Starting phenix.real_space_refine on Sun Aug 9 06:10:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9y3v_72468/08_2026/9y3v_72468.cif Found real_map, /net/cci-nas-00/data/ceres_data/9y3v_72468/08_2026/9y3v_72468.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9y3v_72468/08_2026/9y3v_72468.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9y3v_72468/08_2026/9y3v_72468.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9y3v_72468/08_2026/9y3v_72468.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9y3v_72468/08_2026/9y3v_72468.map" } resolution = 2.9 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= 0.004 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: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 Mg 1 5.21 5 S 184 5.16 5 Cl 8 4.86 5 C 20456 2.51 5 N 5600 2.21 5 O 5993 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 244 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 32243 Number of models: 1 Model: "" Number of chains: 19 Chain: "A" Number of atoms: 3423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 3423 Classifications: {'peptide': 437} Link IDs: {'PCIS': 3, 'PTRANS': 18, 'TRANS': 415} Chain breaks: 1 Chain: "B" Number of atoms: 3423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 3423 Classifications: {'peptide': 437} Link IDs: {'PCIS': 3, 'PTRANS': 18, 'TRANS': 415} Chain breaks: 1 Chain: "C" Number of atoms: 2693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2693 Classifications: {'peptide': 344} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 329} Chain: "D" Number of atoms: 2693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2693 Classifications: {'peptide': 344} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 329} Chain: "E" Number of atoms: 2770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 356, 2770 Classifications: {'peptide': 356} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 337} Chain: "F" Number of atoms: 2770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 356, 2770 Classifications: {'peptide': 356} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 337} Chain: "G" Number of atoms: 2302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 296, 2302 Classifications: {'peptide': 296} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 286} Chain breaks: 1 Chain: "H" Number of atoms: 2302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 296, 2302 Classifications: {'peptide': 296} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 286} Chain breaks: 1 Chain: "I" Number of atoms: 3260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 420, 3260 Classifications: {'peptide': 420} Link IDs: {'PTRANS': 18, 'TRANS': 401} Chain breaks: 1 Chain: "J" Number of atoms: 3260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 420, 3260 Classifications: {'peptide': 420} Link IDs: {'PTRANS': 18, 'TRANS': 401} Chain breaks: 1 Chain: "K" Number of atoms: 1668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1668 Classifications: {'peptide': 210} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 197} Chain: "L" Number of atoms: 1668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1668 Classifications: {'peptide': 210} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 197} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CL': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CL': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CL': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CL': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CL': 2, ' MG': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CL': 2, ' ZN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 13583 SG CYS E 338 66.424 87.135 63.291 1.00 19.18 S ATOM 24406 SG CYS I 281 66.419 86.390 59.747 1.00 18.98 S ATOM 16353 SG CYS F 338 80.275 74.213 126.319 1.00 18.30 S ATOM 27666 SG CYS J 281 82.445 72.975 128.848 1.00 18.53 S Time building chain proxies: 7.10, per 1000 atoms: 0.22 Number of scatterers: 32243 At special positions: 0 Unit cell: (147.444, 153.699, 188.55, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 Cl 8 17.00 S 184 16.00 Mg 1 11.99 O 5993 8.00 N 5600 7.00 C 20456 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: 2.33 Conformation dependent library (CDL) restraints added in 1.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN F 602 " pdb="ZN ZN F 602 " - pdb=" ND1 HIS F 371 " pdb="ZN ZN F 602 " - pdb=" SG CYS J 281 " pdb="ZN ZN F 602 " - pdb=" SG CYS F 338 " 8180 Ramachandran restraints generated. 4090 Oldfield, 0 Emsley, 4090 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7780 Finding SS restraints... Secondary structure from input PDB file: 194 helices and 44 sheets defined 46.0% alpha, 15.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.17 Creating SS restraints... Processing helix chain 'A' and resid 58 through 62 Processing helix chain 'A' and resid 64 through 67 Processing helix chain 'A' and resid 75 through 86 Processing helix chain 'A' and resid 98 through 109 removed outlier: 3.672A pdb=" N LYS A 108 " --> pdb=" O GLU A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 113 Processing helix chain 'A' and resid 130 through 141 Processing helix chain 'A' and resid 161 through 175 Processing helix chain 'A' and resid 229 through 232 Processing helix chain 'A' and resid 253 through 263 removed outlier: 4.247A pdb=" N ALA A 257 " --> pdb=" O SER A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 279 Processing helix chain 'A' and resid 279 through 284 Processing helix chain 'A' and resid 302 through 315 Processing helix chain 'A' and resid 322 through 326 removed outlier: 3.750A pdb=" N ASN A 326 " --> pdb=" O PRO A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 489 Processing helix chain 'B' and resid 58 through 62 Processing helix chain 'B' and resid 64 through 67 Processing helix chain 'B' and resid 75 through 86 Processing helix chain 'B' and resid 98 through 109 removed outlier: 3.574A pdb=" N LYS B 108 " --> pdb=" O GLU B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 113 Processing helix chain 'B' and resid 130 through 142 Processing helix chain 'B' and resid 161 through 175 Processing helix chain 'B' and resid 229 through 232 Processing helix chain 'B' and resid 253 through 263 removed outlier: 4.297A pdb=" N ALA B 257 " --> pdb=" O SER B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 268 through 279 Processing helix chain 'B' and resid 279 through 284 Processing helix chain 'B' and resid 302 through 315 Processing helix chain 'B' and resid 322 through 326 removed outlier: 3.718A pdb=" N ASN B 326 " --> pdb=" O PRO B 323 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 334 removed outlier: 3.831A pdb=" N SER B 334 " --> pdb=" O THR B 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 484 through 489 Processing helix chain 'C' and resid 9 through 24 Processing helix chain 'C' and resid 30 through 49 Processing helix chain 'C' and resid 53 through 72 removed outlier: 4.053A pdb=" N GLN C 72 " --> pdb=" O MET C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 75 through 98 removed outlier: 3.993A pdb=" N GLY C 79 " --> pdb=" O GLU C 75 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU C 96 " --> pdb=" O GLU C 92 " (cutoff:3.500A) Processing helix chain 'C' and resid 108 through 115 Processing helix chain 'C' and resid 128 through 146 removed outlier: 3.641A pdb=" N ASN C 132 " --> pdb=" O GLN C 128 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLY C 146 " --> pdb=" O VAL C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 153 Processing helix chain 'C' and resid 154 through 158 Processing helix chain 'C' and resid 171 through 183 removed outlier: 3.866A pdb=" N ARG C 183 " --> pdb=" O LYS C 179 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 210 removed outlier: 3.563A pdb=" N ALA C 210 " --> pdb=" O ASN C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 226 Processing helix chain 'C' and resid 227 through 229 No H-bonds generated for 'chain 'C' and resid 227 through 229' Processing helix chain 'C' and resid 250 through 261 Processing helix chain 'C' and resid 270 through 274 Processing helix chain 'C' and resid 282 through 286 Processing helix chain 'C' and resid 290 through 294 Processing helix chain 'C' and resid 317 through 321 Processing helix chain 'C' and resid 332 through 334 No H-bonds generated for 'chain 'C' and resid 332 through 334' Processing helix chain 'C' and resid 335 through 344 removed outlier: 3.640A pdb=" N LEU C 339 " --> pdb=" O TYR C 335 " (cutoff:3.500A) Processing helix chain 'C' and resid 345 through 349 removed outlier: 3.705A pdb=" N HIS C 349 " --> pdb=" O PRO C 346 " (cutoff:3.500A) Processing helix chain 'D' and resid 9 through 24 Processing helix chain 'D' and resid 30 through 49 Processing helix chain 'D' and resid 53 through 72 removed outlier: 4.166A pdb=" N GLN D 72 " --> pdb=" O MET D 68 " (cutoff:3.500A) Processing helix chain 'D' and resid 75 through 98 removed outlier: 4.095A pdb=" N GLY D 79 " --> pdb=" O GLU D 75 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LEU D 96 " --> pdb=" O GLU D 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 108 through 113 Processing helix chain 'D' and resid 128 through 153 removed outlier: 3.690A pdb=" N ASN D 132 " --> pdb=" O GLN D 128 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLY D 146 " --> pdb=" O VAL D 142 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N MET D 148 " --> pdb=" O LEU D 144 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N GLU D 149 " --> pdb=" O GLU D 145 " (cutoff:3.500A) Processing helix chain 'D' and resid 154 through 158 Processing helix chain 'D' and resid 171 through 183 removed outlier: 3.793A pdb=" N ARG D 183 " --> pdb=" O LYS D 179 " (cutoff:3.500A) Processing helix chain 'D' and resid 199 through 210 removed outlier: 3.553A pdb=" N ALA D 210 " --> pdb=" O ASN D 206 " (cutoff:3.500A) Processing helix chain 'D' and resid 221 through 226 Processing helix chain 'D' and resid 227 through 229 No H-bonds generated for 'chain 'D' and resid 227 through 229' Processing helix chain 'D' and resid 250 through 261 removed outlier: 3.502A pdb=" N HIS D 261 " --> pdb=" O ALA D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 270 through 274 Processing helix chain 'D' and resid 282 through 286 Processing helix chain 'D' and resid 290 through 294 Processing helix chain 'D' and resid 296 through 305 removed outlier: 6.467A pdb=" N ASP D 301 " --> pdb=" O THR D 298 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N ILE D 302 " --> pdb=" O GLU D 299 " (cutoff:3.500A) Processing helix chain 'D' and resid 317 through 321 Processing helix chain 'D' and resid 332 through 334 No H-bonds generated for 'chain 'D' and resid 332 through 334' Processing helix chain 'D' and resid 335 through 344 removed outlier: 3.658A pdb=" N LEU D 339 " --> pdb=" O TYR D 335 " (cutoff:3.500A) Processing helix chain 'D' and resid 345 through 349 removed outlier: 3.535A pdb=" N HIS D 349 " --> pdb=" O PRO D 346 " (cutoff:3.500A) Processing helix chain 'E' and resid 191 through 196 removed outlier: 3.714A pdb=" N GLN E 194 " --> pdb=" O SER E 191 " (cutoff:3.500A) Processing helix chain 'E' and resid 204 through 216 Processing helix chain 'E' and resid 221 through 239 removed outlier: 3.767A pdb=" N CYS E 226 " --> pdb=" O SER E 222 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLN E 235 " --> pdb=" O ARG E 231 " (cutoff:3.500A) Processing helix chain 'E' and resid 247 through 267 removed outlier: 5.232A pdb=" N VAL E 253 " --> pdb=" O SER E 249 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LYS E 257 " --> pdb=" O VAL E 253 " (cutoff:3.500A) Proline residue: E 258 - end of helix Processing helix chain 'E' and resid 270 through 286 Processing helix chain 'E' and resid 292 through 312 Processing helix chain 'E' and resid 312 through 324 removed outlier: 3.994A pdb=" N GLN E 317 " --> pdb=" O VAL E 313 