Starting phenix.real_space_refine on Sat Aug 8 16:42:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9y3t_72466/08_2026/9y3t_72466.cif Found real_map, /net/cci-nas-00/data/ceres_data/9y3t_72466/08_2026/9y3t_72466.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9y3t_72466/08_2026/9y3t_72466.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9y3t_72466/08_2026/9y3t_72466.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9y3t_72466/08_2026/9y3t_72466.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9y3t_72466/08_2026/9y3t_72466.map" } resolution = 2.5 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= 0.005 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 4 6.06 5 P 2 5.49 5 S 161 5.16 5 Cl 2 4.86 5 C 18055 2.51 5 N 4947 2.21 5 O 5321 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 225 residue(s): 0.02s 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: 28492 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 3423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 3423 Classifications: {'peptide': 437} Link IDs: {'PCIS': 3, 'PTRANS': 18, 'TRANS': 415} Chain breaks: 1 Chain: "B" Number of atoms: 3423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 3423 Classifications: {'peptide': 437} Link IDs: {'PCIS': 3, 'PTRANS': 18, 'TRANS': 415} Chain breaks: 1 Chain: "C" Number of atoms: 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: 2294 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 2294 Classifications: {'peptide': 295} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 285} 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: 3164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 409, 3164 Classifications: {'peptide': 409} Link IDs: {'PTRANS': 18, 'TRANS': 390} Chain breaks: 2 Chain: "J" Number of atoms: 3164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 409, 3164 Classifications: {'peptide': 409} Link IDs: {'PTRANS': 18, 'TRANS': 390} Chain breaks: 2 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 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: "F" 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} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1270 SG CYS A 196 59.202 60.612 140.101 1.00 76.89 S ATOM 4693 SG CYS B 196 57.323 68.005 24.709 1.00 57.47 S ATOM 13363 SG CYS E 338 65.562 77.747 112.168 1.00 36.48 S ATOM 24178 SG CYS I 281 67.211 79.477 114.722 1.00 50.28 S ATOM 16133 SG CYS F 338 62.846 50.504 52.155 1.00 32.29 S ATOM 27342 SG CYS J 281 64.213 48.647 49.551 1.00 52.63 S Time building chain proxies: 5.43, per 1000 atoms: 0.19 Number of scatterers: 28492 At special positions: 0 Unit cell: (152.29, 130.004, 166.219, 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 4 29.99 Cl 2 17.00 S 161 16.00 P 2 15.00 O 5321 8.00 N 4947 7.00 C 18055 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: 2.23 Conformation dependent library (CDL) restraints added in 1.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1000 " pdb="ZN ZN A1000 " - pdb=" SG CYS A 196 " pdb="ZN ZN A1000 " - pdb=" ND1 HIS A 304 " pdb=" ZN B1000 " pdb="ZN ZN B1000 " - pdb=" SG CYS B 196 " pdb="ZN ZN B1000 " - pdb=" ND1 HIS B 304 " pdb=" ZN E 601 " pdb="ZN ZN E 601 " - pdb=" ND1 HIS E 371 " pdb="ZN ZN E 601 " - pdb=" SG CYS I 281 " pdb="ZN ZN E 601 " - pdb=" SG CYS E 338 " pdb=" ZN F 602 " pdb="ZN ZN F 602 " - pdb=" SG CYS J 281 " pdb="ZN ZN F 602 " - pdb=" ND1 HIS F 371 " pdb="ZN ZN F 602 " - pdb=" SG CYS F 338 " 7242 Ramachandran restraints generated. 3621 Oldfield, 0 Emsley, 3621 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6898 Finding SS restraints... Secondary structure from input PDB file: 169 helices and 37 sheets defined 45.5% alpha, 14.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.12 Creating SS restraints... Processing helix chain 'A' and resid 58 through 63 removed outlier: 4.325A pdb=" N ASP A 62 " --> pdb=" O PRO A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 67 Processing helix chain 'A' and resid 75 through 87 Processing helix chain 'A' and resid 98 through 108 removed outlier: 3.577A pdb=" N ILE A 102 " --> pdb=" O LYS A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 113 Processing helix chain 'A' and resid 130 through 141 Processing helix chain 'A' and resid 161 through 175 Processing helix chain 'A' and resid 229 through 232 Processing helix chain 'A' and resid 253 through 263 removed outlier: 4.365A pdb=" N ALA A 257 " --> pdb=" O SER A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 284 removed outlier: 6.017A pdb=" N GLU A 281 " --> pdb=" O LEU A 277 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N ILE A 282 " --> pdb=" O VAL A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 315 Processing helix chain 'A' and resid 322 through 326 removed outlier: 3.661A pdb=" N ASN A 326 " --> pdb=" O PRO A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 334 removed outlier: 4.061A pdb=" N SER A 334 " --> pdb=" O THR A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 489 Processing helix chain 'B' and resid 58 through 62 Processing helix chain 'B' and resid 64 through 67 Processing helix chain 'B' and resid 75 through 87 Processing helix chain 'B' and resid 98 through 109 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 254 through 263 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 Processing helix chain 'B' and resid 484 through 489 Processing helix chain 'C' and resid 9 through 24 removed outlier: 3.587A pdb=" N GLU C 13 " --> pdb=" O SER C 9 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 48 Processing helix chain 'C' and resid 53 through 72 removed outlier: 3.942A pdb=" N GLN C 72 " --> pdb=" O MET C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 75 through 98 removed outlier: 4.020A pdb=" N GLY C 79 " --> pdb=" O GLU C 75 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LEU C 96 " --> pdb=" O GLU C 92 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 153 removed outlier: 4.623A pdb=" N MET C 148 " --> pdb=" O LEU C 144 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N GLU C 149 " --> pdb=" O GLU C 145 " (cutoff:3.500A) Processing helix chain 'C' and resid 154 through 158 Processing helix chain 'C' and resid 171 through 183 Processing helix chain 'C' and resid 199 through 210 Processing helix chain 'C' and resid 218 through 220 No H-bonds generated for 'chain 'C' and resid 218 through 220' Processing helix chain 'C' and resid 221 through 227 removed outlier: 4.459A 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 removed outlier: 3.969A pdb=" N HIS C 286 " --> pdb=" O ASP C 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 290 through 294 Processing helix chain 'C' and resid 296 through 305 removed outlier: 6.311A pdb=" N ASP C 301 " --> pdb=" O THR C 298 " (cutoff:3.500A) removed outlier: 4.383A 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: 3.601A 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 48 Processing helix chain 'D' and resid 53 through 72 removed outlier: 3.947A pdb=" N GLN D 72 " --> pdb=" O MET D 68 " (cutoff:3.500A) Processing helix chain 'D' and resid 75 through 98 removed outlier: 3.996A pdb=" N GLY D 79 " --> pdb=" O GLU D 75 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU D 96 " --> pdb=" O GLU D 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 128 through 153 removed outlier: 4.742A pdb=" N MET D 148 " --> pdb=" O LEU D 144 " (cutoff:3.500A) removed outlier: 5.302A 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 Processing helix chain 'D' and resid 198 through 210 removed outlier: 4.222A pdb=" N GLU D 202 " --> pdb=" O CYS D 198 " (cutoff:3.500A) Processing helix chain 'D' and resid 221 through 227 removed outlier: 4.353A 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 290 through 294 Processing helix chain 'D' and resid 296 through 305 removed outlier: 6.078A pdb=" N ASP D 301 " --> pdb=" O THR D 298 " (cutoff:3.500A) removed outlier: 3.952A 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: 3.765A 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 196 Processing helix chain 'E' and resid 204 through 216 Processing helix chain 'E' and resid 221 through 240 removed outlier: 3.504A pdb=" N CYS E 226 " --> pdb=" O SER E 222 " (cutoff:3.500A) Processing helix chain 'E' and resid 247 through 267 removed outlier: 5.001A 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 325 removed outlier: 3.887A pdb=" N GLN E 325 " --> pdb=" O ARG E 321 " (cutoff:3.500A) Processing helix chain 'E' and resid 339 through 352 Processing helix chain 'E' and resid 368 through 379 removed outlier: 3.594A 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 463 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 519 Processing helix chain 'F' and resid 177 through 181 Processing helix chain 'F' and resid 191 through 196 Processing helix chain 'F' and resid 204 through 216 Processing helix chain 'F' and resid 221 through 240 removed outlier: 3.545A pdb=" N CYS F 226 " --> pdb=" O SER F 222 " (cutoff:3.500A) Processing helix chain 'F' and resid 247 through 267 removed outlier: 5.240A pdb=" N VAL F 253 " --> pdb=" O SER F 249 " (cutoff:3.500A) Proline residue: F 258 - end of helix Processing helix chain 'F' and resid 270 through 286 Processing helix chain 'F' and resid 292 through 312 Processing helix chain 'F' and resid 312 through 324 Processing helix chain 'F' and resid 339 through 352 Processing helix chain 'F' and resid 368 through 379 removed outlier: 3.717A pdb=" N THR F 372 " --> pdb=" O GLU F 368 " (cutoff:3.500A) Processing helix chain 'F' and resid 390 through 395 removed outlier: 3.509A pdb=" N VAL F 394 " --> pdb=" O ALA F 390 " (cutoff:3.500A) 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 443 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 519 removed outlier: 3.723A pdb=" N ARG F 517 " --> pdb=" O PRO F 513 " (cutoff:3.500A) Processing helix chain 'G' and resid 4 through 14 Processing helix chain 'G' and resid 21 through 37 Processing helix chain 'G' and resid 41 through 57 Processing helix chain 'G' and resid 62 through 77 removed outlier: 3.719A pdb=" N SER G 66 " --> pdb=" O SER G 62 " (cutoff:3.500A) Processing helix chain 'G' and resid 85 through 116 removed outlier: 4.501A pdb=" N ARG G 108 " --> pdb=" O ILE G 104 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N ASN G 109 " --> pdb=" O SER G 105 " (cutoff:3.500A) 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 Processing helix chain 'G' and resid 159 through 170 removed outlier: 3.741A pdb=" N LYS G 163 " --> pdb=" O LEU G 159 " (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 292 through 304 removed outlier: 3.579A pdb=" N VAL G 296 " --> pdb=" O THR G 292 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N SER G 297 " --> pdb=" O PRO G 293 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ASP G 298 " --> pdb=" O SER G 294 " (cutoff:3.500A) Processing helix chain 'H' and resid 3 through 15 Processing helix chain 'H' and resid 21 through 37 Processing helix chain 'H' and resid 41 through 60 removed outlier: 3.589A pdb=" N VAL H 59 " --> pdb=" O THR H 55 " (cutoff:3.500A) Processing helix chain 'H' and resid 62 through 77 removed outlier: 3.813A pdb=" N SER H 66 " --> pdb=" O SER H 62 " (cutoff:3.500A) Processing helix chain 'H' and resid 80 through 84 removed outlier: 3.909A pdb=" N TYR H 83 " --> pdb=" O SER H 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 85 through 116 removed outlier: 3.630A pdb=" N LYS H 91 " --> pdb=" O SER H 87 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU H 106 " --> pdb=" O ARG H 102 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N SER H 107 " --> pdb=" O ARG H 103 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N ARG H 108 " --> pdb=" O ILE H 104 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N ASN H 109 " --> pdb=" O SER H 105 " (cutoff:3.500A) 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 171 removed outlier: 3.854A pdb=" N LYS H 163 " --> pdb=" O LEU H 159 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N HIS H 170 " --> pdb=" O LYS H 166 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU H 171 " --> pdb=" O ALA H 167 " (cutoff:3.500A) 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 292 through 305 removed outlier: 3.744A pdb=" N VAL H 296 " --> pdb=" O THR H 292 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N SER H 297 " --> pdb=" O PRO H 293 