Starting phenix.real_space_refine on Sun Aug 9 00:11:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9y4w_72499/08_2026/9y4w_72499.cif Found real_map, /net/cci-nas-00/data/ceres_data/9y4w_72499/08_2026/9y4w_72499.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9y4w_72499/08_2026/9y4w_72499.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9y4w_72499/08_2026/9y4w_72499.map" model { file = "/net/cci-nas-00/data/ceres_data/9y4w_72499/08_2026/9y4w_72499.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9y4w_72499/08_2026/9y4w_72499.cif" } resolution = 2.4 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= -0.000 sd= 0.006 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 2 6.06 5 P 3 5.49 5 S 173 5.16 5 Cl 3 4.86 5 C 19343 2.51 5 N 5302 2.21 5 O 5686 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 230 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: 30512 Number of models: 1 Model: "" Number of chains: 19 Chain: "A" Number of atoms: 3492 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3492 Classifications: {'peptide': 445} Link IDs: {'PCIS': 3, 'PTRANS': 18, 'TRANS': 423} Chain breaks: 2 Chain: "B" Number of atoms: 3492 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3492 Classifications: {'peptide': 445} Link IDs: {'PCIS': 3, 'PTRANS': 18, 'TRANS': 423} Chain breaks: 2 Chain: "C" Number of atoms: 2583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2583 Classifications: {'peptide': 331} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 316} Chain: "D" Number of atoms: 2583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2583 Classifications: {'peptide': 331} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 316} 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: 3268 Number of conformers: 1 Conformer: "" Number of residues, atoms: 421, 3268 Classifications: {'peptide': 421} Link IDs: {'PTRANS': 18, 'TRANS': 402} Chain breaks: 1 Chain: "J" Number of atoms: 3268 Number of conformers: 1 Conformer: "" Number of residues, atoms: 421, 3268 Classifications: {'peptide': 421} Link IDs: {'PTRANS': 18, 'TRANS': 402} Chain breaks: 1 Chain: "K" Number of atoms: 1660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1660 Classifications: {'peptide': 209} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 196} 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: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'PO4': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'PO4': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CL': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CL': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'PO4': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "H" 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 13501 SG CYS E 338 65.874 55.877 52.735 1.00 24.47 S ATOM 24332 SG CYS I 281 67.387 54.555 50.314 1.00 29.24 S ATOM 16271 SG CYS F 338 63.867 76.799 115.434 1.00 28.63 S ATOM 27600 SG CYS J 281 65.252 78.281 117.913 1.00 27.20 S Time building chain proxies: 6.84, per 1000 atoms: 0.22 Number of scatterers: 30512 At special positions: 0 Unit cell: (152.29, 133.718, 169.934, 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 2 29.99 Cl 3 17.00 S 173 16.00 P 3 15.00 O 5686 8.00 N 5302 7.00 C 19343 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: 2.11 Conformation dependent library (CDL) restraints added in 1.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN E 602 " pdb="ZN ZN E 602 " - pdb=" SG CYS I 281 " pdb="ZN ZN E 602 " - pdb=" SG CYS E 338 " pdb="ZN ZN E 602 " - pdb=" ND1 HIS E 371 " pdb=" ZN J 501 " pdb="ZN ZN J 501 " - pdb=" SG CYS J 281 " pdb="ZN ZN J 501 " - pdb=" SG CYS F 338 " pdb="ZN ZN J 501 " - pdb=" ND1 HIS F 371 " 7738 Ramachandran restraints generated. 3869 Oldfield, 0 Emsley, 3869 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7362 Finding SS restraints... Secondary structure from input PDB file: 185 helices and 43 sheets defined 46.0% alpha, 15.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.10 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 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 196 through 199 Processing helix chain 'A' and resid 229 through 232 Processing helix chain 'A' and resid 253 through 263 removed outlier: 4.319A 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 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: 3.547A 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 141 Processing helix chain 'B' and resid 161 through 175 Processing helix chain 'B' and resid 196 through 199 Processing helix chain 'B' and resid 229 through 232 Processing helix chain 'B' and resid 253 through 263 removed outlier: 4.293A 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: 3.523A pdb=" N ASN B 326 " --> pdb=" O PRO B 323 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 334 removed outlier: 3.629A 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 25 Processing helix chain 'C' and resid 30 through 49 Processing helix chain 'C' and resid 53 through 72 removed outlier: 3.844A pdb=" N GLN C 72 " --> pdb=" O MET C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 75 through 97 removed outlier: 4.094A pdb=" N GLY C 79 " --> pdb=" O GLU C 75 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 118 removed outlier: 4.071A pdb=" N SER C 101 " --> pdb=" O GLY C 98 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N GLY C 102 " --> pdb=" O ARG C 99 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 146 removed outlier: 3.567A 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: 3.636A pdb=" N ARG C 183 " --> pdb=" O LYS C 179 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 210 Processing helix chain 'C' and resid 221 through 227 removed outlier: 4.351A pdb=" N SER C 227 " --> pdb=" O PHE C 223 " (cutoff:3.500A) 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 296 through 305 removed outlier: 6.447A pdb=" N ASP C 301 " --> pdb=" O THR C 298 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N ILE C 302 " --> pdb=" O GLU C 299 " (cutoff:3.500A) 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 Processing helix chain 'C' and resid 345 through 349 removed outlier: 3.678A 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: 3.780A pdb=" N GLN D 72 " --> pdb=" O MET D 68 " (cutoff:3.500A) Processing helix chain 'D' and resid 75 through 97 removed outlier: 4.115A pdb=" N GLY D 79 " --> pdb=" O GLU D 75 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 118 removed outlier: 4.271A pdb=" N GLY D 104 " --> pdb=" O SER D 101 " (cutoff:3.500A) Processing helix chain 'D' and resid 128 through 153 removed outlier: 3.549A pdb=" N ASN D 132 " --> pdb=" O GLN D 128 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLY D 146 " --> pdb=" O VAL D 142 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N MET D 148 " --> pdb=" O LEU D 144 " (cutoff:3.500A) removed outlier: 5.366A 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: 3.620A pdb=" N ARG D 183 " --> pdb=" O LYS D 179 " (cutoff:3.500A) Processing helix chain 'D' and resid 199 through 210 Processing helix chain 'D' and resid 221 through 227 removed outlier: 4.478A pdb=" N SER D 227 " --> pdb=" O PHE D 223 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 261 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 304 removed outlier: 6.302A pdb=" N ASP D 301 " --> pdb=" O THR D 298 " (cutoff:3.500A) removed outlier: 4.209A 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 Processing helix chain 'D' and resid 345 through 349 removed outlier: 3.641A pdb=" N HIS D 349 " --> pdb=" O PRO D 346 " (cutoff:3.500A) Processing helix chain 'E' and resid 177 through 181 Processing helix chain 'E' and resid 191 through 195 Processing helix chain 'E' and resid 204 through 216 Processing helix chain 'E' and resid 221 through 240 removed outlier: 3.526A pdb=" N CYS E 226 " --> pdb=" O SER E 222 " (cutoff:3.500A) Processing helix chain 'E' and resid 247 through 267 removed outlier: 5.211A pdb=" N VAL E 253 " --> pdb=" O SER E 249 " (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: 3.622A pdb=" N GLN E 317 " --> pdb=" O VAL E 313 " (cutoff:3.500A) Processing helix chain 'E' and resid 339 through 352 Processing helix chain 'E' and resid 368 through 379 removed outlier: 3.808A pdb=" N THR E 372 " --> pdb=" O GLU E 368 " (cutoff:3.500A) Processing helix chain 'E' and resid 390 through 395 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 443 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 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 521 Processing helix chain 'F' and resid 191 through 196 removed outlier: 3.759A 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: 3.714A pdb=" N CYS F 226 " --> pdb=" O SER F 222 " (cutoff:3.500A) Processing helix chain 'F' and resid 247 through 267 removed outlier: 4.978A pdb=" N VAL F 253 " --> pdb=" O SER F 249 " (cutoff:3.500A) removed outlier: 3.659A 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 removed outlier: 3.500A pdb=" N SER F 298 " --> pdb=" O GLU F 294 " (cutoff:3.500A) Processing helix chain 'F' and resid 312 through 325 removed outlier: 3.748A pdb=" N GLN F 317 " --> pdb=" O VAL F 313 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N GLN F 325 " --> pdb=" O ARG F 321 " (cutoff:3.500A) Processing helix chain 'F' and resid 339 through 352 Processing helix chain 'F' and resid 368 through 380 removed outlier: 3.769A pdb=" N THR F 372 " --> pdb=" O GLU F 368 " (cutoff:3.500A) Processing helix chain 'F' and resid 390 through 395 Processing helix chain 'F' and resid 396 through 398 No H-bonds generated for 'chain 'F' and resid 396 through 398' 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 464 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 521 Processing helix chain 'G' and resid 2 through 17 removed outlier: 3.690A pdb=" N LEU G 6 " --> pdb=" O ASP G 2 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ASP G 17 " --> pdb=" O GLN G 13 " (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 78 removed outlier: 3.729A pdb=" N SER G 66 " --> pdb=" O SER G 62 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N LEU G 78 " --> pdb=" O ARG G 74 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 82 Processing helix chain 'G' and resid 85 through 105 removed outlier: 4.631A pdb=" N LYS G 91 " --> pdb=" O SER G 87 " (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: 3.695A pdb=" N LYS G 163 " --> pdb=" O LEU G 159 " (cutoff:3.500A) removed outlier: 3.537A 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: 4.313A pdb=" N SER G 297 " --> pdb=" O PRO G 293 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ASP G 298 " --> pdb=" O SER G 294 " (cutoff:3.500A) Processing helix chain 'H' and resid 2 through 17 removed outlier: 3.709A pdb=" N LEU H 6 " --> pdb=" O ASP H 2 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N MET H 14 " --> pdb=" O PHE H 10 " (cutoff:3.500A) Processing helix chain 'H' and resid 21 through 37 Processing helix chain 'H' and resid 41 through 60 removed outlier: 3.510A pdb=" N VAL H 59 " --> pdb=" O THR H 55 " (cutoff:3.500A) Processing helix chain 'H' and resid 62 through 78 removed outlier: 3.619A pdb=" N SER H 66 " --> pdb=" O SER H 62 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU H 78 " --> pdb=" O ARG H 74 " (cutoff:3.500A) Processing helix chain 'H' and resid 79 through 82 Processing helix chain 'H' and resid 85 through 106 removed outlier: 3.797A pdb=" N LYS H 91 " --> pdb=" O SER H 87 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N LEU H 106 " --> pdb=" O ARG H 102 " (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 Processing helix chain 'H' and resid 159 through 170 removed outlier: 3.795A pdb=" N LYS H 163 " --> pdb=" O LEU H 159 " (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 242 through 246 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 304 removed outlier: 4.333A pdb=" N SER H 297 " --> pdb=" O PRO H 293 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ASP H 298 " --> pdb=" O SER H 294 " (cutoff:3.500A) 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 66 removed outlier: 3.580A pdb=" N GLN I 60 " --> pdb=" O THR I 56 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LYS I 61 " --> pdb=" O ARG I 57 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N ALA I 62 " --> pdb=" O ASP I 58 " (cutoff:3.500A) Processing helix chain 'I' and resid 85 through 93 removed outlier: 3.635A 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: 4.562A pdb=" N LEU I 120 " --> pdb=" O GLU I 116 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N PHE I 121 " --> pdb=" O VAL I 117 " (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 216 removed outlier: 3.921A pdb=" N VAL I 212 " --> pdb=" O LYS I 208 " (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: 4.021A pdb=" N SER I 331 " --> pdb=" O PRO I 327 " (cutoff:3.500A) removed outlier: 4.097A 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 13 through 15 No H-bonds generated for 'chain 'J' and resid 13 through 15' 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: 3.521A pdb=" N GLN J 60 " --> pdb=" O THR J 56 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LYS J 61 " --> pdb=" O ARG J 57 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N ALA J 62 " --> pdb=" O ASP J 58 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU J 63 " --> pdb=" O VAL J 59 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N