Starting phenix.real_space_refine on Sun Sep 13 01:33:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6znn_11318/09_2026/6znn_11318_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6znn_11318/09_2026/6znn_11318.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6znn_11318/09_2026/6znn_11318.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6znn_11318/09_2026/6znn_11318.map" model { file = "/net/cci-nas-00/data/ceres_data/6znn_11318/09_2026/6znn_11318_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6znn_11318/09_2026/6znn_11318_neut.cif" } resolution = 4.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.010 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 Zn 3 6.06 5 P 9 5.49 5 S 97 5.16 5 C 12313 2.51 5 N 3417 2.21 5 O 3618 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 47 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 19457 Number of models: 1 Model: "" Number of chains: 17 Chain: "G" Number of atoms: 2956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2956 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 19, 'TRANS': 350} Chain: "H" Number of atoms: 2885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2885 Classifications: {'peptide': 370} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 350} Chain: "I" Number of atoms: 2941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2941 Classifications: {'peptide': 370} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 19, 'TRANS': 350} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "J" Number of atoms: 2932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 379, 2932 Classifications: {'peptide': 379} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 24, 'TRANS': 354} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 14 Chain: "M" Number of atoms: 583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 583 Classifications: {'peptide': 75} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 69} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "S" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 340 Classifications: {'peptide': 68} Incomplete info: {'truncation_to_alanine': 68} Link IDs: {'TRANS': 67} Unresolved non-hydrogen bonds: 136 Unresolved non-hydrogen angles: 204 Unresolved non-hydrogen dihedrals: 68 Planarities with less than four sites: {'UNK:plan-1': 68} Unresolved non-hydrogen planarities: 68 Chain: "T" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 340 Classifications: {'peptide': 68} Incomplete info: {'truncation_to_alanine': 68} Link IDs: {'TRANS': 67} Unresolved non-hydrogen bonds: 136 Unresolved non-hydrogen angles: 204 Unresolved non-hydrogen dihedrals: 68 Planarities with less than four sites: {'UNK:plan-1': 68} Unresolved non-hydrogen planarities: 68 Chain: "U" Number of atoms: 1224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1224 Classifications: {'peptide': 167} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 12, 'TRANS': 154} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'HIS:plan': 1, 'ASP:plan': 3, 'ASN:plan1': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 25 Chain: "V" Number of atoms: 1260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1260 Classifications: {'peptide': 179} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PTRANS': 10, 'TRANS': 168} Unresolved non-hydrogen bonds: 125 Unresolved non-hydrogen angles: 152 Unresolved non-hydrogen dihedrals: 100 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 9, 'GLN:plan1': 1, 'ASN:plan1': 2, 'ASP:plan': 6, 'ARG:plan': 3, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 85 Chain: "X" Number of atoms: 465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 465 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 93} Link IDs: {'TRANS': 92} Unresolved non-hydrogen bonds: 186 Unresolved non-hydrogen angles: 279 Unresolved non-hydrogen dihedrals: 93 Planarities with less than four sites: {'UNK:plan-1': 93} Unresolved non-hydrogen planarities: 93 Chain: "Y" Number of atoms: 2956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 410, 2956 Classifications: {'peptide': 410} Incomplete info: {'truncation_to_alanine': 96} Link IDs: {'PTRANS': 30, 'TRANS': 379} Chain breaks: 2 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 335 Unresolved non-hydrogen angles: 425 Unresolved non-hydrogen dihedrals: 266 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'GLU:plan': 21, 'ASP:plan': 14, 'ARG:plan': 4, 'ASN:plan1': 5, 'TYR:plan': 2, 'PHE:plan': 3, 'GLN:plan1': 4, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 219 Chain: "x" Number of atoms: 460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 460 Classifications: {'peptide': 92} Incomplete info: {'truncation_to_alanine': 92} Link IDs: {'TRANS': 91} Unresolved non-hydrogen bonds: 184 Unresolved non-hydrogen angles: 276 Unresolved non-hydrogen dihedrals: 92 Planarities with less than four sites: {'UNK:plan-1': 92} Unresolved non-hydrogen planarities: 92 Chain: "G" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "Y" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 16189 SG CYS Y 33 81.546 41.291 50.527 1.00176.12 S ATOM 17746 SG CYS Y 287 82.674 38.608 52.763 1.00182.93 S ATOM 16324 SG CYS Y 51 112.896 30.834 68.620 1.00172.70 S ATOM 16468 SG CYS Y 70 112.797 27.626 71.431 1.00168.75 S ATOM 16509 SG CYS Y 76 121.782 39.737 72.509 1.00177.86 S ATOM 16664 SG CYS Y 114 125.834 42.054 72.654 1.00177.90 S Time building chain proxies: 3.80, per 1000 atoms: 0.20 Number of scatterers: 19457 At special positions: 0 Unit cell: (171.52, 119.26, 176.88, 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) Zn 3 29.99 S 97 16.00 P 9 15.00 O 3618 8.00 N 3417 7.00 C 12313 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: 1.64 Conformation dependent library (CDL) restraints added in 765.2 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN Y 501 " pdb="ZN ZN Y 501 " - pdb=" SG CYS Y 287 " pdb="ZN ZN Y 501 " - pdb=" SG CYS Y 33 " pdb=" ZN Y 502 " pdb="ZN ZN Y 502 " - pdb=" SG CYS Y 51 " pdb="ZN ZN Y 502 " - pdb=" SG CYS Y 70 " pdb=" ZN Y 503 " pdb="ZN ZN Y 503 " - pdb=" SG CYS Y 114 " pdb="ZN ZN Y 503 " - pdb=" SG CYS Y 76 " 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4970 Finding SS restraints... Secondary structure from input PDB file: 86 helices and 38 sheets defined 49.0% alpha, 13.