Starting phenix.real_space_refine on Sun Aug 9 00:04:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ya8_72724/08_2026/9ya8_72724.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ya8_72724/08_2026/9ya8_72724.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.32 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ya8_72724/08_2026/9ya8_72724.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ya8_72724/08_2026/9ya8_72724.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ya8_72724/08_2026/9ya8_72724.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ya8_72724/08_2026/9ya8_72724.map" } resolution = 4.32 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= 0.198 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 8 5.49 5 Mg 4 5.21 5 S 177 5.16 5 C 19447 2.51 5 N 5243 2.21 5 O 5952 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.03s 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: 30831 Number of models: 1 Model: "" Number of chains: 17 Chain: "A" Number of atoms: 2932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2932 Classifications: {'peptide': 375} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 355} Chain: "B" Number of atoms: 2932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2932 Classifications: {'peptide': 375} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 355} Chain: "C" Number of atoms: 2932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2932 Classifications: {'peptide': 375} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 355} Chain: "D" Number of atoms: 2932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2932 Classifications: {'peptide': 375} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 355} Chain: "E" Number of atoms: 930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 930 Classifications: {'peptide': 115} Modifications used: {'COO': 1} Link IDs: {'TRANS': 114} Chain: "F" Number of atoms: 930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 930 Classifications: {'peptide': 115} Modifications used: {'COO': 1} Link IDs: {'TRANS': 114} Chain: "G" Number of atoms: 562 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 562 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 1, 'TRANS': 68} Chain: "H" Number of atoms: 562 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 562 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 1, 'TRANS': 68} Chain: "I" Number of atoms: 595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 595 Classifications: {'peptide': 68} Link IDs: {'TRANS': 67} Chain: "J" Number of atoms: 6489 Number of conformers: 1 Conformer: "" Number of residues, atoms: 807, 6489 Classifications: {'peptide': 807} Link IDs: {'PTRANS': 30, 'TRANS': 776} Chain: "K" Number of atoms: 6489 Number of conformers: 1 Conformer: "" Number of residues, atoms: 807, 6489 Classifications: {'peptide': 807} Link IDs: {'CIS': 2, 'PTRANS': 30, 'TRANS': 774} Chain: "L" Number of atoms: 1217 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1217 Classifications: {'peptide': 153} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 146} Chain: "M" Number of atoms: 1217 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1217 Classifications: {'peptide': 153} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 146} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 6.72, per 1000 atoms: 0.22 Number of scatterers: 30831 At special positions: 0 Unit cell: (170.856, 143.736, 271.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 177 16.00 P 8 15.00 Mg 4 11.99 O 5952 8.00 N 5243 7.00 C 19447 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: 2.82 Conformation dependent library (CDL) restraints added in 1.4 seconds 7664 Ramachandran restraints generated. 3832 Oldfield, 0 Emsley, 3832 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7236 Finding SS restraints... Secondary structure from input PDB file: 174 helices and 40 sheets defined 57.3% alpha, 10.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.95 Creating SS restraints... Processing helix chain 'A' and resid 55 through 60 removed outlier: 3.754A pdb=" N GLN A 59 " --> pdb=" O GLY A 55 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N SER A 60 " --> pdb=" O ASP A 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 55 through 60' Processing helix chain 'A' and resid 61 through 63 No H-bonds generated for 'chain 'A' and resid 61 through 63' Processing helix chain 'A' and resid 78 through 93 removed outlier: 3.957A pdb=" N LYS A 84 " --> pdb=" O ASP A 80 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE A 85 " --> pdb=" O ASP A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 128 removed outlier: 4.206A pdb=" N GLU A 117 " --> pdb=" O LYS A 113 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LYS A 118 " --> pdb=" O ALA A 114 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N MET A 123 " --> pdb=" O MET A 119 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N PHE A 124 " --> pdb=" O THR A 120 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLU A 125 " --> pdb=" O GLN A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 145 Processing helix chain 'A' and resid 172 through 175 Processing helix chain 'A' and resid 181 through 193 Processing helix chain 'A' and resid 194 through 197 Processing helix chain 'A' and resid 202 through 217 removed outlier: 3.964A pdb=" N GLU A 207 " --> pdb=" O THR A 203 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ILE A 208 " --> pdb=" O ALA A 204 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LYS A 215 " --> pdb=" O ASP A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 233 removed outlier: 3.604A pdb=" N SER A 232 " --> pdb=" O ALA A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 257 removed outlier: 3.685A pdb=" N CYS A 257 " --> pdb=" O GLU A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 262 Processing helix chain 'A' and resid 263 through 268 Processing helix chain 'A' and resid 273 through 285 Processing helix chain 'A' and resid 286 through 288 No H-bonds generated for 'chain 'A' and resid 286 through 288' Processing helix chain 'A' and resid 289 through 296 Processing helix chain 'A' and resid 308 through 321 Processing helix chain 'A' and resid 337 through 348 Processing helix chain 'A' and resid 350 through 355 removed outlier: 3.628A pdb=" N GLN A 354 " --> pdb=" O THR A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 364 Processing helix chain 'A' and resid 365 through 369 removed outlier: 4.212A pdb=" N SER A 368 " --> pdb=" O ALA A 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 61 Processing helix chain 'B' and resid 78 through 92 Processing helix chain 'B' and resid 97 through 101 Processing helix chain 'B' and resid 112 through 127 removed outlier: 4.233A pdb=" N ARG B 116 " --> pdb=" O PRO B 112 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLU B 117 " --> pdb=" O LYS B 113 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N MET B 123 " --> pdb=" O MET B 119 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N PHE B 124 " --> pdb=" O THR B 120 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLU B 125 " --> pdb=" O GLN B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 145 removed outlier: 3.647A pdb=" N TYR B 143 " --> pdb=" O VAL B 139 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA B 144 " --> pdb=" O LEU B 140 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N SER B 145 " --> pdb=" O SER B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 193 Processing helix chain 'B' and resid 194 through 196 No H-bonds generated for 'chain 'B' and resid 194 through 196' Processing helix chain 'B' and resid 202 through 217 removed outlier: 3.626A pdb=" N ARG B 206 " --> pdb=" O THR B 202 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N GLU B 207 " --> pdb=" O THR B 203 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N ILE B 208 " --> pdb=" O ALA B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 233 Processing helix chain 'B' and resid 252 through 257 removed outlier: 3.888A pdb=" N CYS B 257 " --> pdb=" O GLU B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 262 Processing helix chain 'B' and resid 263 through 267 Processing helix chain 'B' and resid 273 through 284 Processing helix chain 'B' and resid 289 through 296 removed outlier: 3.622A pdb=" N ALA B 295 " --> pdb=" O LYS B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 306 removed outlier: 4.288A pdb=" N TYR B 306 " --> pdb=" O THR B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 321 removed outlier: 3.969A pdb=" N GLN B 314 " --> pdb=" O ALA B 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 349 Processing helix chain 'B' and resid 351 through 356 removed outlier: 3.732A pdb=" N GLN B 354 " --> pdb=" O THR B 351 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N TRP B 356 " --> pdb=" O GLN B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 364 Processing helix chain 'B' and resid 366 through 372 removed outlier: 3.647A pdb=" N VAL B 370 " --> pdb=" O PRO B 367 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ARG B 372 " --> pdb=" O ILE B 369 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 61 Processing helix chain 'C' and resid 78 through 92 Processing helix chain 'C' and resid 97 through 101 Processing helix chain 'C' and resid 112 through 128 removed outlier: 4.237A pdb=" N ARG C 116 " --> pdb=" O PRO C 112 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLU C 117 " --> pdb=" O LYS C 113 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N MET C 123 " --> pdb=" O MET C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 145 removed outlier: 3.647A pdb=" N SER C 145 " --> pdb=" O SER C 141 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 175 Processing helix chain 'C' and resid 181 through 193 Processing helix chain 'C' and resid 194 through 197 Processing helix chain 'C' and resid 202 through 217 removed outlier: 4.016A pdb=" N GLU C 207 " --> pdb=" O THR C 203 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N ILE C 208 " --> pdb=" O ALA C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 233 Processing helix chain 'C' and resid 252 through 257 removed outlier: 3.826A pdb=" N CYS C 257 " --> pdb=" O GLU C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 262 Processing helix chain 'C' and resid 263 through 268 removed outlier: 3.526A pdb=" N PHE C 266 " --> pdb=" O GLN C 263 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 285 Processing helix chain 'C' and resid 289 through 296 Processing helix chain 'C' and resid 301 through 305 Processing helix chain 'C' and resid 308 through 321 removed outlier: 3.523A pdb=" N ARG C 312 " --> pdb=" O GLY C 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 334 through 336 No H-bonds generated for 'chain 'C' and resid 334 through 336' Processing helix chain 'C' and resid 337 through 348 Processing helix chain 'C' and resid 350 through 355 removed outlier: 3.806A pdb=" N GLN C 354 " --> pdb=" O THR C 351 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 364 Processing helix chain 'C' and resid 366 through 372 removed outlier: 3.990A pdb=" N VAL C 370 " --> pdb=" O PRO C 367 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N HIS C 371 " --> pdb=" O SER C 368 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ARG C 372 " --> pdb=" O ILE C 369 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 61 removed outlier: 3.719A pdb=" N GLN D 59 " --> pdb=" O GLY D 55 " (cutoff:3.500A) Processing helix chain 'D' and resid 78 through 92 Processing helix chain 'D' and resid 97 through 101 removed outlier: 3.510A pdb=" N GLU D 100 " --> pdb=" O ALA D 97 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N HIS D 101 " --> pdb=" O PRO D 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 97 through 101' Processing helix chain 'D' and resid 112 through 126 removed outlier: 3.919A pdb=" N ARG D 116 " --> pdb=" O PRO D 112 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N MET D 123 " --> pdb=" O MET D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 145 removed outlier: 3.622A pdb=" N SER D 145 " --> pdb=" O SER D 141 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 175 removed