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ARG E 321 " --> pdb=" O GLN E 317 " (cutoff:3.500A) Processing helix chain 'E' and resid 339 through 352 Processing helix chain 'E' and resid 368 through 380 removed outlier: 3.700A pdb=" N THR E 372 " --> pdb=" O GLU E 368 " (cutoff:3.500A) Processing helix chain 'E' and resid 390 through 395 removed outlier: 3.566A pdb=" N VAL E 394 " --> pdb=" O ALA E 390 " (cutoff:3.500A) Processing helix chain 'E' and resid 396 through 398 No H-bonds generated for 'chain 'E' and resid 396 through 398' Processing helix chain 'E' and resid 419 through 430 Processing helix chain 'E' and resid 439 through 441 No H-bonds generated for 'chain 'E' and resid 439 through 441' Processing helix chain 'E' and resid 459 through 464 Processing helix chain 'E' and resid 475 through 479 Processing helix chain 'E' and resid 493 through 497 removed outlier: 3.502A pdb=" N VAL E 497 " --> pdb=" O PRO E 494 " (cutoff:3.500A) Processing helix chain 'E' and resid 508 through 510 No H-bonds generated for 'chain 'E' and resid 508 through 510' Processing helix chain 'E' and resid 511 through 520 Processing helix chain 'F' and resid 191 through 195 removed outlier: 3.612A pdb=" N GLN F 194 " --> pdb=" O SER F 191 " (cutoff:3.500A) Processing helix chain 'F' and resid 204 through 216 Processing helix chain 'F' and resid 221 through 240 removed outlier: 3.846A pdb=" N CYS F 226 " --> pdb=" O SER F 222 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLN F 235 " --> pdb=" O ARG F 231 " (cutoff:3.500A) Processing helix chain 'F' and resid 247 through 267 removed outlier: 5.101A pdb=" N VAL F 253 " --> pdb=" O SER F 249 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LYS F 257 " --> pdb=" O VAL F 253 " (cutoff:3.500A) Proline residue: F 258 - end of helix Processing helix chain 'F' and resid 270 through 286 Processing helix chain 'F' and resid 292 through 312 Processing helix chain 'F' and resid 312 through 324 removed outlier: 3.935A pdb=" N GLN F 317 " --> pdb=" O VAL F 313 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ARG F 321 " --> pdb=" O GLN F 317 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N PHE F 322 " --> pdb=" O ALA F 318 " (cutoff:3.500A) Processing helix chain 'F' and resid 339 through 352 Processing helix chain 'F' and resid 368 through 380 removed outlier: 3.851A pdb=" N THR F 372 " --> pdb=" O GLU F 368 " (cutoff:3.500A) Processing helix chain 'F' and resid 390 through 395 removed outlier: 3.528A pdb=" N VAL F 394 " --> pdb=" O ALA F 390 " (cutoff:3.500A) Processing helix chain 'F' and resid 419 through 430 Processing helix chain 'F' and resid 439 through 441 No H-bonds generated for 'chain 'F' and resid 439 through 441' Processing helix chain 'F' and resid 459 through 463 Processing helix chain 'F' and resid 475 through 479 Processing helix chain 'F' and resid 493 through 497 Processing helix chain 'F' and resid 508 through 510 No H-bonds generated for 'chain 'F' and resid 508 through 510' Processing helix chain 'F' and resid 511 through 520 Processing helix chain 'G' and resid 2 through 17 removed outlier: 3.665A pdb=" N LEU G 6 " --> pdb=" O ASP G 2 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N MET G 14 " --> pdb=" O PHE G 10 " (cutoff:3.500A) Processing helix chain 'G' and resid 21 through 36 Processing helix chain 'G' and resid 41 through 57 Processing helix chain 'G' and resid 62 through 83 removed outlier: 3.660A pdb=" N SER G 66 " --> pdb=" O SER G 62 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLU G 82 " --> pdb=" O LEU G 78 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N TYR G 83 " --> pdb=" O ALA G 79 " (cutoff:3.500A) Processing helix chain 'G' and resid 85 through 105 removed outlier: 3.692A pdb=" N LYS G 91 " --> pdb=" O SER G 87 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU G 99 " --> pdb=" O GLU G 95 " (cutoff:3.500A) Processing helix chain 'G' and resid 106 through 116 Processing helix chain 'G' and resid 117 through 119 No H-bonds generated for 'chain 'G' and resid 117 through 119' Processing helix chain 'G' and resid 131 through 144 removed outlier: 3.612A pdb=" N ARG G 136 " --> pdb=" O ARG G 132 " (cutoff:3.500A) Processing helix chain 'G' and resid 159 through 170 removed outlier: 3.837A pdb=" N LYS G 163 " --> pdb=" O LEU G 159 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N HIS G 170 " --> pdb=" O LYS G 166 " (cutoff:3.500A) Processing helix chain 'G' and resid 179 through 181 No H-bonds generated for 'chain 'G' and resid 179 through 181' Processing helix chain 'G' and resid 182 through 187 Processing helix chain 'G' and resid 188 through 190 No H-bonds generated for 'chain 'G' and resid 188 through 190' Processing helix chain 'G' and resid 211 through 222 Processing helix chain 'G' and resid 231 through 235 Processing helix chain 'G' and resid 247 through 252 Processing helix chain 'G' and resid 277 through 281 Processing helix chain 'G' and resid 293 through 304 removed outlier: 4.301A pdb=" N SER G 297 " --> pdb=" O PRO G 293 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ASP G 298 " --> pdb=" O SER G 294 " (cutoff:3.500A) Processing helix chain 'H' and resid 2 through 16 removed outlier: 3.613A pdb=" N MET H 14 " --> pdb=" O PHE H 10 " (cutoff:3.500A) Processing helix chain 'H' and resid 21 through 36 Processing helix chain 'H' and resid 41 through 57 Processing helix chain 'H' and resid 62 through 83 removed outlier: 3.749A pdb=" N GLU H 82 " --> pdb=" O LEU H 78 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N TYR H 83 " --> pdb=" O ALA H 79 " (cutoff:3.500A) Processing helix chain 'H' and resid 85 through 105 removed outlier: 3.519A pdb=" N LEU H 99 " --> pdb=" O GLU H 95 " (cutoff:3.500A) Processing helix chain 'H' and resid 106 through 116 Processing helix chain 'H' and resid 117 through 119 No H-bonds generated for 'chain 'H' and resid 117 through 119' Processing helix chain 'H' and resid 131 through 144 removed outlier: 3.594A pdb=" N ARG H 136 " --> pdb=" O ARG H 132 " (cutoff:3.500A) Processing helix chain 'H' and resid 159 through 170 removed outlier: 3.831A pdb=" N LYS H 163 " --> pdb=" O LEU H 159 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N HIS H 170 " --> pdb=" O LYS H 166 " (cutoff:3.500A) Processing helix chain 'H' and resid 179 through 181 No H-bonds generated for 'chain 'H' and resid 179 through 181' Processing helix chain 'H' and resid 182 through 187 Processing helix chain 'H' and resid 188 through 190 No H-bonds generated for 'chain 'H' and resid 188 through 190' Processing helix chain 'H' and resid 211 through 222 Processing helix chain 'H' and resid 231 through 235 Processing helix chain 'H' and resid 247 through 252 Processing helix chain 'H' and resid 277 through 281 Processing helix chain 'H' and resid 293 through 305 removed outlier: 4.383A pdb=" N SER H 297 " --> pdb=" O PRO H 293 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ASP H 298 " --> pdb=" O SER H 294 " (cutoff:3.500A) Processing helix chain 'I' and resid 13 through 15 No H-bonds generated for 'chain 'I' and resid 13 through 15' Processing helix chain 'I' and resid 16 through 21 Processing helix chain 'I' and resid 24 through 27 Processing helix chain 'I' and resid 36 through 47 Processing helix chain 'I' and resid 56 through 67 removed outlier: 3.950A pdb=" N ALA I 62 " --> pdb=" O ASP I 58 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N PHE I 67 " --> pdb=" O LEU I 63 " (cutoff:3.500A) Processing helix chain 'I' and resid 85 through 93 removed outlier: 3.654A pdb=" N ILE I 93 " --> pdb=" O SER I 89 " (cutoff:3.500A) Processing helix chain 'I' and resid 94 through 97 Processing helix chain 'I' and resid 114 through 124 removed outlier: 4.136A pdb=" N LEU I 120 " --> pdb=" O GLU I 116 " (cutoff:3.500A) Processing helix chain 'I' and resid 144 through 148 Processing helix chain 'I' and resid 174 through 176 No H-bonds generated for 'chain 'I' and resid 174 through 176' Processing helix chain 'I' and resid 184 through 190 Processing helix chain 'I' and resid 208 through 218 removed outlier: 3.806A pdb=" N VAL I 212 " --> pdb=" O LYS I 208 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLU I 217 " --> pdb=" O ASP I 213 " (cutoff:3.500A) Processing helix chain 'I' and resid 227 through 236 Processing helix chain 'I' and resid 262 through 266 Processing helix chain 'I' and resid 315 through 334 Proline residue: I 327 - end of helix removed outlier: 4.135A pdb=" N SER I 331 " --> pdb=" O PRO I 327 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ALA I 332 " --> pdb=" O LYS I 328 " (cutoff:3.500A) Processing helix chain 'I' and resid 348 through 352 Processing helix chain 'J' and resid 16 through 21 Processing helix chain 'J' and resid 24 through 27 Processing helix chain 'J' and resid 36 through 47 Processing helix chain 'J' and resid 56 through 67 removed outlier: 3.620A pdb=" N ALA J 62 " --> pdb=" O ASP J 58 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N PHE J 67 " --> pdb=" O LEU J 63 " (cutoff:3.500A) Processing helix chain 'J' and resid 85 through 94 Processing helix chain 'J' and resid 95 through 97 No H-bonds generated for 'chain 'J' and resid 95 through 97' Processing helix chain 'J' and resid 114 through 124 removed outlier: 4.174A pdb=" N LEU J 120 " --> pdb=" O GLU J 116 " (cutoff:3.500A) Processing helix chain 'J' and resid 144 through 148 removed outlier: 3.701A pdb=" N GLY J 147 " --> pdb=" O GLY J 144 " (cutoff:3.500A) Processing helix chain 'J' and resid 174 through 176 No H-bonds generated for 'chain 'J' and resid 174 through 176' Processing helix chain 'J' and resid 184 through 188 Processing helix chain 'J' and resid 208 through 218 removed outlier: 3.797A pdb=" N VAL J 212 " --> pdb=" O LYS J 208 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N MET J 216 " --> pdb=" O VAL J 212 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLU J 217 " --> pdb=" O ASP J 213 " (cutoff:3.500A) Processing helix chain 'J' and resid 227 through 236 removed outlier: 3.531A pdb=" N GLN J 236 " --> pdb=" O LEU J 232 " (cutoff:3.500A) Processing helix chain 'J' and resid 237 through 238 No H-bonds generated for 'chain 'J' and resid 237 through 238' Processing helix chain 'J' and resid 262 through 266 Processing helix chain 'J' and resid 315 through 334 Proline residue: J 327 - end of helix removed outlier: 3.899A pdb=" N SER J 331 " --> pdb=" O PRO J 327 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ALA J 332 " --> pdb=" O LYS J 328 " (cutoff:3.500A) Processing helix chain 'J' and resid 348 through 352 Processing helix chain 'K' and resid 15 through 27 Processing helix chain 'K' and resid 30 through 33 removed outlier: 4.053A pdb=" N GLY K 33 " --> pdb=" O PHE K 30 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 30 through 33' Processing helix chain 'K' and resid 41 through 44 removed outlier: 3.730A pdb=" N TYR K 44 " --> pdb=" O ASP K 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 41 through 44' Processing helix chain 'K' and resid 48 through 57 Processing helix chain 'K' and resid 64 through 68 Processing helix chain 'K' and resid 69 through 82 Processing helix chain 'K' and resid 122 through 126 Processing helix chain 'K' and resid 135 through 152 Processing helix chain 'K' and resid 154 through 165 Processing helix chain 'K' and resid 165 through 174 Processing helix chain 'K' and resid 175 through 180 removed outlier: 3.956A pdb=" N LYS K 179 " --> pdb=" O PRO K 176 " (cutoff:3.500A) Processing helix chain 'K' and resid 190 through 207 Proline residue: K 203 - end of helix removed outlier: 3.844A pdb=" N TYR K 207 " --> pdb=" O PRO K 203 " (cutoff:3.500A) Processing helix chain 'L' and resid 15 through 27 Processing helix chain 'L' and resid 30 through 33 removed outlier: 3.879A pdb=" N GLY L 33 " --> pdb=" O PHE L 30 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 30 through 33' Processing helix chain 'L' and resid 41 through 44 Processing helix chain 'L' and resid 