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.46 Creating SS restraints... Processing helix chain 'G' and resid 59 through 65 Processing helix chain 'G' and resid 82 through 95 removed outlier: 3.580A pdb=" N TYR G 94 " --> pdb=" O TRP G 90 " (cutoff:3.500A) Processing helix chain 'G' and resid 117 through 131 removed outlier: 3.779A pdb=" N ARG G 121 " --> pdb=" O PRO G 117 " (cutoff:3.500A) Processing helix chain 'G' and resid 141 through 151 removed outlier: 3.868A pdb=" N LEU G 145 " --> pdb=" O MET G 141 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N TYR G 148 " --> pdb=" O VAL G 144 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N THR G 150 " --> pdb=" O SER G 146 " (cutoff:3.500A) Processing helix chain 'G' and resid 177 through 180 removed outlier: 3.746A pdb=" N ILE G 180 " --> pdb=" O PRO G 177 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 177 through 180' Processing helix chain 'G' and resid 186 through 202 Processing helix chain 'G' and resid 209 through 221 removed outlier: 3.823A pdb=" N ILE G 213 " --> pdb=" O SER G 209 " (cutoff:3.500A) Processing helix chain 'G' and resid 227 through 234 removed outlier: 3.610A pdb=" N THR G 233 " --> pdb=" O GLN G 229 " (cutoff:3.500A) Processing helix chain 'G' and resid 253 through 258 Processing helix chain 'G' and resid 259 through 263 Processing helix chain 'G' and resid 274 through 286 removed outlier: 3.573A pdb=" N VAL G 280 " --> pdb=" O HIS G 276 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N SER G 286 " --> pdb=" O ALA G 282 " (cutoff:3.500A) Processing helix chain 'G' and resid 287 through 289 No H-bonds generated for 'chain 'G' and resid 287 through 289' Processing helix chain 'G' and resid 290 through 297 Processing helix chain 'G' and resid 302 through 306 removed outlier: 3.784A pdb=" N THR G 305 " --> pdb=" O GLY G 302 " (cutoff:3.500A) Processing helix chain 'G' and resid 309 through 322 removed outlier: 3.529A pdb=" N LYS G 319 " --> pdb=" O LEU G 315 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LYS G 320 " --> pdb=" O SER G 316 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU G 321 " --> pdb=" O GLU G 317 " (cutoff:3.500A) Processing helix chain 'G' and resid 338 through 350 Processing helix chain 'G' and resid 352 through 357 Processing helix chain 'G' and resid 360 through 367 Processing helix chain 'G' and resid 367 through 375 removed outlier: 4.366A pdb=" N ILE G 371 " --> pdb=" O GLY G 367 " (cutoff:3.500A) Processing helix chain 'H' and resid 55 through 61 Processing helix chain 'H' and resid 78 through 91 Processing helix chain 'H' and resid 112 through 126 removed outlier: 3.974A pdb=" N ARG H 116 " --> pdb=" O PRO H 112 " (cutoff:3.500A) Processing helix chain 'H' and resid 137 through 144 removed outlier: 3.702A pdb=" N LEU H 142 " --> pdb=" O ALA H 138 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N TYR H 143 " --> pdb=" O VAL H 139 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ALA H 144 " --> pdb=" O LEU H 140 " (cutoff:3.500A) Processing helix chain 'H' and resid 172 through 175 Processing helix chain 'H' and resid 181 through 197 removed outlier: 3.606A pdb=" N LYS H 191 " --> pdb=" O ASP H 187 " (cutoff:3.500A) Processing helix chain 'H' and resid 202 through 217 Processing helix chain 'H' and resid 222 through 233 Processing helix chain 'H' and resid 252 through 257 Processing helix chain 'H' and resid 258 through 263 removed outlier: 4.268A pdb=" N PHE H 262 " --> pdb=" O PRO H 258 " (cutoff:3.500A) Processing helix chain 'H' and resid 273 through 285 removed outlier: 3.629A pdb=" N THR H 278 " --> pdb=" O ILE H 274 " (cutoff:3.500A) Processing helix chain 'H' and resid 289 through 296 Processing helix chain 'H' and resid 301 through 305 removed outlier: 3.733A pdb=" N THR H 304 " --> pdb=" O GLY H 301 " (cutoff:3.500A) Processing helix chain 'H' and resid 308 through 321 removed outlier: 3.510A pdb=" N ARG H 312 " --> pdb=" O GLY H 308 " (cutoff:3.500A) Processing helix chain 'H' and resid 337 through 349 removed outlier: 3.542A pdb=" N GLY H 342 " --> pdb=" O SER H 338 " (cutoff:3.500A) Processing helix chain 'H' and resid 350 through 355 removed outlier: 3.500A pdb=" N GLN H 354 " --> pdb=" O THR H 351 " (cutoff:3.500A) Processing helix chain 'H' and resid 359 through 366 Processing helix chain 'H' and resid 368 through 373 removed outlier: 4.126A pdb=" N ARG H 372 " --> pdb=" O SER H 368 " (cutoff:3.500A) Processing helix chain 'I' and resid 59 through 65 removed outlier: 3.528A pdb=" N HIS I 65 " --> pdb=" O LYS I 61 " (cutoff:3.500A) Processing helix chain 'I' and resid 82 through 94 removed outlier: 3.537A pdb=" N TYR I 94 " --> pdb=" O TRP I 90 " (cutoff:3.500A) Processing helix chain 'I' and resid 117 through 131 removed outlier: 3.596A pdb=" N ARG I 121 " --> pdb=" O PRO I 117 " (cutoff:3.500A) Processing helix chain 'I' and resid 142 through 151 removed outlier: 3.691A pdb=" N LEU I 147 " --> pdb=" O ALA I 143 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N TYR I 148 " --> pdb=" O VAL I 144 " (cutoff:3.500A) Processing helix chain 'I' and resid 186 through 202 Processing helix chain 'I' and resid 209 through 221 removed outlier: 3.842A pdb=" N ILE I 213 " --> pdb=" O SER I 209 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL I 214 " --> pdb=" O GLU I 210 " (cutoff:3.500A) Processing helix chain 'I' and resid 227 through 234 removed outlier: 3.815A pdb=" N ASP I 231 " --> pdb=" O ASN I 227 " (cutoff:3.500A) Processing helix chain 'I' and resid 253 through 258 Processing helix chain 'I' and resid 259 through 263 Processing helix chain 'I' and resid 274 through 286 removed outlier: 3.593A pdb=" N LEU I 279 " --> pdb=" O ILE I 275 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SER I 286 " --> pdb=" O ALA I 282 " (cutoff:3.500A) Processing helix chain 'I' and resid 287 through 296 removed outlier: 4.605A pdb=" N ARG I 292 " --> pdb=" O MET I 288 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N THR I 293 " --> pdb=" O ASP I 289 " (cutoff:3.500A) Processing helix chain 'I' and resid 309 through 322 removed outlier: 3.505A pdb=" N SER I 316 " --> pdb=" O ASP I 312 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LYS I 320 " --> pdb=" O SER I 316 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LEU