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ASP H 298 " --> pdb=" O SER H 294 " (cutoff:3.500A) Processing helix chain 'I' and resid 16 through 21 removed outlier: 3.818A pdb=" N THR I 20 " --> pdb=" O MET I 16 " (cutoff:3.500A) Processing helix chain 'I' and resid 24 through 28 Processing helix chain 'I' and resid 36 through 47 removed outlier: 3.526A pdb=" N LEU I 40 " --> pdb=" O ILE I 36 " (cutoff:3.500A) Processing helix chain 'I' and resid 56 through 67 Processing helix chain 'I' and resid 85 through 92 Processing helix chain 'I' and resid 93 through 97 Processing helix chain 'I' and resid 114 through 124 removed outlier: 4.378A pdb=" N LEU I 120 " --> pdb=" O GLU I 116 " (cutoff:3.500A) Processing helix chain 'I' and resid 144 through 148 removed outlier: 3.895A pdb=" N GLY I 147 " --> pdb=" O GLY I 144 " (cutoff:3.500A) 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 188 Processing helix chain 'I' and resid 208 through 218 removed outlier: 3.738A pdb=" N VAL I 212 " --> pdb=" O LYS I 208 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLU I 217 " --> pdb=" O ASP I 213 " (cutoff:3.500A) Processing helix chain 'I' and resid 227 through 235 Processing helix chain 'I' and resid 236 through 238 No H-bonds generated for 'chain 'I' and resid 236 through 238' Processing helix chain 'I' and resid 262 through 267 Processing helix chain 'I' and resid 315 through 334 Proline residue: I 327 - end of helix removed outlier: 4.145A pdb=" N SER I 331 " --> pdb=" O PRO I 327 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ALA I 332 " --> pdb=" O LYS I 328 " (cutoff:3.500A) Processing helix chain 'I' and resid 348 through 352 removed outlier: 3.753A pdb=" N VAL I 352 " --> pdb=" O LYS I 349 " (cutoff:3.500A) 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 64 Processing helix chain 'J' and resid 87 through 92 Processing helix chain 'J' and resid 93 through 97 Processing helix chain 'J' and resid 114 through 124 removed outlier: 4.222A pdb=" N LEU J 120 " --> pdb=" O GLU J 116 " (cutoff:3.500A) Processing helix chain 'J' and resid 144 through 148 Processing helix chain 'J' and resid 173 through 177 removed outlier: 4.244A pdb=" N ASP J 177 " --> pdb=" O GLU J 173 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 173 through 177' Processing helix chain 'J' and resid 184 through 188 Processing helix chain 'J' and resid 208 through 218 removed outlier: 3.780A pdb=" N VAL J 212 " --> pdb=" O LYS J 208 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N MET J 216 " --> pdb=" O VAL J 212 " (cutoff:3.500A) removed outlier: 3.985A 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 237 through 238 No H-bonds generated for 'chain 'J' and resid 237 through 238' Processing helix chain 'J' and resid 262 through 267 Processing helix chain 'J' and resid 315 through 334 Proline residue: J 327 - end of helix removed outlier: 3.881A pdb=" N SER J 331 " --> pdb=" O PRO J 327 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ALA J 332 " --> pdb=" O LYS J 328 " (cutoff:3.500A) Processing helix chain 'J' and resid 348 through 352 removed outlier: 3.751A pdb=" N VAL J 352 " --> pdb=" O LYS J 349 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 119 through 124 removed outlier: 6.661A pdb=" N THR A 91 " --> pdb=" O ARG A 121 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N ILE A 123 " --> pdb=" O THR A 91 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N VAL A 93 " --> pdb=" O ILE A 123 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N TYR A 152 " --> pdb=" O HIS A 248 " (cutoff:3.500A) removed outlier: 8.728A pdb=" N HIS A 248 " --> pdb=" O TYR A 152 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N CYS A 247 " --> pdb=" O ILE A 184 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N ILE A 184 " --> pdb=" O CYS A 247 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N ILE A 249 " --> pdb=" O THR A 182 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N THR A 182 " --> pdb=" O ILE A 249 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N ILE A 251 " --> pdb=" O VAL A 180 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N VAL A 180 " --> pdb=" O ILE A 251 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N HIS A 288 " --> pdb=" O VAL A 180 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N THR A 182 " --> pdb=" O HIS A 288 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N HIS A 290 " --> pdb=" O THR A 182 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N ILE A 184 " --> pdb=" O HIS A 290 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N THR A 292 " --> pdb=" O ILE A 184 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N LYS A 186 " --> pdb=" O THR A 292 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N ILE A 287 " --> pdb=" O VAL A 212 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ARG A 211 " --> pdb=" O ASP A 206 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N ALA A 204 " --> pdb=" O LEU A 213 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N PHE A 215 " --> pdb=" O VAL A 202 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N VAL A 202 " --> pdb=" O PHE A 215 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N VAL A 238 " --> pdb=" O PHE I 195 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N PHE I 157 " --> pdb=" O MET I 170 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N MET I 170 " --> pdb=" O PHE I 157 " (cutoff:3.500A) removed outlier: 6.454A 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: 6.701A pdb=" N TYR A 343 " --> pdb=" O LEU A 362 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N LEU A 361 " --> pdb=" O ILE A 379 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N VAL A 378 " --> pdb=" O LEU A 396 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N TYR A 395 " --> pdb=" O LEU A 413 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N LEU A 412 " --> pdb=" O LEU A 431 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N VAL A 430 " --> pdb=" O ILE A 449 " (cutoff:3.500A) removed outlier: 4.283A 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: 6.510A pdb=" N SER A 349 " --> pdb=" O ILE A 368 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N VAL A 367 " --> pdb=" O ILE A 385 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N HIS A 384 " --> pdb=" O VAL A 402 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ARG A 401 " --> pdb=" O VAL A 419 " (cutoff:3.500A) removed outlier: 6.648A 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: 6.403A pdb=" N ILE A 355 " --> pdb=" O ILE A 374 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N PHE A 373 " --> pdb=" O LEU A 391 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N VAL A 390 " --> pdb=" O ILE A 408 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N GLN A 407 " --> pdb=" O LEU A 425 " (cutoff:3.500A) removed outlier: 6.895A 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: 4.643A pdb=" N TYR B 152 " --> pdb=" O HIS B 248 " (cutoff:3.500A) removed outlier: 8.583A pdb=" N HIS B 248 " --> pdb=" O TYR B 152 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N CYS B 247 " --> pdb=" O ILE B 184 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N ILE B 184 " --> pdb=" O CYS B 247 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N ILE B 249 " --> pdb=" O THR B 182 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N THR B 182 " --> pdb=" O ILE B 249 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N ILE B 251 " --> pdb=" O VAL B 180 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N VAL B 180 " --> pdb=" O ILE B 251 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N SER B 179 " --> pdb=" O GLN B 286 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N HIS B 288 " --> pdb=" O SER B 179 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N MET B 181 " --> pdb=" O HIS B 288 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N HIS B 290 " --> pdb=" O MET B 181 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N MET B 183 " --> pdb=" O HIS B 290 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N THR B 292 " --> pdb=" O MET B 183 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N PHE B 185 " --> pdb=" O THR B 292 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N ILE B 287 " --> pdb=" O VAL B 212 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ARG B 211 " --> pdb=" O ASP B 206 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N ALA B 204 " --> pdb=" O LEU B 213 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N PHE B 215 " --> pdb=" O VAL B 202 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N VAL B 202 " --> pdb=" O PHE B 215 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N VAL B 238 " --> pdb=" O PHE J 195 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N PHE J 157 " --> pdb=" O MET J 170 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N MET J 170 " --> pdb=" O PHE J 157 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N GLY J 159 " --> pdb=" O LEU J 168 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 69 through 70 Processing sheet with id=AB1, first strand: chain 'B' and resid 155 through 157 Processing sheet with id=AB2, first strand: chain 'B' and resid 223 through 227 Processing sheet with id=AB3, first strand: chain 'B' and resid 336 through 338 removed outlier: 6.330A pdb=" N LEU B 361 " --> pdb=" O ILE B 379 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N VAL B 378 " --> pdb=" O LEU B 396 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N TYR B 395 " --> pdb=" O LEU B 413 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N LEU B 412 " --> pdb=" O LEU B 431 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N VAL B 430 " --> pdb=" O ILE B 449 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N VAL B 448 " --> pdb=" O TRP B 497 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 349 through 350 removed outlier: 6.301A pdb=" N SER B 349 " --> pdb=" O ILE B 368 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N VAL B 367 " --> pdb=" O ILE B 385 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N HIS B 384 " --> pdb=" O VAL B 402 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N ARG B 401 " --> pdb=" O VAL B 419 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N GLU B 418 " --> pdb=" O VAL B 437 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'B' and resid 355 through 356 removed outlier: 6.413A pdb=" N ILE B 355 " --> pdb=" O ILE B 374 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N PHE B 373 " --> pdb=" O LEU B 391 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N VAL B 390 " --> pdb=" O ILE B 408 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N GLN B 407 " --> pdb=" O LEU B 425 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'C' and resid 329 through 331 removed outlier: 6.777A pdb=" N LEU C 265 " --> pdb=" O LEU C 323 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N ILE C 325 " --> pdb=" O LEU C 265 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N VAL C 267 " --> pdb=" O ILE C 325 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N VAL C 232 " --> pdb=" O ILE C 266 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N CYS C 268 " --> pdb=" O VAL C 232 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N ILE C 234 " --> pdb=" O CYS C 268 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N VAL C 164 " --> pdb=" O LYS C 231 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N ILE C 233 " --> pdb=" O VAL C 164 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N MET C 166 " --> pdb=" O ILE C 233 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N ILE C 165 " --> pdb=" O ILE C 190 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N ALA C 192 " --> pdb=" O ILE C 165 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N THR C 167 " --> pdb=" O ALA C 192 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 238 through 239 Processing sheet with id=AB8, first strand: chain 'C' and resid 307 through 308 removed outlier: 6.462A pdb=" N SER C 307 " --> pdb=" O TYR F 385 " (cutoff:3.500A) removed outlier: 8.799A pdb=" N LEU F 387 " --> pdb=" O SER C 307 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N ILE F 333 " --> pdb=" O VAL F 359 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N VAL F 361 " --> pdb=" O ILE F 333 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N