48 through 57 Processing helix chain 'L' and resid 69 through 82 Processing helix chain 'L' and resid 115 through 119 removed outlier: 4.529A pdb=" N LEU L 118 " --> pdb=" O ILE L 115 " (cutoff:3.500A) Processing helix chain 'L' and resid 122 through 126 Processing helix chain 'L' and resid 135 through 152 removed outlier: 3.643A pdb=" N ASN L 148 " --> pdb=" O ALA L 144 " (cutoff:3.500A) Processing helix chain 'L' and resid 154 through 165 Processing helix chain 'L' and resid 165 through 174 Processing helix chain 'L' and resid 175 through 178 Processing helix chain 'L' and resid 190 through 207 Proline residue: L 203 - end of helix removed outlier: 3.770A pdb=" N TYR L 207 " --> pdb=" O PRO L 203 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 119 through 124 removed outlier: 6.351A pdb=" N THR A 91 " --> pdb=" O ARG A 121 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N ILE A 123 " --> pdb=" O THR A 91 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N VAL A 93 " --> pdb=" O ILE A 123 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N TYR A 152 " --> pdb=" O HIS A 248 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N HIS A 248 " --> pdb=" O TYR A 152 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N CYS A 247 " --> pdb=" O ILE A 184 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N ILE A 184 " --> pdb=" O CYS A 247 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N ILE A 249 " --> pdb=" O THR A 182 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N THR A 182 " --> pdb=" O ILE A 249 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N ILE A 251 " --> pdb=" O VAL A 180 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N VAL A 180 " --> pdb=" O ILE A 251 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N GLN A 286 " --> pdb=" O SER A 179 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N MET A 181 " --> pdb=" O GLN A 286 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N ILE A 287 " --> pdb=" O VAL A 212 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ARG A 211 " --> pdb=" O ASP A 206 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N ALA A 204 " --> pdb=" O LEU A 213 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N PHE A 215 " --> pdb=" O VAL A 202 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N VAL A 202 " --> pdb=" O PHE A 215 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N VAL A 238 " --> pdb=" O PHE I 195 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N PHE I 157 " --> pdb=" O MET I 170 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N MET I 170 " --> pdb=" O PHE I 157 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N GLY I 159 " --> pdb=" O LEU I 168 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 69 through 70 Processing sheet with id=AA3, first strand: chain 'A' and resid 155 through 157 Processing sheet with id=AA4, first strand: chain 'A' and resid 223 through 227 Processing sheet with id=AA5, first strand: chain 'A' and resid 336 through 338 removed outlier: 6.289A pdb=" N LEU A 361 " --> pdb=" O ILE A 379 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N VAL A 378 " --> pdb=" O LEU A 396 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N TYR A 395 " --> pdb=" O LEU A 413 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N LEU A 412 " --> pdb=" O LEU A 431 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N VAL A 430 " --> pdb=" O ILE A 449 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N VAL A 448 " --> pdb=" O TRP A 497 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 349 through 350 removed outlier: 6.406A pdb=" N SER A 349 " --> pdb=" O ILE A 368 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N VAL A 367 " --> pdb=" O ILE A 385 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N HIS A 384 " --> pdb=" O VAL A 402 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N ARG A 401 " --> pdb=" O VAL A 419 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N GLU A 418 " --> pdb=" O VAL A 437 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 355 through 356 removed outlier: 6.483A pdb=" N ILE A 355 " --> pdb=" O ILE A 374 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N PHE A 373 " --> pdb=" O LEU A 391 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N VAL A 390 " --> pdb=" O ILE A 408 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N GLN A 407 " --> pdb=" O LEU A 425 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N THR A 424 " --> pdb=" O LEU A 443 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 119 through 124 removed outlier: 6.400A pdb=" N THR B 91 " --> pdb=" O ARG B 121 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N ILE B 123 " --> pdb=" O THR B 91 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N VAL B 93 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N TYR B 152 " --> pdb=" O HIS B 248 " (cutoff:3.500A) removed outlier: 7.995A pdb=" N HIS B 248 " --> pdb=" O TYR B 152 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N CYS B 247 " --> pdb=" O ILE B 184 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N ILE B 184 " --> pdb=" O CYS B 247 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N ILE B 249 " --> pdb=" O THR B 182 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N THR B 182 " --> pdb=" O ILE B 249 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N ILE B 251 " --> pdb=" O VAL B 180 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N VAL B 180 " --> pdb=" O ILE B 251 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N GLN B 286 " --> pdb=" O SER B 179 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N MET B 181 " --> pdb=" O GLN B 286 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N ILE B 287 " --> pdb=" O VAL B 212 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N VAL B 212 " --> pdb=" O ASP B 206 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N ASP B 206 " --> pdb=" O VAL B 212 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N VAL B 238 " --> pdb=" O PHE J 195 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 69 through 70 Processing sheet with id=AB1, first strand: chain 'B' and resid 155 through 157 Processing sheet with id=AB2, first strand: chain 'B' and resid 223 through 227 Processing sheet with id=AB3, first strand: chain 'B' and resid 336 through 338 removed outlier: 6.292A pdb=" N LEU B 361 " --> pdb=" O ILE B 379 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N VAL B 378 " --> pdb=" O LEU B 396 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N TYR B 395 " --> pdb=" O LEU B 413 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N LEU B 412 " --> pdb=" O LEU B 431 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N VAL B 430 " --> pdb=" O ILE B 449 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N VAL B 448 " --> pdb=" O TRP B 497 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 349 through 350 removed outlier: 6.296A pdb=" N SER B 349 " --> pdb=" O ILE B 368 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N VAL B 367 " --> pdb=" O ILE B 385 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N HIS B 384 " --> pdb=" O VAL B 402 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ARG B 401 " --> pdb=" O VAL B 419 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N GLU B 418 " --> pdb=" O VAL B 437 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'B' and resid 355 through 356 removed outlier: 6.398A pdb=" N ILE B 355 " --> pdb=" O ILE B 374 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N PHE B 373 " --> pdb=" O LEU B 391 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N VAL B 390 " --> pdb=" O ILE B 408 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N GLN B 407 " --> pdb=" O LEU B 425 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N THR B 424 " --> pdb=" O LEU B 443 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'C' and resid 329 through 331 removed outlier: 6.657A pdb=" N LEU C 265 " --> pdb=" O LEU C 323 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N ILE C 325 " --> pdb=" O LEU C 265 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N VAL C 267 " --> pdb=" O ILE C 325 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N VAL C 232 " --> pdb=" O ILE C 266 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N CYS C 268 " --> pdb=" O VAL C 232 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N ILE C 234 " --> pdb=" O CYS C 268 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N ILE C 168 " --> pdb=" O ILE C 233 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N GLU C 163 " --> pdb=" O HIS C 188 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N ILE C 190 " --> pdb=" O GLU C 163 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N ILE C 165 " --> pdb=" O ILE C 190 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N ALA C 192 " --> pdb=" O ILE C 165 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N THR C 167 " --> pdb=" O ALA C 192 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N GLU C 213 " --> pdb=" O PHE C 187 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N THR C 214 " --> pdb=" O ARG F 483 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N LEU F 485 " --> pdb=" O THR C 214 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N VAL C 216 " --> pdb=" O LEU F 485 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 238 through 239 Processing sheet with id=AB8, first strand: chain 'C' and resid 306 through 308 removed outlier: 6.388A pdb=" N ILE F 333 " --> pdb=" O VAL F 359 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N VAL F 361 " --> pdb=" O ILE F 333 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N VAL F 335 " --> pdb=" O VAL F 361 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N VAL F 332 " --> pdb=" O LYS F 400 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N LEU F 402 " --> pdb=" O VAL F 332 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N LEU F 334 " --> pdb=" O LEU F 402 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N GLY F 404 " --> pdb=" O LEU F 334 " (cutoff:3.500A) removed outlier: 7.918A pdb=" N TYR F 336 " --> pdb=" O GLY F 404 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N VAL F 401 " --> pdb=" O LEU F 435 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N CYS F 437 " --> pdb=" O VAL F 401 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N LEU F 403 " --> pdb=" O CYS F 437 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N VAL F 434 " --> pdb=" O LEU F 499 " (cutoff:3.500A) removed outlier: 8.078A pdb=" N ILE F 501 " --> pdb=" O VAL F 434 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N VAL F 436 " --> pdb=" O ILE F 501 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 329 through 331 removed outlier: 6.649A pdb=" N LEU D 265 " --> pdb=" O LEU D 323 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N ILE D 325 " --> pdb=" O LEU D 265 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N VAL D 267 " --> pdb=" O ILE D 325 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N VAL D 232 " --> pdb=" O ILE D 266 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N CYS D 268 " --> pdb=" O VAL D 232 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ILE D 234 " --> pdb=" O CYS D 268 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N ILE D 168 " --> pdb=" O ILE D 233 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N GLU D 163 " --> pdb=" O HIS D 188 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N ILE D 190 " --> pdb=" O GLU D 163 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ILE D 165 " --> pdb=" O ILE D 190 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N ALA D 192 " --> pdb=" O ILE D 165 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N THR D 167 " --> pdb=" O ALA D 192 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N GLU D 213 " --> pdb=" O PHE D 187 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N THR