outlier: 3.730A pdb=" N ILE D 175 " --> pdb=" O PRO D 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 172 through 175' Processing helix chain 'D' and resid 181 through 193 Processing helix chain 'D' and resid 194 through 197 Processing helix chain 'D' and resid 205 through 217 Processing helix chain 'D' and resid 223 through 233 removed outlier: 3.554A pdb=" N ALA D 228 " --> pdb=" O GLU D 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 257 removed outlier: 4.001A pdb=" N CYS D 257 " --> pdb=" O GLU D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 262 Processing helix chain 'D' and resid 263 through 268 Processing helix chain 'D' and resid 273 through 283 Processing helix chain 'D' and resid 291 through 296 Processing helix chain 'D' and resid 301 through 306 removed outlier: 3.777A pdb=" N TYR D 306 " --> pdb=" O THR D 303 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 321 removed outlier: 3.827A pdb=" N GLN D 314 " --> pdb=" O ALA D 310 " (cutoff:3.500A) Processing helix chain 'D' and resid 337 through 348 removed outlier: 3.629A pdb=" N SER D 348 " --> pdb=" O SER D 344 " (cutoff:3.500A) Processing helix chain 'D' and resid 351 through 355 removed outlier: 3.811A pdb=" N GLN D 354 " --> pdb=" O THR D 351 " (cutoff:3.500A) Processing helix chain 'D' and resid 359 through 366 Processing helix chain 'D' and resid 367 through 370 removed outlier: 3.582A pdb=" N VAL D 370 " --> pdb=" O PRO D 367 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 367 through 370' Processing helix chain 'E' and resid 171 through 284 removed outlier: 3.684A pdb=" N SER E 283 " --> pdb=" O ASN E 279 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ILE E 284 " --> pdb=" O ASP E 280 " (cutoff:3.500A) Processing helix chain 'F' and resid 171 through 283 removed outlier: 4.595A pdb=" N SER F 283 " --> pdb=" O ASN F 279 " (cutoff:3.500A) Processing helix chain 'G' and resid 2 through 70 Proline residue: G 64 - end of helix removed outlier: 3.515A pdb=" N LYS G 70 " --> pdb=" O ASP G 66 " (cutoff:3.500A) Processing helix chain 'H' and resid 2 through 69 Proline residue: H 64 - end of helix Processing helix chain 'I' and resid 85 through 150 Processing helix chain 'J' and resid 5 through 9 removed outlier: 3.976A pdb=" N ALA J 8 " --> pdb=" O GLU J 5 " (cutoff:3.500A) Processing helix chain 'J' and resid 19 through 29 Processing helix chain 'J' and resid 74 through 76 No H-bonds generated for 'chain 'J' and resid 74 through 76' Processing helix chain 'J' and resid 81 through 85 removed outlier: 3.747A pdb=" N ASP J 85 " --> pdb=" O PRO J 82 " (cutoff:3.500A) Processing helix chain 'J' and resid 97 through 111 removed outlier: 3.633A pdb=" N VAL J 101 " --> pdb=" O HIS J 97 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU J 102 " --> pdb=" O GLU J 98 " (cutoff:3.500A) Processing helix chain 'J' and resid 131 through 134 removed outlier: 3.732A pdb=" N TYR J 134 " --> pdb=" O LEU J 131 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 131 through 134' Processing helix chain 'J' and resid 135 through 142 Processing helix chain 'J' and resid 153 through 169 Processing helix chain 'J' and resid 180 through 202 Processing helix chain 'J' and resid 206 through 210 Processing helix chain 'J' and resid 215 through 231 removed outlier: 4.067A pdb=" N GLN J 219 " --> pdb=" O THR J 215 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ASN J 224 " --> pdb=" O ILE J 220 " (cutoff:3.500A) Proline residue: J 225 - end of helix removed outlier: 3.581A pdb=" N PHE J 230 " --> pdb=" O ALA J 226 " (cutoff:3.500A) Processing helix chain 'J' and resid 269 through 274 removed outlier: 3.627A pdb=" N ARG J 272 " --> pdb=" O GLU J 269 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N VAL J 273 " --> pdb=" O LYS J 270 " (cutoff:3.500A) Processing helix chain 'J' and resid 283 through 291 removed outlier: 4.026A pdb=" N TYR J 287 " --> pdb=" O TYR J 283 " (cutoff:3.500A) Processing helix chain 'J' and resid 294 through 301 removed outlier: 4.191A pdb=" N LEU J 298 " --> pdb=" O LYS J 294 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ASP J 299 " --> pdb=" O PRO J 295 " (cutoff:3.500A) Processing helix chain 'J' and resid 306 through 310 removed outlier: 4.128A pdb=" N TYR J 310 " --> pdb=" O PRO J 307 " (cutoff:3.500A) Processing helix chain 'J' and resid 326 through 339 removed outlier: 3.694A pdb=" N MET J 330 " --> pdb=" O ALA J 326 " (cutoff:3.500A) Processing helix chain 'J' and resid 342 through 360 removed outlier: 3.754A pdb=" N ASN J 347 " --> pdb=" O SER J 343 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N TYR J 350 " --> pdb=" O LYS J 346 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N GLY J 360 " --> pdb=" O ILE J 356 " (cutoff:3.500A) Processing helix chain 'J' and resid 378 through 389 Processing helix chain 'J' and resid 391 through 399 removed outlier: 3.740A pdb=" N LEU J 396 " --> pdb=" O SER J 392 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LYS J 397 " --> pdb=" O ALA J 393 " (cutoff:3.500A) Processing helix chain 'J' and resid 416 through 447 removed outlier: 3.548A pdb=" N THR J 446 " --> pdb=" O ARG J 442 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N LEU J 447 " --> pdb=" O ILE J 443 " (cutoff:3.500A) Processing helix chain 'J' and resid 472 through 505 Processing helix chain 'J' and resid 514 through 526 removed outlier: 4.130A pdb=" N ALA J 519 " --> pdb=" O MET J 515 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N CYS J 520 " --> pdb=" O ASP J 516 " (cutoff:3.500A) Processing helix chain 'J' and resid 529 through 537 removed outlier: 3.601A pdb=" N GLU J 535 " --> pdb=" O MET J 531 " (cutoff:3.500A) Processing helix chain 'J' and resid 538 through 540 No H-bonds generated for 'chain 'J' and resid 538 through 540' Processing helix chain 'J' and resid 544 through 557 Processing helix chain 'J' and resid 592 through 598 removed outlier: 3.562A pdb=" N LYS J 596 " --> pdb=" O GLY J 592 " (cutoff:3.500A) Processing helix chain 'J' and resid 602 through 611 removed outlier: 3.620A pdb=" N VAL J 606 " --> pdb=" O ASN J 602 " (cutoff:3.500A) Processing helix chain 'J' and resid 614 through 621 Processing helix chain 'J' and resid 646 through 663 Processing helix chain 'J' and resid 685 through 696 removed outlier: 3.570A pdb=" N VAL J 689 " --> pdb=" O ASP J 685 " (cutoff:3.500A) Processing helix chain 'J' and resid 697 through 708 removed outlier: 3.546A pdb=" N GLY J 708 " --> pdb=" O ILE J 704 " (cutoff:3.500A) Processing helix chain 'J' and resid 715 through 723 removed outlier: 3.744A pdb=" N ARG J 719 " --> pdb=" O TYR J 715 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLN J 720 " --> pdb=" O GLY J 716 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ARG J 723 " --> pdb=" O ARG J 719 " (cutoff:3.500A) Processing helix chain 'J' and resid 724 through 726 No H-bonds generated for 'chain 'J' and resid 724 through 726' Processing helix chain 'J' and resid 737 through 747 Processing helix chain 'J' and resid 768 through 810 Processing helix chain 'K' and resid 12 through 17 removed outlier: 3.549A pdb=" N LEU K 16 " --> pdb=" O ALA K 12 " (cutoff:3.500A) Processing helix chain 'K' and resid 19 through 27 removed outlier: 4.178A pdb=" N ARG K 23 " --> pdb=" O SER K 19 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLU K 25 " --> pdb=" O LYS K 21 " (cutoff:3.500A) Processing helix chain 'K' and resid 81 through 85 Processing helix chain 'K' and resid 89 through 93 removed outlier: 3.674A pdb=" N MET K 92 " --> pdb=" O ASP K 89 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU K 93 " --> pdb=" O MET K 90 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 89 through 93' Processing helix chain 'K' and resid 97 through 111 Processing helix chain 'K' and resid 131 through 134 removed outlier: 3.841A pdb=" N TYR K 134 " --> pdb=" O LEU K 131 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 131 through 134' Processing helix chain 'K' and resid 135 through 142 Processing helix chain 'K' and resid 146 through 150 removed outlier: 3.978A pdb=" N GLU K 149 " --> pdb=" O LYS K 146 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N ALA K 150 " --> pdb=" O ARG K 147 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 146 through 150' Processing helix chain 'K' and resid 153 through 169 Processing helix chain 'K' and resid 180 through 201 removed outlier: 4.022A pdb=" N LYS K 184 " --> pdb=" O SER K 180 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N VAL K 186 " --> pdb=" O ALA K 182 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LYS K 189 " --> pdb=" O THR K 185 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE K 201 " --> pdb=" O VAL K 197 " (cutoff:3.500A) Processing helix chain 'K' and resid 217 through 231 Proline residue: K 225 - end of helix removed outlier: 3.647A pdb=" N PHE K 230 " --> pdb=" O ALA K 226 " (cutoff:3.500A) Processing helix chain 'K' and resid 270 through 274 Processing helix chain 'K' and resid 283 through 291 removed outlier: 4.355A pdb=" N TYR K 287 " --> pdb=" O TYR K 283 " (cutoff:3.500A) Processing helix chain 'K' and resid 294 through 302 removed outlier: 4.359A pdb=" N LEU K 298 " --> pdb=" O LYS K 294 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASP K 299 " --> pdb=" O PRO K 295 " (cutoff:3.500A) Processing helix chain 'K' and resid 324 through 340 removed outlier: 4.534A pdb=" N GLU K 328 " --> pdb=" O ASP K 324 " (cutoff:3.500A) Processing helix chain 'K' and resid 342 through 360 removed outlier: 3.665A pdb=" N MET K 357 " --> pdb=" O THR K 353 " (cutoff:3.500A) Processing helix chain 'K' and resid 378 through 388 Processing helix chain 'K' and resid 391 through 401 Processing helix chain 'K' and resid 416 through 447 Processing helix chain 'K' and resid 472 through 505 removed outlier: 3.756A pdb=" N GLU K 499 " --> pdb=" O VAL K 495 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLU K 500 " --> pdb=" O LEU K 496 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N TYR K 501 " --> pdb=" O GLU K 497 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LYS K 502 " --> pdb=" O GLN K 498 " (cutoff:3.500A) Processing helix chain 'K' and resid 514 through 526 removed outlier: 4.049A pdb=" N CYS K 520 " --> pdb=" O ASP K 516 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N LEU K 523 " --> pdb=" O ALA K 519 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ILE K 524 " --> pdb=" O CYS K 520 " (cutoff:3.500A) Processing helix chain 'K' and resid 529 through 538 Processing helix chain 'K' and resid 544 through 557 removed outlier: 3.503A pdb=" N HIS K 556 " --> pdb=" O LEU K 552 " (cutoff:3.500A) Processing helix chain 'K' and resid 592 through 598 removed outlier: 3.653A pdb=" N LYS K 596 " --> pdb=" O GLY K 592 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N LYS K 598 " --> pdb=" O LEU K 594 " (cutoff:3.500A) Processing helix chain 'K' and resid 604 through 611 Processing helix chain 'K' and resid 614 through 621 Processing helix chain 'K' and resid 646 through 664 removed outlier: 3.581A pdb=" N LEU K 650 " --> pdb=" O THR K 646 " (cutoff:3.500A) Processing helix chain 'K' and resid 685 through 697 removed outlier: 3.571A pdb=" N GLY K 697 " --> pdb=" O LEU K 693 " (cutoff:3.500A) Processing helix chain 'K' and resid 697 through 708 removed outlier: 3.705A pdb=" N GLY K 708 " --> pdb=" O ILE K 704 " (cutoff:3.500A) Processing helix chain 'K' and resid 715 through 721 Processing helix chain 'K' and resid 737 through 747 Processing helix chain 'K' and resid 768 through 810 removed outlier: 3.771A pdb=" N LEU K 772 " --> pdb=" O GLY K 768 " (cutoff:3.500A) Processing helix chain 'L' and resid 48 through 63 Processing helix chain 'L' and resid 76 through 84 removed outlier: 4.158A pdb=" N VAL L 80 " --> pdb=" O GLN L 76 " (cutoff:3.500A) Processing helix chain 'L' and resid 89 through 97 removed outlier: 3.743A pdb=" N VAL L 93 " --> pdb=" O THR L 89 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU L 97 " --> pdb=" O VAL L 93 " (cutoff:3.500A) Processing helix chain 'L' and resid 101 through 106 removed outlier: 4.058A pdb=" N ASN L 106 " --> pdb=" O GLN L 102 " (cutoff:3.500A) Processing helix chain 'L' and