VAL F 335 " --> pdb=" O VAL F 361 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N VAL F 332 " --> pdb=" O LYS F 400 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N LEU F 402 " --> pdb=" O VAL F 332 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N LEU F 334 " --> pdb=" O LEU F 402 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N GLY F 404 " --> pdb=" O LEU F 334 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N TYR F 336 " --> pdb=" O GLY F 404 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N VAL F 401 " --> pdb=" O LEU F 435 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N CYS F 437 " --> pdb=" O VAL F 401 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N LEU F 403 " --> pdb=" O CYS F 437 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N VAL F 434 " --> pdb=" O LEU F 499 " (cutoff:3.500A) removed outlier: 7.957A pdb=" N ILE F 501 " --> pdb=" O VAL F 434 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N VAL F 436 " --> pdb=" O ILE F 501 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 329 through 331 removed outlier: 6.780A pdb=" N LEU D 265 " --> pdb=" O LEU D 323 " (cutoff:3.500A) removed outlier: 7.856A pdb=" N ILE D 325 " --> pdb=" O LEU D 265 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N VAL D 267 " --> pdb=" O ILE D 325 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N VAL D 232 " --> pdb=" O ILE D 266 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N CYS D 268 " --> pdb=" O VAL D 232 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ILE D 234 " --> pdb=" O CYS D 268 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N VAL D 164 " --> pdb=" O LYS D 231 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N ILE D 233 " --> pdb=" O VAL D 164 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N MET D 166 " --> pdb=" O ILE D 233 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N THR D 214 " --> pdb=" O ARG E 483 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N LEU E 485 " --> pdb=" O THR D 214 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N VAL D 216 " --> pdb=" O LEU E 485 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 238 through 239 Processing sheet with id=AC2, first strand: chain 'D' and resid 307 through 308 removed outlier: 6.610A pdb=" N SER D 307 " --> pdb=" O TYR E 385 " (cutoff:3.500A) removed outlier: 8.811A pdb=" N LEU E 387 " --> pdb=" O SER D 307 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N ILE E 333 " --> pdb=" O VAL E 359 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N VAL E 361 " --> pdb=" O ILE E 333 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N VAL E 335 " --> pdb=" O VAL E 361 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N VAL E 332 " --> pdb=" O LYS E 400 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N LEU E 402 " --> pdb=" O VAL E 332 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N LEU E 334 " --> pdb=" O LEU E 402 " (cutoff:3.500A) removed outlier: 8.011A pdb=" N GLY E 404 " --> pdb=" O LEU E 334 " (cutoff:3.500A) removed outlier: 8.002A pdb=" N TYR E 336 " --> pdb=" O GLY E 404 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N VAL E 401 " --> pdb=" O LEU E 435 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N CYS E 437 " --> pdb=" O VAL E 401 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N LEU E 403 " --> pdb=" O CYS E 437 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N VAL E 434 " --> pdb=" O LEU E 499 " (cutoff:3.500A) removed outlier: 7.971A pdb=" N ILE E 501 " --> pdb=" O VAL E 434 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N VAL E 436 " --> pdb=" O ILE E 501 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 407 through 408 Processing sheet with id=AC4, first strand: chain 'F' and resid 407 through 408 Processing sheet with id=AC5, first strand: chain 'G' and resid 289 through 291 removed outlier: 6.754A pdb=" N PHE G 226 " --> pdb=" O LEU G 283 " (cutoff:3.500A) removed outlier: 8.189A pdb=" N PHE G 285 " --> pdb=" O PHE G 226 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N VAL G 228 " --> pdb=" O PHE G 285 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N VAL G 193 " --> pdb=" O TYR G 227 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N VAL G 229 " --> pdb=" O VAL G 193 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N VAL G 195 " --> pdb=" O VAL G 229 " (cutoff:3.500A) removed outlier: 8.956A pdb=" N THR G 176 " --> pdb=" O PHE G 148 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N VAL G 150 " --> pdb=" O THR G 176 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N VAL G 178 " --> pdb=" O VAL G 150 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N VAL G 152 " --> pdb=" O VAL G 178 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N VAL G 175 " --> pdb=" O LYS H 267 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 199 through 200 Processing sheet with id=AC7, first strand: chain 'G' and resid 267 through 269 removed outlier: 6.935A pdb=" N LYS G 267 " --> pdb=" O VAL H 177 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N VAL H 193 " --> pdb=" O TYR H 227 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N VAL H 229 " --> pdb=" O VAL H 193 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N VAL H 195 " --> pdb=" O VAL H 229 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N PHE H 226 " --> pdb=" O LEU H 283 " (cutoff:3.500A) removed outlier: 8.134A pdb=" N PHE H 285 " --> pdb=" O PHE H 226 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N VAL H 228 " --> pdb=" O PHE H 285 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'H' and resid 199 through 200 Processing sheet with id=AC9, first strand: chain 'I' and resid 72 through 77 removed outlier: 6.632A pdb=" N VAL I 51 " --> pdb=" O ASP I 74 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N VAL I 76 " --> pdb=" O VAL I 51 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N VAL I 53 " --> pdb=" O VAL I 76 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N GLU I 50 " --> pdb=" O PHE I 3 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N ALA I 5 " --> pdb=" O GLU I 50 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N GLN I 4 " --> pdb=" O LEU I 102 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N LEU I 104 " --> pdb=" O GLN I 4 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N VAL I 6 " --> pdb=" O LEU I 104 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N SER I 105 " --> pdb=" O HIS I 203 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N HIS I 203 " --> pdb=" O SER I 105 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N ALA I 202 " --> pdb=" O ARG I 133 " (cutoff:3.500A) removed outlier: 8.249A pdb=" N ARG I 133 " --> pdb=" O ALA I 202 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N LEU I 204 " --> pdb=" O LEU I 131 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N LEU I 128 " --> pdb=" O TYR I 301 " (cutoff:3.500A) removed outlier: 7.975A pdb=" N HIS I 303 " --> pdb=" O LEU I 128 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N MET I 130 " --> pdb=" O HIS I 303 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N MET I 305 " --> pdb=" O MET I 130 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N MET I 132 " --> pdb=" O MET I 305 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 108 through 110 Processing sheet with id=AD2, first strand: chain 'I' and resid 345 through 346 removed outlier: 6.636A pdb=" N GLN I 345 " --> pdb=" O ILE I 364 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N GLN I 363 " --> pdb=" O ILE I 381 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N LEU I 380 " --> pdb=" O VAL I 398 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N THR I 397 " --> pdb=" O ILE I 415 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N VAL I 414 " --> pdb=" O ILE I 432 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'I' and resid 357 through 358 removed outlier: 6.423A pdb=" N LEU I 357 " --> pdb=" O ILE I 375 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N VAL I 374 " --> pdb=" O LEU I 392 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N LEU I 391 " --> pdb=" O ILE I 409 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N VAL I 408 " --> pdb=" O ILE I 426 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N LEU I 425 " --> pdb=" O ILE I 443 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'I' and resid 369 through 371 removed outlier: 6.632A pdb=" N SER I 369 " --> pdb=" O ILE I 387 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ASN I 403 " --> pdb=" O ILE I 421 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ARG I 438 " --> pdb=" O ASP I 420 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'J' and resid 74 through 77 removed outlier: 6.354A pdb=" N VAL J 53 " --> pdb=" O VAL J 76 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N HIS J 203 " --> pdb=" O SER J 105 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N LEU J 131 " --> pdb=" O ALA J 202 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N LEU J 204 " --> pdb=" O ALA J 129 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N ALA J 129 " --> pdb=" O LEU J 204 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N LEU J 128 " --> pdb=" O TYR J 301 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N HIS J 303 " --> pdb=" O LEU J 128 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N MET J 130 " --> pdb=" O HIS J 303 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N MET J 305 " --> pdb=" O MET J 130 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N MET J 132 " --> pdb=" O MET J 305 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'J' and resid 29 through 30 removed outlier: 3.604A pdb=" N LYS J 33 " --> pdb=" O VAL J 30 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'J' and resid 108 through 110 Processing sheet with id=AD8, first strand: chain 'J' and resid 345 through 346 removed outlier: 6.649A pdb=" N GLN J 345 " --> pdb=" O ILE J 364 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N GLN J 363 " --> pdb=" O ILE J 381 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N LEU J 380 " --> pdb=" O VAL J 398 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N THR J 397 " --> pdb=" O ILE J 415 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N VAL J 414 " --> pdb=" O ILE J 432 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'J' and resid 357 through 358 removed outlier: 6.288A pdb=" N LEU J 357 " --> pdb=" O ILE J 375 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N VAL J 374 " --> pdb=" O LEU J 392 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N LEU J 391 " --> pdb=" O ILE J 409 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N VAL J 408 " --> pdb=" O ILE J 426 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N LEU J 425 " --> pdb=" O ILE J 443 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'J' and resid 369 through 371 removed outlier: 6.425A pdb=" N SER J 369 " --> pdb=" O ILE J 387 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N THR J 386 " --> pdb=" O ILE J 404 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N ASN J 403 " --> pdb=" O ILE J 421 " (cutoff:3.500A) 1205 hydrogen bonds defined for protein. 3222 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: 6.86 Time building geometry restraints manager: 3.