I 321 " --> pdb=" O GLU I 317 " (cutoff:3.500A) Processing helix chain 'I' and resid 338 through 350 removed outlier: 3.504A pdb=" N GLY I 344 " --> pdb=" O THR I 340 " (cutoff:3.500A) Processing helix chain 'I' and resid 352 through 357 Processing helix chain 'I' and resid 360 through 367 removed outlier: 3.570A pdb=" N GLY I 367 " --> pdb=" O TYR I 363 " (cutoff:3.500A) Processing helix chain 'I' and resid 369 through 375 Processing helix chain 'J' and resid 60 through 78 Processing helix chain 'J' and resid 98 through 112 Processing helix chain 'J' and resid 122 through 132 removed outlier: 3.584A pdb=" N LEU J 129 " --> pdb=" O LEU J 125 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N THR J 130 " --> pdb=" O MET J 126 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N LEU J 131 " --> pdb=" O ALA J 127 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLY J 132 " --> pdb=" O LEU J 128 " (cutoff:3.500A) Processing helix chain 'J' and resid 158 through 161 Processing helix chain 'J' and resid 167 through 182 Processing helix chain 'J' and resid 203 through 214 Processing helix chain 'J' and resid 219 through 232 removed outlier: 3.564A pdb=" N LYS J 225 " --> pdb=" O THR J 221 " (cutoff:3.500A) Processing helix chain 'J' and resid 259 through 266 removed outlier: 3.769A pdb=" N ARG J 263 " --> pdb=" O LEU J 259 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ASP J 264 " --> pdb=" O GLY J 260 " (cutoff:3.500A) Processing helix chain 'J' and resid 267 through 272 removed outlier: 4.118A pdb=" N PHE J 271 " --> pdb=" O VAL J 267 " (cutoff:3.500A) Processing helix chain 'J' and resid 279 through 291 removed outlier: 4.236A pdb=" N ILE J 284 " --> pdb=" O VAL J 280 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N LEU J 285 " --> pdb=" O ALA J 281 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLN J 290 " --> pdb=" O ASP J 286 " (cutoff:3.500A) Processing helix chain 'J' and resid 295 through 302 Processing helix chain 'J' and resid 307 through 312 removed outlier: 3.630A pdb=" N LEU J 312 " --> pdb=" O THR J 309 " (cutoff:3.500A) Processing helix chain 'J' and resid 314 through 329 removed outlier: 3.586A pdb=" N ARG J 318 " --> pdb=" O GLY J 314 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLU J 328 " --> pdb=" O ARG J 324 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LYS J 329 " --> pdb=" O TYR J 325 " (cutoff:3.500A) Processing helix chain 'J' and resid 329 through 334 removed outlier: 4.355A pdb=" N LYS J 334 " --> pdb=" O PRO J 330 " (cutoff:3.500A) Processing helix chain 'J' and resid 349 through 352 Processing helix chain 'J' and resid 353 through 363 removed outlier: 3.634A pdb=" N GLY J 358 " --> pdb=" O ALA J 354 " (cutoff:3.500A) Processing helix chain 'J' and resid 364 through 372 removed outlier: 4.042A pdb=" N SER J 370 " --> pdb=" O ASP J 366 " (cutoff:3.500A) Processing helix chain 'J' and resid 375 through 382 Processing helix chain 'M' and resid 4 through 9 removed outlier: 3.584A pdb=" N ASP M 8 " --> pdb=" O PRO M 4 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N LEU M 9 " --> pdb=" O LYS M 5 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 4 through 9' Processing helix chain 'M' and resid 51 through 60 removed outlier: 3.504A pdb=" N ASP M 57 " --> pdb=" O ASN M 53 " (cutoff:3.500A) Processing helix chain 'S' and resid 2 through 68 Processing helix chain 'T' and resid 2 through 68 removed outlier: 4.162A pdb=" N UNK T 27 " --> pdb=" O UNK T 23 " (cutoff:3.500A) Processing helix chain 'U' and resid 65 through 70 Processing helix chain 'U' and resid 161 through 171 removed outlier: 3.927A pdb=" N MET U 168 " --> pdb=" O LEU U 164 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N LYS U 169 " --> pdb=" O ASP U 165 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ILE U 170 " --> pdb=" O PHE U 166 " (cutoff:3.500A) Processing helix chain 'V' and resid 161 through 175 removed outlier: 4.141A pdb=" N ILE V 166 " --> pdb=" O GLN V 162 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ASP V 167 " --> pdb=" O GLU V 163 " (cutoff:3.500A) Processing helix chain 'X' and resid 132 through 221 removed outlier: 3.929A pdb=" N UNK X 148 " --> pdb=" O UNK X 144 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N UNK X 154 " --> pdb=" O UNK X 150 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N UNK X 161 " --> pdb=" O UNK X 157 " (cutoff:3.500A) Processing helix chain 'Y' and resid 59 through 67 Processing helix chain 'Y' and resid 117 through 122 removed outlier: 4.373A pdb=" N VAL Y 121 " --> pdb=" O THR Y 117 " (cutoff:3.500A) Processing helix chain 'Y' and resid 141 through 172 removed outlier: 3.517A pdb=" N GLU Y 158 " --> pdb=" O LEU Y 154 " (cutoff:3.500A) Processing helix chain 'Y' and resid 251 through 257 Processing helix chain 'Y' and resid 308 through 312 Processing helix chain 'Y' and resid 446 through 452 Processing helix chain 'x' and resid 132 through 222 removed outlier: 4.129A pdb=" N UNK x 167 " --> pdb=" O UNK x 163 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'G' and resid 33 through 36 Processing sheet with id=AA2, first strand: chain 'G' and resid 57 through 58 Processing sheet with id=AA3, first strand: chain 'G' and resid 75 through 76 Processing sheet with id=AA4, first strand: chain 'G' and resid 174 through 175 Processing sheet with id=AA5, first strand: chain 'G' and resid 174 through 175 removed outlier: 6.121A pdb=" N VAL G 156 " --> pdb=" O VAL G 299 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N SER G 301 " --> pdb=" O VAL G 156 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N LEU G 158 " --> pdb=" O SER G 301 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N ILE G 298 " --> pdb=" O SER G 331 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N LEU G 300 " --> pdb=" O PRO G 333 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'G' and resid 240 through 242 Processing sheet with id=AA7, first strand: chain 'H' and resid 29 through 32 removed outlier: 3.677A pdb=" N PHE H 31 " --> pdb=" O CYS H 17 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N LEU H 8 " --> pdb=" O LEU H 104 " (cutoff:3.500A) removed outlier: 8.484A pdb=" N THR H 106 " --> pdb=" O LEU H 8 " (cutoff:3.500A) removed outlier: 8.205A pdb=" N VAL H 10 " --> pdb=" O THR H 106 