PHE J 67 " --> pdb=" O LEU J 63 " (cutoff:3.500A) Processing helix chain 'J' and resid 85 through 92 Processing helix chain 'J' and resid 93 through 97 Processing helix chain 'J' and resid 114 through 124 removed outlier: 4.320A pdb=" N LEU J 120 " --> pdb=" O GLU J 116 " (cutoff:3.500A) Processing helix chain 'J' and resid 144 through 148 removed outlier: 4.248A 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 190 removed outlier: 3.678A pdb=" N LYS J 189 " --> pdb=" O SER J 185 " (cutoff:3.500A) Processing helix chain 'J' and resid 208 through 218 removed outlier: 3.786A pdb=" N VAL J 212 " --> pdb=" O LYS J 208 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N MET J 216 " --> pdb=" O VAL J 212 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N GLU J 217 " --> pdb=" O ASP J 213 " (cutoff:3.500A) Processing helix chain 'J' and resid 227 through 236 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: 3.724A pdb=" N SER J 331 " --> pdb=" O PRO J 327 " (cutoff:3.500A) removed outlier: 3.916A 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 removed outlier: 3.555A pdb=" N CYS K 27 " --> pdb=" O LEU K 23 " (cutoff:3.500A) Processing helix chain 'K' and resid 41 through 44 Processing helix chain 'K' and resid 48 through 57 removed outlier: 3.977A pdb=" N LEU K 54 " --> pdb=" O ASP K 50 " (cutoff:3.500A) 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 removed outlier: 3.550A pdb=" N TYR K 126 " --> pdb=" O PHE K 123 " (cutoff:3.500A) 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: 3.745A 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: 3.717A pdb=" N TYR K 207 " --> pdb=" O PRO K 203 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 119 through 124 removed outlier: 6.577A pdb=" N THR A 91 " --> pdb=" O ARG A 121 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N ILE A 123 " --> pdb=" O THR A 91 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N VAL A 93 " --> pdb=" O ILE A 123 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N TYR A 152 " --> pdb=" O HIS A 248 " (cutoff:3.500A) removed outlier: 8.627A pdb=" N HIS A 248 " --> pdb=" O TYR A 152 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N CYS A 247 " --> pdb=" O LYS A 186 " (cutoff:3.500A) removed outlier: 8.000A pdb=" N LYS A 186 " --> pdb=" O CYS A 247 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N ILE A 249 " --> pdb=" O ILE A 184 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N GLN A 286 " --> pdb=" O SER A 179 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N MET A 181 " --> pdb=" O GLN A 286 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N ILE A 287 " --> pdb=" O VAL A 212 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ARG A 211 " --> pdb=" O ASP A 206 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N ALA A 204 " --> pdb=" O LEU A 213 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N PHE A 215 " --> pdb=" O VAL A 202 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N VAL A 202 " --> pdb=" O PHE A 215 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N VAL A 238 " --> pdb=" O PHE I 195 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N PHE I 157 " --> pdb=" O MET I 170 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N MET I 170 " --> pdb=" O PHE I 157 " (cutoff:3.500A) removed outlier: 6.427A 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: 6.239A pdb=" N LEU A 361 " --> pdb=" O ILE A 379 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N VAL A 378 " --> pdb=" O LEU A 396 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N TYR A 395 " --> pdb=" O LEU A 413 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N LEU A 412 " --> pdb=" O LEU A 431 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N VAL A 430 " --> pdb=" O ILE A 449 " (cutoff:3.500A) removed outlier: 4.260A 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: 6.156A pdb=" N SER A 349 " --> pdb=" O ILE A 368 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N VAL A 367 " --> pdb=" O ILE A 385 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N HIS A 384 " --> pdb=" O VAL A 402 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N ARG A 401 " --> pdb=" O VAL A 419 " (cutoff:3.500A) removed outlier: 6.890A 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: 6.433A pdb=" N ILE A 355 " --> pdb=" O ILE A 374 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N PHE A 373 " --> pdb=" O LEU A 391 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N VAL A 390 " --> pdb=" O ILE A 408 " (cutoff:3.500A) removed outlier: 6.713A 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: 6.589A pdb=" N THR B 91 " --> pdb=" O ARG B 121 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N ILE B 123 " --> pdb=" O THR B 91 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N VAL B 93 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N TYR B 152 " --> pdb=" O HIS B 248 " (cutoff:3.500A) removed outlier: 8.594A pdb=" N HIS B 248 " --> pdb=" O TYR B 152 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N CYS B 247 " --> pdb=" O ILE B 184 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N ILE B 184 " --> pdb=" O CYS B 247 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N ILE B 249 " --> pdb=" O THR B 182 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N THR B 182 " --> pdb=" O ILE B 249 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N ILE B 251 " --> pdb=" O VAL B 180 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N VAL B 180 " --> pdb=" O ILE B 251 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N GLN B 286 " --> pdb=" O SER B 179 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N MET B 181 " --> pdb=" O GLN B 286 " (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 212 through 217 removed outlier: 6.372A pdb=" N ALA B 204 " --> pdb=" O LEU B 213 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N PHE B 215 " --> pdb=" O VAL B 202 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N VAL B 202 " --> pdb=" O PHE B 215 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N VAL B 238 " --> pdb=" O PHE J 195 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N PHE J 157 " --> pdb=" O MET J 170 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N MET J 170 " --> pdb=" O PHE J 157 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N GLY J 159 " --> pdb=" O LEU J 168 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 223 through 227 Processing sheet with id=AB4, first strand: chain 'B' and resid 336 through 338 removed outlier: 6.248A pdb=" N LEU B 361 " --> pdb=" O ILE B 379 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N VAL B 378 " --> pdb=" O LEU B 396 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N TYR B 395 " --> pdb=" O LEU B 413 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N LEU B 412 " --> pdb=" O LEU B 431 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N VAL B 430 " --> pdb=" O ILE B 449 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N VAL B 448 " --> pdb=" O TRP B 497 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 349 through 350 removed outlier: 6.309A pdb=" N SER B 349 " --> pdb=" O ILE B 368 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N VAL B 367 " --> pdb=" O ILE B 385 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N HIS B 384 " --> pdb=" O VAL B 402 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ARG B 401 " --> pdb=" O VAL B 419 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N GLU B 418 " --> pdb=" O VAL B 437 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'B' and resid 355 through 356 removed outlier: 6.421A pdb=" N ILE B 355 " --> pdb=" O ILE B 374 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N PHE B 373 " --> pdb=" O LEU B 391 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N VAL B 390 " --> pdb=" O ILE B 408 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N GLN B 407 " --> pdb=" O LEU B 425 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N THR B 424 " --> pdb=" O LEU B 443 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'C' and resid 329 through 331 removed outlier: 6.610A pdb=" N LEU C 265 " --> pdb=" O LEU C 323 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N ILE C 325 " --> pdb=" O LEU C 265 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N VAL C 267 " --> pdb=" O ILE C 325 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N VAL C 232 " --> pdb=" O ILE C 266 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N CYS C 268 " --> pdb=" O VAL C 232 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ILE C 234 " --> pdb=" O CYS C 268 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N ILE C 168 " --> pdb=" O ILE C 233 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N GLU C 163 " --> pdb=" O HIS C 188 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N ILE C 190 " --> pdb=" O GLU C 163 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ILE C 165 " --> pdb=" O ILE C 190 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N ALA C 192 " --> pdb=" O ILE C 165 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N THR C 167 " --> pdb=" O ALA C 192 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N GLU C 213 " --> pdb=" O PHE C 187 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N THR C 214 " --> pdb=" O ARG F 483 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N LEU F 485 " --> pdb=" O THR C 214 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N VAL C 216 " --> pdb=" O LEU F 485 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 238 through 239 Processing sheet with id=AB9, first strand: chain 'C' and resid 307 through 308 removed outlier: 6.616A pdb=" N SER C 307 " --> pdb=" O TYR F 385 " (cutoff:3.500A) removed outlier: 8.898A pdb=" N LEU F 387 " --> pdb=" O SER C 307 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N ILE F 333 " --> pdb=" O VAL F 359 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N VAL F 361 " --> pdb=" O ILE F 333 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N VAL F 335 " --> pdb=" O VAL F 361 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N VAL F 332 " --> pdb=" O LYS F 400 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N LEU F 402 " --> pdb=" O VAL F 332 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N LEU F 334 " --> pdb=" O LEU F 402 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N GLY F 404 " --> pdb=" O LEU F 334 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N TYR F 336 " --> pdb=" O GLY F 404 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N VAL F 401 " --> pdb=" O LEU F 435 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N CYS F 437 " --> pdb=" O VAL F 401 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N LEU F 403 " --> pdb=" O CYS F 437 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N VAL F 434 " --> pdb=" O LEU F 499 " (cutoff:3.500A) removed outlier: 7.953A pdb=" N ILE F 501 " --> pdb=" O VAL F 434 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N VAL F 436 " --> pdb=" O ILE F 501 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 329 through 331 removed outlier: 6.659A pdb=" N LEU D 265 " --> pdb=" O LEU D 323 " (cutoff:3.500A) removed outlier: 7.760A pdb=" N ILE D 325 " --> pdb=" O LEU D 265 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N VAL D 267 " --> pdb=" O ILE D 325 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N VAL D 232 " --> pdb=" O ILE D 266 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N CYS D 268 " --> pdb=" O VAL D 232 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N ILE D 234 " --> pdb=" O CYS D 268 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N ILE D 168 " --> pdb=" O ILE D 233 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N GLU D 163 " --> pdb=" O HIS D 188 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N ILE D 190 " --> pdb=" O GLU D 163 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N ILE D 165 " --> pdb=" O ILE D 190 " (cutoff:3.500A) removed outlier: 7.703A pdb=" N ALA D 192 " --> pdb=" O ILE D 165 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N THR D 167 " --> pdb=" O ALA D 192 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N GLU D 213 " --> pdb=" O PHE D 187 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N THR D 214 " --> pdb=" O ARG E 483 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N LEU E 485 " --> pdb=" O THR D 214 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N VAL D 216 " --> pdb=" O LEU E 485 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 238 through 239 Processing sheet with id=AC3, first strand: chain 'D' and resid 306 through 308 removed outlier: 6.605A pdb=" N SER D 307 " --> pdb=" O TYR E 385 " (cutoff:3.500A) removed outlier: 8.904A pdb=" N LEU E 387 " --> pdb=" O SER D 307 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N ILE E 333 " --> pdb=" O VAL E 359 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N VAL E 361 " --> pdb=" O ILE E 333 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N VAL E 335 " --> pdb=" O VAL E 361 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N VAL E 332 " --> pdb=" O LYS E 400 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N LEU E 402 " --> pdb=" O VAL E 332 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N LEU E 334 " --> pdb=" O LEU E 402 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N GLY E 404 " --> pdb=" O LEU E 