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 4966 1.32 - 1.45: 7148 1.45 - 1.57: 16645 1.57 - 1.69: 1 1.69 - 1.82: 242 Bond restraints: 29002 Sorted by residual: bond pdb=" CA PRO E 493 " pdb=" CB PRO E 493 " ideal model delta sigma weight residual 1.539 1.495 0.044 9.30e-03 1.16e+04 2.22e+01 bond pdb=" CA PRO F 493 " pdb=" CB PRO F 493 " ideal model delta sigma weight residual 1.539 1.496 0.044 9.30e-03 1.16e+04 2.20e+01 bond pdb=" CA SER C 326 " pdb=" CB SER C 326 " ideal model delta sigma weight residual 1.532 1.466 0.066 1.45e-02 4.76e+03 2.05e+01 bond pdb=" C VAL F 335 " pdb=" O VAL F 335 " ideal model delta sigma weight residual 1.235 1.196 0.039 9.90e-03 1.02e+04 1.55e+01 bond pdb=" CA SER D 326 " pdb=" CB SER D 326 " ideal model delta sigma weight residual 1.532 1.476 0.055 1.45e-02 4.76e+03 1.46e+01 ... (remaining 28997 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.67: 37955 3.67 - 7.34: 1254 7.34 - 11.01: 79 11.01 - 14.68: 7 14.68 - 18.34: 1 Bond angle restraints: 39296 Sorted by residual: angle pdb=" OG1 THR D 236 " pdb=" CB THR D 236 " pdb=" CG2 THR D 236 " ideal model delta sigma weight residual 109.30 90.96 18.34 2.00e+00 2.50e-01 8.41e+01 angle pdb=" N GLN E 317 " pdb=" CA GLN E 317 " pdb=" CB GLN E 317 " ideal model delta sigma weight residual 110.16 98.49 11.67 1.48e+00 4.57e-01 6.21e+01 angle pdb=" N VAL G 229 " pdb=" CA VAL G 229 " pdb=" CB VAL G 229 " ideal model delta sigma weight residual 111.90 102.30 9.60 1.26e+00 6.30e-01 5.81e+01 angle pdb=" CA ASP A 53 " pdb=" CB ASP A 53 " pdb=" CG ASP A 53 " ideal model delta sigma weight residual 112.60 120.07 -7.47 1.00e+00 1.00e+00 5.58e+01 angle pdb=" C GLU D 193 " pdb=" CA GLU D 193 " pdb=" CB GLU D 193 " ideal model delta sigma weight residual 110.68 98.86 11.82 1.70e+00 3.46e-01 4.84e+01 ... (remaining 39291 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.71: 16204 17.71 - 35.42: 1153 35.42 - 53.13: 229 53.13 - 70.83: 88 70.83 - 88.54: 30 Dihedral angle restraints: 17704 sinusoidal: 7065 harmonic: 10639 Sorted by residual: dihedral pdb=" CA CYS E 465 " pdb=" C CYS E 465 " pdb=" N LYS E 466 " pdb=" CA LYS E 466 " ideal model delta harmonic sigma weight residual -180.00 -140.32 -39.68 0 5.00e+00 4.00e-02 6.30e+01 dihedral pdb=" CA VAL F 167 " pdb=" C VAL F 167 " pdb=" N PRO F 168 " pdb=" CA PRO F 168 " ideal model delta harmonic sigma weight residual -180.00 -143.44 -36.56 0 5.00e+00 4.00e-02 5.35e+01 dihedral pdb=" CA SER F 289 " pdb=" C SER F 289 " pdb=" N SER F 290 " pdb=" CA SER F 290 " ideal model delta harmonic sigma weight residual 180.00 144.31 35.69 0 5.00e+00 4.00e-02 5.10e+01 ... (remaining 17701 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.102: 3537 0.102 - 0.203: 965 0.203 - 0.305: 77 0.305 - 0.407: 11 0.407 - 0.508: 3 Chirality restraints: 4593 Sorted by residual: chirality pdb=" CA ASP C 314 " pdb=" N ASP C 314 " pdb=" C ASP C 314 " pdb=" CB ASP C 314 " both_signs ideal model delta sigma weight residual False 2.51 2.00 0.51 2.00e-01 2.50e+01 6.46e+00 chirality pdb=" CA GLN F 464 " pdb=" N GLN F 464 " pdb=" C GLN F 464 " pdb=" CB GLN F 464 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.47 2.00e-01 2.50e+01 5.56e+00 chirality pdb=" CA ASP D 314 " pdb=" N ASP D 314 " pdb=" C ASP D 314 " pdb=" CB ASP D 314 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.42e+00 ... (remaining 4590 not shown) Planarity restraints: 5029 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG F 225 " 0.525 9.50e-02 1.11e+02 2.36e-01 3.68e+01 pdb=" NE ARG F 225 " -0.022 2.00e-02 2.50e+03 pdb=" CZ ARG F 225 " -0.035 2.00e-02 2.50e+03 pdb=" NH1 ARG F 225 " 0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG F 225 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 172 " 0.489 9.50e-02 1.11e+02 2.20e-01 3.27e+01 pdb=" NE ARG C 172 " -0.019 2.00e-02 2.50e+03 pdb=" CZ ARG C 172 " -0.037 2.00e-02 2.50e+03 pdb=" NH1 ARG C 172 " 0.007 2.00e-02 2.50e+03 pdb=" NH2 ARG C 172 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 172 " -0.480 9.50e-02 1.11e+02 2.16e-01 3.06e+01 pdb=" NE ARG D 172 " 0.020 2.00e-02 2.50e+03 pdb=" CZ ARG D 172 " 0.031 2.00e-02 2.50e+03 pdb=" NH1 ARG D 172 " -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG D 172 " -0.025 2.00e-02 2.50e+03 ... (remaining 5026 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 2331 2.75 - 3.29: 29045 3.29 - 3.82: 46689 3.82 - 4.36: 60407 4.36 - 4.90: 99811 Nonbonded interactions: 238283 Sorted by model distance: nonbonded pdb="CL CL F 601 " pdb="ZN ZN F 602 " model vdw 2.212 2.380 nonbonded pdb="ZN ZN E 601 " pdb="CL CL E 602 " model vdw 2.257 2.380 nonbonded pdb=" OG1 THR F 193 " pdb=" OD2 ASP J 119 " model vdw 2.311 3.040 nonbonded pdb=" OH TYR A 296 " pdb=" OD2 ASP A 312 " model vdw 2.328 3.040 nonbonded pdb=" O LEU C 274 " pdb=" OH TYR C 344 " model vdw 2.365 3.040 ... (remaining 238278 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' } ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = (chain 'E' and resid 167 through 522) selection = (chain 'F' and resid 167 through 522) } ncs_group { reference = chain 'G' selection = (chain 'H' and resid 2 through 305) } ncs_group { reference = chain 'I' selection = chain 'J' } 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: 5.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.460 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 29.660 Find NCS groups from input model: 0.700 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:9.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8670 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 0.395 29012 Z= 0.652 Angle : 1.595 18.344 39296 Z= 1.019 Chirality : 0.087 0.508 4593 Planarity : 0.015 0.236 5029 Dihedral : 14.137 88.543 10806 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 1.74 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.92 % Favored : 95.89 % Rotamer: Outliers : 1.32 % Allowed : 3.62 % Favored : 95.06 % Cbeta Deviations : 0.61 % Peptide Plane: Cis-proline : 8.75 % Cis-general : 0.00 % Twisted Proline : 1.25 % Twisted General : 0.09 % 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: -1.20 (0.13), residues: 3621 helix: -1.34 (0.12), residues: 1314 sheet: -0.47 (0.23), residues: 444 loop : -0.29 (0.14), residues: 1863 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.036 0.004 ARG B 315 TYR 0.065 0.009 TYR F 489 PHE 0.038 0.008 PHE G 285 TRP 0.059 0.008 TRP G 272 HIS 0.023 0.005 HIS C 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00996 / 0.64 (29002) covalent geometry : angle 1.59516 / 1.02 (39296) hydrogen bonds : bond 0.17757 / 11.68 ( 1205) hydrogen bonds : angle 7.01543 / 5.05 ( 3222) metal coordination : bond 0.23228 / 13.86 ( 10) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7242 Ramachandran restraints generated. 3621 Oldfield, 0 Emsley, 3621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7242 Ramachandran restraints generated. 3621 Oldfield, 0 Emsley, 3621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 520 residues out of total 3175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 478 time to evaluate : 1.120 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: D 124 PHE cc_start: 0.8109 (m-80) cc_final: 0.7682 (m-80) REVERT: E 195 PHE cc_start: 0.8387 (m-80) cc_final: 0.8125 (m-80) REVERT: F 511 SER cc_start: 0.8853 (OUTLIER) cc_final: 0.8623 (t) REVERT: G 48 ASN cc_start: 0.8727 (t0) cc_final: 0.8414 (t0) REVERT: H 1 MET cc_start: 0.4042 (tpt) cc_final: 0.3812 (pmt) REVERT: I 74 ASP cc_start: 0.7886 (OUTLIER) cc_final: 0.7393 (t0) REVERT: I 231 TYR cc_start: 0.8492 (t80) cc_final: 0.8241 (t80) REVERT: I 358 ILE cc_start: 0.8506 (mt) cc_final: 0.8306 (mt) REVERT: I 380 LEU cc_start: 0.7945 (mt) cc_final: 0.7568 (pt) REVERT: I 386 THR cc_start: 0.7022 (m) cc_final: 0.6764 (p) REVERT: I 389 ASN cc_start: 0.8559 (m-40) cc_final: 0.7653 (t0) outliers start: 42 outliers final: 14 residues processed: 512 average time/residue: 0.7508 time to fit residues: 438.3187 Evaluate side-chains 271 residues out of total 3175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 255 time to evaluate : 1.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 335 CYS Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 265 ASP Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 335 CYS Chi-restraints excluded: chain F residue 394 VAL Chi-restraints excluded: chain F residue 511 SER Chi-restraints excluded: chain G residue 15 LYS Chi-restraints excluded: chain G residue 279 SER Chi-restraints excluded: chain H residue 192 LEU Chi-restraints excluded: chain H residue 279 SER Chi-restraints excluded: chain I residue 74 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 0.9980 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 0.8980 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 0.9980 chunk 298 optimal weight: 1.9990 overall best weight: 0.9780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 197 HIS A 285 ASN B 263 ASN B 440 ASN C 252 HIS C 280 ASN D 150 ASN D 199 GLN E 347 GLN E 478 ASN F 317 GLN G 244 GLN H 109 ASN I 274 ASN J 136 GLN J 218 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.110703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.074988 restraints weight = 53073.405| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 2.64 r_work: 0.3052 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2937 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.2410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 29012 Z= 0.155 Angle : 0.668 11.094 39296 Z= 0.348 Chirality : 0.046 0.181 4593 Planarity : 0.004 0.049 5029 Dihedral : 6.476 89.536 3973 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.24 % Favored : 97.74 % Rotamer: Outliers : 2.39 % Allowed : 9.92 % Favored : 87.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.75 % Cis-general : 0.00 % Twisted Proline : 0.62 % Twisted General : 0.03 % 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: 0.48 (0.14), residues: 3621 helix: 0.66 (0.14), residues: 1319 sheet: -0.12 (0.24), residues: 458 loop : 0.35 (0.15), residues: 1844 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 63 TYR 0.018 0.002 TYR I 92 PHE 0.026 0.002 PHE B 264 TRP 0.015 0.001 TRP B 111 HIS 0.008 0.001 HIS A 168 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.16 (29002) covalent geometry : angle 0.66829 / 0.35 (39296) hydrogen bonds : bond 0.04428 / 2.95 ( 1205) hydrogen bonds : angle 4.78109 / 3.46 ( 3222) metal coordination : bond 0.00356 / 0.20 ( 10) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7242 Ramachandran restraints generated. 3621 Oldfield, 0 Emsley, 3621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7242 Ramachandran restraints generated. 3621 Oldfield, 0 Emsley, 3621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 3175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 308 time to evaluate : 1.169 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 LYS cc_start: 0.8926 (OUTLIER) cc_final: 0.8614 (tppt) REVERT: A 338 SER cc_start: 0.7964 (OUTLIER) cc_final: 0.7743 (t) REVERT: A 422 ARG cc_start: 0.7822 (OUTLIER) cc_final: 0.7485 (tmm160) REVERT: C 13 GLU cc_start: 0.8563 (mp0) cc_final: 0.8150 (mp0) REVERT: C 37 GLU cc_start: 0.8990 (tp30) cc_final: 0.8787 (mm-30) REVERT: C 56 GLU cc_start: 0.8759 (pt0) cc_final: 0.8519 (pp20) REVERT: C 121 ASP cc_start: 0.8702 (t0) cc_final: 0.8480 (t0) REVERT: C 171 SER cc_start: 0.9016 (OUTLIER) cc_final: 0.8634 (p) REVERT: D 45 ILE cc_start: 0.9100 (mt) cc_final: 0.8759 (mp) REVERT: D 121 ASP cc_start: 0.8649 (t0) cc_final: 0.8322 (t0) REVERT: D 124 PHE cc_start: 0.8189 (m-80) cc_final: 0.7245 (m-80) REVERT: D 340 MET cc_start: 0.8915 (tpp) cc_final: 0.8703 (tpp) REVERT: E 209 ARG cc_start: 0.8515 (OUTLIER) cc_final: 0.8301 (ttt90) REVERT: F 197 SER cc_start: 0.8701 (OUTLIER) cc_final: 0.8140 (p) REVERT: F 453 VAL cc_start: 0.9179 (t) cc_final: 0.8836 (m) REVERT: G 48 ASN cc_start: 0.8787 (t0) cc_final: 0.8375 (t0) REVERT: G 267 LYS cc_start: 0.5893 (mttp) cc_final: 0.4247 (tmtt) REVERT: H 1 MET cc_start: 0.4340 (tpt) cc_final: 0.3927 (pmt) REVERT: I 74 ASP cc_start: 0.7414 (OUTLIER) cc_final: 0.6439 (t0) REVERT: I 136 GLN cc_start: 0.7510 (mt0) cc_final: 0.6619 (mp10) REVERT: I 192 ARG cc_start: 0.8999 (ttt180) cc_final: 0.8764 (ttt-90) REVERT: I 321 GLU cc_start: 0.9258 (tm-30) cc_final: 0.8923 (tp30) REVERT: I 391 LEU cc_start: 0.7967 (OUTLIER) cc_final: 0.7630 (mt) REVERT: J 69 MET cc_start: 0.7195 (pmm) cc_final: 0.6947 (mtp) REVERT: J 71 MET cc_start: 0.8940 (mtm) cc_final: 0.8321 (mtp) REVERT: J 321 GLU cc_start: 0.9277 (tp30) cc_final: 0.8947 (tm-30) REVERT: J 372 ARG cc_start: 0.8933 (mtp85) cc_final: 0.8444 (mmm-85) REVERT: J 380 LEU cc_start: 0.8331 (mt) cc_final: 0.8022 (mp) outliers start: 76 outliers final: 13 residues processed: 358 average time/residue: 0.7186 time to fit residues: 296.9386 Evaluate side-chains 251 residues out of total 3175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 230 time to evaluate : 1.