D 214 " --> pdb=" O ARG E 483 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N LEU E 485 " --> pdb=" O THR D 214 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N VAL D 216 " --> pdb=" O LEU E 485 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 238 through 239 Processing sheet with id=AC2, first strand: chain 'D' and resid 307 through 308 removed outlier: 6.412A pdb=" N ILE E 333 " --> pdb=" O VAL E 359 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N VAL E 361 " --> pdb=" O ILE E 333 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N VAL E 335 " --> pdb=" O VAL E 361 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N VAL E 332 " --> pdb=" O LYS E 400 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N LEU E 402 " --> pdb=" O VAL E 332 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N LEU E 334 " --> pdb=" O LEU E 402 " (cutoff:3.500A) removed outlier: 7.851A pdb=" N GLY E 404 " --> pdb=" O LEU E 334 " (cutoff:3.500A) removed outlier: 7.842A pdb=" N TYR E 336 " --> pdb=" O GLY E 404 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N VAL E 401 " --> pdb=" O LEU E 435 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N CYS E 437 " --> pdb=" O VAL E 401 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N LEU E 403 " --> pdb=" O CYS E 437 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N VAL E 434 " --> pdb=" O LEU E 499 " (cutoff:3.500A) removed outlier: 8.084A pdb=" N ILE E 501 " --> pdb=" O VAL E 434 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N VAL E 436 " --> pdb=" O ILE E 501 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 443 through 444 removed outlier: 6.537A pdb=" N LEU E 408 " --> pdb=" O CYS E 444 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 466 through 467 Processing sheet with id=AC5, first strand: chain 'F' and resid 443 through 444 removed outlier: 6.594A pdb=" N LEU F 408 " --> pdb=" O CYS F 444 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 466 through 467 Processing sheet with id=AC7, first strand: chain 'G' and resid 289 through 291 removed outlier: 6.933A pdb=" N PHE G 226 " --> pdb=" O LEU G 283 " (cutoff:3.500A) removed outlier: 8.034A pdb=" N PHE G 285 " --> pdb=" O PHE G 226 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N VAL G 228 " --> pdb=" O PHE G 285 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N VAL G 193 " --> pdb=" O TYR G 227 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N VAL G 229 " --> pdb=" O VAL G 193 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N VAL G 195 " --> pdb=" O VAL G 229 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N THR G 124 " --> pdb=" O LEU G 192 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N ILE G 194 " --> pdb=" O THR G 124 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N LEU G 126 " --> pdb=" O ILE G 194 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N ILE G 125 " --> pdb=" O TYR G 151 " (cutoff:3.500A) removed outlier: 8.078A pdb=" N THR G 153 " --> pdb=" O ILE G 125 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N THR G 127 " --> pdb=" O THR G 153 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N VAL G 150 " --> pdb=" O THR G 176 " (cutoff:3.500A) removed outlier: 7.693A pdb=" N VAL G 178 " --> pdb=" O VAL G 150 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N VAL G 152 " --> pdb=" O VAL G 178 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 199 through 200 Processing sheet with id=AC9, first strand: chain 'G' and resid 267 through 268 removed outlier: 6.880A pdb=" N LYS G 267 " --> pdb=" O VAL H 177 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N ILE H 125 " --> pdb=" O TYR H 151 " (cutoff:3.500A) removed outlier: 8.119A pdb=" N THR H 153 " --> pdb=" O ILE H 125 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N THR H 127 " --> pdb=" O THR H 153 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N THR H 124 " --> pdb=" O LEU H 192 " (cutoff:3.500A) removed outlier: 7.698A pdb=" N ILE H 194 " --> pdb=" O THR H 124 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N LEU H 126 " --> pdb=" O ILE H 194 " (cutoff:3.500A) removed outlier: 8.283A pdb=" N GLY H 196 " --> pdb=" O LEU H 126 " (cutoff:3.500A) removed outlier: 7.938A pdb=" N HIS H 128 " --> pdb=" O GLY H 196 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N VAL H 193 " --> pdb=" O TYR H 227 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N VAL H 229 " --> pdb=" O VAL H 193 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N VAL H 195 " --> pdb=" O VAL H 229 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N PHE H 226 " --> pdb=" O LEU H 283 " (cutoff:3.500A) removed outlier: 8.124A pdb=" N PHE H 285 " --> pdb=" O PHE H 226 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N VAL H 228 " --> pdb=" O PHE H 285 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'H' and resid 199 through 200 Processing sheet with id=AD2, first strand: chain 'I' and resid 72 through 77 removed outlier: 6.696A pdb=" N VAL I 51 " --> pdb=" O ASP I 74 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N VAL I 76 " --> pdb=" O VAL I 51 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N VAL I 53 " --> pdb=" O VAL I 76 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N ALA I 5 " --> pdb=" O GLU I 50 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N HIS I 203 " --> pdb=" O SER I 105 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N LEU I 131 " --> pdb=" O ALA I 202 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N LEU I 204 " --> pdb=" O ALA I 129 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N ALA I 129 " --> pdb=" O LEU I 204 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N LEU I 128 " --> pdb=" O TYR I 301 " (cutoff:3.500A) removed outlier: 8.104A pdb=" N HIS I 303 " --> pdb=" O LEU I 128 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N MET I 130 " --> pdb=" O HIS I 303 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N MET I 305 " --> pdb=" O MET I 130 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N MET I 132 " --> pdb=" O MET I 305 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'I' and resid 29 through 30 Processing sheet with id=AD4, first strand: chain 'I' and resid 108 through 110 Processing sheet with id=AD5, first strand: chain 'I' and resid 345 through 346 removed outlier: 6.455A pdb=" N GLN I 345 " --> pdb=" O ILE I 364 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N GLN I 363 " --> pdb=" O ILE I 381 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N LEU I 380 " --> pdb=" O VAL I 398 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N THR I 397 " --> pdb=" O ILE I 415 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N VAL I 414 " --> pdb=" O ILE I 432 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'I' and resid 357 through 358 removed outlier: 6.340A pdb=" N LEU I 357 " --> pdb=" O ILE I 375 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N VAL I 374 " --> pdb=" O LEU I 392 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N LEU I 391 " --> pdb=" O ILE I 409 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N VAL I 408 " --> pdb=" O ILE I 426 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N LEU I 425 " --> pdb=" O ILE I 443 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'I' and resid 369 through 371 removed outlier: 6.380A pdb=" N THR I 386 " --> pdb=" O ILE I 404 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ASN I 403 " --> pdb=" O ILE I 421 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'J' and resid 72 through 77 removed outlier: 6.869A pdb=" N VAL J 51 " --> pdb=" O ASP J 74 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N VAL J 76 " --> pdb=" O VAL J 51 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N VAL J 53 " --> pdb=" O VAL J 76 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N ALA J 5 " --> pdb=" O GLU J 50 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N HIS J 203 " --> pdb=" O SER J 105 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N LEU J 131 " --> pdb=" O ALA J 202 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N LEU J 204 " --> pdb=" O ALA J 129 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N ALA J 129 " --> pdb=" O LEU J 204 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N LEU J 128 " --> pdb=" O TYR J 301 " (cutoff:3.500A) removed outlier: 8.064A pdb=" N HIS J 303 " --> pdb=" O LEU J 128 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N MET J 130 " --> pdb=" O HIS J 303 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N MET J 305 " --> pdb=" O MET J 130 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N MET J 132 " --> pdb=" O MET J 305 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'J' and resid 29 through 30 Processing sheet with id=AE1, first strand: chain 'J' and resid 108 through 110 Processing sheet with id=AE2, first strand: chain 'J' and resid 345 through 346 removed outlier: 6.405A pdb=" N GLN J 345 " --> pdb=" O ILE J 364 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N GLN J 363 " --> pdb=" O ILE J 381 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N LEU J 380 " --> pdb=" O VAL J 398 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N THR J 397 " --> pdb=" O ILE J 415 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N VAL J 414 " --> pdb=" O ILE J 432 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'J' and resid 357 through 358 removed outlier: 6.393A pdb=" N LEU J 357 " --> pdb=" O ILE J 375 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N VAL J 374 " --> pdb=" O LEU J 392 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N LEU J 391 " --> pdb=" O ILE J 409 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N VAL J 408 " --> pdb=" O ILE J 426 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N LEU J 425 " --> pdb=" O ILE J 443 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'J' and resid 369 through 371 removed outlier: 6.280A pdb=" N SER J 369 " --> pdb=" O ILE J 387 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N THR J 386 " --> pdb=" O ILE J 404 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N ASN J 403 " --> pdb=" O ILE J 421 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'K' and resid 35 through 39 removed outlier: 6.736A pdb=" N THR K 129 " --> pdb=" O ILE K 183 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N VAL K 185 " --> pdb=" O THR K 129 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N PHE K 131 " --> pdb=" O VAL K 185 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'K' and resid 85 through 92 removed outlier: 3.635A pdb=" N GLY K 100 " --> pdb=" O ILE K 90 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ASP K 92 " --> pdb=" O CYS K 98 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N CYS K 98 " --> pdb=" O ASP K 92 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'L' and resid 35 through 39 removed outlier: 6.145A pdb=" N TYR L 4 " --> pdb=" O VAL L 110 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N VAL L 112 " --> pdb=" O TYR L 4 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N ILE L 6 " --> pdb=" O VAL L 112 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N THR L 129 " --> pdb=" O ILE L 183 " (cutoff:3.500A) removed outlier: 7.851A pdb=" N VAL L 185 " --> pdb=" O THR L 129 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N PHE L 131 " --> pdb=" O VAL L 185 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'L' and resid 85 through 91 removed outlier: 3.810A pdb=" N GLY L 100 " --> pdb=" O ILE L 90 " (cutoff:3.500A) 1361 hydrogen bonds defined for protein. 3699 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.70 Time building geometry restraints manager: 3.