334 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N TYR E 336 " --> pdb=" O GLY E 404 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N VAL E 401 " --> pdb=" O LEU E 435 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N CYS E 437 " --> pdb=" O VAL E 401 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N LEU E 403 " --> pdb=" O CYS E 437 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N VAL E 434 " --> pdb=" O LEU E 499 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N ILE E 501 " --> pdb=" O VAL E 434 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N VAL E 436 " --> pdb=" O ILE E 501 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 407 through 408 Processing sheet with id=AC5, first strand: chain 'E' and resid 466 through 467 Processing sheet with id=AC6, first strand: chain 'F' and resid 443 through 444 removed outlier: 6.458A pdb=" N LEU F 408 " --> pdb=" O CYS F 444 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 466 through 467 Processing sheet with id=AC8, first strand: chain 'G' and resid 289 through 291 removed outlier: 6.731A pdb=" N PHE G 226 " --> pdb=" O LEU G 283 " (cutoff:3.500A) removed outlier: 8.103A pdb=" N PHE G 285 " --> pdb=" O PHE G 226 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N VAL G 228 " --> pdb=" O PHE G 285 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N VAL G 193 " --> pdb=" O TYR G 227 " (cutoff:3.500A) removed outlier: 7.625A pdb=" N VAL G 229 " --> pdb=" O VAL G 193 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N VAL G 195 " --> pdb=" O VAL G 229 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N THR G 124 " --> pdb=" O LEU G 192 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N ILE G 194 " --> pdb=" O THR G 124 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N LEU G 126 " --> pdb=" O ILE G 194 " (cutoff:3.500A) removed outlier: 8.279A pdb=" N GLY G 196 " --> pdb=" O LEU G 126 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N HIS G 128 " --> pdb=" O GLY G 196 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N ILE G 125 " --> pdb=" O TYR G 151 " (cutoff:3.500A) removed outlier: 8.102A pdb=" N THR G 153 " --> pdb=" O ILE G 125 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N THR G 127 " --> pdb=" O THR G 153 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N VAL G 150 " --> pdb=" O THR G 176 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N VAL G 178 " --> pdb=" O VAL G 150 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N VAL G 152 " --> pdb=" O VAL G 178 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 199 through 200 Processing sheet with id=AD1, first strand: chain 'G' and resid 267 through 268 removed outlier: 6.737A pdb=" N LYS G 267 " --> pdb=" O VAL H 177 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N ILE H 125 " --> pdb=" O TYR H 151 " (cutoff:3.500A) removed outlier: 8.051A pdb=" N THR H 153 " --> pdb=" O ILE H 125 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N THR H 127 " --> pdb=" O THR H 153 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N THR H 124 " --> pdb=" O LEU H 192 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N ILE H 194 " --> pdb=" O THR H 124 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N LEU H 126 " --> pdb=" O ILE H 194 " (cutoff:3.500A) removed outlier: 8.226A pdb=" N GLY H 196 " --> pdb=" O LEU H 126 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N HIS H 128 " --> pdb=" O GLY H 196 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N VAL H 193 " --> pdb=" O TYR H 227 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N VAL H 229 " --> pdb=" O VAL H 193 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N VAL H 195 " --> pdb=" O VAL H 229 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N PHE H 226 " --> pdb=" O LEU H 283 " (cutoff:3.500A) removed outlier: 8.093A pdb=" N PHE H 285 " --> pdb=" O PHE H 226 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N VAL H 228 " --> pdb=" O PHE H 285 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 199 through 200 Processing sheet with id=AD3, first strand: chain 'I' and resid 72 through 77 removed outlier: 6.694A pdb=" N VAL I 51 " --> pdb=" O ASP I 74 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N VAL I 76 " --> pdb=" O VAL I 51 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N VAL I 53 " --> pdb=" O VAL I 76 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N ALA I 5 " --> pdb=" O GLU I 50 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N HIS I 203 " --> pdb=" O SER I 105 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N ALA I 202 " --> pdb=" O ARG I 133 " (cutoff:3.500A) removed outlier: 8.519A pdb=" N ARG I 133 " --> pdb=" O ALA I 202 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N LEU I 204 " --> pdb=" O LEU I 131 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N LEU I 128 " --> pdb=" O TYR I 301 " (cutoff:3.500A) removed outlier: 8.013A pdb=" N HIS I 303 " --> pdb=" O LEU I 128 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N MET I 130 " --> pdb=" O HIS I 303 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N MET I 305 " --> pdb=" O MET I 130 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N MET I 132 " --> pdb=" O MET I 305 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'I' and resid 29 through 30 Processing sheet with id=AD5, first strand: chain 'I' and resid 108 through 110 Processing sheet with id=AD6, first strand: chain 'I' and resid 345 through 346 removed outlier: 6.442A pdb=" N GLN I 345 " --> pdb=" O ILE I 364 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N GLN I 363 " --> pdb=" O ILE I 381 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N LEU I 380 " --> pdb=" O VAL I 398 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N THR I 397 " --> pdb=" O ILE I 415 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N VAL I 414 " --> pdb=" O ILE I 432 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'I' and resid 357 through 358 removed outlier: 6.413A pdb=" N LEU I 357 " --> pdb=" O ILE I 375 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N VAL I 374 " --> pdb=" O LEU I 392 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N LEU I 391 " --> pdb=" O ILE I 409 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N VAL I 408 " --> pdb=" O ILE I 426 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N LEU I 425 " --> pdb=" O ILE I 443 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'I' and resid 369 through 371 removed outlier: 6.414A pdb=" N THR I 386 " --> pdb=" O ILE I 404 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ASN I 403 " --> pdb=" O ILE I 421 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'J' and resid 72 through 77 removed outlier: 6.612A pdb=" N VAL J 51 " --> pdb=" O ASP J 74 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N VAL J 76 " --> pdb=" O VAL J 51 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N VAL J 53 " --> pdb=" O VAL J 76 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N ALA J 5 " --> pdb=" O GLU J 50 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N GLN J 4 " --> pdb=" O LEU J 102 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N LEU J 104 " --> pdb=" O GLN J 4 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N VAL J 6 " --> pdb=" O LEU J 104 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N SER J 105 " --> pdb=" O HIS J 203 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N HIS J 203 " --> pdb=" O SER J 105 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N ALA J 202 " --> pdb=" O ARG J 133 " (cutoff:3.500A) removed outlier: 8.518A pdb=" N ARG J 133 " --> pdb=" O ALA J 202 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N LEU J 204 " --> pdb=" O LEU J 131 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N LEU J 128 " --> pdb=" O TYR J 301 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N HIS J 303 " --> pdb=" O LEU J 128 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N MET J 130 " --> pdb=" O HIS J 303 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N MET J 305 " --> pdb=" O MET J 130 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N MET J 132 " --> pdb=" O MET J 305 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'J' and resid 29 through 30 Processing sheet with id=AE2, first strand: chain 'J' and resid 108 through 110 Processing sheet with id=AE3, first strand: chain 'J' and resid 345 through 346 removed outlier: 6.556A pdb=" N GLN J 345 " --> pdb=" O ILE J 364 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N GLN J 363 " --> pdb=" O ILE J 381 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N LEU J 380 " --> pdb=" O VAL J 398 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N THR J 397 " --> pdb=" O ILE J 415 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N VAL J 414 " --> pdb=" O ILE J 432 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'J' and resid 357 through 358 removed outlier: 6.344A pdb=" N LEU J 357 " --> pdb=" O ILE J 375 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N VAL J 374 " --> pdb=" O LEU J 392 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N LEU J 391 " --> pdb=" O ILE J 409 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N VAL J 408 " --> pdb=" O ILE J 426 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N LEU J 425 " --> pdb=" O ILE J 443 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE4 Processing sheet with id=AE5, first strand: chain 'J' and resid 369 through 371 removed outlier: 6.412A pdb=" N THR J 386 " --> pdb=" O ILE J 404 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ASN J 403 " --> pdb=" O ILE J 421 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'K' and resid 35 through 39 removed outlier: 6.553A pdb=" N VAL K 36 " --> pdb=" O ILE K 111 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N GLU K 113 " --> pdb=" O VAL K 36 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N ILE K 38 " --> pdb=" O GLU K 113 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N TYR K 4 " --> pdb=" O VAL K 110 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N VAL K 112 " --> pdb=" O TYR K 4 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N ILE K 6 " --> pdb=" O VAL K 112 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N ILE K 5 " --> pdb=" O ILE K 128 " (cutoff:3.500A) removed outlier: 8.057A pdb=" N ALA K 130 " --> pdb=" O ILE K 5 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N GLY K 7 " --> pdb=" O ALA K 130 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N LEU K 132 " --> pdb=" O GLY K 7 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N SER K 9 " --> pdb=" O LEU K 132 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N THR K 129 " --> pdb=" O ILE K 183 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N VAL K 185 " --> pdb=" O THR K 129 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N PHE K 131 " --> pdb=" O VAL K 185 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE6 Processing sheet with id=AE7, first strand: chain 'K' and resid 85 through 92 removed outlier: 3.734A pdb=" N GLY K 100 " --> pdb=" O ILE K 90 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N ASP K 92 " --> pdb=" O CYS K 98 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N CYS K 98 " --> pdb=" O ASP K 92 " (cutoff:3.500A) 1274 hydrogen bonds defined for protein. 3387 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: 7.91 Time building geometry restraints manager: 2.