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N TYR H 133 " --> pdb=" O VAL H 103 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ILE H 357 " --> pdb=" O MET H 132 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 53 through 54 removed outlier: 3.576A pdb=" N VAL H 35 " --> pdb=" O LYS H 68 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ARG H 37 " --> pdb=" O THR H 66 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 71 through 72 Processing sheet with id=AB1, first strand: chain 'H' and resid 169 through 170 Processing sheet with id=AB2, first strand: chain 'H' and resid 169 through 170 removed outlier: 3.612A pdb=" N VAL H 152 " --> pdb=" O VAL H 163 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ILE H 165 " --> pdb=" O GLY H 150 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N ILE H 151 " --> pdb=" O VAL H 298 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N THR H 297 " --> pdb=" O ILE H 330 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 239 through 241 Processing sheet with id=AB4, first strand: chain 'I' and resid 33 through 36 removed outlier: 3.845A pdb=" N TYR I 33 " --> pdb=" O ALA I 23 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE I 21 " --> pdb=" O PHE I 35 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N THR I 111 " --> pdb=" O ILE I 14 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'I' and resid 57 through 58 Processing sheet with id=AB6, first strand: chain 'I' and resid 75 through 76 Processing sheet with id=AB7, first strand: chain 'I' and resid 181 through 183 removed outlier: 6.231A pdb=" N VAL I 156 " --> pdb=" O VAL I 299 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N SER I 301 " --> pdb=" O VAL I 156 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N LEU I 158 " --> pdb=" O SER I 301 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 240 through 242 Processing sheet with id=AB9, first strand: chain 'I' and resid 329 through 331 Processing sheet with id=AC1, first strand: chain 'J' and resid 37 through 40 removed outlier: 6.979A pdb=" N VAL J 16 " --> pdb=" O VAL J 90 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N ILE J 92 " --> pdb=" O VAL J 16 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ILE J 18 " --> pdb=" O ILE J 92 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'J' and resid 42 through 43 Processing sheet with id=AC3, first strand: chain 'J' and resid 155 through 156 Processing sheet with id=AC4, first strand: chain 'J' and resid 155 through 156 removed outlier: 3.858A pdb=" N VAL J 138 " --> pdb=" O LEU J 149 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N CYS J 141 " --> pdb=" O ILE J 306 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'J' and resid 185 through 186 Processing sheet with id=AC6, first strand: chain 'U' and resid 23 through 25 Processing sheet with id=AC7, first strand: chain 'U' and resid 48 through 49 Processing sheet with id=AC8, first strand: chain 'U' and resid 88 through 90 Processing sheet with id=AC9, first strand: chain 'U' and resid 141 through 143 Processing sheet with id=AD1, first strand: chain 'V' and resid 8 through 10 Processing sheet with id=AD2, first strand: chain 'V' and resid 15 through 17 removed outlier: 7.307A pdb=" N LYS V 21 " --> pdb=" O VAL V 42 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ILE V 41 " --> pdb=" O VAL V 63 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N VAL V 62 " --> pdb=" O ILE V 93 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N PHE V 92 " --> pdb=" O VAL V 110 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N HIS V 109 " --> pdb=" O ILE V 128 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N LYS V 127 " --> pdb=" O PHE V 146 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N VAL V 145 " --> pdb=" O SER V 154 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'V' and resid 35 through 36 removed outlier: 7.755A pdb=" N VAL V 35 " --> pdb=" O VAL V 57 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'V' and resid 68 through 69 removed outlier: 6.370A pdb=" N VAL V 68 " --> pdb=" O VAL V 99 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N VAL V 98 " --> pdb=" O ILE V 116 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N VAL V 115 " --> pdb=" O LEU V 134 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'V' and resid 73 through 74 removed outlier: 3.647A pdb=" N ALA V 81 " --> pdb=" O LYS V 74 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'V' and resid 121 through 122 removed outlier: 7.778A pdb=" N VAL V 121 " --> pdb=" O VAL V 140 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'Y' and resid 21 through 22 removed outlier: 5.083A pdb=" N HIS Y 457 " --> pdb=" O LEU Y 13 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'Y' and resid 57 through 58 removed outlier: 3.954A pdb=" N HIS Y 49 " --> pdb=" O MET Y 58 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N SER Y 281 " --> pdb=" O GLU Y 45 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASP Y 47 " --> pdb=" O LYS Y 279 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N LYS Y 279 " --> pdb=" O ASP Y 47 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N HIS Y 49 " --> pdb=" O LEU Y 277 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N LEU Y 277 " --> pdb=" O HIS Y 49 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'Y' and resid 69 through 74 removed outlier: 4.298A pdb=" N LYS Y 274 " --> pdb=" O CYS Y 70 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'Y' and resid 84 through 86 Processing sheet with id=AE2, first strand: chain 'Y' and resid 316 through 317 926 hydrogen bonds defined for protein. 2592 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: 3.61 Time building geometry restraints manager: 2.