resid 111 through 125 Proline residue: L 117 - end of helix removed outlier: 4.141A pdb=" N ASN L 125 " --> pdb=" O HIS L 121 " (cutoff:3.500A) Processing helix chain 'L' and resid 130 through 139 Processing helix chain 'L' and resid 140 through 142 No H-bonds generated for 'chain 'L' and resid 140 through 142' Processing helix chain 'L' and resid 151 through 159 removed outlier: 3.568A pdb=" N HIS L 156 " --> pdb=" O ALA L 152 " (cutoff:3.500A) Processing helix chain 'L' and resid 166 through 175 Processing helix chain 'L' and resid 186 through 195 removed outlier: 3.752A pdb=" N LYS L 191 " --> pdb=" O GLU L 187 " (cutoff:3.500A) Processing helix chain 'M' and resid 48 through 63 removed outlier: 3.595A pdb=" N ASP M 63 " --> pdb=" O PHE M 59 " (cutoff:3.500A) Processing helix chain 'M' and resid 73 through 84 removed outlier: 3.847A pdb=" N CYS M 77 " --> pdb=" O THR M 73 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N GLY M 78 " --> pdb=" O TYR M 74 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ASP M 79 " --> pdb=" O GLY M 75 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ARG M 82 " --> pdb=" O GLY M 78 " (cutoff:3.500A) Processing helix chain 'M' and resid 101 through 107 Processing helix chain 'M' and resid 111 through 125 Proline residue: M 117 - end of helix removed outlier: 3.781A pdb=" N GLN M 120 " --> pdb=" O LEU M 116 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N HIS M 121 " --> pdb=" O PRO M 117 " (cutoff:3.500A) Processing helix chain 'M' and resid 130 through 142 removed outlier: 3.719A pdb=" N VAL M 140 " --> pdb=" O GLU M 136 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N PHE M 141 " --> pdb=" O GLY M 137 " (cutoff:3.500A) Processing helix chain 'M' and resid 151 through 161 removed outlier: 4.186A pdb=" N ALA M 159 " --> pdb=" O ARG M 155 " (cutoff:3.500A) Processing helix chain 'M' and resid 167 through 174 Processing helix chain 'M' and resid 188 through 194 Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 32 removed outlier: 3.551A pdb=" N THR A 106 " --> pdb=" O CYS A 10 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 54 Processing sheet with id=AA3, first strand: chain 'A' and resid 169 through 170 Processing sheet with id=AA4, first strand: chain 'A' and resid 169 through 170 removed outlier: 4.509A pdb=" N HIS A 161 " --> pdb=" O ASP A 154 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASP A 154 " --> pdb=" O HIS A 161 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL A 163 " --> pdb=" O VAL A 152 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL A 152 " --> pdb=" O VAL A 163 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N ILE A 151 " --> pdb=" O VAL A 298 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N SER A 300 " --> pdb=" O ILE A 151 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N LEU A 153 " --> pdb=" O SER A 300 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ASN A 297 " --> pdb=" O ILE A 330 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 238 through 240 Processing sheet with id=AA6, first strand: chain 'B' and resid 9 through 11 Processing sheet with id=AA7, first strand: chain 'B' and resid 53 through 54 Processing sheet with id=AA8, first strand: chain 'B' and resid 105 through 107 removed outlier: 3.541A pdb=" N ALA B 135 " --> pdb=" O LEU B 105 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 131 through 132 Processing sheet with id=AB1, first strand: chain 'B' and resid 169 through 170 Processing sheet with id=AB2, first strand: chain 'B' and resid 169 through 170 removed outlier: 6.388A pdb=" N ILE B 151 " --> pdb=" O VAL B 298 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ASN B 297 " --> pdb=" O ILE B 330 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 238 through 242 removed outlier: 6.328A pdb=" N LYS B 238 " --> pdb=" O THR B 249 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N THR B 249 " --> pdb=" O LYS B 238 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N TYR B 240 " --> pdb=" O VAL B 247 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N VAL B 247 " --> pdb=" O TYR B 240 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 10 through 11 Processing sheet with id=AB5, first strand: chain 'C' and resid 53 through 54 Processing sheet with id=AB6, first strand: chain 'C' and resid 103 through 107 Processing sheet with id=AB7, first strand: chain 'C' and resid 169 through 170 Processing sheet with id=AB8, first strand: chain 'C' and resid 169 through 170 removed outlier: 6.658A pdb=" N ASN C 297 " --> pdb=" O ILE C 330 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 238 through 242 removed outlier: 4.958A pdb=" N LEU C 242 " --> pdb=" O GLN C 246 " (cutoff:3.500A) removed outlier: 5.646A pdb=" N GLN C 246 " --> pdb=" O LEU C 242 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 29 through 32 removed outlier: 6.583A pdb=" N LEU D 8 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 8.417A pdb=" N THR D 106 " --> pdb=" O LEU D 8 " (cutoff:3.500A) removed outlier: 8.814A pdb=" N CYS D 10 " --> pdb=" O THR D 106 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA D 135 " --> pdb=" O LEU D 105 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 53 through 54 Processing sheet with id=AC3, first strand: chain 'D' and resid 169 through 170 Processing sheet with id=AC4, first strand: chain 'D' and resid 169 through 170 removed outlier: 7.677A pdb=" N VAL D 298 " --> pdb=" O THR D 149 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N ILE D 151 " --> pdb=" O VAL D 298 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N SER D 300 " --> pdb=" O ILE D 151 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N LEU D 153 " --> pdb=" O SER D 300 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ASN D 297 " --> pdb=" O ILE D 330 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 238 through 242 removed outlier: 5.074A pdb=" N LEU D 242 " --> pdb=" O GLN D 246 " (cutoff:3.500A) removed outlier: 5.523A pdb=" N GLN D 246 " --> pdb=" O LEU D 242 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'J' and resid 68 through 72 removed outlier: 7.103A pdb=" N LYS J 58 " --> pdb=" O ARG J 54 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N ARG J 54 " --> pdb=" O LYS J 58 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N THR J 60 " --> pdb=" O LEU J 52 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'J' and resid 115 through 118 removed outlier: 5.969A pdb=" N CYS J 122 " --> pdb=" O ARG J 671 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N ILE J 673 " --> pdb=" O CYS J 122 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N THR J 124 " --> pdb=" O ILE J 673 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N SER J 173 " --> pdb=" O HIS J 668 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N VAL J 670 " --> pdb=" O SER J 173 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N LEU J 175 " --> pdb=" O VAL J 670 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N CYS J 672 " --> pdb=" O LEU J 175 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N THR J 177 " --> pdb=" O CYS J 672 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N GLN J 172 " --> pdb=" O GLY J 458 " (cutoff:3.500A) removed outlier: 8.066A pdb=" N LEU J 460 " --> pdb=" O GLN J 172 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N ILE J 174 " --> pdb=" O LEU J 460 " (cutoff:3.500A) removed outlier: 8.227A pdb=" N ILE J 462 " --> pdb=" O ILE J 174 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N ILE J 176 " --> pdb=" O ILE J 462 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LYS J 246 " --> pdb=" O ASP J 461 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'J' and resid 232 through 233 removed outlier: 3.514A pdb=" N SER J 241 " --> pdb=" O ALA J 233 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'J' and resid 364 through 366 Processing sheet with id=AD1, first strand: chain 'J' and resid 403 through 406 Processing sheet with id=AD2, first strand: chain 'J' and resid 563 through 564 removed outlier: 3.717A pdb=" N PHE J 577 " --> pdb=" O TYR J 588 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'J' and resid 711 through 714 removed outlier: 3.513A pdb=" N LYS J 757 " --> pdb=" O PHE J 764 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'K' and resid 68 through 72 removed outlier: 7.188A pdb=" N LYS K 58 " --> pdb=" O ARG K 54 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N ARG K 54 " --> pdb=" O LYS K 58 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N THR K 60 " --> pdb=" O LEU K 52 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'K' and resid 115 through 118 removed outlier: 6.111A pdb=" N CYS K 122 " --> pdb=" O ARG K 671 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N ILE K 673 " --> pdb=" O CYS K 122 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N THR K 124 " --> pdb=" O ILE K 673 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N THR K 177 " --> pdb=" O VAL K 670 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N CYS K 672 " --> pdb=" O THR K 177 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N GLN K 172 " --> pdb=" O GLY K 458 " (cutoff:3.500A) removed outlier: 8.051A pdb=" N LEU K 460 " --> pdb=" O GLN K 172 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ILE K 174 " --> pdb=" O LEU K 460 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N SER K 260 " --> pdb=" O HIS K 251 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'K' and resid 232 through 233 removed outlier: 3.546A pdb=" N ALA K 233 " --> pdb=" O SER K 241 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'K' and resid 364 through 366 Processing sheet with id=AD8, first strand: chain 'K' and resid 403 through 406 Processing sheet with id=AD9, first strand: chain 'K' and resid 563 through 564 removed outlier: 4.088A pdb=" N PHE K 577 " --> pdb=" O TYR K 588 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'K' and resid 711 through 714 removed outlier: 3.547A pdb=" N ASN K 711 " --> pdb=" O PHE K 765 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'L' and resid 72 through 73 removed outlier: 4.122A pdb=" N ILE L 72 " --> pdb=" O MET L 110 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N MET L 110 " --> pdb=" O ILE L 72 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'L' and resid 148 through 150 removed outlier: 3.519A pdb=" N VAL L 149 " --> pdb=" O ILE L 184 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'M' and resid 148 through 150 1645 hydrogen bonds defined for protein. 4602 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: 9.23 Time building geometry restraints manager: 3.