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 LYS Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 422 ARG Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 335 CYS Chi-restraints excluded: chain C residue 171 SER Chi-restraints excluded: chain C residue 305 LYS Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain E residue 209 ARG Chi-restraints excluded: chain F residue 171 LYS Chi-restraints excluded: chain F residue 197 SER Chi-restraints excluded: chain G residue 15 LYS Chi-restraints excluded: chain G residue 186 ILE Chi-restraints excluded: chain G residue 279 SER Chi-restraints excluded: chain I residue 74 ASP Chi-restraints excluded: chain I residue 391 LEU Chi-restraints excluded: chain J residue 17 THR Chi-restraints excluded: chain J residue 425 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 15 optimal weight: 0.8980 chunk 7 optimal weight: 0.0470 chunk 44 optimal weight: 5.9990 chunk 307 optimal weight: 9.9990 chunk 189 optimal weight: 3.9990 chunk 84 optimal weight: 0.7980 chunk 331 optimal weight: 0.9980 chunk 82 optimal weight: 0.9990 chunk 303 optimal weight: 7.9990 chunk 217 optimal weight: 5.9990 chunk 28 optimal weight: 0.0570 overall best weight: 0.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 277 GLN D 260 HIS F 317 GLN G 244 GLN I 4 GLN I 154 GLN ** I 405 GLN ** 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 = 0.3774 r_free = 0.3774 target = 0.111595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.076278 restraints weight = 53337.398| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 2.64 r_work: 0.3051 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2930 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.2834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 29012 Z= 0.117 Angle : 0.578 9.991 39296 Z= 0.300 Chirality : 0.044 0.165 4593 Planarity : 0.004 0.053 5029 Dihedral : 5.571 88.622 3962 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.24 % Allowed : 11.91 % Favored : 85.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.75 % 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: 0.98 (0.14), residues: 3621 helix: 1.31 (0.15), residues: 1317 sheet: -0.13 (0.24), residues: 452 loop : 0.53 (0.15), residues: 1852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 50 TYR 0.028 0.001 TYR G 9 PHE 0.029 0.001 PHE G 72 TRP 0.011 0.001 TRP B 111 HIS 0.007 0.001 HIS A 168 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 (29002) covalent geometry : angle 0.57781 / 0.30 (39296) hydrogen bonds : bond 0.03987 / 2.66 ( 1205) hydrogen bonds : angle 4.37936 / 3.16 ( 3222) metal coordination : bond 0.00220 / 0.13 ( 10) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7242 Ramachandran restraints generated. 3621 Oldfield, 0 Emsley, 3621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7242 Ramachandran restraints generated. 3621 Oldfield, 0 Emsley, 3621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 3175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 261 time to evaluate : 1.210 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 ARG cc_start: 0.7608 (OUTLIER) cc_final: 0.7165 (mtp85) REVERT: A 422 ARG cc_start: 0.7771 (OUTLIER) cc_final: 0.7531 (tmm160) REVERT: B 108 LYS cc_start: 0.8984 (ttmm) cc_final: 0.8695 (ttpt) REVERT: C 13 GLU cc_start: 0.8480 (mp0) cc_final: 0.7915 (mp0) REVERT: C 56 GLU cc_start: 0.8757 (pt0) cc_final: 0.8504 (pp20) REVERT: C 121 ASP cc_start: 0.8780 (t0) cc_final: 0.8435 (t0) REVERT: C 171 SER cc_start: 0.9073 (OUTLIER) cc_final: 0.8665 (p) REVERT: D 121 ASP cc_start: 0.8699 (t0) cc_final: 0.8437 (t0) REVERT: D 124 PHE cc_start: 0.8113 (m-80) cc_final: 0.7166 (m-80) REVERT: E 188 ARG cc_start: 0.7679 (ttm110) cc_final: 0.7209 (ttm-80) REVERT: E 295 GLU cc_start: 0.8462 (tm-30) cc_final: 0.7812 (tm-30) REVERT: F 197 SER cc_start: 0.8655 (OUTLIER) cc_final: 0.8158 (p) REVERT: F 246 GLU cc_start: 0.7799 (mm-30) cc_final: 0.7103 (mm-30) REVERT: F 247 GLU cc_start: 0.7958 (mt-10) cc_final: 0.7514 (pm20) REVERT: F 250 ARG cc_start: 0.8752 (OUTLIER) cc_final: 0.8442 (ttm-80) REVERT: F 453 VAL cc_start: 0.9148 (t) cc_final: 0.8792 (m) REVERT: G 48 ASN cc_start: 0.8724 (t0) cc_final: 0.8282 (t0) REVERT: G 267 LYS cc_start: 0.6031 (mttp) cc_final: 0.4451 (tmtt) REVERT: H 1 MET cc_start: 0.4082 (tpt) cc_final: 0.3834 (pmt) REVERT: H 237 ARG cc_start: 0.8762 (OUTLIER) cc_final: 0.8429 (mpp80) REVERT: I 74 ASP cc_start: 0.7590 (OUTLIER) cc_final: 0.6684 (t0) REVERT: I 92 TYR cc_start: 0.7856 (t80) cc_final: 0.7326 (t80) REVERT: I 136 GLN cc_start: 0.7499 (mt0) cc_final: 0.6639 (mp10) REVERT: I 188 GLN cc_start: 0.8948 (OUTLIER) cc_final: 0.8733 (tp40) REVERT: I 216 MET cc_start: 0.8576 (mmm) cc_final: 0.8306 (mmt) REVERT: I 231 TYR cc_start: 0.9055 (t80) cc_final: 0.8585 (t80) REVERT: I 319 TYR cc_start: 0.8587 (t80) cc_final: 0.8383 (t80) REVERT: I 320 MET cc_start: 0.8772 (tpp) cc_final: 0.8419 (ppp) REVERT: I 358 ILE cc_start: 0.8209 (mt) cc_final: 0.8000 (mm) REVERT: I 391 LEU cc_start: 0.7986 (mm) cc_final: 0.7736 (mt) REVERT: J 66 GLU cc_start: 0.6679 (OUTLIER) cc_final: 0.6166 (pm20) REVERT: J 69 MET cc_start: 0.7368 (pmm) cc_final: 0.7068 (mtp) REVERT: J 71 MET cc_start: 0.8870 (mtm) cc_final: 0.8161 (mtp) REVERT: J 170 MET cc_start: 0.9220 (OUTLIER) cc_final: 0.8980 (ttm) REVERT: J 216 MET cc_start: 0.8986 (mmm) cc_final: 0.8735 (mmm) REVERT: J 321 GLU cc_start: 0.9357 (tp30) cc_final: 0.8994 (tm-30) REVERT: J 372 ARG cc_start: 0.8949 (mtp85) cc_final: 0.8510 (mmm-85) outliers start: 71 outliers final: 20 residues processed: 309 average time/residue: 0.7013 time to fit residues: 251.7387 Evaluate side-chains 258 residues out of total 3175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 228 time to evaluate : 1.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ARG Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 422 ARG Chi-restraints excluded: chain B residue 57 PHE Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 335 CYS Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain B residue 411 SER Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 131 SER Chi-restraints excluded: chain C residue 171 SER Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 347 ASP Chi-restraints excluded: chain E residue 196 MET Chi-restraints excluded: chain E residue 445 GLU Chi-restraints excluded: chain F residue 197 SER Chi-restraints excluded: chain F residue 250 ARG Chi-restraints excluded: chain G residue 15 LYS Chi-restraints excluded: chain G residue 186 ILE Chi-restraints excluded: chain G residue 279 SER Chi-restraints excluded: chain H residue 237 ARG Chi-restraints excluded: chain I residue 74 ASP Chi-restraints excluded: chain I residue 188 GLN Chi-restraints excluded: chain J residue 17 THR Chi-restraints excluded: chain J residue 66 GLU Chi-restraints excluded: chain J residue 170 MET Chi-restraints excluded: chain J residue 425 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 352 optimal weight: 0.9980 chunk 282 optimal weight: 20.0000 chunk 35 optimal weight: 5.9990 chunk 109 optimal weight: 0.9980 chunk 243 optimal weight: 3.9990 chunk 299 optimal weight: 7.9990 chunk 14 optimal weight: 5.9990 chunk 70 optimal weight: 0.0020 chunk 321 optimal weight: 9.9990 chunk 334 optimal weight: 5.9990 chunk 150 optimal weight: 0.5980 overall best weight: 1.3190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 89 GLN D 44 GLN G 172 ASN H 270 HIS I 363 GLN I 405 GLN J 303 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.110370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.074867 restraints weight = 53321.803| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 2.64 r_work: 0.3037 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2921 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 moved from start: 0.2985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 29012 Z= 0.152 Angle : 0.567 9.104 39296 Z= 0.293 Chirality : 0.045 0.324 4593 Planarity : 0.004 0.054 5029 Dihedral : 5.298 85.896 3961 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.17 % Allowed : 12.66 % Favored : 85.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.75 % 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: 1.10 (0.14), residues: 3621 helix: 1.45 (0.15), residues: 1328 sheet: -0.17 (0.24), residues: 454 loop : 0.58 (0.15), residues: 1839 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG H 74 TYR 0.030 0.001 TYR H 9 PHE 0.022 0.001 PHE D 177 TRP 0.010 0.001 TRP B 111 HIS 0.007 0.001 HIS A 168 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.15 (29002) covalent geometry : angle 0.56688 / 0.29 (39296) hydrogen bonds : bond 0.03885 / 2.58 ( 1205) hydrogen bonds : angle 4.28021 / 3.08 ( 3222) metal coordination : bond 0.00243 / 0.15 ( 10) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7242 Ramachandran restraints generated. 3621 Oldfield, 0 Emsley, 3621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7242 Ramachandran restraints generated. 3621 Oldfield, 0 Emsley, 3621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 3175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 243 time to evaluate : 1.082 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 ARG cc_start: 0.7629 (OUTLIER) cc_final: 0.7190 (mtp85) REVERT: A 108 LYS cc_start: 0.8818 (OUTLIER) cc_final: 0.8472 (tppt) REVERT: A 422 ARG cc_start: 0.7713 (OUTLIER) cc_final: 0.7501 (tmm160) REVERT: B 89 GLN cc_start: 0.8818 (OUTLIER) cc_final: 0.8528 (mt0) REVERT: B 108 LYS cc_start: 0.9003 (ttmm) cc_final: 0.8724 (ttpt) REVERT: C 13 GLU cc_start: 0.8513 (mp0) cc_final: 0.8306 (mt-10) REVERT: C 56 GLU cc_start: 0.8735 (pt0) cc_final: 0.8490 (pp20) REVERT: C 121 ASP cc_start: 0.8814 (t0) cc_final: 0.8400 (t0) REVERT: C 171 SER cc_start: 0.9114 (OUTLIER) cc_final: 0.8691 (p) REVERT: D 45 ILE cc_start: 0.9018 (mt) cc_final: 0.8720 (mp) REVERT: D 121 ASP cc_start: 0.8707 (t0) cc_final: 0.8463 (t0) REVERT: D 124 PHE cc_start: 0.8138 (m-80) cc_final: 0.7170 (m-80) REVERT: D 199 GLN cc_start: 0.8908 (OUTLIER) cc_final: 0.8622 (mt0) REVERT: F 197 SER cc_start: 0.8711 (OUTLIER) cc_final: 0.8306 (p) REVERT: F 246 GLU cc_start: 0.7946 (mm-30) cc_final: 0.7326 (mm-30) REVERT: F 247 GLU cc_start: 0.7927 (mt-10) cc_final: 0.7322 (pm20) REVERT: F 299 GLU cc_start: 0.8584 (mp0) cc_final: 0.8287 (mp0) REVERT: G 48 ASN cc_start: 0.8736 (t0) cc_final: 0.8343 (t0) REVERT: G 267 LYS cc_start: 0.6277 (mttp) cc_final: 0.4638 (tmtt) REVERT: H 1 MET cc_start: 0.4018 (tpt) cc_final: 0.3764 (pmt) REVERT: H 237 ARG cc_start: 0.8719 (OUTLIER) cc_final: 0.8392 (mpp80) REVERT: I 74 ASP cc_start: 0.7833 (OUTLIER) cc_final: 0.7025 (t0) REVERT: I 216 MET cc_start: 0.8542 (mmm) cc_final: 0.8180 (mmm) REVERT: I 320 MET cc_start: 0.8753 (tpp) cc_final: 0.8391 (ppp) REVERT: I 391 LEU cc_start: 0.8056 (mm) cc_final: 0.7807 (mt) REVERT: J 16 MET cc_start: 0.6761 (OUTLIER) cc_final: 0.6450 (tpt) REVERT: J 66 GLU cc_start: 0.6766 (OUTLIER) cc_final: 0.6261 (pm20) REVERT: J 69 MET cc_start: 0.7368 (pmm) cc_final: 0.7066 (mtp) REVERT: J 71 MET cc_start: 0.8936 (mtm) cc_final: 0.8314 (mtp) REVERT: J 170 MET cc_start: 0.9194 (OUTLIER) cc_final: 0.8970 (ttp) REVERT: J 321 GLU cc_start: 0.9370 (tp30) cc_final: 0.8945 (tm-30) REVERT: J 372 ARG cc_start: 0.8929 (mtp85) cc_final: 0.8621 (mmm-85) outliers start: 69 outliers final: 21 residues processed: 288 average time/residue: 0.7280 time to fit residues: 242.1302 Evaluate side-chains 248 residues out of total 3175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 215 time to evaluate : 1.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ARG Chi-restraints excluded: chain A residue 108 LYS Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 422 ARG Chi-restraints excluded: chain B residue 57 PHE Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 89 GLN Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 335 CYS Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain B residue 411 SER Chi-restraints excluded: chain C residue 131 SER Chi-restraints excluded: chain C residue 171 SER Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 199 GLN Chi-restraints excluded: chain D residue 347 ASP Chi-restraints excluded: chain F residue 171 LYS Chi-restraints excluded: chain F residue 197 SER Chi-restraints excluded: chain F residue 241 THR Chi-restraints excluded: chain G residue 15 LYS Chi-restraints excluded: chain G residue 186 ILE Chi-restraints excluded: chain G residue 279 SER Chi-restraints excluded: chain H residue 120 LYS Chi-restraints excluded: chain H residue 237 ARG Chi-restraints excluded: chain I residue 74 ASP Chi-restraints excluded: chain J residue 16 MET Chi-restraints excluded: chain J residue 17 THR Chi-restraints excluded: chain J residue 66 GLU Chi-restraints excluded: chain J residue 170 MET Chi-restraints excluded: chain J residue 425 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 323 optimal weight: 2.9990 chunk 115 optimal weight: 0.4980 chunk 316 optimal weight: 4.9990 chunk 121 optimal weight: 5.9990 chunk 358 optimal weight: 6.9990 chunk 286 optimal weight: 6.9990 chunk 55 optimal weight: 0.6980 chunk 265 optimal weight: 0.7980 chunk 189 optimal weight: 2.9990 chunk 188 optimal weight: 0.9990 chunk 285 optimal weight: 1.