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6489 1.33 - 1.46: 7355 1.46 - 1.58: 18718 1.58 - 1.70: 0 1.70 - 1.82: 278 Bond restraints: 32840 Sorted by residual: bond pdb=" C VAL D 316 " pdb=" N PRO D 317 " ideal model delta sigma weight residual 1.331 1.363 -0.032 8.70e-03 1.32e+04 1.34e+01 bond pdb=" C SER D 275 " pdb=" N PRO D 276 " ideal model delta sigma weight residual 1.334 1.363 -0.029 8.40e-03 1.42e+04 1.23e+01 bond pdb=" C VAL C 316 " pdb=" N PRO C 317 " ideal model delta sigma weight residual 1.331 1.360 -0.029 8.70e-03 1.32e+04 1.10e+01 bond pdb=" CA PRO C 317 " pdb=" C PRO C 317 " ideal model delta sigma weight residual 1.514 1.532 -0.018 5.50e-03 3.31e+04 1.02e+01 bond pdb=" C THR F 242 " pdb=" N PRO F 243 " ideal model delta sigma weight residual 1.331 1.357 -0.026 8.70e-03 1.32e+04 8.86e+00 ... (remaining 32835 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.49: 35348 1.49 - 2.98: 7498 2.98 - 4.46: 1464 4.46 - 5.95: 156 5.95 - 7.44: 24 Bond angle restraints: 44490 Sorted by residual: angle pdb=" CA ASP D 314 " pdb=" CB ASP D 314 " pdb=" CG ASP D 314 " ideal model delta sigma weight residual 112.60 119.79 -7.19 1.00e+00 1.00e+00 5.18e+01 angle pdb=" CA ASP C 314 " pdb=" CB ASP C 314 " pdb=" CG ASP C 314 " ideal model delta sigma weight residual 112.60 118.94 -6.34 1.00e+00 1.00e+00 4.02e+01 angle pdb=" CA ASP H 274 " pdb=" CB ASP H 274 " pdb=" CG ASP H 274 " ideal model delta sigma weight residual 112.60 118.16 -5.56 1.00e+00 1.00e+00 3.09e+01 angle pdb=" N PRO C 317 " pdb=" CA PRO C 317 " pdb=" C PRO C 317 " ideal model delta sigma weight residual 110.47 115.80 -5.33 9.60e-01 1.09e+00 3.08e+01 angle pdb=" CA ASP G 274 " pdb=" CB ASP G 274 " pdb=" CG ASP G 274 " ideal model delta sigma weight residual 112.60 117.91 -5.31 1.00e+00 1.00e+00 2.82e+01 ... (remaining 44485 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 18943 17.95 - 35.90: 814 35.90 - 53.85: 175 53.85 - 71.80: 67 71.80 - 89.75: 33 Dihedral angle restraints: 20032 sinusoidal: 8020 harmonic: 12012 Sorted by residual: dihedral pdb=" CA ASN D 280 " pdb=" C ASN D 280 " pdb=" N GLU D 281 " pdb=" CA GLU D 281 " ideal model delta harmonic sigma weight residual -180.00 -148.38 -31.62 0 5.00e+00 4.00e-02 4.00e+01 dihedral pdb=" CA LEU D 245 " pdb=" C LEU D 245 " pdb=" N ARG D 246 " pdb=" CA ARG D 246 " ideal model delta harmonic sigma weight residual 180.00 148.79 31.21 0 5.00e+00 4.00e-02 3.90e+01 dihedral pdb=" CA LEU C 245 " pdb=" C LEU C 245 " pdb=" N ARG C 246 " pdb=" CA ARG C 246 " ideal model delta harmonic sigma weight residual 180.00 149.14 30.86 0 5.00e+00 4.00e-02 3.81e+01 ... (remaining 20029 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 3113 0.066 - 0.132: 1677 0.132 - 0.198: 329 0.198 - 0.264: 38 0.264 - 0.330: 5 Chirality restraints: 5162 Sorted by residual: chirality pdb=" CA ASN E 245 " pdb=" N ASN E 245 " pdb=" C ASN E 245 " pdb=" CB ASN E 245 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.73e+00 chirality pdb=" CA ASN C 132 " pdb=" N ASN C 132 " pdb=" C ASN C 132 " pdb=" CB ASN C 132 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.49e+00 chirality pdb=" CA ARG B 422 " pdb=" N ARG B 422 " pdb=" C ARG B 422 " pdb=" CB ARG B 422 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.08e+00 ... (remaining 5159 not shown) Planarity restraints: 5704 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG D 14 " -0.364 9.50e-02 1.11e+02 1.64e-01 1.89e+01 pdb=" NE ARG D 14 " 0.013 2.00e-02 2.50e+03 pdb=" CZ ARG D 14 " 0.032 2.00e-02 2.50e+03 pdb=" NH1 ARG D 14 " -0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG D 14 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG H 132 " -0.282 9.50e-02 1.11e+02 1.27e-01 1.07e+01 pdb=" NE ARG H 132 " 0.012 2.00e-02 2.50e+03 pdb=" CZ ARG H 132 " 0.020 2.00e-02 2.50e+03 pdb=" NH1 ARG H 132 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG H 132 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG I 192 " -0.279 9.50e-02 1.11e+02 1.26e-01 1.05e+01 pdb=" NE ARG I 192 " 0.011 2.00e-02 2.50e+03 pdb=" CZ ARG I 192 " 0.019 2.00e-02 2.50e+03 pdb=" NH1 ARG I 192 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG I 192 " -0.015 2.00e-02 2.50e+03 ... (remaining 5701 not shown) Histogram of nonbonded interaction distances: 1.87 - 2.47: 6 2.47 - 3.08: 20282 3.08 - 3.69: 46456 3.69 - 4.29: 72347 4.29 - 4.90: 120140 Nonbonded interactions: 259231 Sorted by model distance: nonbonded pdb=" O SER E 363 " pdb=" O HOH E 701 " model vdw 1.866 3.040 nonbonded pdb="ZN ZN F 602 " pdb="CL CL F 603 " model vdw 2.031 2.380 nonbonded pdb=" ND1 HIS E 371 " pdb="MG MG E 601 " model vdw 2.094 2.250 nonbonded pdb=" SG CYS I 281 " pdb="MG MG E 601 " model vdw 2.354 2.530 nonbonded pdb="MG MG E 601 " pdb="CL CL E 602 " model vdw 2.355 2.320 ... (remaining 259226 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = (chain 'E' and (resid 167 through 522 or resid 603)) selection = (chain 'F' and (resid 167 through 522 or resid 603)) } ncs_group { reference = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.570 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: 0.040 Extract box with map and model: 0.780 Check model and map are aligned: 0.120 Set scattering table: 0.120 Process input model: 33.860 Find NCS groups from input model: 0.680 Set up NCS constraints: 0.080 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:6.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 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 : 0.009 0.322 32843 Z= 0.561 Angle : 1.283 7.441 44490 Z= 0.844 Chirality : 0.075 0.330 5162 Planarity : 0.010 0.164 5704 Dihedral : 12.353 89.747 12252 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 0.17 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.47 % Favored : 97.51 % Rotamer: Outliers : 0.33 % Allowed : 1.48 % Favored : 98.19 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 7.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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 are not related in a simple way. whole: -0.31 (0.12), residues: 4090 helix: -0.64 (0.12), residues: 1484 sheet: 0.34 (0.20), residues: 638 loop : 0.17 (0.14), residues: 1968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.027 0.002 ARG D 14 TYR 0.036 0.004 TYR C 337 PHE 0.029 0.003 PHE C 272 TRP 0.041 0.005 TRP A 111 HIS 0.015 0.003 HIS D 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00861 / 0.56 (32840) covalent geometry : angle 1.28259 / 0.84 (44490) hydrogen bonds : bond 0.18879 / 12.47 ( 1361) hydrogen bonds : angle 6.73680 / 4.80 ( 3699) metal coordination : bond 0.19762 / 14.00 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8180 Ramachandran restraints generated. 4090 Oldfield, 0 Emsley, 4090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8180 Ramachandran restraints generated. 4090 Oldfield, 0 Emsley, 4090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 3584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 241 time to evaluate : 1.366 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 187 MET cc_start: 0.8258 (tpp) cc_final: 0.7981 (tpt) REVERT: J 290 TRP cc_start: 0.5370 (p90) cc_final: 0.1681 (t-100) outliers start: 12 outliers final: 2 residues processed: 252 average time/residue: 0.8761 time to fit residues: 255.2309 Evaluate side-chains 154 residues out of total 3584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 152 time to evaluate : 1.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 104 GLU Chi-restraints excluded: chain D residue 121 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 197 optimal weight: 0.9980 chunk 388 optimal weight: 6.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 0.6980 chunk 207 optimal weight: 0.7980 chunk 401 optimal weight: 10.0000 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 44 GLN E 470 HIS G 244 GLN J 218 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.078857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.048119 restraints weight = 85022.344| |-----------------------------------------------------------------------------| r_work (start): 0.2801 rms_B_bonded: 3.24 r_work: 0.2637 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.2637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9026 moved from start: 0.1610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 32843 Z= 0.130 Angle : 0.594 8.136 44490 Z= 0.315 Chirality : 0.046 0.240 5162 Planarity : 0.004 0.045 5704 Dihedral : 6.167 109.336 4477 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 2.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 0.95 % Allowed : 4.16 % Favored : 94.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.61 % 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 are not related in a simple way. whole: 0.90 (0.13), residues: 4090 helix: 1.01 (0.13), residues: 1514 sheet: 0.34 (0.19), residues: 698 loop : 0.54 (0.14), residues: 1878 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 102 TYR 0.020 0.001 TYR L 66 PHE 0.024 0.001 PHE J 214 TRP 0.016 0.001 TRP B 111 HIS 0.006 0.001 HIS K 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 (32840) covalent geometry : angle 0.59401 / 0.32 (44490) hydrogen bonds : bond 0.04661 / 3.10 ( 1361) hydrogen bonds : angle 4.58010 / 3.28 ( 3699) metal coordination : bond 0.01067 / 0.70 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8180 Ramachandran restraints generated. 4090 Oldfield, 0 Emsley, 4090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8180 Ramachandran restraints generated. 4090 Oldfield, 0 Emsley, 4090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 3584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 151 time to evaluate : 1.454 Fit side-chains revert: symmetry clash REVERT: C 121 ASP cc_start: 0.8446 (t0) cc_final: 0.8106 (t0) REVERT: D 121 ASP cc_start: 0.9094 (t0) cc_final: 0.8824 (t0) REVERT: E 207 MET cc_start: 0.9587 (mmt) cc_final: 0.9050 (mmt) REVERT: E 415 MET cc_start: 0.9123 (OUTLIER) cc_final: 0.8897 (tpp) REVERT: H 83 TYR cc_start: 0.8924 (m-80) cc_final: 0.8642 (m-80) REVERT: H 223 ASN cc_start: 0.9104 (OUTLIER) cc_final: 0.8733 (t0) REVERT: I 67 PHE cc_start: 0.7375 (m-80) cc_final: 0.7074 (m-80) REVERT: I 84 MET cc_start: 0.7378 (mtp) cc_final: 0.6748 (ttm) REVERT: J 290 TRP cc_start: 0.4064 (p90) cc_final: 0.1017 (t-100) REVERT: K 169 MET cc_start: 0.8695 (mmp) cc_final: 0.8168 (mmt) REVERT: L 16 LYS cc_start: 0.7327 (OUTLIER) cc_final: 0.6805 (pttt) REVERT: L 64 HIS cc_start: 0.8567 (t-90) cc_final: 0.8283 (t70) outliers start: 34 outliers final: 7 residues processed: 172 average time/residue: 0.7761 time to fit residues: 157.3779 Evaluate side-chains 145 residues out of total 3584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 135 time to evaluate : 1.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain E residue 415 MET Chi-restraints excluded: chain H residue 223 ASN Chi-restraints excluded: chain J residue 346 ILE Chi-restraints excluded: chain J residue 381 ILE Chi-restraints excluded: chain K residue 18 THR Chi-restraints excluded: chain K residue 141 SER Chi-restraints excluded: chain L residue 16 LYS Chi-restraints excluded: chain L residue 46 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 117 optimal weight: 2.9990 chunk 50 optimal weight: 0.8980 chunk 109 optimal weight: 4.9990 chunk 324 optimal weight: 6.9990 chunk 152 optimal weight: 0.1980 chunk 196 optimal weight: 0.1980 chunk 20 optimal weight: 5.9990 chunk 315 optimal weight: 20.0000 chunk 174 optimal weight: 3.9990 chunk 164 optimal weight: 7.9990 chunk 285 optimal weight: 0.6980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 106 GLN F 470 HIS G 244 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.078090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2809 r_free = 0.2809 target = 0.048018 restraints weight = 83137.160| |-----------------------------------------------------------------------------| r_work (start): 0.2747 rms_B_bonded: 3.32 r_work: 0.2575 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.2575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8747 moved from start: 0.1985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 32843 Z= 0.115 Angle : 0.514 8.608 44490 Z= 0.271 Chirality : 0.045 0.169 5162 Planarity : 0.004 0.050 5704 Dihedral : 5.301 83.596 4472 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 2.