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7658 1.34 - 1.46: 8075 1.46 - 1.58: 15076 1.58 - 1.70: 0 1.70 - 1.81: 260 Bond restraints: 31069 Sorted by residual: bond pdb=" C VAL D 316 " pdb=" N PRO D 317 " ideal model delta sigma weight residual 1.331 1.359 -0.028 8.70e-03 1.32e+04 1.04e+01 bond pdb=" C PRO A 40 " pdb=" N PRO A 41 " ideal model delta sigma weight residual 1.331 1.358 -0.027 8.70e-03 1.32e+04 9.40e+00 bond pdb=" C VAL C 316 " pdb=" N PRO C 317 " ideal model delta sigma weight residual 1.331 1.358 -0.026 8.70e-03 1.32e+04 9.24e+00 bond pdb=" C HIS I 190 " pdb=" N PRO I 191 " ideal model delta sigma weight residual 1.334 1.358 -0.024 8.40e-03 1.42e+04 8.18e+00 bond pdb=" CA PRO D 317 " pdb=" C PRO D 317 " ideal model delta sigma weight residual 1.514 1.529 -0.015 5.50e-03 3.31e+04 7.20e+00 ... (remaining 31064 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.47: 33311 1.47 - 2.93: 7225 2.93 - 4.40: 1403 4.40 - 5.86: 137 5.86 - 7.33: 18 Bond angle restraints: 42094 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 112.60 119.44 -6.84 1.00e+00 1.00e+00 4.68e+01 angle pdb=" CA ASP C 283 " pdb=" CB ASP C 283 " pdb=" CG ASP C 283 " ideal model delta sigma weight residual 112.60 119.26 -6.66 1.00e+00 1.00e+00 4.44e+01 angle pdb=" CA ASP C 314 " pdb=" CB ASP C 314 " pdb=" CG ASP C 314 " ideal model delta sigma weight residual 112.60 118.82 -6.22 1.00e+00 1.00e+00 3.87e+01 angle pdb=" CA ASP G 274 " pdb=" CB ASP G 274 " pdb=" CG ASP G 274 " ideal model delta sigma weight residual 112.60 118.35 -5.75 1.00e+00 1.00e+00 3.31e+01 angle pdb=" CA ASP H 274 " pdb=" CB ASP H 274 " pdb=" CG ASP H 274 " ideal model delta sigma weight residual 112.60 118.31 -5.71 1.00e+00 1.00e+00 3.26e+01 ... (remaining 42089 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.49: 17808 17.49 - 34.98: 857 34.98 - 52.47: 177 52.47 - 69.96: 62 69.96 - 87.45: 35 Dihedral angle restraints: 18939 sinusoidal: 7576 harmonic: 11363 Sorted by residual: 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 180.00 147.93 32.07 0 5.00e+00 4.00e-02 4.11e+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 180.00 148.41 31.59 0 5.00e+00 4.00e-02 3.99e+01 dihedral pdb=" CA ASN C 280 " pdb=" C ASN C 280 " pdb=" N GLU C 281 " pdb=" CA GLU C 281 " ideal model delta harmonic sigma weight residual -180.00 -149.00 -31.00 0 5.00e+00 4.00e-02 3.84e+01 ... (remaining 18936 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 3120 0.071 - 0.142: 1520 0.142 - 0.213: 230 0.213 - 0.284: 20 0.284 - 0.354: 2 Chirality restraints: 4892 Sorted by residual: 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 2.16 0.35 2.00e-01 2.50e+01 3.14e+00 chirality pdb=" CA ASN D 132 " pdb=" N ASN D 132 " pdb=" C ASN D 132 " pdb=" CB ASN D 132 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.77e+00 chirality pdb=" CA ASP B 199 " pdb=" N ASP B 199 " pdb=" C ASP B 199 " pdb=" CB ASP B 199 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.79e+00 ... (remaining 4889 not shown) Planarity restraints: 5391 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 55 " 0.366 9.50e-02 1.11e+02 1.64e-01 1.87e+01 pdb=" NE ARG B 55 " -0.014 2.00e-02 2.50e+03 pdb=" CZ ARG B 55 " -0.030 2.00e-02 2.50e+03 pdb=" NH1 ARG B 55 " 0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG B 55 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG E 374 " -0.313 9.50e-02 1.11e+02 1.40e-01 1.32e+01 pdb=" NE ARG E 374 " 0.013 2.00e-02 2.50e+03 pdb=" CZ ARG E 374 " 0.022 2.00e-02 2.50e+03 pdb=" NH1 ARG E 374 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG E 374 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG G 132 " 0.304 9.50e-02 1.11e+02 1.36e-01 1.19e+01 pdb=" NE ARG G 132 " -0.014 2.00e-02 2.50e+03 pdb=" CZ ARG G 132 " -0.016 2.00e-02 2.50e+03 pdb=" NH1 ARG G 132 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG G 132 " 0.015 2.00e-02 2.50e+03 ... (remaining 5388 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 398 2.70 - 3.25: 29299 3.25 - 3.80: 46372 3.80 - 4.35: 67707 4.35 - 4.90: 108283 Nonbonded interactions: 252059 Sorted by model distance: nonbonded pdb=" O PHE H 235 " pdb=" O HOH H 401 " model vdw 2.150 3.040 nonbonded pdb="CL CL E 601 " pdb="ZN ZN E 602 " model vdw 2.224 2.380 nonbonded pdb="ZN ZN J 501 " pdb="CL CL J 502 " model vdw 2.244 2.380 nonbonded pdb=" OG1 THR F 440 " pdb=" OE2 GLU F 503 " model vdw 2.463 3.040 nonbonded pdb=" OG SER C 171 " pdb=" O2 PO4 C1000 " model vdw 2.486 3.040 ... (remaining 252054 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and resid 39 through 516) } ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = (chain 'E' and resid 167 through 522) selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'I' selection = (chain 'J' and resid 1 through 443) } 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: 7.130 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: 0.630 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 31.540 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 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 : 0.011 0.813 31075 Z= 0.592 Angle : 1.269 7.326 42094 Z= 0.836 Chirality : 0.075 0.354 4892 Planarity : 0.010 0.164 5391 Dihedral : 12.366 87.453 11577 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 0.24 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.74 % Favored : 97.23 % Rotamer: Outliers : 0.12 % Allowed : 1.27 % Favored : 98.61 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 8.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -0.44 (0.12), residues: 3869 helix: -0.63 (0.12), residues: 1422 sheet: -0.21 (0.22), residues: 516 loop : 0.15 (0.14), residues: 1931 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.025 0.002 ARG B 55 TYR 0.046 0.005 TYR D 337 PHE 0.029 0.004 PHE D 272 TRP 0.044 0.005 TRP A 111 HIS 0.010 0.002 HIS F 371 Details of bonding type rmsd/Z covalent geometry : bond 0.00844 / 0.55 (31069) covalent geometry : angle 1.26892 / 0.84 (42094) hydrogen bonds : bond 0.17732 / 11.87 ( 1274) hydrogen bonds : angle 6.62579 / 4.69 ( 3387) metal coordination : bond 0.49991 / 35.68 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7738 Ramachandran restraints generated. 3869 Oldfield, 0 Emsley, 3869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7738 Ramachandran restraints generated. 3869 Oldfield, 0 Emsley, 3869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 580 residues out of total 3391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 576 time to evaluate : 1.206 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 515 TRP cc_start: 0.6362 (m100) cc_final: 0.6125 (t-100) REVERT: F 207 MET cc_start: 0.8698 (mmt) cc_final: 0.8233 (mmt) REVERT: J 132 MET cc_start: 0.7968 (mtt) cc_final: 0.7665 (mtt) outliers start: 4 outliers final: 2 residues processed: 580 average time/residue: 0.7716 time to fit residues: 512.0300 Evaluate side-chains 299 residues out of total 3391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 297 time to evaluate : 0.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 36 ILE Chi-restraints excluded: chain J residue 78 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 386 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 0.6980 chunk 155 optimal weight: 9.9990 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 2.9990 chunk 298 optimal weight: 0.0670 overall best weight: 1.1322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 197 HIS B 285 ASN B 333 GLN C 44 GLN C 49 HIS D 199 GLN E 190 ASN E 194 GLN F 189 GLN F 190 ASN H 223 ASN ** I 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 325 GLN I 405 GLN I 440 ASN ** J 403 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 22 ASN K 173 HIS K 189 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.119719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.078913 restraints weight = 48138.132| |-----------------------------------------------------------------------------| r_work (start): 0.3099 rms_B_bonded: 2.43 r_work: 0.2971 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2852 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.2221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 31075 Z= 0.151 Angle : 0.616 8.932 42094 Z= 0.325 Chirality : 0.047 0.170 4892 Planarity : 0.004 0.047 5391 Dihedral : 5.797 82.909 4233 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 2.24 % Allowed : 8.43 % Favored : 89.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.14 % 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: 0.79 (0.13), residues: 3869 helix: 0.99 (0.14), residues: 1419 sheet: -0.18 (0.20), residues: 620 loop : 0.60 (0.15), residues: 1830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 428 TYR 0.021 0.002 TYR K 102 PHE 0.028 0.002 PHE C 272 TRP 0.019 0.001 TRP B 111 HIS 0.010 0.001 HIS K 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.15 (31069) covalent geometry : angle 0.61608 / 0.32 (42094) hydrogen bonds : bond 0.04547 / 3.01 ( 1274) hydrogen bonds : angle 4.68857 / 3.37 ( 3387) metal coordination : bond 0.00778 / 0.58 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7738 Ramachandran restraints generated. 3869 Oldfield, 0 Emsley, 3869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7738 Ramachandran restraints generated. 3869 Oldfield, 0 Emsley, 3869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 3391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 328 time to evaluate : 0.868 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 ARG cc_start: 0.8289 (ttm110) cc_final: 0.7926 (ttp80) REVERT: A 329 ASP cc_start: 0.8306 (t0) cc_final: 0.7961 (t0) REVERT: A 387 ASP cc_start: 0.8613 (OUTLIER) cc_final: 0.8340 (m-30) REVERT: B 422 ARG cc_start: 0.8581 (ptt-90) cc_final: 0.8330 (ptt-90) REVERT: B 440 ASN cc_start: 0.8801 (m-40) cc_final: 0.8512 (m-40) REVERT: B 515 TRP cc_start: 0.5945 (m100) cc_final: 0.5545 (t-100) REVERT: C 283 ASP cc_start: 0.6854 (OUTLIER) cc_final: 0.6326 (t70) REVERT: D 56 GLU cc_start: 0.8469 (pt0) cc_final: 0.8242 (pp20) REVERT: E 265 GLN cc_start: 0.8404 (mm110) cc_final: 0.8105 (mm110) REVERT: F 207 MET cc_start: 0.9448 (mmt) cc_final: 0.9105 (mmt) REVERT: F 352 GLU cc_start: 0.8589 (OUTLIER) cc_final: 0.7808 (mp0) REVERT: F 415 MET cc_start: 0.9274 (OUTLIER) cc_final: 0.8949 (ttm) REVERT: F 506 MET cc_start: 0.9374 (OUTLIER) cc_final: 0.8911 (mtp) REVERT: I 49 GLU cc_start: 0.7835 (OUTLIER) cc_final: 0.7306 (mt-10) REVERT: I 71 MET cc_start: 0.6868 (OUTLIER) cc_final: 0.6636 (ttm) REVERT: I 216 MET cc_start: 0.7585 (OUTLIER) cc_final: 0.7223 (mmm) REVERT: J 49 GLU cc_start: 0.9041 (OUTLIER) cc_final: 0.8690 (mt-10) REVERT: J 92 TYR cc_start: 0.8817 (t80) cc_final: 0.8587 (t80) REVERT: J 355 ASP cc_start: 0.7758 (p0) cc_final: 0.7540 (p0) REVERT: J 409 ILE cc_start: 0.8084 (mm) cc_final: 0.7876 (mm) REVERT: K 34 ASP cc_start: 0.8650 (OUTLIER) cc_final: 0.8247 (t0) REVERT: K 74 ARG cc_start: 0.8477 (OUTLIER) cc_final: 0.8271 (mtp-110) REVERT: K 82 ASP cc_start: 0.8082 (m-30) cc_final: 0.7869 (m-30) REVERT: K 133 GLU cc_start: 0.6574 (OUTLIER) cc_final: 0.6274 (mp0) REVERT: K 161 MET cc_start: 0.8009 (mmm) cc_final: 0.7609 (mmp) outliers start: 76 outliers final: 13 residues processed: 373 average time/residue: 0.7451 time to fit residues: 321.1791 Evaluate side-chains 301 residues out of total 3391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 276 time to evaluate : 1.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 387 ASP Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 283 ASP Chi-restraints excluded: chain D residue 131 SER Chi-restraints excluded: chain D residue 148 MET Chi-restraints excluded: chain E residue 179 LEU Chi-restraints excluded: chain E residue 509 CYS Chi-restraints excluded: chain F residue 352 GLU Chi-restraints excluded: chain F residue 415 MET Chi-restraints excluded: chain F residue 506 MET Chi-restraints excluded: chain G residue 71 LEU Chi-restraints excluded: chain G residue 145 LYS Chi-restraints excluded: chain I residue 49 GLU Chi-restraints excluded: chain I residue 71 MET Chi-restraints excluded: chain I residue 216 MET Chi-restraints excluded: chain I residue 311 SER Chi-restraints excluded: chain J residue 49 GLU Chi-restraints excluded: chain J residue 58 ASP Chi-restraints excluded: chain J residue 306 LYS Chi-restraints excluded: chain K residue 34 ASP Chi-restraints excluded: chain K residue 74 ARG Chi-restraints excluded: chain K residue 78 SER Chi-restraints excluded: chain K residue 105 ASN Chi-restraints excluded: chain K residue 133 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 386 random chunks: chunk 366 optimal weight: 1.9990 chunk 270 optimal weight: 3.9990 chunk 319 optimal weight: 0.9990 chunk 321 optimal weight: 10.0000 chunk 25 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 226 optimal weight: 10.0000 chunk 116 optimal weight: 1.9990 chunk 31 optimal weight: 10.0000 chunk 335 optimal weight: 3.9990 chunk 362 optimal weight: 6.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 197 HIS B 333 GLN F 190 ASN G 109 ASN H 13 GLN H 170 HIS ** I 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 403 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.118450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.078469 restraints weight = 49731.401| |-----------------------------------------------------------------------------| r_work (start): 0.3133 rms_B_bonded: 2.39 r_work: 0.3026 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2916 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8676 moved from start: 0.2620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 31075 Z= 0.232 Angle : 0.616 8.898 42094 Z= 0.320 Chirality : 0.048 0.180 4892 Planarity : 0.005 0.056 5391 Dihedral : 5.477 84.176 4229 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 2.27 % Allowed : 9.82 % Favored : 87.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.14 % 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: 0.99 (0.14), residues: 3869 helix: 1.38 (0.14), residues: 1407 sheet: -0.19 (0.21), residues: 612 loop : 0.57 (0.15), residues: 1850 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 250 TYR 0.023 0.002 TYR K 102 PHE 0.023 0.002 PHE C 272 TRP 0.016 0.002 TRP B 111 HIS 0.009 0.001 HIS B 168 Details of bonding type rmsd/Z covalent geometry : bond 0.00561 / 0.23 (31069) covalent geometry : angle 0.61569 / 0.32 (42094) hydrogen bonds : bond 0.04592 / 3.05 ( 1274) hydrogen bonds : angle 4.47160 / 3.20 ( 3387) metal coordination : bond 0.00493 / 0.37 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7738 Ramachandran restraints generated. 3869 Oldfield, 0 Emsley, 3869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7738 Ramachandran restraints generated. 