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 277 GLN D 44 GLN G 244 GLN I 363 GLN I 405 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.110853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.075467 restraints weight = 53408.285| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 2.64 r_work: 0.3038 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2918 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.3169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 29012 Z= 0.129 Angle : 0.545 7.973 39296 Z= 0.282 Chirality : 0.044 0.268 4593 Planarity : 0.004 0.053 5029 Dihedral : 5.089 83.505 3961 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.95 % Allowed : 13.70 % Favored : 84.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.75 % 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: 1.20 (0.14), residues: 3621 helix: 1.60 (0.15), residues: 1325 sheet: -0.16 (0.24), residues: 454 loop : 0.62 (0.15), residues: 1842 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 74 TYR 0.022 0.001 TYR H 9 PHE 0.034 0.001 PHE G 72 TRP 0.009 0.001 TRP B 111 HIS 0.006 0.001 HIS A 168 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.13 (29002) covalent geometry : angle 0.54541 / 0.28 (39296) hydrogen bonds : bond 0.03679 / 2.45 ( 1205) hydrogen bonds : angle 4.17307 / 3.01 ( 3222) metal coordination : bond 0.00177 / 0.11 ( 10) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7242 Ramachandran restraints generated. 3621 Oldfield, 0 Emsley, 3621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7242 Ramachandran restraints generated. 3621 Oldfield, 0 Emsley, 3621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 3175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 238 time to evaluate : 1.237 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 ARG cc_start: 0.7633 (OUTLIER) cc_final: 0.7364 (mtp85) REVERT: A 108 LYS cc_start: 0.8755 (OUTLIER) cc_final: 0.8427 (tppt) REVERT: B 108 LYS cc_start: 0.9013 (ttmm) cc_final: 0.8713 (ttpt) REVERT: C 56 GLU cc_start: 0.8716 (pt0) cc_final: 0.8481 (pp20) REVERT: C 121 ASP cc_start: 0.8820 (t0) cc_final: 0.8329 (t0) REVERT: C 124 PHE cc_start: 0.8396 (m-80) cc_final: 0.8028 (m-80) REVERT: C 171 SER cc_start: 0.9089 (OUTLIER) cc_final: 0.8670 (p) REVERT: D 44 GLN cc_start: 0.8244 (OUTLIER) cc_final: 0.7790 (tt0) REVERT: D 45 ILE cc_start: 0.8945 (mt) cc_final: 0.8592 (mp) REVERT: D 121 ASP cc_start: 0.8699 (t0) cc_final: 0.8467 (t0) REVERT: D 124 PHE cc_start: 0.8125 (m-80) cc_final: 0.7186 (m-80) REVERT: D 199 GLN cc_start: 0.8866 (OUTLIER) cc_final: 0.8539 (mt0) REVERT: F 169 THR cc_start: 0.8010 (OUTLIER) cc_final: 0.7585 (m) REVERT: F 197 SER cc_start: 0.8695 (OUTLIER) cc_final: 0.8330 (p) REVERT: F 246 GLU cc_start: 0.7873 (mm-30) cc_final: 0.7179 (mm-30) REVERT: F 247 GLU cc_start: 0.7873 (mt-10) cc_final: 0.7211 (pm20) REVERT: F 250 ARG cc_start: 0.8749 (ttm110) cc_final: 0.8358 (ttm110) REVERT: F 299 GLU cc_start: 0.8709 (OUTLIER) cc_final: 0.8390 (mp0) REVERT: G 48 ASN cc_start: 0.8729 (t0) cc_final: 0.8321 (t0) REVERT: G 191 ASP cc_start: 0.8889 (m-30) cc_final: 0.8585 (m-30) REVERT: G 267 LYS cc_start: 0.6291 (mttp) cc_final: 0.4636 (tmtt) REVERT: H 1 MET cc_start: 0.3985 (tpt) cc_final: 0.3766 (pmt) REVERT: H 237 ARG cc_start: 0.8715 (OUTLIER) cc_final: 0.8372 (mpp80) REVERT: I 74 ASP cc_start: 0.7955 (OUTLIER) cc_final: 0.7092 (t0) REVERT: I 216 MET cc_start: 0.8498 (mmm) cc_final: 0.8228 (mmm) REVERT: I 320 MET cc_start: 0.8734 (tpp) cc_final: 0.8341 (ppp) REVERT: I 391 LEU cc_start: 0.8052 (OUTLIER) cc_final: 0.7819 (mt) REVERT: J 16 MET cc_start: 0.6777 (mmm) cc_final: 0.6451 (tpt) REVERT: J 66 GLU cc_start: 0.6817 (OUTLIER) cc_final: 0.6321 (pm20) REVERT: J 170 MET cc_start: 0.9179 (OUTLIER) cc_final: 0.8920 (ttp) REVERT: J 216 MET cc_start: 0.8917 (mmm) cc_final: 0.8666 (mmm) REVERT: J 321 GLU cc_start: 0.9341 (tp30) cc_final: 0.8962 (tm-30) REVERT: J 372 ARG cc_start: 0.8935 (mtp85) cc_final: 0.8640 (mmm-85) outliers start: 62 outliers final: 21 residues processed: 282 average time/residue: 0.6886 time to fit residues: 226.1045 Evaluate side-chains 249 residues out of total 3175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 215 time to evaluate : 1.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ARG Chi-restraints excluded: chain A residue 95 CYS Chi-restraints excluded: chain A residue 108 LYS Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain B residue 57 PHE Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain B residue 411 SER Chi-restraints excluded: chain C residue 131 SER Chi-restraints excluded: chain C residue 171 SER Chi-restraints excluded: chain D residue 44 GLN Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 199 GLN Chi-restraints excluded: chain D residue 326 SER Chi-restraints excluded: chain D residue 347 ASP Chi-restraints excluded: chain F residue 169 THR Chi-restraints excluded: chain F residue 171 LYS Chi-restraints excluded: chain F residue 197 SER Chi-restraints excluded: chain F residue 241 THR Chi-restraints excluded: chain F residue 299 GLU Chi-restraints excluded: chain G residue 15 LYS Chi-restraints excluded: chain G residue 186 ILE Chi-restraints excluded: chain H residue 120 LYS Chi-restraints excluded: chain H residue 237 ARG Chi-restraints excluded: chain I residue 74 ASP Chi-restraints excluded: chain I residue 386 THR Chi-restraints excluded: chain I residue 391 LEU Chi-restraints excluded: chain J residue 17 THR Chi-restraints excluded: chain J residue 66 GLU Chi-restraints excluded: chain J residue 170 MET Chi-restraints excluded: chain J residue 425 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 231 optimal weight: 0.8980 chunk 160 optimal weight: 4.9990 chunk 86 optimal weight: 5.9990 chunk 212 optimal weight: 0.3980 chunk 279 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 chunk 283 optimal weight: 0.0980 chunk 297 optimal weight: 9.9990 chunk 14 optimal weight: 2.9990 chunk 130 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 288 HIS C 150 ASN C 280 ASN G 172 ASN G 244 GLN I 363 GLN I 405 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.110891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.075407 restraints weight = 53106.467| |-----------------------------------------------------------------------------| r_work (start): 0.3152 rms_B_bonded: 2.64 r_work: 0.3024 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2903 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.3297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 29012 Z= 0.134 Angle : 0.550 9.257 39296 Z= 0.282 Chirality : 0.044 0.277 4593 Planarity : 0.004 0.054 5029 Dihedral : 4.948 80.756 3959 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.02 % Allowed : 14.17 % Favored : 83.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.75 % 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: 1.21 (0.14), residues: 3621 helix: 1.61 (0.15), residues: 1336 sheet: -0.11 (0.25), residues: 448 loop : 0.58 (0.15), residues: 1837 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 292 TYR 0.025 0.001 TYR H 9 PHE 0.020 0.001 PHE D 177 TRP 0.008 0.001 TRP B 111 HIS 0.006 0.001 HIS A 168 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.13 (29002) covalent geometry : angle 0.55017 / 0.28 (39296) hydrogen bonds : bond 0.03607 / 2.40 ( 1205) hydrogen bonds : angle 4.13267 / 2.98 ( 3222) metal coordination : bond 0.00196 / 0.12 ( 10) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7242 Ramachandran restraints generated. 3621 Oldfield, 0 Emsley, 3621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7242 Ramachandran restraints generated. 3621 Oldfield, 0 Emsley, 3621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 3175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 237 time to evaluate : 1.138 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 ARG cc_start: 0.7629 (OUTLIER) cc_final: 0.7116 (mtp85) REVERT: A 108 LYS cc_start: 0.8729 (OUTLIER) cc_final: 0.8381 (tppt) REVERT: B 108 LYS cc_start: 0.9030 (ttmm) cc_final: 0.8779 (ttpt) REVERT: C 13 GLU cc_start: 0.8607 (mt-10) cc_final: 0.7988 (mp0) REVERT: C 60 LEU cc_start: 0.9167 (OUTLIER) cc_final: 0.8941 (pp) REVERT: C 121 ASP cc_start: 0.8829 (t0) cc_final: 0.8303 (t0) REVERT: C 124 PHE cc_start: 0.8413 (m-80) cc_final: 0.8048 (m-80) REVERT: C 171 SER cc_start: 0.9095 (OUTLIER) cc_final: 0.8695 (p) REVERT: D 45 ILE cc_start: 0.8886 (mt) cc_final: 0.8684 (mt) REVERT: D 121 ASP cc_start: 0.8702 (t0) cc_final: 0.8443 (t0) REVERT: D 124 PHE cc_start: 0.8134 (m-80) cc_final: 0.7196 (m-80) REVERT: E 246 GLU cc_start: 0.6725 (tp30) cc_final: 0.6408 (tp30) REVERT: E 250 ARG cc_start: 0.8173 (ttm110) cc_final: 0.7745 (mtm-85) REVERT: F 169 THR cc_start: 0.7994 (OUTLIER) cc_final: 0.7651 (m) REVERT: F 197 SER cc_start: 0.8737 (OUTLIER) cc_final: 0.8373 (p) REVERT: F 246 GLU cc_start: 0.7833 (mm-30) cc_final: 0.7115 (mm-30) REVERT: F 247 GLU cc_start: 0.7892 (mt-10) cc_final: 0.7200 (pm20) REVERT: F 250 ARG cc_start: 0.8742 (ttm110) cc_final: 0.8373 (ttm110) REVERT: F 299 GLU cc_start: 0.8750 (OUTLIER) cc_final: 0.8428 (mp0) REVERT: G 48 ASN cc_start: 0.8748 (t0) cc_final: 0.8320 (t0) REVERT: G 191 ASP cc_start: 0.8895 (m-30) cc_final: 0.8559 (m-30) REVERT: G 267 LYS cc_start: 0.6419 (mttp) cc_final: 0.4780 (tmtt) REVERT: H 1 MET cc_start: 0.4030 (tpt) cc_final: 0.3735 (pmt) REVERT: H 237 ARG cc_start: 0.8728 (OUTLIER) cc_final: 0.8380 (mpp80) REVERT: I 74 ASP cc_start: 0.7891 (OUTLIER) cc_final: 0.7085 (t0) REVERT: I 92 TYR cc_start: 0.7826 (t80) cc_final: 0.7326 (t80) REVERT: I 216 MET cc_start: 0.8517 (mmm) cc_final: 0.8212 (mmm) REVERT: I 320 MET cc_start: 0.8724 (tpp) cc_final: 0.8326 (ppp) REVERT: I 391 LEU cc_start: 0.8022 (OUTLIER) cc_final: 0.7818 (mt) REVERT: J 16 MET cc_start: 0.6791 (OUTLIER) cc_final: 0.6488 (tpt) REVERT: J 66 GLU cc_start: 0.6699 (OUTLIER) cc_final: 0.6227 (pm20) REVERT: J 170 MET cc_start: 0.9188 (OUTLIER) cc_final: 0.8928 (ttp) REVERT: J 216 MET cc_start: 0.8894 (mmm) cc_final: 0.8681 (mmm) REVERT: J 321 GLU cc_start: 0.9358 (tp30) cc_final: 0.8987 (tm-30) REVERT: J 372 ARG cc_start: 0.8944 (mtp85) cc_final: 0.8563 (mmm-85) outliers start: 64 outliers final: 22 residues processed: 277 average time/residue: 0.6623 time to fit residues: 214.8026 Evaluate side-chains 252 residues out of total 3175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 217 time to evaluate : 1.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ARG Chi-restraints excluded: chain A residue 95 CYS Chi-restraints excluded: chain A residue 108 LYS Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain B residue 57 PHE Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain B residue 411 SER Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 131 SER Chi-restraints excluded: chain C residue 171 SER Chi-restraints excluded: chain D residue 50 ARG Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain E residue 196 MET Chi-restraints excluded: chain F residue 169 THR Chi-restraints excluded: chain F residue 197 SER Chi-restraints excluded: chain F residue 241 THR Chi-restraints excluded: chain F residue 299 GLU Chi-restraints excluded: chain F residue 447 VAL Chi-restraints excluded: chain G residue 63 VAL Chi-restraints excluded: chain G residue 186 ILE Chi-restraints excluded: chain H residue 120 LYS Chi-restraints excluded: chain H residue 237 ARG Chi-restraints excluded: chain I residue 74 ASP Chi-restraints excluded: chain I residue 386 THR Chi-restraints excluded: chain I residue 391 LEU Chi-restraints excluded: chain J residue 16 MET Chi-restraints excluded: chain J residue 17 THR Chi-restraints excluded: chain J residue 66 GLU Chi-restraints excluded: chain J residue 170 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 83 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 chunk 100 optimal weight: 0.0980 chunk 137 optimal weight: 0.7980 chunk 275 optimal weight: 5.9990 chunk 81 optimal weight: 0.8980 chunk 163 optimal weight: 0.7980 chunk 351 optimal weight: 3.9990 chunk 311 optimal weight: 0.7980 chunk 354 optimal weight: 8.9990 chunk 121 optimal weight: 4.