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3716 1.33 - 1.45: 4525 1.45 - 1.58: 11434 1.58 - 1.70: 14 1.70 - 1.82: 145 Bond restraints: 19834 Sorted by residual: bond pdb=" C4 ADP G 800 " pdb=" C5 ADP G 800 " ideal model delta sigma weight residual 1.490 1.383 0.107 2.00e-02 2.50e+03 2.88e+01 bond pdb=" C4 ADP I 800 " pdb=" C5 ADP I 800 " ideal model delta sigma weight residual 1.490 1.383 0.107 2.00e-02 2.50e+03 2.85e+01 bond pdb=" C4 ADP J 800 " pdb=" C5 ADP J 800 " ideal model delta sigma weight residual 1.490 1.383 0.107 2.00e-02 2.50e+03 2.84e+01 bond pdb=" N ILE Y 321 " pdb=" CA ILE Y 321 " ideal model delta sigma weight residual 1.456 1.496 -0.040 8.70e-03 1.32e+04 2.08e+01 bond pdb=" N VAL V 140 " pdb=" CA VAL V 140 " ideal model delta sigma weight residual 1.456 1.496 -0.040 8.70e-03 1.32e+04 2.07e+01 ... (remaining 19829 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.59: 23039 2.59 - 5.17: 3791 5.17 - 7.76: 151 7.76 - 10.35: 11 10.35 - 12.93: 2 Bond angle restraints: 26994 Sorted by residual: angle pdb=" N PRO Y 438 " pdb=" CA PRO Y 438 " pdb=" CB PRO Y 438 " ideal model delta sigma weight residual 103.30 110.04 -6.74 8.00e-01 1.56e+00 7.09e+01 angle pdb=" PB ATP H 401 " pdb=" O3B ATP H 401 " pdb=" PG ATP H 401 " ideal model delta sigma weight residual 139.87 132.11 7.76 1.00e+00 1.00e+00 6.01e+01 angle pdb=" PA ATP H 401 " pdb=" O3A ATP H 401 " pdb=" PB ATP H 401 " ideal model delta sigma weight residual 136.83 129.79 7.04 1.00e+00 1.00e+00 4.96e+01 angle pdb=" N PRO Y 447 " pdb=" CA PRO Y 447 " pdb=" CB PRO Y 447 " ideal model delta sigma weight residual 103.25 110.16 -6.91 1.05e+00 9.07e-01 4.33e+01 angle pdb=" N PRO Y 441 " pdb=" CA PRO Y 441 " pdb=" CB PRO Y 441 " ideal model delta sigma weight residual 103.25 110.09 -6.84 1.05e+00 9.07e-01 4.24e+01 ... (remaining 26989 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.85: 11717 30.85 - 61.70: 275 61.70 - 92.55: 11 92.55 - 123.39: 4 123.39 - 154.24: 2 Dihedral angle restraints: 12009 sinusoidal: 4332 harmonic: 7677 Sorted by residual: dihedral pdb=" C5' ADP G 800 " pdb=" O5' ADP G 800 " pdb=" PA ADP G 800 " pdb=" O2A ADP G 800 " ideal model delta sinusoidal sigma weight residual -60.00 94.25 -154.24 1 2.00e+01 2.50e-03 4.56e+01 dihedral pdb=" O1B ADP G 800 " pdb=" O3A ADP G 800 " pdb=" PB ADP G 800 " pdb=" PA ADP G 800 " ideal model delta sinusoidal sigma weight residual -60.00 71.57 -131.58 1 2.00e+01 2.50e-03 3.99e+01 dihedral pdb=" C5' ADP J 800 " pdb=" O5' ADP J 800 " pdb=" PA ADP J 800 " pdb=" O2A ADP J 800 " ideal model delta sinusoidal sigma weight residual -60.00 62.62 -122.62 1 2.00e+01 2.50e-03 3.69e+01 ... (remaining 12006 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 1149 0.047 - 0.093: 984 0.093 - 0.140: 666 0.140 - 0.186: 266 0.186 - 0.233: 65 Chirality restraints: 3130 Sorted by residual: chirality pdb=" CA VAL H 9 " pdb=" N VAL H 9 " pdb=" C VAL H 9 " pdb=" CB VAL H 9 " both_signs ideal model delta sigma weight residual False 2.44 2.67 -0.23 2.00e-01 2.50e+01 1.35e+00 chirality pdb=" CB VAL G 318 " pdb=" CA VAL G 318 " pdb=" CG1 VAL G 318 " pdb=" CG2 VAL G 318 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.22 2.00e-01 2.50e+01 1.25e+00 chirality pdb=" CA ILE G 185 " pdb=" N ILE G 185 " pdb=" C ILE G 185 " pdb=" CB ILE G 185 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.22 2.00e-01 2.50e+01 1.23e+00 ... (remaining 3127 not shown) Planarity restraints: 3494 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP G 357 " 0.035 2.00e-02 2.50e+03 2.81e-02 1.97e+01 pdb=" CG TRP G 357 " -0.078 2.00e-02 2.50e+03 pdb=" CD1 TRP G 357 " 0.018 2.00e-02 2.50e+03 pdb=" CD2 TRP G 357 " 0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP G 357 " 0.008 2.00e-02 2.50e+03 pdb=" CE2 TRP G 357 " 0.007 2.00e-02 2.50e+03 pdb=" CE3 TRP G 357 " 0.008 2.00e-02 2.50e+03 pdb=" CZ2 TRP G 357 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP G 357 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP G 357 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP G 357 " 0.012 2.00e-02 2.50e+03 2.48e-02 6.15e+00 pdb=" C TRP G 357 " -0.043 2.00e-02 2.50e+03 pdb=" O TRP G 357 " 0.016 2.00e-02 2.50e+03 pdb=" N VAL G 358 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR G 375 " 0.009 2.00e-02 2.50e+03 1.92e-02 3.67e+00 pdb=" C THR G 375 " -0.033 2.00e-02 2.50e+03 pdb=" O THR G 375 " 0.012 2.00e-02 2.50e+03 pdb=" N PHE G 376 " 0.011 2.00e-02 2.50e+03 ... (remaining 3491 not shown) Histogram of nonbonded interaction distances: 1.79 - 2.41: 9 2.41 - 3.03: 9578 3.03 - 3.66: 29544 3.66 - 4.28: 41207 4.28 - 4.90: 70290 Nonbonded interactions: 150628 Sorted by model distance: nonbonded pdb=" NH2 ARG Y 37 " pdb="ZN ZN Y 501 " model vdw 1.790 2.310 nonbonded pdb=" O LEU G 267 " pdb=" NE2 HIS H 173 " model vdw 2.215 3.120 nonbonded pdb=" N ALA G 49 " pdb=" OH TYR I 148 " model vdw 2.235 3.120 nonbonded pdb=" O THR G 111 " pdb=" OG1 THR G 111 " model vdw 2.265 3.040 nonbonded pdb=" O GLY G 67 " pdb=" OD2 ASP I 287 " model vdw 2.308 3.040 ... (remaining 150623 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 'G' and (resid 7 through 361 or (resid 362 and (name N or name CA or name \ C or name O or name CB )) or resid 363 or (resid 364 through 366 and (name N or \ name CA or name C or name O or name CB )) or resid 367 through 800)) selection = chain 'I' } ncs_group { reference = chain 'S' selection = chain 'T' } ncs_group { reference = (chain 'X' and resid 132 through 223) selection = chain 'x' } 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: 1.620 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: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 19.020 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7213 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 : 0.015 0.515 19840 Z= 1.048 Angle : 1.766 12.934 26994 Z= 1.285 Chirality : 0.087 0.233 3130 Planarity : 0.003 0.028 3494 Dihedral : 13.322 154.242 7039 Min Nonbonded Distance : 1.790 Molprobity Statistics. All-atom Clashscore : 1.72 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.70 % Favored : 92.17 % Rotamer: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.13 (0.14), residues: 2298 helix: -1.58 (0.16), residues: 669 sheet: -2.29 (0.28), residues: 283 loop : -2.37 (0.14), residues: 1346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG G 329 TYR 0.019 0.002 TYR I 38 PHE 0.017 0.002 PHE M 71 TRP 0.078 0.003 TRP G 357 HIS 0.017 0.002 HIS G 372 Details of bonding type rmsd/Z covalent geometry : bond 0.01378 / 1.03 (19834) covalent geometry : angle 1.76596 / 1.28 (26994) hydrogen bonds : bond 0.24266 / 16.57 ( 920) hydrogen bonds : angle 7.80923 / 5.54 ( 2592) metal coordination : bond 0.29073 / 16.70 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 614 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 614 time to evaluate : 