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 0.81 % Allowed : 5.19 % Favored : 94.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.61 % 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 are not related in a simple way. whole: 1.19 (0.13), residues: 4090 helix: 1.48 (0.14), residues: 1516 sheet: 0.37 (0.19), residues: 772 loop : 0.55 (0.14), residues: 1802 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 15 TYR 0.015 0.001 TYR G 83 PHE 0.018 0.001 PHE D 177 TRP 0.012 0.001 TRP B 111 HIS 0.006 0.001 HIS A 168 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 (32840) covalent geometry : angle 0.51379 / 0.27 (44490) hydrogen bonds : bond 0.04033 / 2.69 ( 1361) hydrogen bonds : angle 4.17684 / 3.01 ( 3699) metal coordination : bond 0.00263 / 0.14 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8180 Ramachandran restraints generated. 4090 Oldfield, 0 Emsley, 4090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8180 Ramachandran restraints generated. 4090 Oldfield, 0 Emsley, 4090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 3584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 147 time to evaluate : 1.563 Fit side-chains REVERT: B 175 GLU cc_start: 0.8606 (tt0) cc_final: 0.8380 (pp20) REVERT: C 121 ASP cc_start: 0.8485 (t0) cc_final: 0.8066 (t0) REVERT: D 104 ASP cc_start: 0.7404 (m-30) cc_final: 0.7184 (m-30) REVERT: D 121 ASP cc_start: 0.9140 (t0) cc_final: 0.8847 (t0) REVERT: E 207 MET cc_start: 0.9368 (mmt) cc_final: 0.8909 (mmt) REVERT: H 83 TYR cc_start: 0.8835 (m-80) cc_final: 0.8513 (m-80) REVERT: H 93 MET cc_start: 0.8944 (mtp) cc_final: 0.8619 (mtm) REVERT: H 223 ASN cc_start: 0.9060 (OUTLIER) cc_final: 0.8744 (t0) REVERT: I 67 PHE cc_start: 0.7396 (m-80) cc_final: 0.6998 (m-80) REVERT: J 84 MET cc_start: 0.8080 (mtp) cc_final: 0.7712 (ttm) REVERT: J 290 TRP cc_start: 0.3678 (p90) cc_final: 0.0851 (t-100) REVERT: K 129 THR cc_start: 0.8370 (p) cc_final: 0.7854 (p) REVERT: K 169 MET cc_start: 0.8726 (mmp) cc_final: 0.8185 (mmt) REVERT: L 16 LYS cc_start: 0.6773 (OUTLIER) cc_final: 0.6361 (pttt) REVERT: L 161 MET cc_start: 0.8843 (tpt) cc_final: 0.8626 (mtt) outliers start: 29 outliers final: 5 residues processed: 164 average time/residue: 0.6836 time to fit residues: 133.5989 Evaluate side-chains 142 residues out of total 3584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 135 time to evaluate : 1.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain H residue 223 ASN Chi-restraints excluded: chain J residue 346 ILE Chi-restraints excluded: chain J residue 381 ILE Chi-restraints excluded: chain K residue 18 THR Chi-restraints excluded: chain L residue 16 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 216 optimal weight: 3.9990 chunk 154 optimal weight: 2.9990 chunk 204 optimal weight: 1.9990 chunk 381 optimal weight: 6.9990 chunk 82 optimal weight: 9.9990 chunk 63 optimal weight: 6.9990 chunk 206 optimal weight: 0.9980 chunk 361 optimal weight: 30.0000 chunk 175 optimal weight: 3.9990 chunk 357 optimal weight: 10.0000 chunk 125 optimal weight: 6.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 317 GLN J 440 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.076196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2749 r_free = 0.2749 target = 0.045941 restraints weight = 83552.545| |-----------------------------------------------------------------------------| r_work (start): 0.2688 rms_B_bonded: 3.32 r_work: 0.2517 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8786 moved from start: 0.2214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 32843 Z= 0.224 Angle : 0.563 9.344 44490 Z= 0.290 Chirality : 0.047 0.184 5162 Planarity : 0.004 0.055 5704 Dihedral : 5.246 84.398 4472 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 2.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 0.92 % Allowed : 5.94 % Favored : 93.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.61 % 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 are not related in a simple way. whole: 1.31 (0.13), residues: 4090 helix: 1.66 (0.14), residues: 1510 sheet: 0.28 (0.21), residues: 634 loop : 0.60 (0.14), residues: 1946 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 237 TYR 0.021 0.001 TYR L 66 PHE 0.020 0.001 PHE D 177 TRP 0.012 0.001 TRP B 111 HIS 0.006 0.001 HIS A 168 Details of bonding type rmsd/Z covalent geometry : bond 0.00546 / 0.22 (32840) covalent geometry : angle 0.56286 / 0.29 (44490) hydrogen bonds : bond 0.04388 / 2.93 ( 1361) hydrogen bonds : angle 4.18605 / 3.02 ( 3699) metal coordination : bond 0.00653 / 0.38 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8180 Ramachandran restraints generated. 4090 Oldfield, 0 Emsley, 4090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8180 Ramachandran restraints generated. 4090 Oldfield, 0 Emsley, 4090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 3584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 140 time to evaluate : 1.260 Fit side-chains REVERT: C 121 ASP cc_start: 0.8472 (t0) cc_final: 0.8058 (t0) REVERT: D 121 ASP cc_start: 0.9097 (t0) cc_final: 0.8881 (t0) REVERT: E 207 MET cc_start: 0.9338 (mmt) cc_final: 0.9055 (mmm) REVERT: E 415 MET cc_start: 0.8962 (OUTLIER) cc_final: 0.8677 (tpp) REVERT: H 145 LYS cc_start: 0.9374 (OUTLIER) cc_final: 0.9098 (mtpp) REVERT: I 16 MET cc_start: 0.5739 (mtm) cc_final: 0.5225 (mtm) REVERT: I 67 PHE cc_start: 0.7488 (m-80) cc_final: 0.6925 (m-80) REVERT: I 320 MET cc_start: 0.9532 (mmm) cc_final: 0.9331 (tmm) REVERT: J 8 MET cc_start: 0.9010 (OUTLIER) cc_final: 0.8284 (mmm) REVERT: J 84 MET cc_start: 0.8194 (mtp) cc_final: 0.7678 (ttm) REVERT: J 290 TRP cc_start: 0.3533 (p90) cc_final: 0.0655 (t-100) REVERT: K 113 GLU cc_start: 0.7370 (OUTLIER) cc_final: 0.6603 (pp20) REVERT: K 129 THR cc_start: 0.8347 (p) cc_final: 0.7828 (p) REVERT: K 169 MET cc_start: 0.8707 (mmp) cc_final: 0.8089 (mmt) REVERT: L 1 MET cc_start: 0.7115 (pmm) cc_final: 0.6703 (ppp) REVERT: L 16 LYS cc_start: 0.6807 (OUTLIER) cc_final: 0.6387 (pttt) REVERT: L 64 HIS cc_start: 0.8480 (t-90) cc_final: 0.8169 (t-90) REVERT: L 158 THR cc_start: 0.8303 (t) cc_final: 0.8032 (p) REVERT: L 161 MET cc_start: 0.8836 (tpt) cc_final: 0.8623 (mtt) outliers start: 33 outliers final: 9 residues processed: 155 average time/residue: 0.6927 time to fit residues: 127.7491 Evaluate side-chains 147 residues out of total 3584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 133 time to evaluate : 1.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain E residue 220 SER Chi-restraints excluded: chain E residue 415 MET Chi-restraints excluded: chain H residue 145 LYS Chi-restraints excluded: chain H residue 266 LEU Chi-restraints excluded: chain J residue 8 MET Chi-restraints excluded: chain J residue 346 ILE Chi-restraints excluded: chain J residue 381 ILE Chi-restraints excluded: chain K residue 18 THR Chi-restraints excluded: chain K residue 113 GLU Chi-restraints excluded: chain K residue 141 SER Chi-restraints excluded: chain L residue 16 LYS Chi-restraints excluded: chain L residue 46 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 156 optimal weight: 4.9990 chunk 380 optimal weight: 20.0000 chunk 88 optimal weight: 7.9990 chunk 232 optimal weight: 9.9990 chunk 312 optimal weight: 2.9990 chunk 340 optimal weight: 3.9990 chunk 98 optimal weight: 0.9980 chunk 93 optimal weight: 2.9990 chunk 134 optimal weight: 1.9990 chunk 149 optimal weight: 2.9990 chunk 269 optimal weight: 3.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 106 GLN I 283 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.076931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2800 r_free = 0.2800 target = 0.046228 restraints weight = 83090.287| |-----------------------------------------------------------------------------| r_work (start): 0.2730 rms_B_bonded: 3.31 r_work: 0.2561 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9047 moved from start: 0.2413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 32843 Z= 0.191 Angle : 0.525 8.294 44490 Z= 0.271 Chirality : 0.046 0.243 5162 Planarity : 0.004 0.053 5704 Dihedral : 5.125 86.832 4472 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 0.98 % Allowed : 6.28 % Favored : 92.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.61 % 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 are not related in a simple way. whole: 1.38 (0.13), residues: 4090 helix: 1.71 (0.14), residues: 1520 sheet: 0.33 (0.22), residues: 622 loop : 0.62 (0.14), residues: 1948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 172 TYR 0.011 0.001 TYR J 210 PHE 0.019 0.001 PHE D 177 TRP 0.010 0.001 TRP A 111 HIS 0.007 0.001 HIS B 168 Details of bonding type rmsd/Z covalent geometry : bond 0.00460 / 0.19 (32840) covalent geometry : angle 0.52477 / 0.27 (44490) hydrogen bonds : bond 0.04012 / 2.68 ( 1361) hydrogen bonds : angle 4.07000 / 2.93 ( 3699) metal coordination : bond 0.00474 / 0.27 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8180 Ramachandran restraints generated. 4090 Oldfield, 0 Emsley, 4090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8180 Ramachandran restraints generated. 4090 Oldfield, 0 Emsley, 4090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 3584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 138 time to evaluate : 0.834 Fit side-chains REVERT: C 121 ASP cc_start: 0.8543 (t0) cc_final: 0.8134 (t0) REVERT: E 207 MET cc_start: 0.9514 (mmt) cc_final: 0.9263 (mmm) REVERT: E 415 MET cc_start: 0.9126 (OUTLIER) cc_final: 0.8919 (tpp) REVERT: H 145 LYS cc_start: 0.9505 (OUTLIER) cc_final: 0.9285 (mmmt) REVERT: H 164 MET cc_start: 0.9054 (tpt) cc_final: 0.8728 (tpt) REVERT: H 223 ASN cc_start: 0.9235 (OUTLIER) cc_final: 0.8913 (t0) REVERT: I 8 MET cc_start: 0.8848 (mmm) cc_final: 0.8639 (mmt) REVERT: I 16 MET cc_start: 0.5730 (mtm) cc_final: 0.5451 (ptp) REVERT: J 290 TRP cc_start: 0.3727 (p90) cc_final: 0.0695 (t-100) REVERT: J 384 ARG cc_start: 0.8358 (OUTLIER) cc_final: 0.8157 (tpt90) REVERT: K 113 GLU cc_start: 0.7627 (OUTLIER) cc_final: 0.6840 (pp20) REVERT: K 129 THR cc_start: 0.8662 (p) cc_final: 0.8149 (p) REVERT: K 169 MET cc_start: 0.8695 (mmp) cc_final: 0.8141 (mmt) REVERT: K 173 HIS cc_start: 0.8002 (m-70) cc_final: 0.7733 (m90) REVERT: L 16 LYS cc_start: 0.7225 (OUTLIER) cc_final: 0.6663 (pttt) REVERT: L 64 HIS cc_start: 0.8451 (t-90) cc_final: 0.7752 (t-90) REVERT: L 66 TYR cc_start: 0.7321 (OUTLIER) cc_final: 0.7061 (p90) REVERT: L 136 MET cc_start: 0.8716 (mpp) cc_final: 0.8361 (tpp) REVERT: L 158 THR cc_start: 0.8341 (t) cc_final: 0.8082 (p) REVERT: L 161 MET cc_start: 0.8833 (tpt) cc_final: 0.8626 (mtt) outliers start: 35 outliers final: 11 residues processed: 159 average time/residue: 0.6724 time to fit residues: 126.4289 Evaluate side-chains 150 residues out of total 3584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 132 time to evaluate : 0.