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 277 GLN C 280 ASN G 244 GLN I 363 GLN ** I 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.111670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.076235 restraints weight = 53183.107| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 2.65 r_work: 0.3038 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2918 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.3469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 29012 Z= 0.112 Angle : 0.537 9.981 39296 Z= 0.276 Chirality : 0.044 0.257 4593 Planarity : 0.004 0.055 5029 Dihedral : 4.758 77.870 3955 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.64 % Allowed : 14.93 % Favored : 83.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.75 % 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: 3621 helix: 1.79 (0.15), residues: 1316 sheet: -0.11 (0.25), residues: 448 loop : 0.67 (0.15), residues: 1857 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG E 292 TYR 0.023 0.001 TYR H 9 PHE 0.036 0.001 PHE G 72 TRP 0.007 0.001 TRP B 111 HIS 0.013 0.001 HIS G 270 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.11 (29002) covalent geometry : angle 0.53740 / 0.28 (39296) hydrogen bonds : bond 0.03382 / 2.25 ( 1205) hydrogen bonds : angle 4.03993 / 2.91 ( 3222) metal coordination : bond 0.00131 / 0.08 ( 10) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7242 Ramachandran restraints generated. 3621 Oldfield, 0 Emsley, 3621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7242 Ramachandran restraints generated. 3621 Oldfield, 0 Emsley, 3621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 3175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 247 time to evaluate : 1.140 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 ARG cc_start: 0.7586 (OUTLIER) cc_final: 0.7293 (mtp85) REVERT: A 108 LYS cc_start: 0.8724 (OUTLIER) cc_final: 0.8379 (tppt) REVERT: B 108 LYS cc_start: 0.9007 (ttmm) cc_final: 0.8750 (ttpt) REVERT: C 13 GLU cc_start: 0.8571 (mt-10) cc_final: 0.7920 (mp0) REVERT: C 56 GLU cc_start: 0.8780 (pt0) cc_final: 0.8573 (pp20) REVERT: C 121 ASP cc_start: 0.8833 (t0) cc_final: 0.8314 (t0) REVERT: C 124 PHE cc_start: 0.8443 (m-80) cc_final: 0.8086 (m-80) REVERT: C 171 SER cc_start: 0.9082 (OUTLIER) cc_final: 0.8701 (p) REVERT: D 45 ILE cc_start: 0.8831 (mt) cc_final: 0.8459 (mp) REVERT: D 121 ASP cc_start: 0.8698 (t0) cc_final: 0.8421 (t0) REVERT: D 124 PHE cc_start: 0.8128 (m-80) cc_final: 0.7159 (m-80) REVERT: F 169 THR cc_start: 0.8006 (OUTLIER) cc_final: 0.7706 (m) REVERT: F 197 SER cc_start: 0.8716 (OUTLIER) cc_final: 0.8394 (p) REVERT: F 246 GLU cc_start: 0.7861 (mm-30) cc_final: 0.6347 (mm-30) REVERT: F 247 GLU cc_start: 0.7825 (mt-10) cc_final: 0.7300 (pm20) REVERT: F 250 ARG cc_start: 0.8731 (ttm110) cc_final: 0.8188 (mtp-110) REVERT: F 299 GLU cc_start: 0.8756 (OUTLIER) cc_final: 0.8414 (mp0) REVERT: G 48 ASN cc_start: 0.8709 (t0) cc_final: 0.8257 (t0) REVERT: G 191 ASP cc_start: 0.8881 (m-30) cc_final: 0.8543 (m-30) REVERT: G 198 GLU cc_start: 0.9159 (mm-30) cc_final: 0.8915 (mm-30) REVERT: H 1 MET cc_start: 0.3957 (tpt) cc_final: 0.3622 (pmt) REVERT: H 45 LEU cc_start: 0.7468 (OUTLIER) cc_final: 0.7205 (mt) REVERT: H 237 ARG cc_start: 0.8739 (OUTLIER) cc_final: 0.8408 (mpp80) REVERT: H 249 LYS cc_start: 0.9107 (OUTLIER) cc_final: 0.8746 (ptpp) REVERT: I 16 MET cc_start: 0.5711 (ptm) cc_final: 0.5374 (ptm) REVERT: I 74 ASP cc_start: 0.7811 (OUTLIER) cc_final: 0.7069 (t0) REVERT: I 92 TYR cc_start: 0.7836 (t80) cc_final: 0.7330 (t80) REVERT: I 188 GLN cc_start: 0.8983 (OUTLIER) cc_final: 0.8741 (tp40) REVERT: I 216 MET cc_start: 0.8517 (mmm) cc_final: 0.8244 (mmm) REVERT: I 320 MET cc_start: 0.8738 (tpp) cc_final: 0.8368 (ppp) REVERT: J 16 MET cc_start: 0.6702 (OUTLIER) cc_final: 0.6403 (tpt) REVERT: J 66 GLU cc_start: 0.6698 (OUTLIER) cc_final: 0.6294 (pm20) REVERT: J 216 MET cc_start: 0.8871 (mmm) cc_final: 0.8596 (mmm) REVERT: J 321 GLU cc_start: 0.9358 (tp30) cc_final: 0.8982 (tm-30) REVERT: J 372 ARG cc_start: 0.8941 (mtp85) cc_final: 0.8529 (mmm-85) outliers start: 52 outliers final: 20 residues processed: 282 average time/residue: 0.6552 time to fit residues: 216.4666 Evaluate side-chains 256 residues out of total 3175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 223 time to evaluate : 1.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ARG Chi-restraints excluded: chain A residue 95 CYS Chi-restraints excluded: chain A residue 108 LYS Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain B residue 57 PHE Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain B residue 411 SER Chi-restraints excluded: chain C residue 131 SER Chi-restraints excluded: chain C residue 171 SER Chi-restraints excluded: chain C residue 280 ASN Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain F residue 169 THR Chi-restraints excluded: chain F residue 171 LYS Chi-restraints excluded: chain F residue 197 SER Chi-restraints excluded: chain F residue 241 THR Chi-restraints excluded: chain F residue 299 GLU Chi-restraints excluded: chain F residue 447 VAL Chi-restraints excluded: chain G residue 63 VAL Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 120 LYS Chi-restraints excluded: chain H residue 237 ARG Chi-restraints excluded: chain H residue 249 LYS Chi-restraints excluded: chain I residue 74 ASP Chi-restraints excluded: chain I residue 188 GLN Chi-restraints excluded: chain I residue 386 THR Chi-restraints excluded: chain J residue 16 MET Chi-restraints excluded: chain J residue 17 THR Chi-restraints excluded: chain J residue 66 GLU Chi-restraints excluded: chain J residue 316 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 164 optimal weight: 9.9990 chunk 306 optimal weight: 7.9990 chunk 121 optimal weight: 4.9990 chunk 139 optimal weight: 3.9990 chunk 299 optimal weight: 1.9990 chunk 232 optimal weight: 0.6980 chunk 339 optimal weight: 1.9990 chunk 313 optimal weight: 8.9990 chunk 11 optimal weight: 0.9980 chunk 326 optimal weight: 10.0000 chunk 65 optimal weight: 2.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 280 ASN G 172 ASN G 244 GLN I 363 GLN I 405 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.110082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.074465 restraints weight = 53284.147| |-----------------------------------------------------------------------------| r_work (start): 0.3134 rms_B_bonded: 2.64 r_work: 0.3006 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2885 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 moved from start: 0.3427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 29012 Z= 0.180 Angle : 0.579 10.145 39296 Z= 0.294 Chirality : 0.045 0.303 4593 Planarity : 0.004 0.052 5029 Dihedral : 4.818 74.306 3955 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.39 % Allowed : 15.84 % Favored : 82.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.75 % 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: 1.23 (0.14), residues: 3621 helix: 1.69 (0.15), residues: 1332 sheet: -0.26 (0.24), residues: 478 loop : 0.62 (0.15), residues: 1811 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 292 TYR 0.028 0.001 TYR I 94 PHE 0.031 0.001 PHE G 72 TRP 0.009 0.001 TRP B 111 HIS 0.006 0.001 HIS A 168 Details of bonding type rmsd/Z covalent geometry : bond 0.00429 / 0.18 (29002) covalent geometry : angle 0.57887 / 0.29 (39296) hydrogen bonds : bond 0.03713 / 2.46 ( 1205) hydrogen bonds : angle 4.09317 / 2.95 ( 3222) metal coordination : bond 0.00303 / 0.19 ( 10) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7242 Ramachandran restraints generated. 3621 Oldfield, 0 Emsley, 3621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7242 Ramachandran restraints generated. 3621 Oldfield, 0 Emsley, 3621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 3175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 228 time to evaluate : 1.125 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 ARG cc_start: 0.7711 (OUTLIER) cc_final: 0.7246 (mtp85) REVERT: A 108 LYS cc_start: 0.8711 (OUTLIER) cc_final: 0.8333 (tppt) REVERT: C 13 GLU cc_start: 0.8556 (mt-10) cc_final: 0.8331 (mt-10) REVERT: C 121 ASP cc_start: 0.8867 (t0) cc_final: 0.8351 (t0) REVERT: C 124 PHE cc_start: 0.8494 (m-80) cc_final: 0.8135 (m-80) REVERT: C 171 SER cc_start: 0.9108 (OUTLIER) cc_final: 0.8711 (p) REVERT: D 45 ILE cc_start: 0.8843 (mt) cc_final: 0.8628 (mt) REVERT: D 121 ASP cc_start: 0.8701 (t0) cc_final: 0.8424 (t0) REVERT: D 124 PHE cc_start: 0.8137 (m-80) cc_final: 0.7172 (m-80) REVERT: F 169 THR cc_start: 0.8039 (OUTLIER) cc_final: 0.7768 (m) REVERT: F 197 SER cc_start: 0.8763 (OUTLIER) cc_final: 0.8421 (p) REVERT: F 246 GLU cc_start: 0.7845 (mm-30) cc_final: 0.6634 (mm-30) REVERT: F 247 GLU cc_start: 0.7842 (mt-10) cc_final: 0.7467 (pm20) REVERT: F 250 ARG cc_start: 0.8755 (ttm110) cc_final: 0.8261 (mtp-110) REVERT: F 299 GLU cc_start: 0.8745 (OUTLIER) cc_final: 0.8413 (mp0) REVERT: G 48 ASN cc_start: 0.8703 (t0) cc_final: 0.8364 (t0) REVERT: G 191 ASP cc_start: 0.8861 (m-30) cc_final: 0.8561 (m-30) REVERT: H 1 MET cc_start: 0.3915 (tpt) cc_final: 0.3643 (pmt) REVERT: H 45 LEU cc_start: 0.7572 (OUTLIER) cc_final: 0.7313 (mt) REVERT: H 237 ARG cc_start: 0.8770 (OUTLIER) cc_final: 0.8422 (mpp80) REVERT: I 74 ASP cc_start: 0.7923 (OUTLIER) cc_final: 0.7213 (t0) REVERT: I 216 MET cc_start: 0.8524 (mmm) cc_final: 0.8289 (mmm) REVERT: I 320 MET cc_start: 0.8615 (tpp) cc_final: 0.8260 (ppp) REVERT: J 66 GLU cc_start: 0.6739 (OUTLIER) cc_final: 0.6298 (pm20) REVERT: J 216 MET cc_start: 0.8838 (mmm) cc_final: 0.8586 (mmm) REVERT: J 321 GLU cc_start: 0.9344 (tp30) cc_final: 0.8979 (tm-30) REVERT: J 372 ARG cc_start: 0.8955 (mtp85) cc_final: 0.8547 (mmm-85) outliers start: 44 outliers final: 22 residues processed: 258 average time/residue: 0.6481 time to fit residues: 196.1679 Evaluate side-chains 248 residues out of total 3175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 216 time to evaluate : 1.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ARG Chi-restraints excluded: chain A residue 95 CYS Chi-restraints excluded: chain A residue 108 LYS Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain B residue 57 PHE Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain B residue 411 SER Chi-restraints excluded: chain C residue 131 SER Chi-restraints excluded: chain C residue 171 SER Chi-restraints excluded: chain C residue 280 ASN Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 217 MET Chi-restraints excluded: chain F residue 169 THR Chi-restraints excluded: chain F residue 171 LYS Chi-restraints excluded: chain F residue 197 SER Chi-restraints excluded: chain F residue 241 THR Chi-restraints excluded: chain F residue 299 GLU Chi-restraints excluded: chain F residue 447 VAL Chi-restraints excluded: chain G residue 63 VAL Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 120 LYS Chi-restraints excluded: chain H residue 237 ARG Chi-restraints excluded: chain I residue 74 ASP Chi-restraints excluded: chain I residue 386 THR Chi-restraints excluded: chain J residue 17 THR Chi-restraints excluded: chain J residue 66 GLU Chi-restraints excluded: chain J residue 316 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 194 optimal weight: 5.9990 chunk 5 optimal weight: 4.9990 chunk 213 optimal weight: 0.9990 chunk 266 optimal weight: 2.9990 chunk 28 optimal weight: 0.4980 chunk 182 optimal weight: 8.9990 chunk 90 optimal weight: 0.8980 chunk 222 optimal weight: 4.9990 chunk 163 optimal weight: 3.9990 chunk 47 optimal weight: 0.9990 chunk 202 optimal weight: 0.5980 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 277 GLN C 280 ASN G 244 GLN G 270 HIS I 363 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.111370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.075945 restraints weight = 53087.059| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 2.64 r_work: 0.3035 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2913 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.3557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 29012 Z= 0.120 Angle : 0.562 10.965 39296 Z= 0.283 Chirality : 0.044 0.279 4593 Planarity : 0.004 0.059 5029 Dihedral : 4.695 71.264 3955 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.10 % Allowed : 16.31 % Favored : 82.