0.687 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: 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: G 37 ASN cc_start: 0.8697 (t0) cc_final: 0.8095 (t0) REVERT: G 63 GLU cc_start: 0.9255 (tp30) cc_final: 0.8948 (tp30) REVERT: G 86 MET cc_start: 0.9532 (tpp) cc_final: 0.9258 (tpp) REVERT: G 157 VAL cc_start: 0.8674 (t) cc_final: 0.8201 (t) REVERT: G 210 GLU cc_start: 0.9409 (mt-10) cc_final: 0.9205 (mt-10) REVERT: G 279 LEU cc_start: 0.8581 (tp) cc_final: 0.8159 (tp) REVERT: G 318 VAL cc_start: 0.8867 (m) cc_final: 0.8608 (p) REVERT: G 342 ILE cc_start: 0.9480 (mt) cc_final: 0.9243 (tp) REVERT: G 346 ILE cc_start: 0.9408 (mt) cc_final: 0.9029 (tp) REVERT: G 347 LEU cc_start: 0.8742 (tp) cc_final: 0.8535 (tp) REVERT: H 8 LEU cc_start: 0.9521 (mt) cc_final: 0.9310 (mm) REVERT: H 78 ASN cc_start: 0.8597 (t0) cc_final: 0.7950 (t0) REVERT: H 82 MET cc_start: 0.9574 (tpt) cc_final: 0.9184 (tpp) REVERT: H 90 PHE cc_start: 0.9669 (m-80) cc_final: 0.9278 (m-80) REVERT: H 119 MET cc_start: 0.9715 (ttm) cc_final: 0.9405 (tmm) REVERT: H 120 THR cc_start: 0.9701 (p) cc_final: 0.8852 (t) REVERT: H 123 MET cc_start: 0.9620 (mmm) cc_final: 0.9368 (tpp) REVERT: H 129 THR cc_start: 0.9038 (p) cc_final: 0.7989 (t) REVERT: H 153 MET cc_start: 0.8774 (tmm) cc_final: 0.8423 (tmm) REVERT: H 184 ASP cc_start: 0.9071 (m-30) cc_final: 0.8832 (m-30) REVERT: H 192 ILE cc_start: 0.9676 (pt) cc_final: 0.9230 (pt) REVERT: H 272 CYS cc_start: 0.8714 (p) cc_final: 0.8019 (p) REVERT: H 296 ASN cc_start: 0.9443 (m-40) cc_final: 0.9129 (t0) REVERT: H 305 MET cc_start: 0.9114 (mtp) cc_final: 0.8741 (mmt) REVERT: I 21 ILE cc_start: 0.9176 (pt) cc_final: 0.8879 (mm) REVERT: I 37 ASN cc_start: 0.8891 (t0) cc_final: 0.8583 (t0) REVERT: I 75 MET cc_start: 0.7845 (ttm) cc_final: 0.7296 (tpp) REVERT: I 76 GLU cc_start: 0.8908 (mt-10) cc_final: 0.8564 (mp0) REVERT: I 85 ASP cc_start: 0.9290 (m-30) cc_final: 0.9078 (m-30) REVERT: I 86 MET cc_start: 0.9699 (tpt) cc_final: 0.9056 (tpt) REVERT: I 91 GLN cc_start: 0.9664 (tt0) cc_final: 0.9383 (tp-100) REVERT: I 115 LEU cc_start: 0.9289 (mt) cc_final: 0.8956 (tt) REVERT: I 142 GLN cc_start: 0.8699 (mt0) cc_final: 0.8289 (tt0) REVERT: I 157 VAL cc_start: 0.9733 (t) cc_final: 0.9493 (m) REVERT: I 160 SER cc_start: 0.9477 (m) cc_final: 0.9095 (p) REVERT: I 166 HIS cc_start: 0.8917 (p-80) cc_final: 0.8364 (p90) REVERT: I 172 GLU cc_start: 0.9073 (mm-30) cc_final: 0.8855 (mm-30) REVERT: I 189 ASP cc_start: 0.9200 (m-30) cc_final: 0.8385 (m-30) REVERT: I 288 MET cc_start: 0.9057 (mtp) cc_final: 0.8848 (tpp) REVERT: I 290 LEU cc_start: 0.9600 (mt) cc_final: 0.9331 (mt) REVERT: I 314 LEU cc_start: 0.9871 (tp) cc_final: 0.9666 (tp) REVERT: I 330 ILE cc_start: 0.9600 (mt) cc_final: 0.9359 (mp) REVERT: J 18 ILE cc_start: 0.9760 (pt) cc_final: 0.9250 (mm) REVERT: J 27 CYS cc_start: 0.8291 (m) cc_final: 0.7727 (m) REVERT: J 64 LEU cc_start: 0.9795 (tp) cc_final: 0.9550 (tp) REVERT: J 70 GLU cc_start: 0.9554 (mm-30) cc_final: 0.9014 (tp30) REVERT: J 114 GLU cc_start: 0.9460 (mt-10) cc_final: 0.8963 (mp0) REVERT: J 145 GLU cc_start: 0.9167 (pt0) cc_final: 0.8962 (mm-30) REVERT: J 178 GLN cc_start: 0.9742 (mm-40) cc_final: 0.9353 (mm-40) REVERT: J 326 LEU cc_start: 0.9682 (mt) cc_final: 0.9362 (mt) REVERT: J 327 VAL cc_start: 0.9683 (t) cc_final: 0.9375 (t) REVERT: J 341 PHE cc_start: 0.9062 (m-80) cc_final: 0.8640 (m-10) REVERT: J 368 LEU cc_start: 0.9716 (tp) cc_final: 0.9483 (mt) REVERT: M 50 VAL cc_start: 0.7766 (t) cc_final: 0.7565 (m) REVERT: M 64 VAL cc_start: 0.8065 (m) cc_final: 0.7255 (m) REVERT: M 69 LEU cc_start: 0.7791 (tt) cc_final: 0.6906 (tt) REVERT: V 103 GLN cc_start: 0.8979 (tp40) cc_final: 0.8656 (tm-30) REVERT: V 110 VAL cc_start: 0.9356 (t) cc_final: 0.9047 (t) REVERT: V 123 LYS cc_start: 0.9448 (mmtt) cc_final: 0.9215 (mmmm) REVERT: V 153 PHE cc_start: 0.9373 (t80) cc_final: 0.8561 (t80) REVERT: V 156 GLU cc_start: 0.7745 (mp0) cc_final: 0.7183 (mp0) REVERT: V 164 LEU cc_start: 0.9607 (tp) cc_final: 0.9380 (tt) REVERT: V 167 ASP cc_start: 0.9175 (t70) cc_final: 0.8918 (t0) REVERT: Y 36 LEU cc_start: 0.8600 (pt) cc_final: 0.8331 (tt) REVERT: Y 120 ASP cc_start: 0.8837 (m-30) cc_final: 0.8619 (m-30) REVERT: Y 230 ASP cc_start: 0.8892 (m-30) cc_final: 0.7349 (p0) REVERT: Y 252 LEU cc_start: 0.9588 (tt) cc_final: 0.9364 (tp) REVERT: Y 257 LEU cc_start: 0.9736 (mt) cc_final: 0.9329 (pp) REVERT: Y 261 PHE cc_start: 0.9139 (p90) cc_final: 0.8298 (p90) REVERT: Y 289 HIS cc_start: 0.6523 (t70) cc_final: 0.6275 (t-90) REVERT: Y 290 ASN cc_start: 0.8662 (t0) cc_final: 0.8176 (t0) REVERT: Y 297 ASN cc_start: 0.7917 (m110) cc_final: 0.7518 (m-40) outliers start: 0 outliers final: 0 residues processed: 614 average time/residue: 0.1379 time to fit residues: 129.7847 Evaluate side-chains 364 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 364 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 197 optimal weight: 4.9990 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 0.9980 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 40.0000 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 8.9990 chunk 111 optimal weight: 0.9990 chunk 258 optimal weight: 20.0000 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 120 ASN G 166 HIS G 297 ASN ** G 372 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 88 HIS H 161 HIS I 16 ASN ** I 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 380 GLN U 140 ASN ** U 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 20 ASN ** V 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 162 GLN ** Y 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 306 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.050379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2640 r_free = 0.2640 target = 0.034113 restraints weight = 117552.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2683 r_free = 0.2683 target = 0.035512 restraints weight = 68166.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2715 r_free = 0.2715 target = 0.036539 restraints weight = 45984.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.2736 r_free = 0.2736 target = 0.037279 restraints weight = 34021.