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 10229 1.34 - 1.46: 6471 1.46 - 1.58: 14386 1.58 - 1.70: 12 1.70 - 1.81: 310 Bond restraints: 31408 Sorted by residual: bond pdb=" C LYS J 526 " pdb=" N PRO J 527 " ideal model delta sigma weight residual 1.332 1.354 -0.022 1.33e-02 5.65e+03 2.81e+00 bond pdb=" N THR C 6 " pdb=" CA THR C 6 " ideal model delta sigma weight residual 1.457 1.471 -0.014 1.29e-02 6.01e+03 1.14e+00 bond pdb=" C4 ADP A 401 " pdb=" C5 ADP A 401 " ideal model delta sigma weight residual 1.490 1.469 0.021 2.00e-02 2.50e+03 1.09e+00 bond pdb=" C4 ADP C 401 " pdb=" C5 ADP C 401 " ideal model delta sigma weight residual 1.490 1.469 0.021 2.00e-02 2.50e+03 1.06e+00 bond pdb=" C4 ADP D 401 " pdb=" C5 ADP D 401 " ideal model delta sigma weight residual 1.490 1.470 0.020 2.00e-02 2.50e+03 1.04e+00 ... (remaining 31403 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.85: 42158 2.85 - 5.70: 180 5.70 - 8.54: 8 8.54 - 11.39: 0 11.39 - 14.24: 3 Bond angle restraints: 42349 Sorted by residual: angle pdb=" C ASP K 628 " pdb=" N THR K 629 " pdb=" CA THR K 629 " ideal model delta sigma weight residual 121.70 135.94 -14.24 1.80e+00 3.09e-01 6.26e+01 angle pdb=" C GLY M 182 " pdb=" N CYS M 183 " pdb=" CA CYS M 183 " ideal model delta sigma weight residual 121.70 134.78 -13.08 1.80e+00 3.09e-01 5.28e+01 angle pdb=" C GLY L 182 " pdb=" N CYS L 183 " pdb=" CA CYS L 183 " ideal model delta sigma weight residual 121.70 133.37 -11.67 1.80e+00 3.09e-01 4.21e+01 angle pdb=" C GLN K 79 " pdb=" N ASN K 80 " pdb=" CA ASN K 80 " ideal model delta sigma weight residual 120.68 125.97 -5.29 1.52e+00 4.33e-01 1.21e+01 angle pdb=" N VAL J 631 " pdb=" CA VAL J 631 " pdb=" C VAL J 631 " ideal model delta sigma weight residual 111.91 108.85 3.06 8.90e-01 1.26e+00 1.18e+01 ... (remaining 42344 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 17804 17.96 - 35.93: 1065 35.93 - 53.89: 264 53.89 - 71.85: 61 71.85 - 89.82: 25 Dihedral angle restraints: 19219 sinusoidal: 7994 harmonic: 11225 Sorted by residual: dihedral pdb=" CA ALA C 7 " pdb=" C ALA C 7 " pdb=" N LEU C 8 " pdb=" CA LEU C 8 " ideal model delta harmonic sigma weight residual 180.00 156.89 23.11 0 5.00e+00 4.00e-02 2.14e+01 dihedral pdb=" C5' ADP D 401 " pdb=" O5' ADP D 401 " pdb=" PA ADP D 401 " pdb=" O2A ADP D 401 " ideal model delta sinusoidal sigma weight residual -60.00 18.78 -78.78 1 2.00e+01 2.50e-03 1.93e+01 dihedral pdb=" CA THR C 6 " pdb=" C THR C 6 " pdb=" N ALA C 7 " pdb=" CA ALA C 7 " ideal model delta harmonic sigma weight residual 180.00 -159.28 -20.72 0 5.00e+00 4.00e-02 1.72e+01 ... (remaining 19216 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 2861 0.028 - 0.056: 1141 0.056 - 0.085: 368 0.085 - 0.113: 214 0.113 - 0.141: 49 Chirality restraints: 4633 Sorted by residual: chirality pdb=" CA ILE J 569 " pdb=" N ILE J 569 " pdb=" C ILE J 569 " pdb=" CB ILE J 569 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.98e-01 chirality pdb=" CA ILE K 730 " pdb=" N ILE K 730 " pdb=" C ILE K 730 " pdb=" CB ILE K 730 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.32e-01 chirality pdb=" CA ILE K 684 " pdb=" N ILE K 684 " pdb=" C ILE K 684 " pdb=" CB ILE K 684 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.17e-01 ... (remaining 4630 not shown) Planarity restraints: 5495 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR K 629 " -0.036 5.00e-02 4.00e+02 5.46e-02 4.76e+00 pdb=" N PRO K 630 " 0.094 5.00e-02 4.00e+02 pdb=" CA PRO K 630 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO K 630 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL J 39 " 0.027 5.00e-02 4.00e+02 4.08e-02 2.67e+00 pdb=" N PRO J 40 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO J 40 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO J 40 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS J 666 " -0.024 5.00e-02 4.00e+02 3.67e-02 2.16e+00 pdb=" N PRO J 667 " 0.064 5.00e-02 4.00e+02 pdb=" CA PRO J 667 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO J 667 " -0.020 5.00e-02 4.00e+02 ... (remaining 5492 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 173 2.53 - 3.13: 23052 3.13 - 3.72: 47368 3.72 - 4.31: 61991 4.31 - 4.90: 105411 Nonbonded interactions: 237995 Sorted by model distance: nonbonded pdb=" O1B ADP A 401 " pdb="MG MG A 402 " model vdw 1.943 2.170 nonbonded pdb=" OE1 GLN B 137 " pdb="MG MG B 402 " model vdw 1.955 2.170 nonbonded pdb=" OE1 GLN D 137 " pdb="MG MG D 402 " model vdw 1.958 2.170 nonbonded pdb=" OE1 GLN C 137 " pdb="MG MG C 402 " model vdw 1.963 2.170 nonbonded pdb=" O3B ADP B 401 " pdb="MG MG B 402 " model vdw 1.987 2.170 ... (remaining 237990 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' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'J' selection = chain 'K' } ncs_group { reference = chain 'L' selection = chain 'M' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.380 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: 0.030 Extract box with map and model: 0.360 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 31.510 Find NCS groups from input model: 0.770 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 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 : 0.002 0.028 31408 Z= 0.113 Angle : 0.532 14.239 42349 Z= 0.289 Chirality : 0.039 0.141 4633 Planarity : 0.004 0.055 5495 Dihedral : 12.986 89.818 11983 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 2.38 % Allowed : 6.50 % Favored : 91.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.11 % 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: 0.95 (0.14), residues: 3832 helix: 1.63 (0.12), residues: 1939 sheet: 0.12 (0.27), residues: 406 loop : -0.51 (0.16), residues: 1487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 39 TYR 0.008 0.001 TYR K 756 PHE 0.015 0.001 PHE L 59 TRP 0.007 0.001 TRP D 340 HIS 0.003 0.001 HIS C 73 Details of bonding type rmsd/Z covalent geometry : bond 0.00208 / 0.11 (31408) covalent geometry : angle 0.53192 / 0.29 (42349) hydrogen bonds : bond 0.16341 / 11.20 ( 1637) hydrogen bonds : angle 5.60205 / 3.92 ( 4602) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7664 Ramachandran restraints generated. 3832 Oldfield, 0 Emsley, 3832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7664 Ramachandran restraints generated. 3832 Oldfield, 0 Emsley, 3832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1111 residues out of total 3322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 1032 time to evaluate : 1.200 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: 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: A 59 GLN cc_start: 0.6655 (mm110) cc_final: 0.6201 (mm110) REVERT: A 192 ILE cc_start: 0.9271 (pt) cc_final: 0.8976 (mm) REVERT: A 375 PHE cc_start: 0.7668 (t80) cc_final: 0.7452 (t80) REVERT: B 53 TYR cc_start: 0.6985 (m-80) cc_final: 0.6651 (m-80) REVERT: B 132 MET cc_start: 0.8364 (ppp) cc_final: 0.7924 (ttp) REVERT: B 154 ASP cc_start: 0.8611 (t0) cc_final: 0.8155 (t0) REVERT: B 227 MET cc_start: 0.8390 (mmm) cc_final: 0.8186 (mmm) REVERT: B 283 MET cc_start: 0.9321 (mmm) cc_final: 0.8832 (tpp) REVERT: B 330 ILE cc_start: 0.9343 (mp) cc_final: 0.9020 (mm) REVERT: B 355 MET cc_start: 0.8382 (mmm) cc_final: 0.8168 (tpp) REVERT: C 123 MET cc_start: 0.8894 (mmm) cc_final: 0.8670 (tpp) REVERT: C 143 TYR cc_start: 0.6620 (m-10) cc_final: 0.6411 (m-10) REVERT: C 154 ASP cc_start: 0.7880 (t0) cc_final: 0.7618 (t0) REVERT: C 167 GLU cc_start: 0.6287 (tp30) cc_final: 0.6083 (tp30) REVERT: D 47 MET cc_start: 0.5636 (mmm) cc_final: 0.4979 (tpp) REVERT: D 59 GLN cc_start: 0.8699 (OUTLIER) cc_final: 0.8235 (tp-100) REVERT: D 76 ILE cc_start: 0.9419 (mt) cc_final: 0.9168 (mt) REVERT: D 123 MET cc_start: 0.7213 (mmm) cc_final: 0.6919 (mmm) REVERT: D 129 VAL cc_start: 0.8077 (m) cc_final: 0.7806 (m) REVERT: D 186 THR cc_start: 0.9173 (m) cc_final: 0.8533 (p) REVERT: D 201 VAL cc_start: 0.8939 (m) cc_final: 0.8675 (t) REVERT: D 304 THR cc_start: 0.8930 (p) cc_final: 0.8587 (t) REVERT: D 305 MET cc_start: 0.8496 (mmm) cc_final: 0.7976 (ttm) REVERT: F 230 ASP cc_start: 0.9007 (OUTLIER) cc_final: 0.8762 (t0) REVERT: F 234 GLU cc_start: 0.8347 (tt0) cc_final: 0.8115 (tm-30) REVERT: F 268 LYS cc_start: 0.5541 (tppt) cc_final: 0.5263 (tptt) REVERT: G 17 ASN cc_start: 0.6924 (t0) cc_final: 0.6468 (t0) REVERT: I 88 ASP cc_start: 0.5354 (m-30) cc_final: 0.5103 (m-30) REVERT: I 141 ARG cc_start: 0.7478 (mmt-90) cc_final: 0.7270 (tpp-160) REVERT: J 71 VAL cc_start: 0.8154 (OUTLIER) cc_final: 0.7874 (m) REVERT: J 164 TYR cc_start: 0.5638 (m-80) cc_final: 0.5434 (m-80) REVERT: J 324 ASP cc_start: 0.5976 (t0) cc_final: 0.5603 (t70) REVERT: J 379 GLU cc_start: 0.5993 (tm-30) cc_final: 0.5176 (tm-30) REVERT: J 435 MET cc_start: 0.7859 (tmm) cc_final: 0.7633 (tmm) REVERT: J 476 LEU cc_start: 0.8800 (tp) cc_final: 0.8534 (tt) REVERT: J 702 ILE cc_start: 0.9074 (mm) cc_final: 0.8841 (tp) REVERT: K 38 TYR cc_start: 0.7448 (m-80) cc_final: 0.7096 (m-10) REVERT: K 71 VAL cc_start: 0.7579 (OUTLIER) cc_final: 0.7356 (m) REVERT: K 142 TYR cc_start: 0.6520 (m-80) cc_final: 0.6309 (m-80) REVERT: K 304 THR cc_start: 0.8543 (t) cc_final: 0.8337 (t) REVERT: K 435 MET cc_start: 0.7689 (ttp) cc_final: 0.6298 (ttp) REVERT: K 446 THR cc_start: 0.7843 (OUTLIER) cc_final: 0.7524 (t) REVERT: K 534 LEU cc_start: 0.9199 (tp) cc_final: 0.8735 (tp) REVERT: K 619 ASN cc_start: 0.7004 (t0) cc_final: 0.6656 (t0) REVERT: K 665 THR cc_start: 0.8825 (t) cc_final: 0.8521 (m) REVERT: M 194 MET cc_start: 0.7099 (mmm) cc_final: 0.6767 (tpp) outliers start: 79 outliers final: 28 residues processed: 1084 average time/residue: 0.1996 time to fit residues: 340.4266 Evaluate side-chains 684 residues out of total 3322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 651 time to evaluate : 1.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 197 optimal weight: 4.9990 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 0.0000 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 0.8980 chunk 183 optimal weight: 0.8980 chunk 298 optimal weight: 1.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 246 GLN C 49 GLN C 353 GLN D 12 ASN D 263 GLN E 263 GLN F 210 GLN G 68 GLN H 17 ASN H 47 GLN I 107 HIS J 171 ASN J 251 HIS J 368 GLN J 419 GLN J 444 ASN J 492 HIS J 581 HIS K 65 HIS K 75 GLN K 187 ASN ** K 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 284 HIS K 347 ASN K 358 HIS K 437 ASN K 444 ASN K 589 ASN K 595 GLN ** K 666 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 691 HIS L 156 HIS M 146 ASN ** M 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.122160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.108693 restraints weight = 75090.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.109010 restraints weight = 56809.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.109243 restraints weight = 44297.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.109362 restraints weight = 41465.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.109565 restraints weight = 38978.945| |-----------------------------------------------------------------------------| r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.2638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 31408 Z= 0.197 Angle : 0.653 13.484 42349 Z= 0.337 Chirality : 0.044 0.160 4633 Planarity : 0.005 0.057 5495 Dihedral : 5.715 85.729 4229 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.41 % Favored : 95.56 % Rotamer: Outliers : 0.12 % Allowed : 3.25 % Favored : 96.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.11 % 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: 0.64 (0.14), residues: 3832 helix: 1.23 (0.12), residues: 1972 sheet: 0.14 (0.27), residues: 394 loop : -0.53 (0.16), residues: 1466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG K 780 TYR 0.021 0.002 TYR C 337 PHE 0.027 0.002 PHE K 764 TRP 0.015 0.002 TRP K 438 HIS 0.009 0.001 HIS K 65 Details of bonding type rmsd/Z covalent geometry : bond 0.00445 / 0.20 (31408) covalent geometry : angle 0.65322 / 0.34 (42349) hydrogen bonds : bond 0.05328 / 3.64 ( 1637) hydrogen bonds : angle 4.73737 / 3.35 ( 4602) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7664 Ramachandran restraints generated. 3832 Oldfield, 0 Emsley, 3832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7664 Ramachandran restraints generated. 