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 289 MET Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain E residue 220 SER Chi-restraints excluded: chain E residue 386 LEU Chi-restraints excluded: chain E residue 415 MET Chi-restraints excluded: chain H residue 145 LYS Chi-restraints excluded: chain H residue 223 ASN Chi-restraints excluded: chain J residue 381 ILE Chi-restraints excluded: chain J residue 384 ARG Chi-restraints excluded: chain K residue 18 THR Chi-restraints excluded: chain K residue 113 GLU Chi-restraints excluded: chain K residue 141 SER Chi-restraints excluded: chain L residue 16 LYS Chi-restraints excluded: chain L residue 46 SER Chi-restraints excluded: chain L residue 66 TYR Chi-restraints excluded: chain L residue 169 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 394 optimal weight: 7.9990 chunk 70 optimal weight: 0.9990 chunk 403 optimal weight: 20.0000 chunk 65 optimal weight: 1.9990 chunk 197 optimal weight: 2.9990 chunk 143 optimal weight: 0.9980 chunk 205 optimal weight: 2.9990 chunk 51 optimal weight: 5.9990 chunk 25 optimal weight: 8.9990 chunk 121 optimal weight: 1.9990 chunk 350 optimal weight: 0.4980 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 106 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.077362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.046716 restraints weight = 82298.353| |-----------------------------------------------------------------------------| r_work (start): 0.2750 rms_B_bonded: 3.31 r_work: 0.2581 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9030 moved from start: 0.2554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 32843 Z= 0.124 Angle : 0.490 9.434 44490 Z= 0.254 Chirality : 0.044 0.163 5162 Planarity : 0.004 0.052 5704 Dihedral : 4.960 86.547 4472 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.00 % Allowed : 6.84 % Favored : 92.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.61 % 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 are not related in a simple way. whole: 1.49 (0.13), residues: 4090 helix: 1.80 (0.14), residues: 1526 sheet: 0.38 (0.22), residues: 612 loop : 0.69 (0.14), residues: 1952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 344 TYR 0.011 0.001 TYR L 66 PHE 0.018 0.001 PHE L 162 TRP 0.009 0.001 TRP A 111 HIS 0.005 0.001 HIS B 168 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.12 (32840) covalent geometry : angle 0.49039 / 0.25 (44490) hydrogen bonds : bond 0.03602 / 2.40 ( 1361) hydrogen bonds : angle 3.95248 / 2.85 ( 3699) metal coordination : bond 0.00252 / 0.14 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8180 Ramachandran restraints generated. 4090 Oldfield, 0 Emsley, 4090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8180 Ramachandran restraints generated. 4090 Oldfield, 0 Emsley, 4090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 3584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 135 time to evaluate : 1.287 Fit side-chains REVERT: C 121 ASP cc_start: 0.8566 (t0) cc_final: 0.8162 (t0) REVERT: D 203 MET cc_start: 0.9280 (OUTLIER) cc_final: 0.9003 (tpp) REVERT: E 415 MET cc_start: 0.9103 (OUTLIER) cc_final: 0.8835 (tpp) REVERT: F 415 MET cc_start: 0.9270 (OUTLIER) cc_final: 0.8620 (ttm) REVERT: H 145 LYS cc_start: 0.9509 (OUTLIER) cc_final: 0.9290 (mmmt) REVERT: H 164 MET cc_start: 0.9039 (tpt) cc_final: 0.8748 (tpt) REVERT: H 223 ASN cc_start: 0.9210 (OUTLIER) cc_final: 0.8917 (t0) REVERT: I 67 PHE cc_start: 0.8141 (m-80) cc_final: 0.7295 (m-80) REVERT: J 8 MET cc_start: 0.9187 (OUTLIER) cc_final: 0.8451 (mmm) REVERT: J 84 MET cc_start: 0.8334 (mtp) cc_final: 0.8133 (ttm) REVERT: J 290 TRP cc_start: 0.3657 (p90) cc_final: 0.0664 (t-100) REVERT: K 169 MET cc_start: 0.8808 (mmp) cc_final: 0.8223 (mmt) REVERT: K 173 HIS cc_start: 0.7977 (m-70) cc_final: 0.7667 (m90) REVERT: L 1 MET cc_start: 0.7177 (pmm) cc_final: 0.6919 (ppp) REVERT: L 16 LYS cc_start: 0.7162 (OUTLIER) cc_final: 0.6627 (pttt) REVERT: L 64 HIS cc_start: 0.8444 (t-90) cc_final: 0.7745 (t-90) REVERT: L 66 TYR cc_start: 0.7243 (OUTLIER) cc_final: 0.6966 (p90) REVERT: L 136 MET cc_start: 0.8748 (mpp) cc_final: 0.8418 (tpp) REVERT: L 161 MET cc_start: 0.8827 (tpt) cc_final: 0.8608 (mtt) REVERT: L 180 LYS cc_start: 0.9049 (OUTLIER) cc_final: 0.8805 (mtmm) outliers start: 36 outliers final: 8 residues processed: 153 average time/residue: 0.7557 time to fit residues: 136.5864 Evaluate side-chains 147 residues out of total 3584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 130 time to evaluate : 1.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 289 MET Chi-restraints excluded: chain D residue 203 MET Chi-restraints excluded: chain E residue 220 SER Chi-restraints excluded: chain E residue 415 MET Chi-restraints excluded: chain F residue 415 MET Chi-restraints excluded: chain H residue 145 LYS Chi-restraints excluded: chain H residue 223 ASN Chi-restraints excluded: chain J residue 8 MET Chi-restraints excluded: chain J residue 381 ILE Chi-restraints excluded: chain K residue 18 THR Chi-restraints excluded: chain L residue 16 LYS Chi-restraints excluded: chain L residue 46 SER Chi-restraints excluded: chain L residue 66 TYR Chi-restraints excluded: chain L residue 169 MET Chi-restraints excluded: chain L residue 180 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 55 optimal weight: 0.0870 chunk 49 optimal weight: 3.9990 chunk 199 optimal weight: 4.9990 chunk 164 optimal weight: 4.9990 chunk 347 optimal weight: 2.9990 chunk 234 optimal weight: 4.9990 chunk 273 optimal weight: 0.9980 chunk 350 optimal weight: 0.3980 chunk 272 optimal weight: 0.9990 chunk 279 optimal weight: 2.9990 chunk 87 optimal weight: 6.9990 overall best weight: 1.0962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 106 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.077636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2824 r_free = 0.2824 target = 0.047002 restraints weight = 83179.187| |-----------------------------------------------------------------------------| r_work (start): 0.2759 rms_B_bonded: 3.32 r_work: 0.2590 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9024 moved from start: 0.2655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 32843 Z= 0.114 Angle : 0.487 9.986 44490 Z= 0.251 Chirality : 0.044 0.162 5162 Planarity : 0.004 0.050 5704 Dihedral : 4.857 86.299 4472 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 0.81 % Allowed : 7.53 % Favored : 91.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.61 % 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 are not related in a simple way. whole: 1.54 (0.13), residues: 4090 helix: 1.87 (0.14), residues: 1526 sheet: 0.28 (0.22), residues: 638 loop : 0.76 (0.14), residues: 1926 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG I 57 TYR 0.011 0.001 TYR L 66 PHE 0.017 0.001 PHE L 162 TRP 0.009 0.001 TRP A 111 HIS 0.005 0.001 HIS B 168 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.11 (32840) covalent geometry : angle 0.48745 / 0.25 (44490) hydrogen bonds : bond 0.03446 / 2.29 ( 1361) hydrogen bonds : angle 3.89967 / 2.81 ( 3699) metal coordination : bond 0.00212 / 0.12 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8180 Ramachandran restraints generated. 4090 Oldfield, 0 Emsley, 4090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8180 Ramachandran restraints generated. 4090 Oldfield, 0 Emsley, 4090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 3584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 135 time to evaluate : 1.301 Fit side-chains revert: symmetry clash REVERT: C 121 ASP cc_start: 0.8584 (t0) cc_final: 0.8171 (t0) REVERT: D 203 MET cc_start: 0.9279 (OUTLIER) cc_final: 0.8981 (tpp) REVERT: E 415 MET cc_start: 0.9092 (OUTLIER) cc_final: 0.8831 (tpp) REVERT: F 415 MET cc_start: 0.9270 (OUTLIER) cc_final: 0.8617 (ttm) REVERT: H 145 LYS cc_start: 0.9507 (OUTLIER) cc_final: 0.9305 (mmmt) REVERT: H 164 MET cc_start: 0.9032 (tpt) cc_final: 0.8724 (tpt) REVERT: H 223 ASN cc_start: 0.9205 (OUTLIER) cc_final: 0.8942 (t0) REVERT: J 8 MET cc_start: 0.9195 (OUTLIER) cc_final: 0.8423 (mmm) REVERT: J 84 MET cc_start: 0.8346 (mtp) cc_final: 0.8022 (ttm) REVERT: J 290 TRP cc_start: 0.3710 (p90) cc_final: 0.0707 (t-100) REVERT: K 113 GLU cc_start: 0.7676 (OUTLIER) cc_final: 0.6905 (pp20) REVERT: K 169 MET cc_start: 0.8853 (mmp) cc_final: 0.8295 (mmt) REVERT: K 173 HIS cc_start: 0.8041 (m-70) cc_final: 0.7692 (m90) REVERT: L 16 LYS cc_start: 0.7237 (OUTLIER) cc_final: 0.6797 (pttt) REVERT: L 64 HIS cc_start: 0.8477 (t-90) cc_final: 0.8256 (t-90) REVERT: L 136 MET cc_start: 0.8753 (mpp) cc_final: 0.8446 (tpp) REVERT: L 161 MET cc_start: 0.8805 (tpt) cc_final: 0.8581 (mtt) outliers start: 29 outliers final: 9 residues processed: 151 average time/residue: 0.7151 time to fit residues: 128.6594 Evaluate side-chains 150 residues out of total 3584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 133 time to evaluate : 1.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 289 MET Chi-restraints excluded: chain D residue 203 MET Chi-restraints excluded: chain E residue 220 SER Chi-restraints excluded: chain E residue 415 MET Chi-restraints excluded: chain F residue 415 MET Chi-restraints excluded: chain H residue 145 LYS Chi-restraints excluded: chain H residue 223 ASN Chi-restraints excluded: chain J residue 8 MET Chi-restraints excluded: chain J residue 381 ILE Chi-restraints excluded: chain K residue 18 THR Chi-restraints excluded: chain K residue 113 GLU Chi-restraints excluded: chain L residue 16 LYS Chi-restraints excluded: chain L residue 46 SER Chi-restraints excluded: chain L residue 141 SER Chi-restraints excluded: chain L residue 169 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 223 optimal weight: 1.9990 chunk 309 optimal weight: 10.0000 chunk 189 optimal weight: 3.9990 chunk 367 optimal weight: 7.9990 chunk 262 optimal weight: 5.9990 chunk 144 optimal weight: 0.7980 chunk 96 optimal weight: 6.9990 chunk 372 optimal weight: 30.0000 chunk 306 optimal weight: 5.9990 chunk 314 optimal weight: 0.0370 chunk 316 optimal weight: 30.0000 overall best weight: 2.5664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 106 GLN ** G 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.076407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2790 r_free = 0.2790 target = 0.045700 restraints weight = 83246.280| |-----------------------------------------------------------------------------| r_work (start): 0.2722 rms_B_bonded: 3.29 r_work: 0.2552 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9055 moved from start: 0.2690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 32843 Z= 0.210 Angle : 0.542 10.979 44490 Z= 0.276 Chirality : 0.046 0.162 5162 Planarity : 0.004 0.052 5704 Dihedral : 4.931 87.193 4472 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 0.92 % Allowed : 7.67 % Favored : 91.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.61 % 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 are not related in a simple way. whole: 1.48 (0.13), residues: 4090 helix: 1.86 (0.14), residues: 1524 sheet: 0.23 (0.22), residues: 634 loop : 0.69 (0.14), residues: 1932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 57 TYR 0.014 0.001 TYR I 210 PHE 0.020 0.001 PHE L 162 TRP 0.009 0.001 TRP A 111 HIS 0.006 0.001 HIS B 168 Details of bonding type rmsd/Z covalent geometry : bond 0.00507 / 0.21 (32840) covalent geometry : angle 0.54207 / 0.28 (44490) hydrogen bonds : bond 0.04003 / 2.67 ( 1361) hydrogen bonds : angle 4.00855 / 2.89 ( 3699) metal coordination : bond 0.00633 / 0.36 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8180 Ramachandran restraints generated. 4090 Oldfield, 0 Emsley, 4090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8180 Ramachandran restraints generated. 4090 Oldfield, 0 Emsley, 4090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 3584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 137 time to evaluate : 1.026 Fit side-chains REVERT: C 121 ASP cc_start: 0.8573 (t0) cc_final: 0.8175 (t0) REVERT: D 203 MET cc_start: 0.9285 (OUTLIER) cc_final: 0.8985 (tpp) REVERT: E 415 MET cc_start: 0.9119 (OUTLIER) cc_final: 0.8862 (tpp) REVERT: F 415 MET cc_start: 0.9296 (OUTLIER) cc_final: 0.8665 (ttm) REVERT: H 164 MET cc_start: 0.9050 (tpt) cc_final: 0.8666 (tpt) REVERT: J 8 MET cc_start: 0.9192 (OUTLIER) cc_final: 0.8457 (mmm) REVERT: J 84 MET cc_start: 0.8313 (mtp) cc_final: 0.7846 (ttm) REVERT: J 290 TRP cc_start: 0.3856 (p90) cc_final: 0.0823 (t-100) REVERT: K 113 GLU cc_start: 0.7726 (OUTLIER) cc_final: 0.6970 (pp20) REVERT: K 169 MET cc_start: 0.8869 (mmp) cc_final: 0.8308 (mmt) REVERT: K 173 HIS cc_start: 0.8010 (m-70) cc_final: 0.7655 (m90) REVERT: L 16 LYS cc_start: 0.7428 (OUTLIER) cc_final: 0.6928 (pttt) REVERT: L 64 HIS cc_start: 0.8420 (t-90) cc_final: 0.7764 (t-90) REVERT: L 66 TYR cc_start: 0.7289 (OUTLIER) cc_final: 0.6872 (p90) REVERT: L 136 MET cc_start: 0.8771 (mpp) cc_final: 0.8450 (tpp) REVERT: L 158 THR cc_start: 0.8369 (t) cc_final: 0.8101 (p) REVERT: L 161 MET cc_start: 0.8813 (tpt) cc_final: 0.8603 (mtt) outliers start: 33 outliers final: 12 residues processed: 157 average time/residue: 0.6535 time to fit residues: 122.4397 Evaluate side-chains 150 residues out of total 3584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 131 time to evaluate : 1.