3869 Oldfield, 0 Emsley, 3869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 3391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 298 time to evaluate : 1.180 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 GLN cc_start: 0.8838 (OUTLIER) cc_final: 0.8370 (mt0) REVERT: A 163 ARG cc_start: 0.8421 (ttm110) cc_final: 0.8101 (ttp80) REVERT: A 270 ASP cc_start: 0.8558 (m-30) cc_final: 0.8053 (p0) REVERT: A 329 ASP cc_start: 0.8504 (t0) cc_final: 0.8067 (t0) REVERT: A 387 ASP cc_start: 0.8635 (OUTLIER) cc_final: 0.8348 (m-30) REVERT: B 57 PHE cc_start: 0.8903 (OUTLIER) cc_final: 0.8321 (m-80) REVERT: B 163 ARG cc_start: 0.8555 (ttm-80) cc_final: 0.7784 (ttm-80) REVERT: B 329 ASP cc_start: 0.9114 (OUTLIER) cc_final: 0.8890 (m-30) REVERT: B 422 ARG cc_start: 0.8666 (ptt-90) cc_final: 0.8435 (ptt-90) REVERT: B 440 ASN cc_start: 0.8741 (m-40) cc_final: 0.8475 (m-40) REVERT: C 10 GLU cc_start: 0.8428 (tt0) cc_final: 0.8129 (tp30) REVERT: C 186 LYS cc_start: 0.8750 (tppt) cc_final: 0.8292 (tptp) REVERT: C 283 ASP cc_start: 0.6953 (OUTLIER) cc_final: 0.6583 (t70) REVERT: D 48 ASP cc_start: 0.7977 (m-30) cc_final: 0.7683 (m-30) REVERT: D 56 GLU cc_start: 0.8461 (pt0) cc_final: 0.8158 (pp20) REVERT: D 145 GLU cc_start: 0.8115 (OUTLIER) cc_final: 0.7707 (mp0) REVERT: E 265 GLN cc_start: 0.8576 (mm110) cc_final: 0.8292 (mm110) REVERT: F 171 LYS cc_start: 0.8384 (pttt) cc_final: 0.8165 (pttp) REVERT: F 352 GLU cc_start: 0.8657 (OUTLIER) cc_final: 0.7971 (mp0) REVERT: F 415 MET cc_start: 0.9304 (OUTLIER) cc_final: 0.9028 (ttm) REVERT: F 506 MET cc_start: 0.9418 (OUTLIER) cc_final: 0.9030 (mtp) REVERT: G 268 GLU cc_start: 0.7677 (tt0) cc_final: 0.7344 (tm-30) REVERT: I 71 MET cc_start: 0.6998 (OUTLIER) cc_final: 0.6482 (ttm) REVERT: I 216 MET cc_start: 0.7713 (OUTLIER) cc_final: 0.7394 (mmm) REVERT: I 318 LEU cc_start: 0.8483 (tp) cc_final: 0.7838 (tt) REVERT: I 320 MET cc_start: 0.8542 (OUTLIER) cc_final: 0.8235 (mtm) REVERT: I 417 LYS cc_start: 0.7698 (mmtt) cc_final: 0.7447 (mmtt) REVERT: J 49 GLU cc_start: 0.9080 (OUTLIER) cc_final: 0.8733 (mt-10) REVERT: J 92 TYR cc_start: 0.8774 (t80) cc_final: 0.8528 (t80) REVERT: J 307 GLU cc_start: 0.8361 (OUTLIER) cc_final: 0.8145 (mm-30) REVERT: J 355 ASP cc_start: 0.7742 (p0) cc_final: 0.7470 (p0) REVERT: J 404 ILE cc_start: 0.7873 (OUTLIER) cc_final: 0.7526 (tt) REVERT: K 34 ASP cc_start: 0.8670 (OUTLIER) cc_final: 0.8437 (t0) REVERT: K 74 ARG cc_start: 0.8482 (ttp80) cc_final: 0.8189 (mtp-110) REVERT: K 82 ASP cc_start: 0.8074 (m-30) cc_final: 0.7871 (m-30) REVERT: K 121 LYS cc_start: 0.8607 (mttt) cc_final: 0.8296 (tppp) REVERT: K 133 GLU cc_start: 0.6703 (OUTLIER) cc_final: 0.6367 (mp0) REVERT: K 161 MET cc_start: 0.7924 (mmm) cc_final: 0.6984 (tpt) REVERT: K 167 LEU cc_start: 0.7518 (tm) cc_final: 0.7224 (mt) outliers start: 77 outliers final: 16 residues processed: 343 average time/residue: 0.7627 time to fit residues: 303.9789 Evaluate side-chains 306 residues out of total 3391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 273 time to evaluate : 1.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 GLN Chi-restraints excluded: chain A residue 387 ASP Chi-restraints excluded: chain B residue 57 PHE Chi-restraints excluded: chain B residue 329 ASP Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 283 ASP Chi-restraints excluded: chain D residue 131 SER Chi-restraints excluded: chain D residue 145 GLU Chi-restraints excluded: chain E residue 509 CYS Chi-restraints excluded: chain F residue 282 LYS Chi-restraints excluded: chain F residue 352 GLU Chi-restraints excluded: chain F residue 415 MET Chi-restraints excluded: chain F residue 506 MET Chi-restraints excluded: chain G residue 71 LEU Chi-restraints excluded: chain G residue 73 LEU Chi-restraints excluded: chain G residue 145 LYS Chi-restraints excluded: chain I residue 30 VAL Chi-restraints excluded: chain I residue 58 ASP Chi-restraints excluded: chain I residue 71 MET Chi-restraints excluded: chain I residue 216 MET Chi-restraints excluded: chain I residue 279 ASP Chi-restraints excluded: chain I residue 320 MET Chi-restraints excluded: chain I residue 372 ARG Chi-restraints excluded: chain J residue 49 GLU Chi-restraints excluded: chain J residue 58 ASP Chi-restraints excluded: chain J residue 307 GLU Chi-restraints excluded: chain J residue 346 ILE Chi-restraints excluded: chain J residue 404 ILE Chi-restraints excluded: chain K residue 34 ASP Chi-restraints excluded: chain K residue 78 SER Chi-restraints excluded: chain K residue 133 GLU Chi-restraints excluded: chain K residue 138 VAL Chi-restraints excluded: chain K residue 188 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 386 random chunks: chunk 157 optimal weight: 2.9990 chunk 381 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 295 optimal weight: 3.9990 chunk 71 optimal weight: 0.9980 chunk 149 optimal weight: 0.9980 chunk 339 optimal weight: 6.9990 chunk 350 optimal weight: 5.9990 chunk 13 optimal weight: 0.9980 chunk 69 optimal weight: 1.9990 chunk 264 optimal weight: 1.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 197 HIS B 333 GLN C 44 GLN F 190 ASN H 170 HIS ** I 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 119 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.119553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.079788 restraints weight = 49157.226| |-----------------------------------------------------------------------------| r_work (start): 0.3154 rms_B_bonded: 2.38 r_work: 0.3047 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2937 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8657 moved from start: 0.2801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 31075 Z= 0.155 Angle : 0.551 9.290 42094 Z= 0.288 Chirality : 0.046 0.166 4892 Planarity : 0.004 0.052 5391 Dihedral : 5.206 84.130 4229 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 2.21 % Allowed : 10.70 % Favored : 87.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.14 % 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: 1.14 (0.14), residues: 3869 helix: 1.58 (0.14), residues: 1411 sheet: -0.28 (0.21), residues: 626 loop : 0.66 (0.15), residues: 1832 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 292 TYR 0.022 0.001 TYR K 102 PHE 0.023 0.001 PHE G 72 TRP 0.012 0.001 TRP B 111 HIS 0.007 0.001 HIS B 168 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.16 (31069) covalent geometry : angle 0.55069 / 0.29 (42094) hydrogen bonds : bond 0.03921 / 2.60 ( 1274) hydrogen bonds : angle 4.30036 / 3.08 ( 3387) metal coordination : bond 0.00195 / 0.14 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7738 Ramachandran restraints generated. 3869 Oldfield, 0 Emsley, 3869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7738 Ramachandran restraints generated. 3869 Oldfield, 0 Emsley, 3869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 3391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 297 time to evaluate : 1.241 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 GLN cc_start: 0.8820 (OUTLIER) cc_final: 0.8275 (mt0) REVERT: A 163 ARG cc_start: 0.8401 (ttm110) cc_final: 0.8110 (ttp80) REVERT: A 270 ASP cc_start: 0.8545 (m-30) cc_final: 0.8060 (p0) REVERT: A 329 ASP cc_start: 0.8541 (t0) cc_final: 0.8064 (t0) REVERT: A 387 ASP cc_start: 0.8691 (OUTLIER) cc_final: 0.8405 (m-30) REVERT: B 57 PHE cc_start: 0.8929 (OUTLIER) cc_final: 0.8222 (m-80) REVERT: B 127 LEU cc_start: 0.9230 (OUTLIER) cc_final: 0.9002 (mt) REVERT: B 329 ASP cc_start: 0.9114 (OUTLIER) cc_final: 0.8892 (m-30) REVERT: B 422 ARG cc_start: 0.8696 (ptt-90) cc_final: 0.8429 (ptt-90) REVERT: B 440 ASN cc_start: 0.8669 (m-40) cc_final: 0.8384 (m110) REVERT: B 493 LYS cc_start: 0.7861 (mttt) cc_final: 0.7589 (mtmt) REVERT: C 10 GLU cc_start: 0.8434 (tt0) cc_final: 0.8107 (tp30) REVERT: C 13 GLU cc_start: 0.8230 (pt0) cc_final: 0.7808 (pt0) REVERT: C 139 GLU cc_start: 0.8731 (tm-30) cc_final: 0.8244 (tm-30) REVERT: C 186 LYS cc_start: 0.8742 (tppt) cc_final: 0.8313 (tptp) REVERT: C 283 ASP cc_start: 0.6935 (OUTLIER) cc_final: 0.6490 (t70) REVERT: D 56 GLU cc_start: 0.8434 (pt0) cc_final: 0.8185 (pp20) REVERT: D 67 ARG cc_start: 0.8604 (OUTLIER) cc_final: 0.8108 (ptm160) REVERT: D 145 GLU cc_start: 0.8031 (OUTLIER) cc_final: 0.7674 (mp0) REVERT: E 265 GLN cc_start: 0.8565 (mm110) cc_final: 0.8295 (mm110) REVERT: F 171 LYS cc_start: 0.8383 (pttt) cc_final: 0.8166 (pttp) REVERT: F 348 GLU cc_start: 0.8976 (mt-10) cc_final: 0.8476 (mt-10) REVERT: F 352 GLU cc_start: 0.8680 (OUTLIER) cc_final: 0.7998 (mp0) REVERT: F 506 MET cc_start: 0.9372 (OUTLIER) cc_final: 0.9140 (mtp) REVERT: G 268 GLU cc_start: 0.7628 (tt0) cc_final: 0.7298 (tm-30) REVERT: I 71 MET cc_start: 0.6956 (OUTLIER) cc_final: 0.5823 (ttm) REVERT: I 216 MET cc_start: 0.7669 (OUTLIER) cc_final: 0.7364 (mmm) REVERT: I 320 MET cc_start: 0.8650 (OUTLIER) cc_final: 0.8319 (mtm) REVERT: I 417 LYS cc_start: 0.7576 (mmtt) cc_final: 0.7291 (mmtt) REVERT: J 44 GLU cc_start: 0.9004 (OUTLIER) cc_final: 0.8656 (tt0) REVERT: J 49 GLU cc_start: 0.9083 (OUTLIER) cc_final: 0.8743 (mt-10) REVERT: J 92 TYR cc_start: 0.8782 (t80) cc_final: 0.8530 (t80) REVERT: J 264 TYR cc_start: 0.8820 (m-80) cc_final: 0.8474 (m-80) REVERT: J 355 ASP cc_start: 0.7569 (p0) cc_final: 0.7226 (p0) REVERT: J 404 ILE cc_start: 0.8041 (OUTLIER) cc_final: 0.7644 (tt) REVERT: K 74 ARG cc_start: 0.8528 (ttp80) cc_final: 0.8232 (ttt-90) REVERT: K 82 ASP cc_start: 0.8085 (m-30) cc_final: 0.7873 (m-30) REVERT: K 115 ILE cc_start: 0.8733 (OUTLIER) cc_final: 0.8402 (tt) REVERT: K 133 GLU cc_start: 0.6647 (OUTLIER) cc_final: 0.6326 (mp0) REVERT: K 167 LEU cc_start: 0.7454 (tm) cc_final: 0.7190 (mt) REVERT: K 169 MET cc_start: 0.7826 (OUTLIER) cc_final: 0.7414 (mmm) outliers start: 75 outliers final: 17 residues processed: 345 average time/residue: 0.7333 time to fit residues: 294.4494 Evaluate side-chains 303 residues out of total 3391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 267 time to evaluate : 1.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 GLN Chi-restraints excluded: chain A residue 95 CYS Chi-restraints excluded: chain A residue 387 ASP Chi-restraints excluded: chain B residue 57 PHE Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 329 ASP Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 283 ASP Chi-restraints excluded: chain D residue 67 ARG Chi-restraints excluded: chain D residue 131 SER Chi-restraints excluded: chain D residue 145 GLU Chi-restraints excluded: chain E residue 169 THR Chi-restraints excluded: chain E residue 179 LEU Chi-restraints excluded: chain E residue 286 SER Chi-restraints excluded: chain E residue 509 CYS Chi-restraints excluded: chain E residue 520 SER Chi-restraints excluded: chain F residue 282 LYS Chi-restraints excluded: chain F residue 352 GLU Chi-restraints excluded: chain F residue 506 MET Chi-restraints excluded: chain G residue 71 LEU Chi-restraints excluded: chain G residue 73 LEU Chi-restraints excluded: chain G residue 145 LYS Chi-restraints excluded: chain I residue 58 ASP Chi-restraints excluded: chain I residue 71 MET Chi-restraints excluded: chain I residue 216 MET Chi-restraints excluded: chain I residue 320 MET Chi-restraints excluded: chain J residue 44 GLU Chi-restraints excluded: chain J residue 49 GLU Chi-restraints excluded: chain J residue 58 ASP Chi-restraints excluded: chain J residue 165 LYS Chi-restraints excluded: chain J residue 367 LYS Chi-restraints excluded: chain J residue 404 ILE Chi-restraints excluded: chain K residue 78 SER Chi-restraints excluded: chain K residue 115 ILE Chi-restraints excluded: chain K residue 133 GLU Chi-restraints excluded: chain K residue 169 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 386 random chunks: chunk 39 optimal weight: 5.9990 chunk 340 optimal weight: 2.9990 chunk 353 optimal weight: 6.9990 chunk 64 optimal weight: 0.0070 chunk 206 optimal weight: 0.9990 chunk 273 optimal weight: 2.9990 chunk 98 optimal weight: 4.9990 chunk 146 optimal weight: 0.9980 chunk 310 optimal weight: 4.9990 chunk 190 optimal weight: 7.9990 chunk 131 optimal weight: 0.2980 overall best weight: 1.0602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 197 HIS B 333 GLN C 44 GLN E 194 GLN E 265 GLN H 170 HIS ** I 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 119 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.119208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.077754 restraints weight = 48470.782| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 2.50 r_work: 0.2960 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2840 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.2961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 31075 Z= 0.131 Angle : 0.532 9.690 42094 Z= 0.276 Chirality : 0.045 0.170 4892 Planarity : 0.004 0.052 5391 Dihedral : 5.009 84.537 4229 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 2.09 % Allowed : 11.15 % Favored : 86.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.14 % 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: 1.33 (0.14), residues: 3869 helix: 1.69 (0.14), residues: 1425 sheet: 0.05 (0.23), residues: 504 loop : 0.65 (0.14), residues: 1940 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG F 188 TYR 0.024 0.001 TYR K 102 PHE 0.025 0.001 PHE G 72 TRP 0.012 0.001 TRP A 97 HIS 0.007 0.001 HIS B 168 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.13 (31069) covalent geometry : angle 0.53153 / 0.28 (42094) hydrogen bonds : bond 0.03633 / 2.41 ( 1274) hydrogen bonds : angle 4.19007 / 3.00 ( 3387) metal coordination : bond 0.00134 / 0.09 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7738 Ramachandran restraints generated. 3869 Oldfield, 0 Emsley, 3869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7738 Ramachandran restraints generated. 