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.2755 r_free = 0.2755 target = 0.037894 restraints weight = 26831.257| |-----------------------------------------------------------------------------| r_work (final): 0.2719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.3196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 19840 Z= 0.182 Angle : 0.686 11.803 26994 Z= 0.349 Chirality : 0.043 0.204 3130 Planarity : 0.005 0.071 3494 Dihedral : 8.472 167.376 2898 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.87 % Favored : 96.04 % Rotamer: Outliers : 0.16 % Allowed : 3.40 % Favored : 96.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.43 (0.16), residues: 2298 helix: 0.44 (0.19), residues: 702 sheet: -1.28 (0.27), residues: 317 loop : -1.70 (0.15), residues: 1279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG U 150 TYR 0.023 0.002 TYR G 73 PHE 0.028 0.002 PHE U 90 TRP 0.031 0.002 TRP G 357 HIS 0.014 0.002 HIS V 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.18 (19834) covalent geometry : angle 0.68595 / 0.35 (26994) hydrogen bonds : bond 0.05030 / 3.34 ( 920) hydrogen bonds : angle 5.02932 / 3.63 ( 2592) metal coordination : bond 0.00631 / 0.36 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 396 time to evaluate : 0.598 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: symmetry clash REVERT: G 15 ASP cc_start: 0.9413 (t70) cc_final: 0.8951 (t0) REVERT: G 37 ASN cc_start: 0.9586 (t0) cc_final: 0.9158 (t0) REVERT: G 75 MET cc_start: 0.9275 (ptp) cc_final: 0.9036 (ptp) REVERT: G 86 MET cc_start: 0.9760 (tpp) cc_final: 0.9427 (tpp) REVERT: G 94 TYR cc_start: 0.8519 (m-80) cc_final: 0.8265 (m-80) REVERT: G 97 ASP cc_start: 0.9525 (m-30) cc_final: 0.8987 (t0) REVERT: G 109 LEU cc_start: 0.9763 (tp) cc_final: 0.9519 (tp) REVERT: G 120 ASN cc_start: 0.9430 (OUTLIER) cc_final: 0.9207 (t0) REVERT: G 142 GLN cc_start: 0.9199 (mt0) cc_final: 0.8963 (mm110) REVERT: G 184 ASP cc_start: 0.8936 (p0) cc_final: 0.8581 (p0) REVERT: G 189 ASP cc_start: 0.9089 (m-30) cc_final: 0.8766 (m-30) REVERT: G 210 GLU cc_start: 0.9429 (mt-10) cc_final: 0.9219 (mt-10) REVERT: G 215 LYS cc_start: 0.9492 (ptpt) cc_final: 0.9119 (ptpt) REVERT: G 227 ASN cc_start: 0.8420 (t0) cc_final: 0.8127 (t0) REVERT: G 347 LEU cc_start: 0.9860 (tp) cc_final: 0.9477 (tp) REVERT: H 8 LEU cc_start: 0.9567 (mt) cc_final: 0.9334 (mm) REVERT: H 16 MET cc_start: 0.9344 (mmm) cc_final: 0.8663 (mmm) REVERT: H 78 ASN cc_start: 0.8690 (t0) cc_final: 0.8068 (t0) REVERT: H 81 ASP cc_start: 0.9621 (m-30) cc_final: 0.9181 (m-30) REVERT: H 82 MET cc_start: 0.9708 (tpt) cc_final: 0.9309 (tpp) REVERT: H 90 PHE cc_start: 0.9768 (m-80) cc_final: 0.9257 (m-80) REVERT: H 119 MET cc_start: 0.9662 (ttm) cc_final: 0.9409 (tmm) REVERT: H 120 THR cc_start: 0.9688 (p) cc_final: 0.9158 (t) REVERT: H 129 THR cc_start: 0.9243 (p) cc_final: 0.8537 (t) REVERT: H 132 MET cc_start: 0.9195 (tmm) cc_final: 0.8942 (ttp) REVERT: H 154 ASP cc_start: 0.9502 (t0) cc_final: 0.9143 (t0) REVERT: H 190 MET cc_start: 0.9365 (mmm) cc_final: 0.9064 (mmm) REVERT: H 195 GLU cc_start: 0.9545 (mt-10) cc_final: 0.9247 (mt-10) REVERT: H 217 CYS cc_start: 0.9468 (m) cc_final: 0.9206 (m) REVERT: H 272 CYS cc_start: 0.8912 (p) cc_final: 0.8539 (p) REVERT: H 292 ASP cc_start: 0.9404 (m-30) cc_final: 0.8547 (p0) REVERT: H 293 LEU cc_start: 0.9846 (mm) cc_final: 0.9195 (mm) REVERT: H 296 ASN cc_start: 0.9335 (m-40) cc_final: 0.9092 (t0) REVERT: H 313 MET cc_start: 0.9586 (mmp) cc_final: 0.9264 (mmm) REVERT: H 374 CYS cc_start: 0.8004 (p) cc_final: 0.7402 (t) REVERT: I 16 ASN cc_start: 0.9529 (m110) cc_final: 0.9225 (m-40) REVERT: I 21 ILE cc_start: 0.9253 (pt) cc_final: 0.8779 (mm) REVERT: I 37 ASN cc_start: 0.9058 (t0) cc_final: 0.8632 (t0) REVERT: I 75 MET cc_start: 0.7988 (ttm) cc_final: 0.7033 (ttp) REVERT: I 76 GLU cc_start: 0.9202 (mt-10) cc_final: 0.8764 (mp0) REVERT: I 86 MET cc_start: 0.9823 (tpt) cc_final: 0.9307 (tpt) REVERT: I 87 GLU cc_start: 0.9499 (OUTLIER) cc_final: 0.9232 (pt0) REVERT: I 91 GLN cc_start: 0.9740 (tt0) cc_final: 0.9511 (tp-100) REVERT: I 115 LEU cc_start: 0.9357 (mt) cc_final: 0.9155 (mp) REVERT: I 157 VAL cc_start: 0.9735 (t) cc_final: 0.9456 (t) REVERT: I 160 SER cc_start: 0.9627 (m) cc_final: 0.9379 (p) REVERT: I 166 HIS cc_start: 0.9273 (p-80) cc_final: 0.8563 (p90) REVERT: I 172 GLU cc_start: 0.9433 (mm-30) cc_final: 0.9020 (mm-30) REVERT: I 181 MET cc_start: 0.9231 (tpp) cc_final: 0.8935 (mmm) REVERT: I 189 ASP cc_start: 0.9299 (m-30) cc_final: 0.8737 (m-30) REVERT: I 300 LEU cc_start: 0.9810 (mt) cc_final: 0.9467 (mm) REVERT: J 18 ILE cc_start: 0.9740 (pt) cc_final: 0.9503 (tp) REVERT: J 64 LEU cc_start: 0.9867 (tp) cc_final: 0.9622 (tp) REVERT: J 70 GLU cc_start: 0.9714 (mm-30) cc_final: 0.9380 (mm-30) REVERT: J 145 GLU cc_start: 0.9483 (pt0) cc_final: 0.9036 (tp30) REVERT: J 178 GLN cc_start: 0.9753 (mm-40) cc_final: 0.9417 (mm-40) REVERT: J 298 GLN cc_start: 0.9193 (mp10) cc_final: 0.8978 (pm20) REVERT: J 311 MET cc_start: 0.9267 (mmt) cc_final: 0.8638 (mmt) REVERT: J 322 GLU cc_start: 0.9571 (tt0) cc_final: 0.8894 (mt-10) REVERT: J 387 TRP cc_start: 0.9129 (p-90) cc_final: 0.8792 (p-90) REVERT: U 38 LYS cc_start: 0.8652 (ttpp) cc_final: 0.8101 (tmmt) REVERT: U 52 GLU cc_start: 0.9667 (pm20) cc_final: 0.9457 (pm20) REVERT: U 90 PHE cc_start: 0.9165 (m-80) cc_final: 0.8752 (m-80) REVERT: U 108 GLU cc_start: 0.9336 (mt-10) cc_final: 0.9062 (mt-10) REVERT: U 125 ILE cc_start: 0.9157 (tp) cc_final: 0.8711 (tp) REVERT: U 139 GLU cc_start: 0.8786 (tp30) cc_final: 0.8524 (tp30) REVERT: U 144 TYR cc_start: 0.8760 (p90) cc_final: 0.7879 (p90) REVERT: V 123 LYS cc_start: 0.9355 (mmtt) cc_final: 0.8879 (mmtm) REVERT: V 138 THR cc_start: 0.9662 (t) cc_final: 0.9187 (m) REVERT: V 143 PHE cc_start: 0.9553 (m-80) cc_final: 0.9211 (m-80) REVERT: V 165 MET cc_start: 0.9502 (mmp) cc_final: 0.9228 (mmm) REVERT: Y 36 LEU cc_start: 0.9016 (pt) cc_final: 0.8215 (tt) REVERT: Y 230 ASP cc_start: 0.9269 (m-30) cc_final: 0.8438 (p0) REVERT: Y 261 PHE cc_start: 0.9379 (p90) cc_final: 0.9167 (p90) REVERT: Y 276 LEU cc_start: 0.9722 (mt) cc_final: 0.9433 (mt) REVERT: Y 289 HIS cc_start: 0.8268 (t70) cc_final: 0.7671 (t70) REVERT: Y 290 ASN cc_start: 0.8965 (t0) cc_final: 0.8215 (t0) REVERT: Y 296 PHE cc_start: 0.9518 (t80) cc_final: 0.9292 (t80) REVERT: Y 305 ILE cc_start: 0.8975 (tp) cc_final: 0.8530 (tp) REVERT: Y 411 ILE cc_start: 0.9289 (mm) cc_final: 0.9028 (mp) outliers start: 3 