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.75 % 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: 3621 helix: 1.77 (0.15), residues: 1326 sheet: -0.26 (0.24), residues: 476 loop : 0.62 (0.15), residues: 1819 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG E 292 TYR 0.020 0.001 TYR H 9 PHE 0.038 0.001 PHE G 72 TRP 0.009 0.001 TRP B 111 HIS 0.013 0.001 HIS G 270 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.12 (29002) covalent geometry : angle 0.56171 / 0.28 (39296) hydrogen bonds : bond 0.03404 / 2.26 ( 1205) hydrogen bonds : angle 4.03152 / 2.90 ( 3222) metal coordination : bond 0.00149 / 0.09 ( 10) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7242 Ramachandran restraints generated. 3621 Oldfield, 0 Emsley, 3621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7242 Ramachandran restraints generated. 3621 Oldfield, 0 Emsley, 3621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 3175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 230 time to evaluate : 0.897 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 ARG cc_start: 0.7661 (OUTLIER) cc_final: 0.7328 (mtp85) REVERT: A 108 LYS cc_start: 0.8717 (OUTLIER) cc_final: 0.8356 (tppt) REVERT: B 108 LYS cc_start: 0.8976 (ttmm) cc_final: 0.8650 (ttpt) REVERT: C 13 GLU cc_start: 0.8531 (mt-10) cc_final: 0.8278 (mt-10) REVERT: C 121 ASP cc_start: 0.8823 (t0) cc_final: 0.8315 (t0) REVERT: C 124 PHE cc_start: 0.8469 (m-80) cc_final: 0.8122 (m-80) REVERT: C 171 SER cc_start: 0.9114 (OUTLIER) cc_final: 0.8742 (p) REVERT: D 44 GLN cc_start: 0.8232 (OUTLIER) cc_final: 0.7775 (tt0) REVERT: D 45 ILE cc_start: 0.8823 (mt) cc_final: 0.8602 (mt) REVERT: D 121 ASP cc_start: 0.8695 (t0) cc_final: 0.8417 (t0) REVERT: D 124 PHE cc_start: 0.8141 (m-80) cc_final: 0.7200 (m-80) REVERT: E 246 GLU cc_start: 0.8329 (tt0) cc_final: 0.7939 (tp30) REVERT: F 169 THR cc_start: 0.7977 (OUTLIER) cc_final: 0.7755 (m) REVERT: F 197 SER cc_start: 0.8722 (OUTLIER) cc_final: 0.8399 (p) REVERT: F 246 GLU cc_start: 0.7813 (mm-30) cc_final: 0.7309 (mm-30) REVERT: F 247 GLU cc_start: 0.7800 (mt-10) cc_final: 0.7247 (pm20) REVERT: F 299 GLU cc_start: 0.8750 (OUTLIER) cc_final: 0.8419 (mp0) REVERT: G 48 ASN cc_start: 0.8680 (t0) cc_final: 0.8331 (t0) REVERT: G 191 ASP cc_start: 0.8843 (m-30) cc_final: 0.8575 (m-30) REVERT: H 1 MET cc_start: 0.3922 (tpt) cc_final: 0.3547 (pmt) REVERT: H 45 LEU cc_start: 0.7546 (OUTLIER) cc_final: 0.7267 (mt) REVERT: H 237 ARG cc_start: 0.8785 (OUTLIER) cc_final: 0.8450 (mpp80) REVERT: I 16 MET cc_start: 0.5769 (ptm) cc_final: 0.5427 (ptm) REVERT: I 71 MET cc_start: 0.6565 (ptp) cc_final: 0.6025 (ptm) REVERT: I 74 ASP cc_start: 0.7828 (m-30) cc_final: 0.7168 (t0) REVERT: I 320 MET cc_start: 0.8669 (tpp) cc_final: 0.8319 (ppp) REVERT: J 66 GLU cc_start: 0.6667 (OUTLIER) cc_final: 0.6275 (pm20) REVERT: J 69 MET cc_start: 0.7362 (pmm) cc_final: 0.7156 (pmm) REVERT: J 216 MET cc_start: 0.8812 (mmm) cc_final: 0.8577 (mmm) REVERT: J 321 GLU cc_start: 0.9345 (tp30) cc_final: 0.8976 (tm-30) REVERT: J 372 ARG cc_start: 0.8946 (mtp85) cc_final: 0.8545 (mmm-85) REVERT: J 425 LEU cc_start: 0.8327 (tm) cc_final: 0.7928 (tt) outliers start: 35 outliers final: 23 residues processed: 255 average time/residue: 0.6433 time to fit residues: 192.6834 Evaluate side-chains 248 residues out of total 3175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 215 time to evaluate : 1.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ARG Chi-restraints excluded: chain A residue 95 CYS Chi-restraints excluded: chain A residue 108 LYS Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain B residue 57 PHE Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain B residue 411 SER Chi-restraints excluded: chain C residue 131 SER Chi-restraints excluded: chain C residue 171 SER Chi-restraints excluded: chain C residue 280 ASN Chi-restraints excluded: chain D residue 44 GLN Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain F residue 169 THR Chi-restraints excluded: chain F residue 171 LYS Chi-restraints excluded: chain F residue 197 SER Chi-restraints excluded: chain F residue 241 THR Chi-restraints excluded: chain F residue 299 GLU Chi-restraints excluded: chain F residue 447 VAL Chi-restraints excluded: chain G residue 63 VAL Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 120 LYS Chi-restraints excluded: chain H residue 237 ARG Chi-restraints excluded: chain I residue 386 THR Chi-restraints excluded: chain J residue 17 THR Chi-restraints excluded: chain J residue 51 VAL Chi-restraints excluded: chain J residue 66 GLU Chi-restraints excluded: chain J residue 316 LEU Chi-restraints excluded: chain J residue 320 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 22 optimal weight: 3.9990 chunk 39 optimal weight: 7.9990 chunk 105 optimal weight: 3.9990 chunk 345 optimal weight: 20.0000 chunk 210 optimal weight: 0.3980 chunk 306 optimal weight: 6.9990 chunk 323 optimal weight: 5.9990 chunk 247 optimal weight: 3.9990 chunk 120 optimal weight: 0.8980 chunk 98 optimal weight: 4.9990 chunk 284 optimal weight: 1.9990 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 280 ASN G 172 ASN G 244 GLN I 363 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.109081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.072837 restraints weight = 53142.698| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 2.68 r_work: 0.2990 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2869 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8642 moved from start: 0.3478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 29012 Z= 0.218 Angle : 0.622 11.820 39296 Z= 0.312 Chirality : 0.047 0.326 4593 Planarity : 0.004 0.052 5029 Dihedral : 4.845 69.123 3953 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 1.13 % Allowed : 16.69 % Favored : 82.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.75 % 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: 1.15 (0.14), residues: 3621 helix: 1.65 (0.15), residues: 1334 sheet: -0.37 (0.24), residues: 490 loop : 0.58 (0.15), residues: 1797 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG E 292 TYR 0.017 0.002 TYR I 205 PHE 0.023 0.002 PHE D 177 TRP 0.009 0.001 TRP B 111 HIS 0.007 0.001 HIS A 168 Details of bonding type rmsd/Z covalent geometry : bond 0.00521 / 0.22 (29002) covalent geometry : angle 0.62200 / 0.31 (39296) hydrogen bonds : bond 0.03888 / 2.57 ( 1205) hydrogen bonds : angle 4.16753 / 3.00 ( 3222) metal coordination : bond 0.00395 / 0.25 ( 10) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7242 Ramachandran restraints generated. 3621 Oldfield, 0 Emsley, 3621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7242 Ramachandran restraints generated. 3621 Oldfield, 0 Emsley, 3621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 3175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 222 time to evaluate : 1.137 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 ARG cc_start: 0.7796 (OUTLIER) cc_final: 0.7370 (mtp85) REVERT: A 108 LYS cc_start: 0.8721 (OUTLIER) cc_final: 0.8360 (tppt) REVERT: B 108 LYS cc_start: 0.8990 (ttmm) cc_final: 0.8656 (ttpt) REVERT: C 13 GLU cc_start: 0.8548 (mt-10) cc_final: 0.8329 (mt-10) REVERT: C 121 ASP cc_start: 0.8874 (t0) cc_final: 0.8355 (t0) REVERT: C 124 PHE cc_start: 0.8515 (m-80) cc_final: 0.8172 (m-80) REVERT: C 171 SER cc_start: 0.9119 (OUTLIER) cc_final: 0.8735 (p) REVERT: D 45 ILE cc_start: 0.8827 (mt) cc_final: 0.8617 (mt) REVERT: D 121 ASP cc_start: 0.8710 (t0) cc_final: 0.8420 (t0) REVERT: D 124 PHE cc_start: 0.8194 (m-80) cc_final: 0.7673 (m-80) REVERT: F 169 THR cc_start: 0.8042 (OUTLIER) cc_final: 0.7806 (m) REVERT: F 197 SER cc_start: 0.8764 (OUTLIER) cc_final: 0.8402 (p) REVERT: F 246 GLU cc_start: 0.7798 (mm-30) cc_final: 0.6555 (mm-30) REVERT: F 247 GLU cc_start: 0.7807 (mt-10) cc_final: 0.7386 (pm20) REVERT: F 250 ARG cc_start: 0.8809 (ttm110) cc_final: 0.8302 (mtp-110) REVERT: F 299 GLU cc_start: 0.8759 (OUTLIER) cc_final: 0.8423 (mp0) REVERT: G 48 ASN cc_start: 0.8644 (t0) cc_final: 0.8287 (t0) REVERT: G 191 ASP cc_start: 0.8834 (m-30) cc_final: 0.8542 (m-30) REVERT: H 1 MET cc_start: 0.3956 (tpt) cc_final: 0.3590 (pmt) REVERT: H 45 LEU cc_start: 0.7626 (OUTLIER) cc_final: 0.7381 (mt) REVERT: H 237 ARG cc_start: 0.8766 (OUTLIER) cc_final: 0.8395 (mpp80) REVERT: I 16 MET cc_start: 0.5442 (ptm) cc_final: 0.5085 (ptm) REVERT: I 71 MET cc_start: 0.6506 (ptp) cc_final: 0.5963 (ptm) REVERT: I 74 ASP cc_start: 0.7975 (m-30) cc_final: 0.7326 (t0) REVERT: I 319 TYR cc_start: 0.8309 (t80) cc_final: 0.8079 (t80) REVERT: I 320 MET cc_start: 0.8744 (tpp) cc_final: 0.8270 (ppp) REVERT: I 321 GLU cc_start: 0.9228 (tp30) cc_final: 0.8552 (mm-30) REVERT: I 380 LEU cc_start: 0.7114 (mm) cc_final: 0.6850 (mm) REVERT: J 66 GLU cc_start: 0.6581 (OUTLIER) cc_final: 0.6126 (pm20) REVERT: J 216 MET cc_start: 0.8817 (mmm) cc_final: 0.8598 (mmm) REVERT: J 321 GLU cc_start: 0.9344 (tp30) cc_final: 0.8958 (tm-30) REVERT: J 372 ARG cc_start: 0.8951 (mtp85) cc_final: 0.8539 (mmm-85) REVERT: J 425 LEU cc_start: 0.8311 (tm) cc_final: 0.7910 (tt) outliers start: 36 outliers final: 22 residues processed: 249 average time/residue: 0.6465 time to fit residues: 188.5128 Evaluate side-chains 244 residues out of total 3175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 213 time to evaluate : 1.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ARG Chi-restraints excluded: chain A residue 95 CYS Chi-restraints excluded: chain A residue 108 LYS Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain B residue 57 PHE Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain B residue 411 SER Chi-restraints excluded: chain C residue 131 SER Chi-restraints excluded: chain C residue 171 SER Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain F residue 169 THR Chi-restraints excluded: chain F residue 171 LYS Chi-restraints excluded: chain F residue 197 SER Chi-restraints excluded: chain F residue 241 THR Chi-restraints excluded: chain F residue 299 GLU Chi-restraints excluded: chain F residue 447 VAL Chi-restraints excluded: chain G residue 63 VAL Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 120 LYS Chi-restraints excluded: chain H residue 237 ARG Chi-restraints excluded: chain I residue 363 GLN Chi-restraints excluded: chain I residue 386 THR Chi-restraints excluded: chain J residue 17 THR Chi-restraints excluded: chain J residue 66 GLU Chi-restraints excluded: chain J residue 316 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 181 optimal weight: 2.9990 chunk 320 optimal weight: 5.9990 chunk 27 optimal weight: 0.6980 chunk 265 optimal weight: 0.8980 chunk 85 optimal weight: 8.9990 chunk 216 optimal weight: 2.9990 chunk 199 optimal weight: 10.0000 chunk 23 optimal weight: 3.9990 chunk 62 optimal weight: 4.9990 chunk 239 optimal weight: 0.9990 chunk 212 optimal weight: 0.6980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 277 GLN C 280 ASN G 270 HIS I 363 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.110267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.074636 restraints weight = 53254.855| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 2.64 r_work: 0.3033 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2912 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 moved from start: 0.3551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 29012 Z= 0.150 Angle : 0.593 12.243 39296 Z= 0.299 Chirality : 0.045 0.333 4593 Planarity : 0.004 0.056 5029 Dihedral : 4.761 67.514 3953 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.13 % Allowed : 16.76 % Favored : 82.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.75 % 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: 1.18 (0.14), residues: 3621 helix: 1.68 (0.15), residues: 1334 sheet: -0.34 (0.24), residues: 480 loop : 0.57 (0.15), residues: 1807 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG E 292 TYR 0.040 0.001 TYR I 94 PHE 0.024 0.001 PHE H 72 TRP 0.009 0.001 TRP B 111 HIS 0.007 0.001 HIS G 270 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.15 (29002) covalent geometry : angle 0.59290 / 0.30 (39296) hydrogen bonds : bond 0.03632 / 2.41 ( 1205) hydrogen bonds : angle 4.11559 / 2.96 ( 3222) metal coordination : bond 0.00245 / 0.15 ( 10) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12827.07 seconds wall clock time: 218 minutes 46.89 seconds (13126.89 seconds total)