3869 Oldfield, 0 Emsley, 3869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 3391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 294 time to evaluate : 1.257 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 GLN cc_start: 0.8784 (OUTLIER) cc_final: 0.8263 (mt0) REVERT: A 163 ARG cc_start: 0.8380 (ttm110) cc_final: 0.8119 (tpp80) REVERT: A 270 ASP cc_start: 0.8515 (m-30) cc_final: 0.7974 (p0) REVERT: A 329 ASP cc_start: 0.8510 (t0) cc_final: 0.7983 (t0) REVERT: A 387 ASP cc_start: 0.8628 (OUTLIER) cc_final: 0.8333 (m-30) REVERT: B 57 PHE cc_start: 0.8912 (OUTLIER) cc_final: 0.8218 (m-80) REVERT: B 163 ARG cc_start: 0.8450 (ttm-80) cc_final: 0.7862 (ttm-80) REVERT: B 232 GLN cc_start: 0.7803 (OUTLIER) cc_final: 0.7602 (pm20) REVERT: B 329 ASP cc_start: 0.9081 (OUTLIER) cc_final: 0.8834 (m-30) REVERT: B 422 ARG cc_start: 0.8726 (ptt-90) cc_final: 0.8419 (ptt-90) REVERT: B 440 ASN cc_start: 0.8718 (m-40) cc_final: 0.8384 (m110) REVERT: B 493 LYS cc_start: 0.7792 (mttt) cc_final: 0.7534 (mtmt) REVERT: C 10 GLU cc_start: 0.8424 (tt0) cc_final: 0.8040 (tp30) REVERT: C 139 GLU cc_start: 0.8726 (tm-30) cc_final: 0.8219 (tm-30) REVERT: C 186 LYS cc_start: 0.8668 (tppt) cc_final: 0.8216 (tptp) REVERT: C 283 ASP cc_start: 0.6898 (OUTLIER) cc_final: 0.6334 (t70) REVERT: D 56 GLU cc_start: 0.8467 (pt0) cc_final: 0.8132 (pp20) REVERT: D 143 GLU cc_start: 0.8864 (tt0) cc_final: 0.8657 (tt0) REVERT: D 249 THR cc_start: 0.9184 (OUTLIER) cc_final: 0.8966 (m) REVERT: E 292 ARG cc_start: 0.8016 (mpp80) cc_final: 0.7811 (mpp-170) REVERT: F 348 GLU cc_start: 0.8977 (mt-10) cc_final: 0.8412 (mt-10) REVERT: F 352 GLU cc_start: 0.8671 (OUTLIER) cc_final: 0.7921 (mp0) REVERT: F 415 MET cc_start: 0.9264 (OUTLIER) cc_final: 0.8996 (ttm) REVERT: G 268 GLU cc_start: 0.7621 (tt0) cc_final: 0.7187 (tm-30) REVERT: I 8 MET cc_start: 0.8655 (mmm) cc_final: 0.8320 (mmm) REVERT: I 216 MET cc_start: 0.7584 (OUTLIER) cc_final: 0.7269 (mmm) REVERT: I 320 MET cc_start: 0.8702 (OUTLIER) cc_final: 0.8359 (mtm) REVERT: J 16 MET cc_start: 0.7091 (mtm) cc_final: 0.6563 (ptp) REVERT: J 44 GLU cc_start: 0.8928 (OUTLIER) cc_final: 0.8611 (tt0) REVERT: J 49 GLU cc_start: 0.9137 (OUTLIER) cc_final: 0.8817 (mt-10) REVERT: J 92 TYR cc_start: 0.8719 (t80) cc_final: 0.8470 (t80) REVERT: J 140 GLU cc_start: 0.7223 (OUTLIER) cc_final: 0.6876 (mm-30) REVERT: J 264 TYR cc_start: 0.8827 (m-80) cc_final: 0.8415 (m-80) REVERT: J 355 ASP cc_start: 0.7637 (p0) cc_final: 0.7216 (p0) REVERT: J 372 ARG cc_start: 0.8716 (mtt180) cc_final: 0.8437 (mtm180) REVERT: K 74 ARG cc_start: 0.8438 (ttp80) cc_final: 0.8187 (ttt-90) REVERT: K 82 ASP cc_start: 0.8067 (m-30) cc_final: 0.7832 (m-30) REVERT: K 113 GLU cc_start: 0.7420 (OUTLIER) cc_final: 0.6911 (tm-30) REVERT: K 115 ILE cc_start: 0.8758 (OUTLIER) cc_final: 0.8432 (tt) REVERT: K 121 LYS cc_start: 0.8370 (OUTLIER) cc_final: 0.8153 (ttpt) REVERT: K 133 GLU cc_start: 0.6617 (OUTLIER) cc_final: 0.6270 (mp0) REVERT: K 161 MET cc_start: 0.7844 (mmm) cc_final: 0.7137 (tpt) REVERT: K 167 LEU cc_start: 0.7366 (tm) cc_final: 0.7128 (mt) REVERT: K 169 MET cc_start: 0.7771 (OUTLIER) cc_final: 0.7375 (mmm) outliers start: 71 outliers final: 21 residues processed: 337 average time/residue: 0.7611 time to fit residues: 297.7820 Evaluate side-chains 306 residues out of total 3391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 266 time to evaluate : 1.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 GLN Chi-restraints excluded: chain A residue 95 CYS Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 387 ASP Chi-restraints excluded: chain B residue 57 PHE Chi-restraints excluded: chain B residue 232 GLN Chi-restraints excluded: chain B residue 329 ASP Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 283 ASP Chi-restraints excluded: chain D residue 131 SER Chi-restraints excluded: chain D residue 145 GLU Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain E residue 169 THR Chi-restraints excluded: chain E residue 286 SER Chi-restraints excluded: chain E residue 509 CYS Chi-restraints excluded: chain E residue 520 SER Chi-restraints excluded: chain F residue 282 LYS Chi-restraints excluded: chain F residue 352 GLU Chi-restraints excluded: chain F residue 415 MET Chi-restraints excluded: chain G residue 71 LEU Chi-restraints excluded: chain G residue 73 LEU Chi-restraints excluded: chain I residue 16 MET Chi-restraints excluded: chain I residue 58 ASP Chi-restraints excluded: chain I residue 216 MET Chi-restraints excluded: chain I residue 320 MET Chi-restraints excluded: chain I residue 417 LYS Chi-restraints excluded: chain J residue 44 GLU Chi-restraints excluded: chain J residue 49 GLU Chi-restraints excluded: chain J residue 58 ASP Chi-restraints excluded: chain J residue 140 GLU Chi-restraints excluded: chain J residue 364 ILE Chi-restraints excluded: chain J residue 367 LYS Chi-restraints excluded: chain K residue 78 SER Chi-restraints excluded: chain K residue 113 GLU Chi-restraints excluded: chain K residue 115 ILE Chi-restraints excluded: chain K residue 121 LYS Chi-restraints excluded: chain K residue 133 GLU Chi-restraints excluded: chain K residue 169 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 386 random chunks: chunk 43 optimal weight: 8.9990 chunk 260 optimal weight: 3.9990 chunk 352 optimal weight: 0.0970 chunk 234 optimal weight: 7.9990 chunk 201 optimal weight: 6.9990 chunk 256 optimal weight: 4.9990 chunk 223 optimal weight: 1.9990 chunk 248 optimal weight: 0.3980 chunk 276 optimal weight: 0.8980 chunk 19 optimal weight: 7.9990 chunk 370 optimal weight: 10.0000 overall best weight: 1.4782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 197 HIS B 333 GLN C 44 GLN F 190 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.118548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.077461 restraints weight = 48302.779| |-----------------------------------------------------------------------------| r_work (start): 0.3075 rms_B_bonded: 2.47 r_work: 0.2943 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2819 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.3050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 31075 Z= 0.158 Angle : 0.538 10.454 42094 Z= 0.278 Chirality : 0.045 0.166 4892 Planarity : 0.004 0.056 5391 Dihedral : 4.965 85.940 4229 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.18 % Allowed : 11.44 % Favored : 86.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.14 % 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: 1.36 (0.14), residues: 3869 helix: 1.74 (0.14), residues: 1431 sheet: 0.05 (0.23), residues: 504 loop : 0.66 (0.14), residues: 1934 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG F 188 TYR 0.024 0.001 TYR K 102 PHE 0.026 0.001 PHE G 72 TRP 0.010 0.001 TRP B 111 HIS 0.007 0.001 HIS B 168 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.16 (31069) covalent geometry : angle 0.53843 / 0.28 (42094) hydrogen bonds : bond 0.03708 / 2.46 ( 1274) hydrogen bonds : angle 4.17126 / 2.98 ( 3387) metal coordination : bond 0.00188 / 0.14 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7738 Ramachandran restraints generated. 3869 Oldfield, 0 Emsley, 3869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7738 Ramachandran restraints generated. 3869 Oldfield, 0 Emsley, 3869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 3391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 271 time to evaluate : 1.219 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 GLN cc_start: 0.8794 (OUTLIER) cc_final: 0.8274 (mt0) REVERT: A 163 ARG cc_start: 0.8358 (ttm110) cc_final: 0.8089 (tpp80) REVERT: A 270 ASP cc_start: 0.8503 (m-30) cc_final: 0.7961 (p0) REVERT: A 387 ASP cc_start: 0.8603 (OUTLIER) cc_final: 0.8305 (m-30) REVERT: B 57 PHE cc_start: 0.8893 (OUTLIER) cc_final: 0.8171 (m-80) REVERT: B 145 ARG cc_start: 0.8389 (mmm160) cc_final: 0.8153 (mmm-85) REVERT: B 329 ASP cc_start: 0.9066 (OUTLIER) cc_final: 0.8818 (m-30) REVERT: B 422 ARG cc_start: 0.8765 (ptt-90) cc_final: 0.8378 (ptt-90) REVERT: B 440 ASN cc_start: 0.8751 (m-40) cc_final: 0.8393 (m110) REVERT: B 493 LYS cc_start: 0.7757 (mttt) cc_final: 0.7494 (mtmt) REVERT: C 10 GLU cc_start: 0.8392 (tt0) cc_final: 0.8022 (tp30) REVERT: C 13 GLU cc_start: 0.8155 (pt0) cc_final: 0.7639 (pt0) REVERT: C 186 LYS cc_start: 0.8672 (tppt) cc_final: 0.8218 (tptp) REVERT: C 283 ASP cc_start: 0.6873 (OUTLIER) cc_final: 0.6221 (t70) REVERT: D 48 ASP cc_start: 0.7860 (m-30) cc_final: 0.7548 (m-30) REVERT: D 143 GLU cc_start: 0.8780 (tt0) cc_final: 0.8540 (tt0) REVERT: D 184 LYS cc_start: 0.8887 (OUTLIER) cc_final: 0.8564 (ttmp) REVERT: D 249 THR cc_start: 0.9178 (OUTLIER) cc_final: 0.8962 (m) REVERT: E 292 ARG cc_start: 0.8003 (mpp80) cc_final: 0.7658 (mpp-170) REVERT: F 250 ARG cc_start: 0.8871 (mtp-110) cc_final: 0.8145 (ttm110) REVERT: F 348 GLU cc_start: 0.8964 (mt-10) cc_final: 0.8400 (mt-10) REVERT: F 352 GLU cc_start: 0.8641 (OUTLIER) cc_final: 0.7875 (mp0) REVERT: F 386 LEU cc_start: 0.9133 (mp) cc_final: 0.8876 (pt) REVERT: F 415 MET cc_start: 0.9282 (OUTLIER) cc_final: 0.9003 (ttm) REVERT: G 268 GLU cc_start: 0.7612 (tt0) cc_final: 0.7155 (tm-30) REVERT: I 8 MET cc_start: 0.8563 (mmm) cc_final: 0.8346 (mmm) REVERT: I 216 MET cc_start: 0.7568 (OUTLIER) cc_final: 0.7248 (mmm) REVERT: I 318 LEU cc_start: 0.8347 (OUTLIER) cc_final: 0.7890 (tp) REVERT: I 320 MET cc_start: 0.8752 (OUTLIER) cc_final: 0.8456 (mtm) REVERT: J 16 MET cc_start: 0.7047 (mtm) cc_final: 0.6541 (ptp) REVERT: J 44 GLU cc_start: 0.8903 (OUTLIER) cc_final: 0.8630 (tt0) REVERT: J 49 GLU cc_start: 0.9126 (OUTLIER) cc_final: 0.8829 (mt-10) REVERT: J 140 GLU cc_start: 0.7247 (OUTLIER) cc_final: 0.7001 (mm-30) REVERT: J 355 ASP cc_start: 0.7712 (p0) cc_final: 0.7320 (p0) REVERT: J 404 ILE cc_start: 0.7992 (OUTLIER) cc_final: 0.7653 (tt) REVERT: K 82 ASP cc_start: 0.8062 (m-30) cc_final: 0.7822 (m-30) REVERT: K 113 GLU cc_start: 0.7378 (OUTLIER) cc_final: 0.6805 (tm-30) REVERT: K 115 ILE cc_start: 0.8802 (OUTLIER) cc_final: 0.8506 (tt) REVERT: K 133 GLU cc_start: 0.6603 (OUTLIER) cc_final: 0.6251 (mp0) REVERT: K 169 MET cc_start: 0.7665 (OUTLIER) cc_final: 0.7299 (mmm) outliers start: 74 outliers final: 24 residues processed: 318 average time/residue: 0.7735 time to fit residues: 285.7477 Evaluate side-chains 305 residues out of total 3391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 261 time to evaluate : 1.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 GLN Chi-restraints excluded: chain A residue 95 CYS Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 387 ASP Chi-restraints excluded: chain B residue 57 PHE Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 329 ASP Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 283 ASP Chi-restraints excluded: chain D residue 131 SER Chi-restraints excluded: chain D residue 184 LYS Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain E residue 169 THR Chi-restraints excluded: chain E residue 179 LEU Chi-restraints excluded: chain E residue 286 SER Chi-restraints excluded: chain E residue 509 CYS Chi-restraints excluded: chain F residue 282 LYS Chi-restraints excluded: chain F residue 352 GLU Chi-restraints excluded: chain F residue 415 MET Chi-restraints excluded: chain G residue 71 LEU Chi-restraints excluded: chain G residue 73 LEU Chi-restraints excluded: chain G residue 223 ASN Chi-restraints excluded: chain H residue 49 LEU Chi-restraints excluded: chain I residue 16 MET Chi-restraints excluded: chain I residue 58 ASP Chi-restraints excluded: chain I residue 216 MET Chi-restraints excluded: chain I residue 318 LEU Chi-restraints excluded: chain I residue 320 MET Chi-restraints excluded: chain I residue 372 ARG Chi-restraints excluded: chain I residue 417 LYS Chi-restraints excluded: chain J residue 44 GLU Chi-restraints excluded: chain J residue 49 GLU Chi-restraints excluded: chain J residue 58 ASP Chi-restraints excluded: chain J residue 140 GLU Chi-restraints excluded: chain J residue 165 LYS Chi-restraints excluded: chain J residue 357 LEU Chi-restraints excluded: chain J residue 367 LYS Chi-restraints excluded: chain J residue 404 ILE Chi-restraints excluded: chain K residue 78 SER Chi-restraints excluded: chain K residue 113 GLU Chi-restraints excluded: chain K residue 115 ILE Chi-restraints excluded: chain K residue 133 GLU Chi-restraints excluded: chain K residue 169 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 386 random chunks: chunk 36 optimal weight: 9.9990 chunk 257 optimal weight: 6.9990 chunk 349 optimal weight: 4.9990 chunk 103 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 chunk 129 optimal weight: 6.9990 chunk 358 optimal weight: 9.9990 chunk 344 optimal weight: 4.9990 chunk 54 optimal weight: 5.9990 chunk 123 optimal weight: 3.9990 chunk 50 optimal weight: 0.5980 overall best weight: 3.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 197 HIS B 333 GLN C 44 GLN D 44 GLN E 194 GLN F 190 ASN H 13 GLN H 170 HIS ** I 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 136 GLN K 119 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.116304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.074903 restraints weight = 48419.902| |-----------------------------------------------------------------------------| r_work (start): 0.3030 rms_B_bonded: 2.48 r_work: 0.2898 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2776 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.3103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.063 31075 Z= 0.290 Angle : 0.632 11.682 42094 Z= 0.324 Chirality : 0.049 0.170 4892 Planarity : 0.005 0.057 5391 Dihedral : 5.246 89.882 4229 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.21 % Allowed : 11.80 % Favored : 85.