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 MET Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 289 MET Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 203 MET Chi-restraints excluded: chain E residue 220 SER Chi-restraints excluded: chain E residue 386 LEU Chi-restraints excluded: chain E residue 415 MET Chi-restraints excluded: chain F residue 415 MET Chi-restraints excluded: chain J residue 8 MET Chi-restraints excluded: chain J residue 381 ILE Chi-restraints excluded: chain K residue 18 THR Chi-restraints excluded: chain K residue 113 GLU Chi-restraints excluded: chain L residue 16 LYS Chi-restraints excluded: chain L residue 46 SER Chi-restraints excluded: chain L residue 66 TYR Chi-restraints excluded: chain L residue 141 SER Chi-restraints excluded: chain L residue 169 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 320 optimal weight: 5.9990 chunk 262 optimal weight: 0.9980 chunk 232 optimal weight: 9.9990 chunk 234 optimal weight: 0.8980 chunk 97 optimal weight: 8.9990 chunk 315 optimal weight: 6.9990 chunk 371 optimal weight: 50.0000 chunk 313 optimal weight: 20.0000 chunk 31 optimal weight: 4.9990 chunk 161 optimal weight: 2.9990 chunk 103 optimal weight: 0.8980 overall best weight: 2.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 106 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.076963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2809 r_free = 0.2809 target = 0.046360 restraints weight = 84168.218| |-----------------------------------------------------------------------------| r_work (start): 0.2736 rms_B_bonded: 3.23 r_work: 0.2570 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9020 moved from start: 0.2770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 32843 Z= 0.177 Angle : 0.534 11.655 44490 Z= 0.271 Chirality : 0.045 0.214 5162 Planarity : 0.004 0.051 5704 Dihedral : 4.892 87.838 4472 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 0.84 % Allowed : 8.01 % Favored : 91.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.61 % 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 are not related in a simple way. whole: 1.50 (0.13), residues: 4090 helix: 1.86 (0.14), residues: 1524 sheet: 0.26 (0.23), residues: 592 loop : 0.70 (0.14), residues: 1974 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 57 TYR 0.013 0.001 TYR L 66 PHE 0.021 0.001 PHE L 162 TRP 0.010 0.001 TRP A 111 HIS 0.005 0.001 HIS B 168 Details of bonding type rmsd/Z covalent geometry : bond 0.00428 / 0.18 (32840) covalent geometry : angle 0.53402 / 0.27 (44490) hydrogen bonds : bond 0.03775 / 2.51 ( 1361) hydrogen bonds : angle 3.97202 / 2.86 ( 3699) metal coordination : bond 0.00448 / 0.26 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8180 Ramachandran restraints generated. 4090 Oldfield, 0 Emsley, 4090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8180 Ramachandran restraints generated. 4090 Oldfield, 0 Emsley, 4090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 3584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 131 time to evaluate : 1.314 Fit side-chains revert: symmetry clash REVERT: C 121 ASP cc_start: 0.8537 (t0) cc_final: 0.8134 (t0) REVERT: E 415 MET cc_start: 0.9100 (OUTLIER) cc_final: 0.8823 (tpp) REVERT: F 415 MET cc_start: 0.9271 (OUTLIER) cc_final: 0.8637 (ttm) REVERT: H 164 MET cc_start: 0.9041 (tpt) cc_final: 0.8719 (tpt) REVERT: I 84 MET cc_start: 0.8363 (mmp) cc_final: 0.7788 (ptm) REVERT: I 286 ARG cc_start: 0.6379 (OUTLIER) cc_final: 0.5762 (mtm110) REVERT: J 8 MET cc_start: 0.9165 (OUTLIER) cc_final: 0.8427 (mmm) REVERT: J 84 MET cc_start: 0.8277 (mtp) cc_final: 0.7819 (ttm) REVERT: J 290 TRP cc_start: 0.3872 (p90) cc_final: 0.0843 (t-100) REVERT: K 113 GLU cc_start: 0.7744 (OUTLIER) cc_final: 0.7054 (pp20) REVERT: K 169 MET cc_start: 0.8850 (mmp) cc_final: 0.8309 (mmt) REVERT: K 173 HIS cc_start: 0.8063 (m-70) cc_final: 0.7734 (m90) REVERT: L 16 LYS cc_start: 0.7297 (OUTLIER) cc_final: 0.7066 (pttt) REVERT: L 64 HIS cc_start: 0.8414 (t-90) cc_final: 0.8204 (t-90) REVERT: L 136 MET cc_start: 0.8787 (mpp) cc_final: 0.8480 (tpp) REVERT: L 161 MET cc_start: 0.8802 (tpt) cc_final: 0.8586 (mtt) REVERT: L 180 LYS cc_start: 0.9001 (OUTLIER) cc_final: 0.8786 (mtmm) outliers start: 30 outliers final: 12 residues processed: 149 average time/residue: 0.7320 time to fit residues: 129.0278 Evaluate side-chains 145 residues out of total 3584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 126 time to evaluate : 1.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 MET Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 289 MET Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain E residue 220 SER Chi-restraints excluded: chain E residue 386 LEU Chi-restraints excluded: chain E residue 415 MET Chi-restraints excluded: chain F residue 415 MET Chi-restraints excluded: chain I residue 286 ARG Chi-restraints excluded: chain J residue 8 MET Chi-restraints excluded: chain J residue 381 ILE Chi-restraints excluded: chain K residue 18 THR Chi-restraints excluded: chain K residue 113 GLU Chi-restraints excluded: chain L residue 16 LYS Chi-restraints excluded: chain L residue 46 SER Chi-restraints excluded: chain L residue 141 SER Chi-restraints excluded: chain L residue 169 MET Chi-restraints excluded: chain L residue 180 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 108 optimal weight: 3.9990 chunk 2 optimal weight: 0.9990 chunk 339 optimal weight: 10.0000 chunk 336 optimal weight: 5.9990 chunk 261 optimal weight: 10.0000 chunk 42 optimal weight: 0.5980 chunk 68 optimal weight: 4.9990 chunk 210 optimal weight: 0.6980 chunk 94 optimal weight: 1.9990 chunk 185 optimal weight: 4.9990 chunk 73 optimal weight: 2.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 106 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.077649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.046487 restraints weight = 84769.612| |-----------------------------------------------------------------------------| r_work (start): 0.2744 rms_B_bonded: 3.32 r_work: 0.2581 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.2581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9009 moved from start: 0.2838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 32843 Z= 0.136 Angle : 0.516 11.807 44490 Z= 0.262 Chirality : 0.044 0.176 5162 Planarity : 0.004 0.050 5704 Dihedral : 4.810 87.737 4472 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 0.61 % Allowed : 8.26 % Favored : 91.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.61 % 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 are not related in a simple way. whole: 1.53 (0.13), residues: 4090 helix: 1.90 (0.14), residues: 1526 sheet: 0.24 (0.23), residues: 590 loop : 0.72 (0.14), residues: 1974 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 57 TYR 0.016 0.001 TYR L 66 PHE 0.023 0.001 PHE L 162 TRP 0.010 0.001 TRP A 111 HIS 0.005 0.001 HIS B 168 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.14 (32840) covalent geometry : angle 0.51634 / 0.26 (44490) hydrogen bonds : bond 0.03542 / 2.36 ( 1361) hydrogen bonds : angle 3.91652 / 2.81 ( 3699) metal coordination : bond 0.00315 / 0.18 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8180 Ramachandran restraints generated. 4090 Oldfield, 0 Emsley, 4090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8180 Ramachandran restraints generated. 4090 Oldfield, 0 Emsley, 4090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 3584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 132 time to evaluate : 1.339 Fit side-chains REVERT: C 121 ASP cc_start: 0.8547 (t0) cc_final: 0.8128 (t0) REVERT: E 415 MET cc_start: 0.9082 (OUTLIER) cc_final: 0.8807 (tpp) REVERT: F 415 MET cc_start: 0.9265 (OUTLIER) cc_final: 0.8625 (ttm) REVERT: H 164 MET cc_start: 0.8991 (tpt) cc_final: 0.8666 (tpt) REVERT: I 8 MET cc_start: 0.8849 (mmm) cc_final: 0.8611 (mmt) REVERT: I 84 MET cc_start: 0.8320 (mmp) cc_final: 0.7937 (ptm) REVERT: J 8 MET cc_start: 0.9188 (OUTLIER) cc_final: 0.8458 (mmm) REVERT: J 84 MET cc_start: 0.8291 (mtp) cc_final: 0.7854 (ttm) REVERT: J 290 TRP cc_start: 0.3855 (p90) cc_final: 0.0814 (t-100) REVERT: K 113 GLU cc_start: 0.7804 (OUTLIER) cc_final: 0.7111 (pp20) REVERT: K 169 MET cc_start: 0.8822 (mmp) cc_final: 0.8302 (mmt) REVERT: K 173 HIS cc_start: 0.8049 (m-70) cc_final: 0.7706 (m90) REVERT: L 16 LYS cc_start: 0.7330 (OUTLIER) cc_final: 0.7115 (pttt) REVERT: L 64 HIS cc_start: 0.8411 (t-90) cc_final: 0.8200 (t-90) REVERT: L 136 MET cc_start: 0.8793 (mpp) cc_final: 0.8484 (tpp) REVERT: L 161 MET cc_start: 0.8813 (tpt) cc_final: 0.8599 (mtt) outliers start: 22 outliers final: 10 residues processed: 145 average time/residue: 0.7398 time to fit residues: 127.9351 Evaluate side-chains 142 residues out of total 3584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 127 time to evaluate : 1.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 MET Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 289 MET Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain E residue 220 SER Chi-restraints excluded: chain E residue 415 MET Chi-restraints excluded: chain F residue 415 MET Chi-restraints excluded: chain J residue 8 MET Chi-restraints excluded: chain K residue 18 THR Chi-restraints excluded: chain K residue 113 GLU Chi-restraints excluded: chain L residue 16 LYS Chi-restraints excluded: chain L residue 46 SER Chi-restraints excluded: chain L residue 141 SER Chi-restraints excluded: chain L residue 169 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 214 optimal weight: 2.9990 chunk 205 optimal weight: 2.9990 chunk 284 optimal weight: 4.9990 chunk 184 optimal weight: 7.9990 chunk 395 optimal weight: 9.9990 chunk 18 optimal weight: 3.9990 chunk 158 optimal weight: 0.5980 chunk 54 optimal weight: 4.9990 chunk 29 optimal weight: 3.9990 chunk 319 optimal weight: 0.0980 chunk 212 optimal weight: 0.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 106 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.077374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2798 r_free = 0.2798 target = 0.046017 restraints weight = 82749.344| |-----------------------------------------------------------------------------| r_work (start): 0.2738 rms_B_bonded: 3.38 r_work: 0.2572 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.2572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9072 moved from start: 0.2891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 32843 Z= 0.140 Angle : 0.521 11.818 44490 Z= 0.263 Chirality : 0.044 0.234 5162 Planarity : 0.004 0.050 5704 Dihedral : 4.755 87.708 4472 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 0.50 % Allowed : 8.51 % Favored : 90.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.61 % 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 are not related in a simple way. whole: 1.56 (0.13), residues: 4090 helix: 1.94 (0.14), residues: 1524 sheet: 0.22 (0.22), residues: 590 loop : 0.73 (0.14), residues: 1976 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 57 TYR 0.017 0.001 TYR L 66 PHE 0.028 0.001 PHE L 162 TRP 0.009 0.001 TRP A 111 HIS 0.006 0.001 HIS B 168 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.14 (32840) covalent geometry : angle 0.52098 / 0.26 (44490) hydrogen bonds : bond 0.03523 / 2.35 ( 1361) hydrogen bonds : angle 3.90807 / 2.81 ( 3699) metal coordination : bond 0.00339 / 0.19 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8897.52 seconds wall clock time: 152 minutes 46.53 seconds (9166.53 seconds total)