3832 Oldfield, 0 Emsley, 3832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 809 residues out of total 3322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 805 time to evaluate : 1.148 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 157 ASP cc_start: 0.6977 (t0) cc_final: 0.6427 (t0) REVERT: A 325 MET cc_start: 0.8756 (mmt) cc_final: 0.8368 (mmt) REVERT: B 105 LEU cc_start: 0.9512 (mm) cc_final: 0.9239 (mp) REVERT: B 116 ARG cc_start: 0.8258 (ttm170) cc_final: 0.8003 (ttm170) REVERT: B 118 LYS cc_start: 0.9014 (mmmt) cc_final: 0.8579 (tppp) REVERT: B 154 ASP cc_start: 0.8625 (t0) cc_final: 0.8185 (t0) REVERT: B 227 MET cc_start: 0.8167 (mmm) cc_final: 0.7950 (mmm) REVERT: B 240 TYR cc_start: 0.8867 (t80) cc_final: 0.8568 (t80) REVERT: B 283 MET cc_start: 0.9395 (mmm) cc_final: 0.8999 (tpp) REVERT: B 330 ILE cc_start: 0.9446 (mp) cc_final: 0.9210 (mm) REVERT: C 44 MET cc_start: 0.7228 (mmm) cc_final: 0.6979 (tpp) REVERT: C 105 LEU cc_start: 0.9079 (mt) cc_final: 0.8610 (mt) REVERT: C 162 ASN cc_start: 0.8492 (t0) cc_final: 0.8089 (t0) REVERT: C 370 VAL cc_start: 0.9132 (t) cc_final: 0.8885 (t) REVERT: D 123 MET cc_start: 0.7892 (mmm) cc_final: 0.7033 (mmm) REVERT: D 129 VAL cc_start: 0.8725 (m) cc_final: 0.8184 (m) REVERT: D 176 MET cc_start: 0.8335 (tpp) cc_final: 0.7763 (ttm) REVERT: D 304 THR cc_start: 0.9420 (p) cc_final: 0.9009 (t) REVERT: E 248 LYS cc_start: 0.9028 (mmmm) cc_final: 0.8723 (mmmm) REVERT: E 254 ASP cc_start: 0.8032 (t0) cc_final: 0.7762 (t0) REVERT: G 8 MET cc_start: 0.5848 (mtp) cc_final: 0.5578 (mtp) REVERT: I 115 GLU cc_start: 0.8286 (tm-30) cc_final: 0.7722 (tm-30) REVERT: I 141 ARG cc_start: 0.7973 (mmt-90) cc_final: 0.7630 (tpp-160) REVERT: J 155 PHE cc_start: 0.8048 (m-10) cc_final: 0.7662 (m-80) REVERT: J 379 GLU cc_start: 0.6232 (tm-30) cc_final: 0.5323 (tm-30) REVERT: J 380 GLU cc_start: 0.7342 (mp0) cc_final: 0.6249 (mp0) REVERT: J 388 MET cc_start: 0.8005 (mpp) cc_final: 0.7692 (mpp) REVERT: J 483 GLU cc_start: 0.8136 (mt-10) cc_final: 0.7872 (mt-10) REVERT: J 508 TRP cc_start: 0.6851 (t-100) cc_final: 0.6243 (t-100) REVERT: J 570 LYS cc_start: 0.8016 (mmmt) cc_final: 0.7795 (mmmm) REVERT: J 702 ILE cc_start: 0.9218 (mm) cc_final: 0.8970 (tp) REVERT: K 38 TYR cc_start: 0.8135 (m-80) cc_final: 0.7411 (m-80) REVERT: K 170 GLU cc_start: 0.8694 (tp30) cc_final: 0.8308 (tp30) REVERT: K 304 THR cc_start: 0.9031 (t) cc_final: 0.8810 (t) REVERT: K 386 TYR cc_start: 0.8393 (t80) cc_final: 0.7976 (t80) REVERT: K 619 ASN cc_start: 0.8274 (t0) cc_final: 0.8062 (t0) REVERT: L 194 MET cc_start: 0.4700 (mmp) cc_final: 0.4094 (mmt) REVERT: M 70 MET cc_start: 0.5088 (mtm) cc_final: 0.4718 (mtm) outliers start: 4 outliers final: 2 residues processed: 807 average time/residue: 0.1848 time to fit residues: 238.2930 Evaluate side-chains 581 residues out of total 3322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 579 time to evaluate : 1.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 276 optimal weight: 1.9990 chunk 321 optimal weight: 0.0370 chunk 290 optimal weight: 0.9990 chunk 53 optimal weight: 0.8980 chunk 333 optimal weight: 0.9980 chunk 296 optimal weight: 1.9990 chunk 310 optimal weight: 0.7980 chunk 170 optimal weight: 0.7980 chunk 119 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 294 optimal weight: 0.5980 overall best weight: 0.6258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 246 GLN B 360 GLN C 353 GLN D 12 ASN J 97 HIS J 153 HIS ** J 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 444 ASN ** K 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 160 ASN ** K 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 358 HIS K 444 ASN K 581 HIS K 666 HIS M 51 GLN M 177 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.122037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.108363 restraints weight = 74859.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.109169 restraints weight = 57264.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.109092 restraints weight = 45819.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.109565 restraints weight = 42131.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.109747 restraints weight = 36002.476| |-----------------------------------------------------------------------------| r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.3117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 31408 Z= 0.149 Angle : 0.600 16.189 42349 Z= 0.308 Chirality : 0.042 0.149 4633 Planarity : 0.004 0.055 5495 Dihedral : 5.556 82.994 4229 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.12 % Favored : 95.85 % Rotamer: Outliers : 0.09 % Allowed : 3.58 % Favored : 96.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.11 % 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: 0.67 (0.14), residues: 3832 helix: 1.28 (0.12), residues: 1972 sheet: 0.24 (0.26), residues: 395 loop : -0.57 (0.16), residues: 1465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG K 403 TYR 0.015 0.001 TYR C 337 PHE 0.027 0.002 PHE K 84 TRP 0.013 0.001 TRP K 438 HIS 0.005 0.001 HIS F 276 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.15 (31408) covalent geometry : angle 0.60025 / 0.31 (42349) hydrogen bonds : bond 0.04884 / 3.37 ( 1637) hydrogen bonds : angle 4.52880 / 3.21 ( 4602) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7664 Ramachandran restraints generated. 3832 Oldfield, 0 Emsley, 3832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7664 Ramachandran restraints generated. 3832 Oldfield, 0 Emsley, 3832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 762 residues out of total 3322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 759 time to evaluate : 1.249 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 157 ASP cc_start: 0.6703 (t0) cc_final: 0.6270 (t0) REVERT: B 105 LEU cc_start: 0.9466 (mm) cc_final: 0.9226 (mp) REVERT: B 227 MET cc_start: 0.8188 (mmm) cc_final: 0.7915 (mmm) REVERT: B 240 TYR cc_start: 0.8938 (t80) cc_final: 0.8554 (t80) REVERT: B 283 MET cc_start: 0.9286 (mmm) cc_final: 0.8961 (tpp) REVERT: B 330 ILE cc_start: 0.9359 (mp) cc_final: 0.9079 (mm) REVERT: B 350 SER cc_start: 0.8841 (p) cc_final: 0.8636 (t) REVERT: B 360 GLN cc_start: 0.7482 (mt0) cc_final: 0.7185 (mt0) REVERT: C 81 ASP cc_start: 0.7566 (m-30) cc_final: 0.7116 (m-30) REVERT: C 105 LEU cc_start: 0.8948 (mt) cc_final: 0.8389 (mt) REVERT: C 350 SER cc_start: 0.8991 (m) cc_final: 0.8781 (m) REVERT: C 355 MET cc_start: 0.8801 (mmm) cc_final: 0.8439 (tpp) REVERT: D 83 GLU cc_start: 0.8178 (tm-30) cc_final: 0.7971 (tm-30) REVERT: D 123 MET cc_start: 0.7821 (mmm) cc_final: 0.7046 (mmm) REVERT: D 176 MET cc_start: 0.8373 (tpp) cc_final: 0.7600 (ttm) REVERT: D 303 THR cc_start: 0.8211 (m) cc_final: 0.7995 (m) REVERT: E 248 LYS cc_start: 0.8904 (mmmm) cc_final: 0.8625 (mmmm) REVERT: F 195 GLU cc_start: 0.4845 (OUTLIER) cc_final: 0.4101 (tt0) REVERT: G 8 MET cc_start: 0.6013 (mtp) cc_final: 0.5745 (mtp) REVERT: I 115 GLU cc_start: 0.8250 (tm-30) cc_final: 0.7789 (tm-30) REVERT: I 141 ARG cc_start: 0.8057 (mmt-90) cc_final: 0.7856 (tpp-160) REVERT: J 72 LYS cc_start: 0.7656 (pptt) cc_final: 0.7380 (pptt) REVERT: J 155 PHE cc_start: 0.7711 (m-10) cc_final: 0.7411 (m-80) REVERT: J 379 GLU cc_start: 0.6159 (tm-30) cc_final: 0.5280 (tm-30) REVERT: J 380 GLU cc_start: 0.7201 (mp0) cc_final: 0.6334 (mp0) REVERT: J 388 MET cc_start: 0.8035 (mpp) cc_final: 0.7661 (mpp) REVERT: J 435 MET cc_start: 0.8308 (tmm) cc_final: 0.7753 (tmm) REVERT: J 476 LEU cc_start: 0.8817 (tp) cc_final: 0.8585 (tt) REVERT: J 508 TRP cc_start: 0.6985 (t-100) cc_final: 0.6304 (t-100) REVERT: J 570 LYS cc_start: 0.8035 (mmmt) cc_final: 0.7682 (mmmm) REVERT: J 702 ILE cc_start: 0.9194 (mm) cc_final: 0.8952 (tp) REVERT: J 746 LEU cc_start: 0.6548 (mm) cc_final: 0.6338 (mm) REVERT: K 38 TYR cc_start: 0.8165 (m-80) cc_final: 0.7433 (m-10) REVERT: K 170 GLU cc_start: 0.8872 (tp30) cc_final: 0.8519 (tp30) REVERT: K 386 TYR cc_start: 0.8435 (t80) cc_final: 0.8146 (t80) REVERT: K 481 THR cc_start: 0.7725 (p) cc_final: 0.7444 (p) REVERT: K 619 ASN cc_start: 0.8216 (t0) cc_final: 0.7890 (t0) REVERT: K 750 ASP cc_start: 0.8704 (t70) cc_final: 0.8336 (t0) REVERT: L 46 GLU cc_start: 0.8527 (tm-30) cc_final: 0.8222 (tt0) REVERT: L 63 ASP cc_start: 0.5634 (t70) cc_final: 0.5344 (t70) REVERT: L 194 MET cc_start: 0.4701 (mmp) cc_final: 0.4148 (mmt) outliers start: 3 outliers final: 0 residues processed: 761 average time/residue: 0.1849 time to fit residues: 226.2896 Evaluate side-chains 578 residues out of total 3322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 577 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 244 optimal weight: 0.9990 chunk 109 optimal weight: 0.8980 chunk 374 optimal weight: 3.9990 chunk 200 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 chunk 170 optimal weight: 1.9990 chunk 176 optimal weight: 0.5980 chunk 307 optimal weight: 2.9990 chunk 376 optimal weight: 3.9990 chunk 243 optimal weight: 0.0770 chunk 198 optimal weight: 0.9980 overall best weight: 0.7138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 49 GLN C 92 ASN D 12 ASN D 275 HIS I 98 ASN I 107 HIS J 97 HIS ** J 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 292 ASN J 444 ASN K 75 GLN ** K 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 160 ASN ** K 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 358 HIS K 444 ASN K 576 HIS K 581 HIS K 789 GLN M 177 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.120607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.106968 restraints weight = 74431.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.107482 restraints weight = 51611.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.107777 restraints weight = 40363.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.108010 restraints weight = 34956.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.108094 restraints weight = 34429.689| |-----------------------------------------------------------------------------| r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.3431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 31408 Z= 0.158 Angle : 0.603 18.543 42349 Z= 0.308 Chirality : 0.042 0.151 4633 Planarity : 0.004 0.057 5495 Dihedral : 5.536 84.885 4229 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 0.09 % Allowed : 3.22 % Favored : 96.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.11 % 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: 0.58 (0.14), residues: 3832 helix: 1.22 (0.12), residues: 1969 sheet: 0.16 (0.26), residues: 400 loop : -0.63 (0.16), residues: 1463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K 281 TYR 0.016 0.001 TYR J 287 PHE 0.019 0.002 PHE J 195 TRP 0.017 0.001 TRP K 438 HIS 0.010 0.001 HIS K 581 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.16 (31408) covalent geometry : angle 0.60261 / 0.31 (42349) hydrogen bonds : bond 0.04781 / 3.29 ( 1637) hydrogen bonds : angle 4.54338 / 3.22 ( 4602) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7664 Ramachandran restraints generated. 3832 Oldfield, 0 Emsley, 3832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7664 Ramachandran restraints generated. 3832 Oldfield, 0 Emsley, 3832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 749 residues out of total 3322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 746 time to evaluate : 1.113 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 157 ASP cc_start: 0.6973 (t0) cc_final: 0.6478 (t0) REVERT: A 176 MET cc_start: 0.6586 (mpp) cc_final: 0.6232 (mpp) REVERT: B 105 LEU cc_start: 0.9427 (mm) cc_final: 0.9176 (mp) REVERT: B 123 MET cc_start: 0.7407 (mmm) cc_final: 0.6913 (mmm) REVERT: B 330 ILE cc_start: 0.9380 (mp) cc_final: 0.9125 (mm) REVERT: B 360 GLN cc_start: 0.7774 (mt0) cc_final: 0.7269 (mt0) REVERT: C 81 ASP cc_start: 0.7507 (m-30) cc_final: 0.7172 (m-30) REVERT: C 300 SER cc_start: 0.9178 (t) cc_final: 0.8800 (p) REVERT: C 355 MET cc_start: 0.8822 (mmm) cc_final: 0.8436 (tpp) REVERT: D 119 MET cc_start: 0.7877 (ttm) cc_final: 0.7588 (ttp) REVERT: D 176 MET cc_start: 0.8435 (tpp) cc_final: 0.7593 (ttm) REVERT: E 189 LYS cc_start: 0.6986 (tmtt) cc_final: 0.6667 (tptp) REVERT: E 248 LYS cc_start: 0.8863 (mmmm) cc_final: 0.8604 (mmmm) REVERT: E 254 ASP cc_start: 0.7942 (t0) cc_final: 0.7681 (t0) REVERT: G 8 MET cc_start: 0.5782 (mtp) cc_final: 0.4818 (mtp) REVERT: G 58 ASP cc_start: 0.5803 (m-30) cc_final: 0.5452 (m-30) REVERT: H 7 LYS cc_start: 0.7180 (mttt) cc_final: 0.6395 (mttt) REVERT: I 115 GLU cc_start: 0.8249 (tm-30) cc_final: 0.7706 (tm-30) REVERT: I 141 ARG cc_start: 0.8063 (mmt-90) cc_final: 0.7799 (tpp-160) REVERT: J 155 PHE cc_start: 0.7811 (m-10) cc_final: 0.7604 (m-80) REVERT: J 380 GLU cc_start: 0.7238 (mp0) cc_final: 0.6880 (mp0) REVERT: J 388 MET cc_start: 0.8023 (mpp) cc_final: 0.7576 (mpp) REVERT: J 476 LEU cc_start: 0.9101 (tp) cc_final: 0.8729 (tt) REVERT: J 508 TRP cc_start: 0.7253 (t-100) cc_final: 0.6659 (t-100) REVERT: J 528 MET cc_start: 0.8583 (mmp) cc_final: 0.8073 (mmm) REVERT: J 570 LYS cc_start: 0.8189 (mmmt) cc_final: 0.7860 (mmmm) REVERT: J 746 LEU cc_start: 0.6554 (mm) cc_final: 0.6349 (mm) REVERT: K 38 TYR cc_start: 0.8111 (m-80) cc_final: 0.7386 (m-10) REVERT: K 45 GLU cc_start: 0.7892 (pt0) cc_final: 0.7618 (pt0) REVERT: K 169 ARG cc_start: 0.8126 (mmm-85) cc_final: 0.7788 (mmm-85) REVERT: K 386 TYR cc_start: 0.8450 (t80) cc_final: 0.7959 (t80) REVERT: K 466 GLU cc_start: 0.7199 (mt-10) cc_final: 0.6882 (mt-10) REVERT: K 481 THR cc_start: 0.7725 (p) cc_final: 0.7498 (p) REVERT: K 619 ASN cc_start: 0.8272 (t0) cc_final: 0.7922 (t0) REVERT: K 750 ASP cc_start: 0.8650 (t70) cc_final: 0.8312 (t0) REVERT: K 799 MET cc_start: 0.7198 (mpp) cc_final: 0.6962 (mpp) REVERT: L 46 GLU cc_start: 0.8518 (tm-30) cc_final: 0.8237 (tt0) REVERT: L 63 ASP cc_start: 0.5487 (t70) cc_final: 0.5081 (t70) REVERT: L 194 MET cc_start: 0.4544 (mmp) cc_final: 0.4029 (mmt) outliers start: 3 outliers final: 1 residues processed: 749 average time/residue: 0.1875 time to fit residues: 226.8302 Evaluate side-chains 574 residues out of total 3322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 573 time to evaluate : 1.