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.14 % 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: 1.07 (0.14), residues: 3869 helix: 1.55 (0.14), residues: 1427 sheet: -0.27 (0.20), residues: 658 loop : 0.58 (0.15), residues: 1784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG F 188 TYR 0.025 0.002 TYR K 102 PHE 0.026 0.002 PHE G 72 TRP 0.013 0.002 TRP A 97 HIS 0.008 0.001 HIS A 168 Details of bonding type rmsd/Z covalent geometry : bond 0.00701 / 0.29 (31069) covalent geometry : angle 0.63167 / 0.32 (42094) hydrogen bonds : bond 0.04459 / 2.98 ( 1274) hydrogen bonds : angle 4.34933 / 3.11 ( 3387) metal coordination : bond 0.00426 / 0.30 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7738 Ramachandran restraints generated. 3869 Oldfield, 0 Emsley, 3869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7738 Ramachandran restraints generated. 3869 Oldfield, 0 Emsley, 3869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 3391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 256 time to evaluate : 1.257 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 GLN cc_start: 0.8806 (OUTLIER) cc_final: 0.8301 (mt0) REVERT: A 163 ARG cc_start: 0.8368 (ttm110) cc_final: 0.8115 (tpp80) REVERT: A 387 ASP cc_start: 0.8600 (OUTLIER) cc_final: 0.8319 (m-30) REVERT: B 57 PHE cc_start: 0.8873 (OUTLIER) cc_final: 0.8302 (m-80) REVERT: B 145 ARG cc_start: 0.8409 (mmm160) cc_final: 0.8145 (mmm-85) REVERT: B 422 ARG cc_start: 0.8727 (ptt-90) cc_final: 0.8414 (ptt-90) REVERT: B 440 ASN cc_start: 0.8775 (m-40) cc_final: 0.8465 (m-40) REVERT: B 493 LYS cc_start: 0.7692 (mttt) cc_final: 0.7421 (mtmt) REVERT: C 10 GLU cc_start: 0.8355 (tt0) cc_final: 0.8009 (tp30) REVERT: C 13 GLU cc_start: 0.8177 (pt0) cc_final: 0.7704 (pt0) REVERT: C 186 LYS cc_start: 0.8775 (tppt) cc_final: 0.8304 (tptp) REVERT: D 48 ASP cc_start: 0.7914 (m-30) cc_final: 0.7668 (m-30) REVERT: D 56 GLU cc_start: 0.8456 (pt0) cc_final: 0.8200 (pp20) REVERT: D 249 THR cc_start: 0.9272 (OUTLIER) cc_final: 0.9053 (m) REVERT: E 292 ARG cc_start: 0.7982 (mpp80) cc_final: 0.7632 (mpp-170) REVERT: F 348 GLU cc_start: 0.8972 (mt-10) cc_final: 0.8399 (mt-10) REVERT: F 352 GLU cc_start: 0.8670 (OUTLIER) cc_final: 0.7866 (mp0) REVERT: F 415 MET cc_start: 0.9296 (OUTLIER) cc_final: 0.8958 (ttm) REVERT: G 268 GLU cc_start: 0.7622 (tt0) cc_final: 0.7180 (tm-30) REVERT: I 140 GLU cc_start: 0.7099 (mm-30) cc_final: 0.6815 (tm-30) REVERT: I 216 MET cc_start: 0.7578 (OUTLIER) cc_final: 0.7211 (mmm) REVERT: I 320 MET cc_start: 0.8769 (OUTLIER) cc_final: 0.8409 (mtm) REVERT: I 381 ILE cc_start: 0.7817 (tt) cc_final: 0.7135 (pp) REVERT: J 49 GLU cc_start: 0.9121 (OUTLIER) cc_final: 0.8845 (mt-10) REVERT: J 140 GLU cc_start: 0.7289 (OUTLIER) cc_final: 0.6988 (mm-30) REVERT: J 355 ASP cc_start: 0.7711 (p0) cc_final: 0.7363 (p0) REVERT: J 367 LYS cc_start: 0.7257 (OUTLIER) cc_final: 0.6899 (ttmt) REVERT: J 404 ILE cc_start: 0.7967 (OUTLIER) cc_final: 0.7626 (tt) REVERT: K 82 ASP cc_start: 0.8107 (m-30) cc_final: 0.7880 (m-30) REVERT: K 113 GLU cc_start: 0.7484 (OUTLIER) cc_final: 0.6911 (tm-30) REVERT: K 115 ILE cc_start: 0.8841 (OUTLIER) cc_final: 0.8591 (tt) REVERT: K 133 GLU cc_start: 0.6620 (OUTLIER) cc_final: 0.6248 (mp0) REVERT: K 169 MET cc_start: 0.7698 (OUTLIER) cc_final: 0.7337 (mmm) outliers start: 75 outliers final: 25 residues processed: 306 average time/residue: 0.7325 time to fit residues: 260.4657 Evaluate side-chains 290 residues out of total 3391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 249 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 GLN Chi-restraints excluded: chain A residue 95 CYS Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 387 ASP Chi-restraints excluded: chain B residue 57 PHE Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 283 ASP Chi-restraints excluded: chain D residue 131 SER Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain E residue 169 THR Chi-restraints excluded: chain E residue 171 LYS Chi-restraints excluded: chain E residue 286 SER Chi-restraints excluded: chain E residue 509 CYS Chi-restraints excluded: chain F residue 282 LYS Chi-restraints excluded: chain F residue 352 GLU Chi-restraints excluded: chain F residue 415 MET Chi-restraints excluded: chain G residue 71 LEU Chi-restraints excluded: chain G residue 73 LEU Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain G residue 223 ASN Chi-restraints excluded: chain I residue 58 ASP Chi-restraints excluded: chain I residue 216 MET Chi-restraints excluded: chain I residue 279 ASP Chi-restraints excluded: chain I residue 320 MET Chi-restraints excluded: chain J residue 49 GLU Chi-restraints excluded: chain J residue 58 ASP Chi-restraints excluded: chain J residue 140 GLU Chi-restraints excluded: chain J residue 165 LYS Chi-restraints excluded: chain J residue 364 ILE Chi-restraints excluded: chain J residue 367 LYS Chi-restraints excluded: chain J residue 404 ILE Chi-restraints excluded: chain K residue 78 SER Chi-restraints excluded: chain K residue 113 GLU Chi-restraints excluded: chain K residue 115 ILE Chi-restraints excluded: chain K residue 133 GLU Chi-restraints excluded: chain K residue 138 VAL Chi-restraints excluded: chain K residue 169 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 386 random chunks: chunk 280 optimal weight: 0.7980 chunk 226 optimal weight: 6.9990 chunk 19 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 107 optimal weight: 3.9990 chunk 197 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 317 optimal weight: 8.9990 chunk 108 optimal weight: 2.9990 chunk 297 optimal weight: 8.9990 chunk 151 optimal weight: 0.9980 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 197 HIS B 333 GLN B 341 ASN C 44 GLN D 44 GLN ** F 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 136 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.117914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.076829 restraints weight = 48209.873| |-----------------------------------------------------------------------------| r_work (start): 0.3062 rms_B_bonded: 2.47 r_work: 0.2931 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2808 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.3195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 31075 Z= 0.165 Angle : 0.561 10.696 42094 Z= 0.288 Chirality : 0.045 0.169 4892 Planarity : 0.004 0.055 5391 Dihedral : 5.049 88.656 4229 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.62 % Allowed : 12.50 % Favored : 85.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.14 % 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 (0.14), residues: 3869 helix: 1.67 (0.14), residues: 1438 sheet: -0.19 (0.21), residues: 642 loop : 0.61 (0.15), residues: 1789 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG F 188 TYR 0.024 0.001 TYR K 102 PHE 0.027 0.001 PHE G 72 TRP 0.013 0.001 TRP A 97 HIS 0.007 0.001 HIS B 168 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.16 (31069) covalent geometry : angle 0.56146 / 0.29 (42094) hydrogen bonds : bond 0.03782 / 2.52 ( 1274) hydrogen bonds : angle 4.20489 / 3.01 ( 3387) metal coordination : bond 0.00209 / 0.14 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7738 Ramachandran restraints generated. 3869 Oldfield, 0 Emsley, 3869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7738 Ramachandran restraints generated. 3869 Oldfield, 0 Emsley, 3869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 3391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 260 time to evaluate : 1.193 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 GLN cc_start: 0.8808 (OUTLIER) cc_final: 0.8322 (mt0) REVERT: A 127 LEU cc_start: 0.8863 (OUTLIER) cc_final: 0.8401 (pp) REVERT: A 163 ARG cc_start: 0.8364 (ttm110) cc_final: 0.8104 (tpp80) REVERT: A 329 ASP cc_start: 0.8525 (t0) cc_final: 0.7893 (t0) REVERT: A 387 ASP cc_start: 0.8600 (OUTLIER) cc_final: 0.8303 (m-30) REVERT: B 57 PHE cc_start: 0.8902 (OUTLIER) cc_final: 0.8249 (m-80) REVERT: B 145 ARG cc_start: 0.8423 (mmm160) cc_final: 0.8138 (mmm-85) REVERT: B 493 LYS cc_start: 0.7691 (mttt) cc_final: 0.7432 (mtmt) REVERT: C 10 GLU cc_start: 0.8354 (tt0) cc_final: 0.7958 (tp30) REVERT: C 186 LYS cc_start: 0.8737 (tppt) cc_final: 0.8287 (tptp) REVERT: D 48 ASP cc_start: 0.7886 (m-30) cc_final: 0.7657 (m-30) REVERT: D 249 THR cc_start: 0.9200 (OUTLIER) cc_final: 0.8997 (m) REVERT: E 292 ARG cc_start: 0.7924 (mpp80) cc_final: 0.7592 (mpp-170) REVERT: F 250 ARG cc_start: 0.8887 (mtp-110) cc_final: 0.8168 (ttm110) REVERT: F 348 GLU cc_start: 0.8950 (mt-10) cc_final: 0.8329 (mt-10) REVERT: F 352 GLU cc_start: 0.8686 (OUTLIER) cc_final: 0.7849 (mp0) REVERT: F 415 MET cc_start: 0.9281 (OUTLIER) cc_final: 0.9001 (ttm) REVERT: F 506 MET cc_start: 0.9387 (OUTLIER) cc_final: 0.8984 (mtp) REVERT: G 268 GLU cc_start: 0.7569 (tt0) cc_final: 0.7137 (tm-30) REVERT: I 48 PHE cc_start: 0.8789 (m-80) cc_final: 0.8409 (m-80) REVERT: I 140 GLU cc_start: 0.7039 (mm-30) cc_final: 0.6764 (tm-30) REVERT: I 216 MET cc_start: 0.7562 (OUTLIER) cc_final: 0.7178 (mmm) REVERT: I 320 MET cc_start: 0.8769 (OUTLIER) cc_final: 0.8390 (mtm) REVERT: I 425 LEU cc_start: 0.6954 (OUTLIER) cc_final: 0.6737 (tm) REVERT: J 16 MET cc_start: 0.7074 (mtm) cc_final: 0.6595 (ptp) REVERT: J 44 GLU cc_start: 0.8895 (OUTLIER) cc_final: 0.8610 (tt0) REVERT: J 49 GLU cc_start: 0.9147 (OUTLIER) cc_final: 0.8877 (mt-10) REVERT: J 140 GLU cc_start: 0.7274 (OUTLIER) cc_final: 0.6971 (mm-30) REVERT: J 355 ASP cc_start: 0.7694 (p0) cc_final: 0.7375 (p0) REVERT: J 404 ILE cc_start: 0.8094 (OUTLIER) cc_final: 0.7780 (tt) REVERT: K 82 ASP cc_start: 0.8104 (m-30) cc_final: 0.7881 (m-30) REVERT: K 113 GLU cc_start: 0.7452 (OUTLIER) cc_final: 0.6894 (tm-30) REVERT: K 115 ILE cc_start: 0.8857 (OUTLIER) cc_final: 0.8610 (tt) REVERT: K 133 GLU cc_start: 0.6588 (OUTLIER) cc_final: 0.6264 (mp0) REVERT: K 167 LEU cc_start: 0.7434 (tm) cc_final: 0.7152 (mt) REVERT: K 169 MET cc_start: 0.7700 (OUTLIER) cc_final: 0.7316 (mmm) outliers start: 55 outliers final: 20 residues processed: 297 average time/residue: 0.7339 time to fit residues: 254.1851 Evaluate side-chains 281 residues out of total 3391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 242 time to evaluate : 1.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 GLN Chi-restraints excluded: chain A residue 95 CYS Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 387 ASP Chi-restraints excluded: chain B residue 57 PHE Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain D residue 131 SER Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain E residue 509 CYS Chi-restraints excluded: chain F residue 282 LYS Chi-restraints excluded: chain F residue 352 GLU Chi-restraints excluded: chain F residue 415 MET Chi-restraints excluded: chain F residue 506 MET Chi-restraints excluded: chain G residue 71 LEU Chi-restraints excluded: chain G residue 73 LEU Chi-restraints excluded: chain I residue 58 ASP Chi-restraints excluded: chain I residue 216 MET Chi-restraints excluded: chain I residue 279 ASP Chi-restraints excluded: chain I residue 320 MET Chi-restraints excluded: chain I residue 417 LYS Chi-restraints excluded: chain I residue 425 LEU Chi-restraints excluded: chain J residue 44 GLU Chi-restraints excluded: chain J residue 49 GLU Chi-restraints excluded: chain J residue 58 ASP Chi-restraints excluded: chain J residue 140 GLU Chi-restraints excluded: chain J residue 165 LYS Chi-restraints excluded: chain J residue 364 ILE Chi-restraints excluded: chain J residue 367 LYS Chi-restraints excluded: chain J residue 404 ILE Chi-restraints excluded: chain K residue 78 SER Chi-restraints excluded: chain K residue 113 GLU Chi-restraints excluded: chain K residue 115 ILE Chi-restraints excluded: chain K residue 133 GLU Chi-restraints excluded: chain K residue 138 VAL Chi-restraints excluded: chain K residue 169 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 386 random chunks: chunk 309 optimal weight: 0.6980 chunk 370 optimal weight: 9.9990 chunk 104 optimal weight: 2.9990 chunk 145 optimal weight: 1.9990 chunk 313 optimal weight: 9.9990 chunk 230 optimal weight: 6.9990 chunk 319 optimal weight: 9.9990 chunk 269 optimal weight: 3.9990 chunk 112 optimal weight: 2.9990 chunk 347 optimal weight: 0.5980 chunk 125 optimal weight: 8.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 197 HIS B 333 GLN C 44 GLN E 194 GLN ** F 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 136 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.117386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.076546 restraints weight = 48151.977| |-----------------------------------------------------------------------------| r_work (start): 0.3058 rms_B_bonded: 2.44 r_work: 0.2925 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2803 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.3249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 31075 Z= 0.190 Angle : 0.576 12.268 42094 Z= 0.295 Chirality : 0.046 0.173 4892 Planarity : 0.004 0.058 5391 Dihedral : 5.013 87.024 4229 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.77 % Allowed : 12.47 % Favored : 85.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.14 % 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 (0.14), residues: 3869 helix: 1.67 (0.14), residues: 1438 sheet: -0.22 (0.21), residues: 642 loop : 0.62 (0.15), residues: 1789 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG E 250 TYR 0.024 0.001 TYR K 102 PHE 0.028 0.001 PHE G 72 TRP 0.016 0.001 TRP A 97 HIS 0.007 0.001 HIS B 168 Details of bonding type rmsd/Z covalent geometry : bond 0.00458 / 0.19 (31069) covalent geometry : angle 0.57636 / 0.29 (42094) hydrogen bonds : bond 0.03872 / 2.58 ( 1274) hydrogen bonds : angle 4.20043 / 3.00 ( 3387) metal coordination : bond 0.00254 / 0.18 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7738 Ramachandran restraints generated. 3869 Oldfield, 0 Emsley, 3869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7738 Ramachandran restraints generated. 3869 Oldfield, 0 Emsley, 3869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 3391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 250 time to evaluate : 0.976 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 GLN cc_start: 0.8815 (OUTLIER) cc_final: 0.8325 (mt0) REVERT: A 127 LEU cc_start: 0.8861 (OUTLIER) cc_final: 0.8397 (pp) REVERT: A 163 ARG cc_start: 0.8382 (ttm110) cc_final: 0.8081 (tpp80) REVERT: A 387 ASP cc_start: 0.8605 (OUTLIER) cc_final: 0.8301 (m-30) REVERT: B 57 PHE cc_start: 0.8878 (OUTLIER) cc_final: 0.8309 (m-80) REVERT: B 145 ARG cc_start: 0.8416 (mmm160) cc_final: 0.8120 (mmm-85) REVERT: B 493 LYS cc_start: 0.7700 (mttt) cc_final: 0.7470 (mtmt) REVERT: C 10 GLU cc_start: 0.8348 (tt0) cc_final: 0.7945 (tp30) REVERT: C 186 LYS cc_start: 0.8740 (tppt) cc_final: 0.8260 (tptp) REVERT: D 44 GLN cc_start: 0.8258 (tp40) cc_final: 0.8012 (tp-100) REVERT: D 48 ASP cc_start: 0.7928 (m-30) cc_final: 0.7654 (m-30) REVERT: D 249 THR cc_start: 0.9211 (OUTLIER) cc_final: 0.8998 (m) REVERT: E 250 ARG cc_start: 0.8170 (mtm110) cc_final: 0.7836 (mtm-85) REVERT: E 292 ARG cc_start: 0.7902 (mpp80) cc_final: 0.7597 (mpp-170) REVERT: F 348 GLU cc_start: 0.8961 (mt-10) cc_final: 0.8354 (mt-10) REVERT: F 352 GLU cc_start: 0.8689 (OUTLIER) cc_final: 0.7881 (mp0) REVERT: F 415 MET cc_start: 0.9288 (OUTLIER) cc_final: 0.8955 (ttm) REVERT: F 506 MET cc_start: 0.9388 (OUTLIER) cc_final: 0.8982 (mtp) REVERT: G 268 GLU cc_start: 0.7495 (tt0) cc_final: 0.7060 (tm-30) REVERT: I 8 MET cc_start: 0.8696 (mmm) cc_final: 0.8490 (mmm) REVERT: I 48 PHE cc_start: 0.8792 (m-80) cc_final: 0.8463 (m-80) REVERT: I 216 MET cc_start: 0.7539 (OUTLIER) cc_final: 0.7151 (mmm) REVERT: I 320 MET cc_start: 0.8799 (OUTLIER) cc_final: 0.8547 (mtm) REVERT: I 425 LEU cc_start: 0.6982 (OUTLIER) cc_final: 0.6762 (tm) REVERT: J 16 MET cc_start: 0.7044 (mtm) cc_final: 0.6617 (ptp) REVERT: J 44 GLU cc_start: 0.8893 (OUTLIER) cc_final: 0.8611 (tt0) REVERT: J 49 GLU cc_start: 0.9160 (OUTLIER) cc_final: 0.8893 (mt-10) REVERT: J 140 GLU cc_start: 0.7347 (OUTLIER) cc_final: 0.7012 (mm-30) REVERT: J 355 ASP cc_start: 0.7709 (p0) cc_final: 0.7389 (p0) REVERT: J 367 LYS cc_start: 0.7352 (OUTLIER) cc_final: 0.7006 (ttmt) REVERT: J 404 ILE cc_start: 0.8084 (OUTLIER) cc_final: 0.7734 (tt) REVERT: K 82 ASP cc_start: 0.8094 (m-30) cc_final: 0.7874 (m-30) REVERT: K 113 GLU cc_start: 0.7500 (OUTLIER) cc_final: 0.6953 (tm-30) REVERT: K 115 ILE cc_start: 0.8837 (OUTLIER) cc_final: 0.8595 (tt) REVERT: K 133 GLU cc_start: 0.6659 (OUTLIER) cc_final: 0.6322 (mp0) REVERT: K 169 MET cc_start: 0.7702 (OUTLIER) cc_final: 0.7342 (mmm) outliers start: 60 outliers final: 22 residues processed: 289 average time/residue: 0.7060 time to fit residues: 238.6479 Evaluate side-chains 285 residues out of total 3391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 243 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 GLN Chi-restraints excluded: chain A residue 95 CYS Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 387 ASP Chi-restraints excluded: chain B residue 57 PHE Chi-restraints excluded: chain B residue 163 ARG Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain D residue 131 SER Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain E residue 169 THR Chi-restraints excluded: chain E residue 509 CYS Chi-restraints excluded: chain F residue 282 LYS Chi-restraints excluded: chain F residue 352 GLU Chi-restraints excluded: chain F residue 415 MET Chi-restraints excluded: chain F residue 506 MET Chi-restraints excluded: chain G residue 71 LEU Chi-restraints excluded: chain G residue 73 LEU Chi-restraints excluded: chain I residue 58 ASP Chi-restraints excluded: chain I residue 216 MET Chi-restraints excluded: chain I residue 279 ASP Chi-restraints excluded: chain I residue 320 MET Chi-restraints excluded: chain I residue 417 LYS Chi-restraints excluded: chain I residue 425 LEU Chi-restraints excluded: chain J residue 44 GLU Chi-restraints excluded: chain J residue 49 GLU Chi-restraints excluded: chain J residue 58 ASP Chi-restraints excluded: chain J residue 140 GLU Chi-restraints excluded: chain J residue 165 LYS Chi-restraints excluded: chain J residue 357 LEU Chi-restraints excluded: chain J residue 364 ILE Chi-restraints excluded: chain J residue 367 LYS Chi-restraints excluded: chain J residue 404 ILE Chi-restraints excluded: chain K residue 78 SER Chi-restraints excluded: chain K residue 113 GLU Chi-restraints excluded: chain K residue 115 ILE Chi-restraints excluded: chain K residue 133 GLU Chi-restraints excluded: chain K residue 138 VAL Chi-restraints excluded: chain K residue 169 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 386 random chunks: chunk 198 optimal weight: 0.7980 chunk 301 optimal weight: 0.6980 chunk 311 optimal weight: 8.9990 chunk 51 optimal weight: 0.0470 chunk 329 optimal weight: 0.9990 chunk 250 optimal weight: 0.7980 chunk 360 optimal weight: 10.0000 chunk 25 optimal weight: 2.9990 chunk 179 optimal weight: 0.9980 chunk 297 optimal weight: 1.9990 chunk 294 optimal weight: 3.9990 overall best weight: 0.6678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 197 HIS B 333 GLN C 44 GLN C 277 GLN D 261 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.119705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.078863 restraints weight = 47732.165| |-----------------------------------------------------------------------------| r_work (start): 0.3098 rms_B_bonded: 2.45 r_work: 0.2969 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2848 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.3367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 31075 Z= 0.112 Angle : 0.534 9.525 42094 Z= 0.274 Chirality : 0.044 0.159 4892 Planarity : 0.004 0.053 5391 Dihedral : 4.782 86.422 4229 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 1.12 % Allowed : 13.27 % Favored : 85.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.14 % 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: 1.40 (0.14), residues: 3869 helix: 1.80 (0.14), residues: 1442 sheet: -0.05 (0.23), residues: 524 loop : 0.69 (0.15), residues: 1903 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.000 ARG F 188 TYR 0.023 0.001 TYR H 86 PHE 0.029 0.001 PHE G 72 TRP 0.017 0.001 TRP A 97 HIS 0.007 0.001 HIS A 168 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.11 (31069) covalent geometry : angle 0.53421 / 0.27 (42094) hydrogen bonds : bond 0.03288 / 2.18 ( 1274) hydrogen bonds : angle 4.05533 / 2.90 ( 3387) metal coordination : bond 0.00111 / 0.08 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7738 Ramachandran restraints generated. 3869 Oldfield, 0 Emsley, 3869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7738 Ramachandran restraints generated. 3869 Oldfield, 0 Emsley, 3869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 3391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 264 time to evaluate : 1.157 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 LEU cc_start: 0.8888 (mm) cc_final: 0.8426 (pp) REVERT: A 163 ARG cc_start: 0.8334 (ttm110) cc_final: 0.8063 (tpp80) REVERT: A 329 ASP cc_start: 0.8536 (t0) cc_final: 0.7875 (t0) REVERT: A 387 ASP cc_start: 0.8665 (OUTLIER) cc_final: 0.8377 (m-30) REVERT: B 57 PHE cc_start: 0.8919 (OUTLIER) cc_final: 0.8205 (m-80) REVERT: B 145 ARG cc_start: 0.8360 (mmm160) cc_final: 0.8067 (mmm-85) REVERT: B 163 ARG cc_start: 0.8414 (OUTLIER) cc_final: 0.7859 (ttm-80) REVERT: B 493 LYS cc_start: 0.7758 (mttt) cc_final: 0.7523 (mtmt) REVERT: C 10 GLU cc_start: 0.8379 (tt0) cc_final: 0.7977 (tp30) REVERT: C 186 LYS cc_start: 0.8645 (tppt) cc_final: 0.8164 (tptp) REVERT: D 44 GLN cc_start: 0.8251 (tp40) cc_final: 0.8017 (tp-100) REVERT: D 48 ASP cc_start: 0.7935 (m-30) cc_final: 0.7652 (m-30) REVERT: D 131 SER cc_start: 0.8888 (OUTLIER) cc_final: 0.8564 (t) REVERT: E 250 ARG cc_start: 0.8156 (mtm110) cc_final: 0.7853 (mtm-85) REVERT: E 292 ARG cc_start: 0.7888 (mpp80) cc_final: 0.7561 (mpp-170) REVERT: F 250 ARG cc_start: 0.8879 (mtp-110) cc_final: 0.8151 (ttm110) REVERT: F 348 GLU cc_start: 0.8878 (mt-10) cc_final: 0.8312 (mt-10) REVERT: F 352 GLU cc_start: 0.8705 (OUTLIER) cc_final: 0.7863 (mp0) REVERT: G 268 GLU cc_start: 0.7396 (tt0) cc_final: 0.7025 (tm-30) REVERT: I 48 PHE cc_start: 0.8695 (m-80) cc_final: 0.8372 (m-80) REVERT: I 216 MET cc_start: 0.7541 (OUTLIER) cc_final: 0.7151 (mmm) REVERT: I 320 MET cc_start: 0.8796 (mtp) cc_final: 0.8543 (mtm) REVERT: I 425 LEU cc_start: 0.6941 (OUTLIER) cc_final: 0.6676 (tm) REVERT: J 16 MET cc_start: 0.6760 (mtm) cc_final: 0.6386 (ptp) REVERT: J 44 GLU cc_start: 0.8877 (OUTLIER) cc_final: 0.8642 (tt0) REVERT: J 49 GLU cc_start: 0.9161 (OUTLIER) cc_final: 0.8866 (mt-10) REVERT: J 140 GLU cc_start: 0.7315 (OUTLIER) cc_final: 0.7068 (mm-30) REVERT: J 355 ASP cc_start: 0.7788 (p0) cc_final: 0.7472 (p0) REVERT: J 367 LYS cc_start: 0.7463 (OUTLIER) cc_final: 0.7183 (ttmt) REVERT: J 404 ILE cc_start: 0.8037 (OUTLIER) cc_final: 0.7706 (tt) REVERT: K 17 SER cc_start: 0.8326 (p) cc_final: 0.7950 (p) REVERT: K 82 ASP cc_start: 0.8103 (m-30) cc_final: 0.7871 (m-30) REVERT: K 113 GLU cc_start: 0.7479 (OUTLIER) cc_final: 0.6948 (tm-30) REVERT: K 133 GLU cc_start: 0.6740 (OUTLIER) cc_final: 0.6430 (mp0) REVERT: K 169 MET cc_start: 0.7773 (OUTLIER) cc_final: 0.7407 (mmm) outliers start: 38 outliers final: 14 residues processed: 289 average time/residue: 0.7240 time to fit residues: 244.4506 Evaluate side-chains 271 residues out of total 3391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 242 time to evaluate : 1.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 CYS Chi-restraints excluded: chain A residue 387 ASP Chi-restraints excluded: chain B residue 57 PHE Chi-restraints excluded: chain B residue 163 ARG Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain D residue 131 SER Chi-restraints excluded: chain E residue 169 THR Chi-restraints excluded: chain E residue 509 CYS Chi-restraints excluded: chain F residue 282 LYS Chi-restraints excluded: chain F residue 352 GLU Chi-restraints excluded: chain G residue 71 LEU Chi-restraints excluded: chain G residue 223 ASN Chi-restraints excluded: chain I residue 58 ASP Chi-restraints excluded: chain I residue 216 MET Chi-restraints excluded: chain I residue 279 ASP Chi-restraints excluded: chain I residue 417 LYS Chi-restraints excluded: chain I residue 425 LEU Chi-restraints excluded: chain J residue 44 GLU Chi-restraints excluded: chain J residue 49 GLU Chi-restraints excluded: chain J residue 140 GLU Chi-restraints excluded: chain J residue 357 LEU Chi-restraints excluded: chain J residue 367 LYS Chi-restraints excluded: chain J residue 404 ILE Chi-restraints excluded: chain J residue 420 ASP Chi-restraints excluded: chain J residue 442 VAL Chi-restraints excluded: chain K residue 78 SER Chi-restraints excluded: chain K residue 113 GLU Chi-restraints excluded: chain K residue 133 GLU Chi-restraints excluded: chain K residue 169 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 386 random chunks: chunk 344 optimal weight: 1.9990 chunk 374 optimal weight: 9.9990 chunk 239 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 chunk 337 optimal weight: 8.9990 chunk 213 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 316 optimal weight: 4.9990 chunk 320 optimal weight: 20.0000 chunk 93 optimal weight: 4.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 177 ASN B 197 HIS B 333 GLN C 44 GLN F 190 ASN I 136 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.117655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.076326 restraints weight = 48270.661| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 2.48 r_work: 0.2925 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2804 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.3342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 31075 Z= 0.215 Angle : 0.581 9.320 42094 Z= 0.297 Chirality : 0.047 0.174 4892 Planarity : 0.004 0.056 5391 Dihedral : 4.908 85.153 4229 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.09 % Allowed : 13.24 % Favored : 85.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.14 % 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: 1.28 (0.14), residues: 3869 helix: 1.72 (0.14), residues: 1438 sheet: -0.14 (0.21), residues: 640 loop : 0.68 (0.15), residues: 1791 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG E 250 TYR 0.025 0.002 TYR H 86 PHE 0.028 0.002 PHE G 72 TRP 0.014 0.001 TRP A 97 HIS 0.008 0.001 HIS A 168 Details of bonding type rmsd/Z covalent geometry : bond 0.00519 / 0.21 (31069) covalent geometry : angle 0.58095 / 0.30 (42094) hydrogen bonds : bond 0.03903 / 2.60 ( 1274) hydrogen bonds : angle 4.17580 / 2.99 ( 3387) metal coordination : bond 0.00278 / 0.20 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14614.57 seconds wall clock time: 248 minutes 23.99 seconds (14903.99 seconds total)