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 158 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 chunk 326 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 114 optimal weight: 1.9990 chunk 215 optimal weight: 6.9990 chunk 87 optimal weight: 0.9980 chunk 241 optimal weight: 2.9990 chunk 269 optimal weight: 2.9990 chunk 193 optimal weight: 3.9990 chunk 359 optimal weight: 2.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 137 GLN C 161 HIS C 353 GLN D 137 GLN D 161 HIS ** J 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 479 ASN K 75 GLN ** K 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 358 HIS K 444 ASN K 602 ASN ** K 666 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 692 GLN M 51 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.113516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.100241 restraints weight = 75892.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.100580 restraints weight = 56783.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.100597 restraints weight = 43796.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.100836 restraints weight = 39896.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.100978 restraints weight = 36809.550| |-----------------------------------------------------------------------------| r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.3955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.089 31408 Z= 0.281 Angle : 0.759 15.430 42349 Z= 0.390 Chirality : 0.047 0.244 4633 Planarity : 0.005 0.052 5495 Dihedral : 6.057 89.493 4229 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 0.06 % Allowed : 3.10 % Favored : 96.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.11 % 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: -0.08 (0.13), residues: 3832 helix: 0.75 (0.12), residues: 1968 sheet: -0.21 (0.25), residues: 430 loop : -1.06 (0.16), residues: 1434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 37 TYR 0.029 0.002 TYR L 74 PHE 0.036 0.003 PHE C 352 TRP 0.019 0.002 TRP K 438 HIS 0.011 0.002 HIS B 371 Details of bonding type rmsd/Z covalent geometry : bond 0.00648 / 0.28 (31408) covalent geometry : angle 0.75865 / 0.39 (42349) hydrogen bonds : bond 0.05477 / 3.75 ( 1637) hydrogen bonds : angle 4.91530 / 3.49 ( 4602) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7664 Ramachandran restraints generated. 3832 Oldfield, 0 Emsley, 3832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7664 Ramachandran restraints generated. 3832 Oldfield, 0 Emsley, 3832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 681 residues out of total 3322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 679 time to evaluate : 1.135 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 157 ASP cc_start: 0.7204 (t0) cc_final: 0.6527 (t0) REVERT: A 313 MET cc_start: 0.8561 (tpp) cc_final: 0.8320 (tpp) REVERT: B 82 MET cc_start: 0.8375 (tpp) cc_final: 0.8110 (tpp) REVERT: B 123 MET cc_start: 0.7407 (mmm) cc_final: 0.6906 (mmm) REVERT: B 176 MET cc_start: 0.8098 (mmt) cc_final: 0.7702 (mmt) REVERT: B 325 MET cc_start: 0.8484 (mmp) cc_final: 0.8072 (mmp) REVERT: B 330 ILE cc_start: 0.9492 (mp) cc_final: 0.9226 (mm) REVERT: B 360 GLN cc_start: 0.7806 (mt0) cc_final: 0.7364 (mt0) REVERT: C 82 MET cc_start: 0.8109 (mmm) cc_final: 0.7622 (mmm) REVERT: C 86 TRP cc_start: 0.9130 (m-10) cc_final: 0.8890 (m-10) REVERT: C 111 ASN cc_start: 0.8318 (m-40) cc_final: 0.7995 (m110) REVERT: C 300 SER cc_start: 0.9252 (t) cc_final: 0.8918 (p) REVERT: C 355 MET cc_start: 0.8834 (mmm) cc_final: 0.8536 (tpp) REVERT: D 61 LYS cc_start: 0.8760 (mmtm) cc_final: 0.8527 (mmtt) REVERT: D 305 MET cc_start: 0.9045 (tpp) cc_final: 0.8538 (ttm) REVERT: E 233 LYS cc_start: 0.7984 (ttpp) cc_final: 0.7766 (tttt) REVERT: E 248 LYS cc_start: 0.8943 (mmmm) cc_final: 0.8662 (mmmm) REVERT: E 254 ASP cc_start: 0.8084 (t0) cc_final: 0.7841 (t0) REVERT: G 58 ASP cc_start: 0.6352 (m-30) cc_final: 0.5861 (m-30) REVERT: I 115 GLU cc_start: 0.8369 (tm-30) cc_final: 0.7887 (tm-30) REVERT: J 237 ARG cc_start: 0.8188 (mmt180) cc_final: 0.7177 (mtp-110) REVERT: J 380 GLU cc_start: 0.7651 (mp0) cc_final: 0.7153 (mp0) REVERT: J 388 MET cc_start: 0.7952 (mpp) cc_final: 0.7379 (mpp) REVERT: J 508 TRP cc_start: 0.7505 (t-100) cc_final: 0.6984 (t-100) REVERT: J 515 MET cc_start: 0.8662 (mtm) cc_final: 0.8385 (mtp) REVERT: J 528 MET cc_start: 0.8639 (mmp) cc_final: 0.8309 (mmm) REVERT: K 38 TYR cc_start: 0.8076 (m-80) cc_final: 0.7113 (m-10) REVERT: K 170 GLU cc_start: 0.8648 (tp30) cc_final: 0.8424 (tp30) REVERT: K 177 THR cc_start: 0.9097 (m) cc_final: 0.8695 (p) REVERT: K 444 ASN cc_start: 0.7094 (t0) cc_final: 0.6830 (t0) REVERT: K 466 GLU cc_start: 0.6980 (mt-10) cc_final: 0.6764 (mt-10) REVERT: K 557 LEU cc_start: 0.8396 (tp) cc_final: 0.7995 (tp) REVERT: K 619 ASN cc_start: 0.8492 (t0) cc_final: 0.8228 (t0) REVERT: K 750 ASP cc_start: 0.8677 (t70) cc_final: 0.8332 (t0) REVERT: L 46 GLU cc_start: 0.8583 (tm-30) cc_final: 0.8287 (tt0) REVERT: L 194 MET cc_start: 0.4302 (mmp) cc_final: 0.3898 (mmt) outliers start: 2 outliers final: 0 residues processed: 680 average time/residue: 0.1757 time to fit residues: 194.2287 Evaluate side-chains 518 residues out of total 3322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 518 time to evaluate : 1.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 243 optimal weight: 0.7980 chunk 52 optimal weight: 0.7980 chunk 337 optimal weight: 0.2980 chunk 296 optimal weight: 0.9990 chunk 158 optimal weight: 0.9990 chunk 266 optimal weight: 0.8980 chunk 288 optimal weight: 0.9980 chunk 348 optimal weight: 0.5980 chunk 213 optimal weight: 0.9990 chunk 43 optimal weight: 0.9980 chunk 88 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 275 HIS F 276 HIS I 107 HIS I 146 GLN J 97 HIS J 172 GLN J 292 ASN J 482 ASN J 691 HIS ** K 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 358 HIS K 734 GLN M 51 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.117637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.104022 restraints weight = 74793.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.104797 restraints weight = 59043.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.104737 restraints weight = 46918.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.105172 restraints weight = 45664.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.105323 restraints weight = 36930.093| |-----------------------------------------------------------------------------| r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.4044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 31408 Z= 0.155 Angle : 0.632 15.944 42349 Z= 0.325 Chirality : 0.044 0.166 4633 Planarity : 0.004 0.058 5495 Dihedral : 5.780 86.601 4229 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 0.06 % Allowed : 2.17 % Favored : 97.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.11 % 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: 0.20 (0.14), residues: 3832 helix: 1.01 (0.12), residues: 1957 sheet: -0.10 (0.26), residues: 420 loop : -0.94 (0.16), residues: 1455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG K 23 TYR 0.033 0.002 TYR K 128 PHE 0.025 0.002 PHE C 352 TRP 0.024 0.002 TRP J 593 HIS 0.007 0.001 HIS J 691 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.16 (31408) covalent geometry : angle 0.63200 / 0.32 (42349) hydrogen bonds : bond 0.04968 / 3.42 ( 1637) hydrogen bonds : angle 4.62443 / 3.29 ( 4602) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7664 Ramachandran restraints generated. 3832 Oldfield, 0 Emsley, 3832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7664 Ramachandran restraints generated. 3832 Oldfield, 0 Emsley, 3832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 702 residues out of total 3322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 700 time to evaluate : 1.360 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: 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: A 157 ASP cc_start: 0.7039 (t0) cc_final: 0.6547 (t0) REVERT: B 75 ILE cc_start: 0.9290 (pt) cc_final: 0.8851 (mt) REVERT: B 82 MET cc_start: 0.8434 (tpp) cc_final: 0.8067 (tpp) REVERT: B 107 GLU cc_start: 0.7812 (tt0) cc_final: 0.7420 (tt0) REVERT: B 123 MET cc_start: 0.7179 (mmm) cc_final: 0.6908 (mmm) REVERT: B 166 TYR cc_start: 0.8937 (t80) cc_final: 0.8653 (t80) REVERT: B 330 ILE cc_start: 0.9524 (mp) cc_final: 0.9270 (mm) REVERT: C 111 ASN cc_start: 0.8150 (m-40) cc_final: 0.7818 (m110) REVERT: C 113 LYS cc_start: 0.9135 (tppt) cc_final: 0.8909 (mmmt) REVERT: C 300 SER cc_start: 0.9212 (t) cc_final: 0.8891 (p) REVERT: D 123 MET cc_start: 0.7633 (mmm) cc_final: 0.6800 (mmm) REVERT: D 136 ILE cc_start: 0.9124 (mm) cc_final: 0.8907 (mt) REVERT: E 233 LYS cc_start: 0.7951 (ttpp) cc_final: 0.7719 (tttt) REVERT: E 248 LYS cc_start: 0.8841 (mmmm) cc_final: 0.8599 (mmmm) REVERT: E 254 ASP cc_start: 0.8092 (t0) cc_final: 0.7756 (t0) REVERT: G 58 ASP cc_start: 0.6094 (m-30) cc_final: 0.5497 (m-30) REVERT: I 115 GLU cc_start: 0.8377 (tm-30) cc_final: 0.7766 (tm-30) REVERT: J 155 PHE cc_start: 0.7912 (m-10) cc_final: 0.7517 (m-80) REVERT: J 237 ARG cc_start: 0.8234 (mmt180) cc_final: 0.7068 (mtp-110) REVERT: J 380 GLU cc_start: 0.7251 (mp0) cc_final: 0.6705 (mp0) REVERT: J 388 MET cc_start: 0.7817 (mpp) cc_final: 0.7503 (mpp) REVERT: J 445 THR cc_start: 0.8539 (p) cc_final: 0.8142 (t) REVERT: J 476 LEU cc_start: 0.8863 (tp) cc_final: 0.8506 (tt) REVERT: J 508 TRP cc_start: 0.7314 (t-100) cc_final: 0.6750 (t-100) REVERT: J 515 MET cc_start: 0.8602 (mtm) cc_final: 0.8284 (mtp) REVERT: J 528 MET cc_start: 0.8560 (mmp) cc_final: 0.8259 (mmm) REVERT: J 746 LEU cc_start: 0.6828 (mm) cc_final: 0.6598 (mm) REVERT: K 33 LEU cc_start: 0.7201 (tp) cc_final: 0.7000 (tp) REVERT: K 38 TYR cc_start: 0.7962 (m-80) cc_final: 0.7081 (m-10) REVERT: K 90 MET cc_start: 0.7905 (mtp) cc_final: 0.7590 (mtp) REVERT: K 95 PHE cc_start: 0.7683 (m-80) cc_final: 0.7442 (m-10) REVERT: K 557 LEU cc_start: 0.8209 (tp) cc_final: 0.7979 (tp) REVERT: K 750 ASP cc_start: 0.8632 (t70) cc_final: 0.8284 (t0) REVERT: L 46 GLU cc_start: 0.8567 (tm-30) cc_final: 0.8290 (tt0) REVERT: L 63 ASP cc_start: 0.5943 (t70) cc_final: 0.5135 (t70) REVERT: L 194 MET cc_start: 0.4319 (mmp) cc_final: 0.3901 (mmt) outliers start: 2 outliers final: 0 residues processed: 702 average time/residue: 0.1795 time to fit residues: 205.3508 Evaluate side-chains 562 residues out of total 3322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 562 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 208 optimal weight: 0.6980 chunk 95 optimal weight: 0.6980 chunk 338 optimal weight: 0.9980 chunk 344 optimal weight: 1.9990 chunk 261 optimal weight: 1.9990 chunk 249 optimal weight: 0.2980 chunk 310 optimal weight: 0.4980 chunk 252 optimal weight: 0.8980 chunk 335 optimal weight: 1.9990 chunk 45 optimal weight: 0.5980 chunk 241 optimal weight: 0.5980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 49 GLN C 371 HIS J 97 HIS ** J 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 75 GLN ** K 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 358 HIS K 444 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.118201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.104580 restraints weight = 74640.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.105139 restraints weight = 53147.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.105223 restraints weight = 41711.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.105482 restraints weight = 39850.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.105532 restraints weight = 39376.397| |-----------------------------------------------------------------------------| r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.4128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 31408 Z= 0.142 Angle : 0.628 20.139 42349 Z= 0.320 Chirality : 0.043 0.166 4633 Planarity : 0.004 0.058 5495 Dihedral : 5.613 84.592 4229 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.11 % 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: 0.32 (0.14), residues: 3832 helix: 1.10 (0.12), residues: 1964 sheet: -0.07 (0.26), residues: 420 loop : -0.86 (0.16), residues: 1448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG M 82 TYR 0.017 0.001 TYR K 128 PHE 0.022 0.001 PHE L 189 TRP 0.023 0.002 TRP K 438 HIS 0.003 0.001 HIS B 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 (31408) covalent geometry : angle 0.62775 / 0.32 (42349) hydrogen bonds : bond 0.04822 / 3.33 ( 1637) hydrogen bonds : angle 4.53856 / 3.22 ( 4602) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7664 Ramachandran restraints generated. 3832 Oldfield, 0 Emsley, 3832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7664 Ramachandran restraints generated. 3832 Oldfield, 0 Emsley, 3832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 717 residues out of total 3322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 717 time to evaluate : 1.155 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 157 ASP cc_start: 0.6984 (t0) cc_final: 0.6465 (t0) REVERT: B 75 ILE cc_start: 0.9335 (pt) cc_final: 0.8858 (mt) REVERT: B 82 MET cc_start: 0.8454 (tpp) cc_final: 0.8171 (tpp) REVERT: B 107 GLU cc_start: 0.7874 (tt0) cc_final: 0.7441 (tt0) REVERT: B 123 MET cc_start: 0.7177 (mmm) cc_final: 0.6884 (mmm) REVERT: B 166 TYR cc_start: 0.8915 (t80) cc_final: 0.8686 (t80) REVERT: B 325 MET cc_start: 0.8455 (mmp) cc_final: 0.8042 (mmt) REVERT: B 330 ILE cc_start: 0.9417 (mp) cc_final: 0.9182 (mm) REVERT: C 81 ASP cc_start: 0.7272 (m-30) cc_final: 0.7035 (m-30) REVERT: C 86 TRP cc_start: 0.9158 (m-10) cc_final: 0.8926 (m-90) REVERT: C 111 ASN cc_start: 0.8010 (m-40) cc_final: 0.7742 (m110) REVERT: C 162 ASN cc_start: 0.8590 (t0) cc_final: 0.8133 (t0) REVERT: C 300 SER cc_start: 0.9134 (t) cc_final: 0.8827 (p) REVERT: D 59 GLN cc_start: 0.9045 (tp40) cc_final: 0.8648 (tp-100) REVERT: D 123 MET cc_start: 0.7655 (mmm) cc_final: 0.6988 (mmm) REVERT: D 176 MET cc_start: 0.8847 (ttm) cc_final: 0.7846 (ttm) REVERT: D 186 THR cc_start: 0.8883 (m) cc_final: 0.8492 (p) REVERT: E 254 ASP cc_start: 0.8043 (t0) cc_final: 0.7764 (t0) REVERT: G 23 GLU cc_start: 0.5910 (mm-30) cc_final: 0.5665 (mm-30) REVERT: G 58 ASP cc_start: 0.5928 (m-30) cc_final: 0.5694 (m-30) REVERT: I 115 GLU cc_start: 0.8410 (tm-30) cc_final: 0.7815 (tm-30) REVERT: J 72 LYS cc_start: 0.7840 (pptt) cc_final: 0.7443 (pptt) REVERT: J 102 LEU cc_start: 0.8435 (tp) cc_final: 0.8007 (tp) REVERT: J 116 THR cc_start: 0.9102 (t) cc_final: 0.8836 (m) REVERT: J 237 ARG cc_start: 0.8153 (mmt180) cc_final: 0.7005 (mtp-110) REVERT: J 380 GLU cc_start: 0.7231 (mp0) cc_final: 0.6786 (mp0) REVERT: J 388 MET cc_start: 0.7880 (mpp) cc_final: 0.7476 (mpp) REVERT: J 445 THR cc_start: 0.8622 (p) cc_final: 0.8220 (t) REVERT: J 476 LEU cc_start: 0.8885 (tp) cc_final: 0.8524 (tt) REVERT: J 508 TRP cc_start: 0.7304 (t-100) cc_final: 0.6754 (t-100) REVERT: J 515 MET cc_start: 0.8598 (mtm) cc_final: 0.8286 (mtp) REVERT: J 528 MET cc_start: 0.8511 (mmp) cc_final: 0.8252 (mmm) REVERT: J 746 LEU cc_start: 0.6784 (mm) cc_final: 0.6569 (mm) REVERT: K 38 TYR cc_start: 0.7972 (m-80) cc_final: 0.7206 (m-10) REVERT: K 90 MET cc_start: 0.8179 (mtp) cc_final: 0.7812 (mtp) REVERT: K 95 PHE cc_start: 0.7702 (m-80) cc_final: 0.7317 (m-10) REVERT: K 219 GLN cc_start: 0.8296 (pt0) cc_final: 0.8028 (pt0) REVERT: K 386 TYR cc_start: 0.8295 (t80) cc_final: 0.7864 (t80) REVERT: K 479 ASN cc_start: 0.9306 (m-40) cc_final: 0.8362 (t0) REVERT: K 750 ASP cc_start: 0.8588 (t70) cc_final: 0.8303 (t0) REVERT: L 46 GLU cc_start: 0.8539 (tm-30) cc_final: 0.8275 (tt0) REVERT: L 63 ASP cc_start: 0.6061 (t70) cc_final: 0.5530 (t70) REVERT: L 194 MET cc_start: 0.4316 (mmp) cc_final: 0.3999 (mmt) REVERT: M 70 MET cc_start: 0.5836 (mtp) cc_final: 0.5240 (mtm) REVERT: M 109 MET cc_start: 0.6559 (mmt) cc_final: 0.6219 (mmt) outliers start: 0 outliers final: 0 residues processed: 717 average time/residue: 0.1835 time to fit residues: 213.0383 Evaluate side-chains 572 residues out of total 3322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 572 time to evaluate : 1.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 222 optimal weight: 0.8980 chunk 250 optimal weight: 0.9990 chunk 349 optimal weight: 3.9990 chunk 87 optimal weight: 0.5980 chunk 49 optimal weight: 1.9990 chunk 86 optimal weight: 0.4980 chunk 373 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 159 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 144 optimal weight: 0.0980 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 49 GLN ** J 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 160 ASN ** K 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 358 HIS K 444 ASN K 486 GLN M 177 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.118286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.104703 restraints weight = 74666.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.105220 restraints weight = 61236.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.105794 restraints weight = 47504.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.106129 restraints weight = 42028.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.106169 restraints weight = 33907.023| |-----------------------------------------------------------------------------| r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.4241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 31408 Z= 0.149 Angle : 0.635 18.228 42349 Z= 0.323 Chirality : 0.043 0.178 4633 Planarity : 0.004 0.060 5495 Dihedral : 5.552 83.435 4229 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.11 % 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: 0.32 (0.14), residues: 3832 helix: 1.11 (0.12), residues: 1965 sheet: -0.03 (0.26), residues: 410 loop : -0.89 (0.16), residues: 1457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K 403 TYR 0.026 0.001 TYR J 194 PHE 0.038 0.001 PHE J 155 TRP 0.028 0.002 TRP A 86 HIS 0.015 0.001 HIS J 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.15 (31408) covalent geometry : angle 0.63492 / 0.32 (42349) hydrogen bonds : bond 0.04785 / 3.31 ( 1637) hydrogen bonds : angle 4.53364 / 3.22 ( 4602) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7664 Ramachandran restraints generated. 3832 Oldfield, 0 Emsley, 3832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7664 Ramachandran restraints generated. 3832 Oldfield, 0 Emsley, 3832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 695 residues out of total 3322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 695 time to evaluate : 1.294 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 157 ASP cc_start: 0.6820 (t0) cc_final: 0.6173 (t0) REVERT: B 75 ILE cc_start: 0.9338 (pt) cc_final: 0.8885 (mt) REVERT: B 82 MET cc_start: 0.8499 (tpp) cc_final: 0.8064 (tpp) REVERT: B 107 GLU cc_start: 0.7845 (tt0) cc_final: 0.7444 (tt0) REVERT: B 325 MET cc_start: 0.8449 (mmp) cc_final: 0.8098 (mmt) REVERT: B 330 ILE cc_start: 0.9358 (mp) cc_final: 0.9152 (mm) REVERT: C 111 ASN cc_start: 0.7903 (m-40) cc_final: 0.7674 (m110) REVERT: C 151 ILE cc_start: 0.9091 (tt) cc_final: 0.8876 (tt) REVERT: C 162 ASN cc_start: 0.8535 (t0) cc_final: 0.8086 (t0) REVERT: C 300 SER cc_start: 0.9091 (t) cc_final: 0.8804 (p) REVERT: C 350 SER cc_start: 0.8936 (m) cc_final: 0.8730 (m) REVERT: D 59 GLN cc_start: 0.9038 (tp40) cc_final: 0.8556 (tp-100) REVERT: D 117 GLU cc_start: 0.8214 (mm-30) cc_final: 0.7905 (mm-30) REVERT: D 123 MET cc_start: 0.7621 (mmm) cc_final: 0.7055 (mmm) REVERT: D 176 MET cc_start: 0.8932 (ttm) cc_final: 0.8441 (ttm) REVERT: D 186 THR cc_start: 0.8882 (m) cc_final: 0.8479 (p) REVERT: E 233 LYS cc_start: 0.8220 (ptmm) cc_final: 0.8005 (ptmt) REVERT: E 254 ASP cc_start: 0.8018 (t0) cc_final: 0.7752 (t0) REVERT: E 281 MET cc_start: 0.3292 (ppp) cc_final: 0.3007 (ppp) REVERT: F 195 GLU cc_start: 0.5594 (pm20) cc_final: 0.5121 (pm20) REVERT: G 58 ASP cc_start: 0.6069 (m-30) cc_final: 0.5746 (m-30) REVERT: I 112 LYS cc_start: 0.7564 (mmtm) cc_final: 0.7267 (mmtm) REVERT: J 72 LYS cc_start: 0.8132 (pptt) cc_final: 0.7789 (pptt) REVERT: J 92 MET cc_start: 0.8381 (mpp) cc_final: 0.8155 (mpp) REVERT: J 116 THR cc_start: 0.9059 (t) cc_final: 0.8824 (m) REVERT: J 237 ARG cc_start: 0.8167 (mmt180) cc_final: 0.7052 (mtp-110) REVERT: J 380 GLU cc_start: 0.7257 (mp0) cc_final: 0.6785 (mp0) REVERT: J 388 MET cc_start: 0.7927 (mpp) cc_final: 0.7491 (mpp) REVERT: J 445 THR cc_start: 0.8621 (p) cc_final: 0.8192 (t) REVERT: J 476 LEU cc_start: 0.8968 (tp) cc_final: 0.8631 (tt) REVERT: J 508 TRP cc_start: 0.7294 (t-100) cc_final: 0.6777 (t-100) REVERT: J 515 MET cc_start: 0.8616 (mtm) cc_final: 0.8272 (mtp) REVERT: J 528 MET cc_start: 0.8552 (mmp) cc_final: 0.8267 (mmm) REVERT: J 570 LYS cc_start: 0.8295 (mmmt) cc_final: 0.7939 (mmmm) REVERT: J 690 MET cc_start: 0.7281 (mmm) cc_final: 0.6986 (mmt) REVERT: J 746 LEU cc_start: 0.6718 (mm) cc_final: 0.6479 (mm) REVERT: K 38 TYR cc_start: 0.8118 (m-80) cc_final: 0.7388 (m-10) REVERT: K 90 MET cc_start: 0.8118 (mtp) cc_final: 0.7723 (mtp) REVERT: K 325 ASP cc_start: 0.7883 (m-30) cc_final: 0.7500 (m-30) REVERT: K 328 GLU cc_start: 0.6471 (mp0) cc_final: 0.5856 (mp0) REVERT: K 386 TYR cc_start: 0.8311 (t80) cc_final: 0.7849 (t80) REVERT: K 479 ASN cc_start: 0.9360 (m-40) cc_final: 0.8398 (t0) REVERT: K 536 GLU cc_start: 0.7752 (tp30) cc_final: 0.7484 (tp30) REVERT: K 539 MET cc_start: 0.7554 (mmm) cc_final: 0.7037 (mmm) REVERT: K 750 ASP cc_start: 0.8633 (t70) cc_final: 0.8308 (t0) REVERT: L 46 GLU cc_start: 0.8504 (tm-30) cc_final: 0.8101 (tt0) REVERT: L 63 ASP cc_start: 0.6321 (t70) cc_final: 0.5901 (t70) REVERT: L 194 MET cc_start: 0.4453 (mmp) cc_final: 0.4082 (mmt) REVERT: M 70 MET cc_start: 0.5995 (mtp) cc_final: 0.5441 (mtm) REVERT: M 109 MET cc_start: 0.6523 (mmt) cc_final: 0.6125 (mmt) REVERT: M 110 MET cc_start: 0.7461 (ttp) cc_final: 0.6594 (mtp) outliers start: 0 outliers final: 0 residues processed: 695 average time/residue: 0.1963 time to fit residues: 220.7344 Evaluate side-chains 564 residues out of total 3322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 564 time to evaluate : 1.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 351 optimal weight: 0.5980 chunk 164 optimal weight: 0.9990 chunk 154 optimal weight: 1.9990 chunk 181 optimal weight: 0.9980 chunk 334 optimal weight: 0.9980 chunk 329 optimal weight: 0.5980 chunk 237 optimal weight: 0.6980 chunk 300 optimal weight: 0.0770 chunk 235 optimal weight: 0.9980 chunk 283 optimal weight: 1.9990 chunk 242 optimal weight: 0.6980 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 246 GLN C 49 GLN ** J 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 444 ASN K 104 ASN ** K 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 288 GLN K 358 HIS K 444 ASN K 486 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.118734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.105169 restraints weight = 74532.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.105552 restraints weight = 51525.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.105719 restraints weight = 44450.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.106098 restraints weight = 37440.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.106237 restraints weight = 34160.497| |-----------------------------------------------------------------------------| r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.4314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 31408 Z= 0.141 Angle : 0.632 18.144 42349 Z= 0.322 Chirality : 0.043 0.187 4633 Planarity : 0.004 0.062 5495 Dihedral : 5.484 82.619 4229 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 0.03 % Allowed : 0.57 % Favored : 99.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.11 % 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: 0.37 (0.14), residues: 3832 helix: 1.17 (0.12), residues: 1953 sheet: -0.10 (0.26), residues: 427 loop : -0.87 (0.16), residues: 1452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG J 663 TYR 0.038 0.001 TYR J 194 PHE 0.037 0.001 PHE C 352 TRP 0.025 0.002 TRP K 438 HIS 0.010 0.001 HIS J 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.14 (31408) covalent geometry : angle 0.63202 / 0.32 (42349) hydrogen bonds : bond 0.04690 / 3.23 ( 1637) hydrogen bonds : angle 4.48609 / 3.19 ( 4602) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7664 Ramachandran restraints generated. 3832 Oldfield, 0 Emsley, 3832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7664 Ramachandran restraints generated. 3832 Oldfield, 0 Emsley, 3832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 695 residues out of total 3322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 694 time to evaluate : 1.278 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 MET cc_start: 0.8403 (ppp) cc_final: 0.6871 (ptm) REVERT: A 157 ASP cc_start: 0.6757 (t0) cc_final: 0.6142 (t0) REVERT: B 75 ILE cc_start: 0.9316 (pt) cc_final: 0.8918 (mt) REVERT: B 107 GLU cc_start: 0.7881 (tt0) cc_final: 0.7453 (tt0) REVERT: B 123 MET cc_start: 0.7233 (mmm) cc_final: 0.6914 (mmm) REVERT: B 193 LEU cc_start: 0.8699 (mm) cc_final: 0.8461 (mt) REVERT: B 325 MET cc_start: 0.8405 (mmp) cc_final: 0.8108 (mmt) REVERT: B 330 ILE cc_start: 0.9360 (mp) cc_final: 0.9125 (mm) REVERT: C 81 ASP cc_start: 0.7359 (m-30) cc_final: 0.7156 (m-30) REVERT: C 111 ASN cc_start: 0.8224 (m-40) cc_final: 0.7939 (m110) REVERT: C 162 ASN cc_start: 0.8533 (t0) cc_final: 0.8094 (t0) REVERT: C 300 SER cc_start: 0.9143 (t) cc_final: 0.8832 (p) REVERT: C 340 TRP cc_start: 0.9267 (t60) cc_final: 0.8596 (t60) REVERT: D 59 GLN cc_start: 0.9042 (tp40) cc_final: 0.8563 (tp-100) REVERT: D 117 GLU cc_start: 0.8270 (mm-30) cc_final: 0.7945 (mm-30) REVERT: D 123 MET cc_start: 0.7720 (mmm) cc_final: 0.7197 (mmm) REVERT: D 128 ASN cc_start: 0.7074 (t0) cc_final: 0.6867 (t0) REVERT: D 176 MET cc_start: 0.8996 (ttm) cc_final: 0.8490 (ttm) REVERT: D 186 THR cc_start: 0.8861 (m) cc_final: 0.8492 (p) REVERT: E 233 LYS cc_start: 0.8219 (ptmm) cc_final: 0.7952 (ptmt) REVERT: E 254 ASP cc_start: 0.8122 (t0) cc_final: 0.7828 (t0) REVERT: G 58 ASP cc_start: 0.6087 (m-30) cc_final: 0.5747 (m-30) REVERT: J 72 LYS cc_start: 0.8090 (pptt) cc_final: 0.7780 (pptt) REVERT: J 92 MET cc_start: 0.8248 (mpp) cc_final: 0.7855 (mpp) REVERT: J 116 THR cc_start: 0.9080 (t) cc_final: 0.8840 (m) REVERT: J 237 ARG cc_start: 0.8143 (mmt180) cc_final: 0.7054 (mtp-110) REVERT: J 380 GLU cc_start: 0.7228 (mp0) cc_final: 0.6835 (mp0) REVERT: J 388 MET cc_start: 0.7904 (mpp) cc_final: 0.7499 (mpp) REVERT: J 445 THR cc_start: 0.8621 (p) cc_final: 0.8230 (t) REVERT: J 476 LEU cc_start: 0.8975 (tp) cc_final: 0.8653 (tt) REVERT: J 508 TRP cc_start: 0.7298 (t-100) cc_final: 0.6755 (t-100) REVERT: J 515 MET cc_start: 0.8597 (mtm) cc_final: 0.8247 (mtp) REVERT: J 528 MET cc_start: 0.8527 (mmp) cc_final: 0.8269 (mmm) REVERT: J 570 LYS cc_start: 0.8371 (mmmt) cc_final: 0.8007 (mmmm) REVERT: J 690 MET cc_start: 0.7125 (mmm) cc_final: 0.6866 (mmm) REVERT: J 746 LEU cc_start: 0.6678 (mm) cc_final: 0.6472 (mm) REVERT: J 802 LYS cc_start: 0.3976 (mmtt) cc_final: 0.3769 (mmtt) REVERT: K 38 TYR cc_start: 0.8126 (m-80) cc_final: 0.7449 (m-10) REVERT: K 90 MET cc_start: 0.8225 (mtp) cc_final: 0.7974 (mtp) REVERT: K 148 SER cc_start: 0.9038 (p) cc_final: 0.8692 (p) REVERT: K 313 ILE cc_start: 0.8139 (pt) cc_final: 0.7850 (pt) REVERT: K 386 TYR cc_start: 0.8287 (t80) cc_final: 0.7847 (t80) REVERT: K 539 MET cc_start: 0.7699 (mmm) cc_final: 0.7327 (mmm) REVERT: K 750 ASP cc_start: 0.8696 (t70) cc_final: 0.8374 (t0) REVERT: L 46 GLU cc_start: 0.8476 (tm-30) cc_final: 0.8075 (tt0) REVERT: L 63 ASP cc_start: 0.6214 (t70) cc_final: 0.5855 (t70) REVERT: M 70 MET cc_start: 0.5704 (mtp) cc_final: 0.5168 (mtm) REVERT: M 194 MET cc_start: 0.6494 (tpp) cc_final: 0.6200 (mmp) outliers start: 1 outliers final: 0 residues processed: 695 average time/residue: 0.1961 time to fit residues: 221.8686 Evaluate side-chains 562 residues out of total 3322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 562 time to evaluate : 1.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 156 optimal weight: 1.9990 chunk 172 optimal weight: 0.9990 chunk 343 optimal weight: 2.9990 chunk 363 optimal weight: 0.0970 chunk 330 optimal weight: 0.7980 chunk 250 optimal weight: 0.8980 chunk 84 optimal weight: 0.9990 chunk 61 optimal weight: 0.9990 chunk 159 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 119 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 49 GLN ** J 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 444 ASN ** K 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 358 HIS K 444 ASN K 486 GLN K 686 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.117429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.104706 restraints weight = 76933.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.104707 restraints weight = 81932.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.105479 restraints weight = 67747.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.105646 restraints weight = 54264.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.105834 restraints weight = 46231.635| |-----------------------------------------------------------------------------| r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.4418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 31408 Z= 0.163 Angle : 0.657 17.714 42349 Z= 0.335 Chirality : 0.044 0.199 4633 Planarity : 0.004 0.062 5495 Dihedral : 5.540 83.053 4229 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.11 % 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: 0.29 (0.14), residues: 3832 helix: 1.10 (0.12), residues: 1960 sheet: -0.15 (0.26), residues: 432 loop : -0.90 (0.16), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG J 143 TYR 0.019 0.002 TYR J 310 PHE 0.035 0.002 PHE C 352 TRP 0.026 0.002 TRP K 438 HIS 0.007 0.001 HIS J 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.16 (31408) covalent geometry : angle 0.65698 / 0.34 (42349) hydrogen bonds : bond 0.04775 / 3.29 ( 1637) hydrogen bonds : angle 4.54795 / 3.23 ( 4602) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7664 Ramachandran restraints generated. 3832 Oldfield, 0 Emsley, 3832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7664 Ramachandran restraints generated. 3832 Oldfield, 0 Emsley, 3832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 688 residues out of total 3322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 688 time to evaluate : 1.242 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 GLU cc_start: 0.8253 (tp30) cc_final: 0.7746 (tm-30) REVERT: A 123 MET cc_start: 0.7028 (mmm) cc_final: 0.6821 (mmm) REVERT: A 157 ASP cc_start: 0.6533 (t0) cc_final: 0.5913 (t0) REVERT: B 75 ILE cc_start: 0.9302 (pt) cc_final: 0.8918 (mt) REVERT: B 107 GLU cc_start: 0.7865 (tt0) cc_final: 0.7425 (tt0) REVERT: B 123 MET cc_start: 0.7189 (mmm) cc_final: 0.6904 (mmm) REVERT: B 193 LEU cc_start: 0.8738 (mm) cc_final: 0.8481 (mt) REVERT: B 325 MET cc_start: 0.8378 (mmp) cc_final: 0.8047 (mmt) REVERT: B 330 ILE cc_start: 0.9405 (mp) cc_final: 0.9195 (mm) REVERT: C 82 MET cc_start: 0.8488 (tpt) cc_final: 0.8090 (mmm) REVERT: C 86 TRP cc_start: 0.9283 (m-10) cc_final: 0.9040 (m-90) REVERT: C 111 ASN cc_start: 0.7980 (m-40) cc_final: 0.7742 (m110) REVERT: C 162 ASN cc_start: 0.8600 (t0) cc_final: 0.8071 (t0) REVERT: C 300 SER cc_start: 0.9137 (t) cc_final: 0.8793 (p) REVERT: C 340 TRP cc_start: 0.9184 (t60) cc_final: 0.8533 (t60) REVERT: D 59 GLN cc_start: 0.9004 (tp40) cc_final: 0.8629 (tp-100) REVERT: D 117 GLU cc_start: 0.8273 (mm-30) cc_final: 0.7913 (mm-30) REVERT: D 123 MET cc_start: 0.7682 (mmm) cc_final: 0.7226 (mmm) REVERT: D 176 MET cc_start: 0.9042 (ttm) cc_final: 0.8576 (ttm) REVERT: D 186 THR cc_start: 0.8923 (m) cc_final: 0.8549 (p) REVERT: E 233 LYS cc_start: 0.8193 (ptmm) cc_final: 0.7867 (ptmt) REVERT: E 254 ASP cc_start: 0.7960 (t0) cc_final: 0.7671 (t0) REVERT: G 58 ASP cc_start: 0.6338 (m-30) cc_final: 0.6076 (m-30) REVERT: J 92 MET cc_start: 0.8245 (mpp) cc_final: 0.7954 (mpp) REVERT: J 116 THR cc_start: 0.9049 (t) cc_final: 0.8814 (m) REVERT: J 237 ARG cc_start: 0.8115 (mmt180) cc_final: 0.7100 (mtp-110) REVERT: J 380 GLU cc_start: 0.7304 (mp0) cc_final: 0.6863 (mp0) REVERT: J 388 MET cc_start: 0.7945 (mpp) cc_final: 0.7554 (mpp) REVERT: J 445 THR cc_start: 0.8754 (p) cc_final: 0.8335 (t) REVERT: J 476 LEU cc_start: 0.8949 (tp) cc_final: 0.8625 (tt) REVERT: J 508 TRP cc_start: 0.7289 (t-100) cc_final: 0.6879 (t-100) REVERT: J 515 MET cc_start: 0.8503 (mtm) cc_final: 0.8175 (mtp) REVERT: J 528 MET cc_start: 0.8585 (mmp) cc_final: 0.8301 (mmm) REVERT: J 570 LYS cc_start: 0.8398 (mmmt) cc_final: 0.8028 (mmmm) REVERT: J 690 MET cc_start: 0.7036 (mmm) cc_final: 0.6677 (mmm) REVERT: J 746 LEU cc_start: 0.6758 (mm) cc_final: 0.6514 (mm) REVERT: J 802 LYS cc_start: 0.4290 (mmtt) cc_final: 0.4074 (mmtt) REVERT: K 38 TYR cc_start: 0.8050 (m-80) cc_final: 0.7326 (m-10) REVERT: K 148 SER cc_start: 0.9043 (p) cc_final: 0.8623 (p) REVERT: K 357 MET cc_start: 0.7872 (mtp) cc_final: 0.6984 (ttm) REVERT: K 386 TYR cc_start: 0.8319 (t80) cc_final: 0.7873 (t80) REVERT: K 479 ASN cc_start: 0.9340 (m-40) cc_final: 0.8435 (t0) REVERT: K 539 MET cc_start: 0.7692 (mmm) cc_final: 0.7258 (mmm) REVERT: K 750 ASP cc_start: 0.8694 (t70) cc_final: 0.8372 (t0) REVERT: L 46 GLU cc_start: 0.8473 (tm-30) cc_final: 0.8068 (tt0) REVERT: M 70 MET cc_start: 0.5528 (mtp) cc_final: 0.4877 (mtm) REVERT: M 109 MET cc_start: 0.6336 (mmt) cc_final: 0.6026 (mmt) outliers start: 0 outliers final: 0 residues processed: 688 average time/residue: 0.1918 time to fit residues: 215.1938 Evaluate side-chains 552 residues out of total 3322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 552 time to evaluate : 1.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 343 optimal weight: 2.9990 chunk 187 optimal weight: 2.9990 chunk 256 optimal weight: 3.9990 chunk 196 optimal weight: 0.0980 chunk 104 optimal weight: 0.5980 chunk 49 optimal weight: 1.9990 chunk 126 optimal weight: 1.9990 chunk 379 optimal weight: 0.9990 chunk 22 optimal weight: 0.4980 chunk 370 optimal weight: 2.9990 chunk 151 optimal weight: 0.6980 overall best weight: 0.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 49 GLN ** J 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 444 ASN ** K 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 358 HIS K 444 ASN K 486 GLN K 686 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.118673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.105304 restraints weight = 74781.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.105804 restraints weight = 51122.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.105925 restraints weight = 39567.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.106213 restraints weight = 38382.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.106261 restraints weight = 36071.597| |-----------------------------------------------------------------------------| r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.4458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 31408 Z= 0.145 Angle : 0.645 17.977 42349 Z= 0.329 Chirality : 0.043 0.196 4633 Planarity : 0.004 0.064 5495 Dihedral : 5.474 82.302 4229 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.11 % 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: 0.33 (0.14), residues: 3832 helix: 1.14 (0.12), residues: 1957 sheet: -0.17 (0.26), residues: 424 loop : -0.86 (0.16), residues: 1451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG M 82 TYR 0.038 0.001 TYR J 194 PHE 0.033 0.001 PHE J 155 TRP 0.026 0.002 TRP K 438 HIS 0.008 0.001 HIS J 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.14 (31408) covalent geometry : angle 0.64471 / 0.33 (42349) hydrogen bonds : bond 0.04694 / 3.23 ( 1637) hydrogen bonds : angle 4.49188 / 3.20 ( 4602) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5441.26 seconds wall clock time: 94 minutes 53.15 seconds (5693.15 seconds total)