outliers final: 0 residues processed: 399 average time/residue: 0.1258 time to fit residues: 79.9084 Evaluate side-chains 283 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 281 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 9 optimal weight: 10.0000 chunk 113 optimal weight: 0.3980 chunk 184 optimal weight: 3.9990 chunk 215 optimal weight: 8.9990 chunk 101 optimal weight: 0.6980 chunk 37 optimal weight: 9.9990 chunk 194 optimal weight: 10.0000 chunk 91 optimal weight: 0.0570 chunk 64 optimal weight: 3.9990 chunk 258 optimal weight: 30.0000 chunk 103 optimal weight: 8.9990 overall best weight: 1.8302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 372 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 10 GLN ** I 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 103 GLN ** V 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 174 GLN ** Y 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.049564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2623 r_free = 0.2623 target = 0.033518 restraints weight = 120111.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2666 r_free = 0.2666 target = 0.034899 restraints weight = 69403.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2697 r_free = 0.2697 target = 0.035919 restraints weight = 47001.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2721 r_free = 0.2721 target = 0.036699 restraints weight = 34801.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2737 r_free = 0.2737 target = 0.037265 restraints weight = 27315.558| |-----------------------------------------------------------------------------| r_work (final): 0.2706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.3748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 19840 Z= 0.150 Angle : 0.607 10.416 26994 Z= 0.305 Chirality : 0.042 0.166 3130 Planarity : 0.004 0.038 3494 Dihedral : 8.076 179.449 2898 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.96 % Favored : 95.95 % Rotamer: Outliers : 0.11 % Allowed : 2.54 % Favored : 97.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.80 (0.17), residues: 2298 helix: 0.86 (0.19), residues: 691 sheet: -0.94 (0.27), residues: 326 loop : -1.21 (0.16), residues: 1281 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 336 TYR 0.019 0.001 TYR G 197 PHE 0.031 0.002 PHE G 193 TRP 0.025 0.002 TRP H 356 HIS 0.009 0.001 HIS G 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.15 (19834) covalent geometry : angle 0.60706 / 0.30 (26994) hydrogen bonds : bond 0.04352 / 2.93 ( 920) hydrogen bonds : angle 4.68632 / 3.37 ( 2592) metal coordination : bond 0.00185 / 0.11 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 357 time to evaluate : 0.581 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: G 15 ASP cc_start: 0.9328 (t70) cc_final: 0.8964 (t0) REVERT: G 37 ASN cc_start: 0.9632 (t0) cc_final: 0.9210 (t0) REVERT: G 75 MET cc_start: 0.9405 (ptp) cc_final: 0.9050 (ptp) REVERT: G 86 MET cc_start: 0.9779 (tpp) cc_final: 0.9413 (tpp) REVERT: G 89 ILE cc_start: 0.9793 (pt) cc_final: 0.9554 (pt) REVERT: G 94 TYR cc_start: 0.8596 (m-80) cc_final: 0.8390 (m-80) REVERT: G 109 LEU cc_start: 0.9797 (tp) cc_final: 0.9429 (tp) REVERT: G 142 GLN cc_start: 0.9451 (mt0) cc_final: 0.8962 (mm110) REVERT: G 184 ASP cc_start: 0.8814 (p0) cc_final: 0.8419 (p0) REVERT: G 189 ASP cc_start: 0.8999 (m-30) cc_final: 0.8643 (m-30) REVERT: G 227 ASN cc_start: 0.8345 (t0) cc_final: 0.7967 (t0) REVERT: G 268 ILE cc_start: 0.9754 (tp) cc_final: 0.9514 (tp) REVERT: G 295 PHE cc_start: 0.9523 (m-80) cc_final: 0.8996 (m-80) REVERT: H 8 LEU cc_start: 0.9630 (mt) cc_final: 0.9383 (mm) REVERT: H 16 MET cc_start: 0.9339 (mmm) cc_final: 0.8638 (mmm) REVERT: H 78 ASN cc_start: 0.8651 (t0) cc_final: 0.8350 (t0) REVERT: H 82 MET cc_start: 0.9648 (tpt) cc_final: 0.9170 (tpt) REVERT: H 90 PHE cc_start: 0.9628 (m-80) cc_final: 0.9176 (m-10) REVERT: H 123 MET cc_start: 0.9658 (tpp) cc_final: 0.9346 (tpp) REVERT: H 129 THR cc_start: 0.9124 (p) cc_final: 0.8779 (t) REVERT: H 154 ASP cc_start: 0.9349 (t0) cc_final: 0.9069 (t0) REVERT: H 184 ASP cc_start: 0.9352 (m-30) cc_final: 0.9088 (m-30) REVERT: H 217 CYS cc_start: 0.9431 (m) cc_final: 0.9025 (m) REVERT: H 272 CYS cc_start: 0.8872 (p) cc_final: 0.8499 (p) REVERT: H 292 ASP cc_start: 0.9425 (m-30) cc_final: 0.8631 (p0) REVERT: H 296 ASN cc_start: 0.9396 (m-40) cc_final: 0.9027 (t0) REVERT: H 305 MET cc_start: 0.9285 (mmt) cc_final: 0.8725 (mmm) REVERT: H 355 MET cc_start: 0.9688 (mmp) cc_final: 0.9460 (mmm) REVERT: H 361 GLU cc_start: 0.9584 (mt-10) cc_final: 0.9374 (mm-30) REVERT: H 374 CYS cc_start: 0.7967 (p) cc_final: 0.7398 (t) REVERT: I 86 MET cc_start: 0.9781 (tpt) cc_final: 0.9331 (tpt) REVERT: I 91 GLN cc_start: 0.9744 (tt0) cc_final: 0.9498 (tp-100) REVERT: I 160 SER cc_start: 0.9639 (m) cc_final: 0.9359 (p) REVERT: I 172 GLU cc_start: 0.9382 (mm-30) cc_final: 0.8953 (mm-30) REVERT: I 189 ASP cc_start: 0.9394 (m-30) cc_final: 0.8785 (m-30) REVERT: I 262 LEU cc_start: 0.9898 (tp) cc_final: 0.9671 (tp) REVERT: I 300 LEU cc_start: 0.9835 (mt) cc_final: 0.9451 (mm) REVERT: J 64 LEU cc_start: 0.9846 (tp) cc_final: 0.9583 (tp) REVERT: J 70 GLU cc_start: 0.9707 (mm-30) cc_final: 0.9388 (mm-30) REVERT: J 109 LEU cc_start: 0.9739 (mm) cc_final: 0.9378 (pp) REVERT: J 145 GLU cc_start: 0.9508 (pt0) cc_final: 0.8986 (tt0) REVERT: J 178 GLN cc_start: 0.9752 (mm-40) cc_final: 0.9376 (mm-40) REVERT: J 208 GLU cc_start: 0.9393 (OUTLIER) cc_final: 0.9176 (pp20) REVERT: J 298 GLN cc_start: 0.9245 (mp10) cc_final: 0.9004 (pm20) REVERT: J 311 MET cc_start: 0.9335 (mmt) cc_final: 0.8837 (mmm) REVERT: J 322 GLU cc_start: 0.9524 (tt0) cc_final: 0.9236 (mt-10) REVERT: J 368 LEU cc_start: 0.9804 (tt) cc_final: 0.9340 (mt) REVERT: J 387 TRP cc_start: 0.9131 (p-90) cc_final: 0.8695 (p-90) REVERT: M 45 VAL cc_start: 0.9308 (m) cc_final: 0.9097 (p) REVERT: U 36 HIS cc_start: 0.9067 (m170) cc_final: 0.8767 (m170) REVERT: U 38 LYS cc_start: 0.8979 (ttpp) cc_final: 0.8483 (tmmt) REVERT: U 90 PHE cc_start: 0.9106 (m-80) cc_final: 0.8804 (m-80) REVERT: U 106 VAL cc_start: 0.8970 (t) cc_final: 0.8480 (t) REVERT: U 139 GLU cc_start: 0.8860 (tp30) cc_final: 0.8635 (tp30) REVERT: U 144 TYR cc_start: 0.8607 (p90) cc_final: 0.7866 (p90) REVERT: U 151 ARG cc_start: 0.9065 (ttm170) cc_final: 0.8087 (tpp80) REVERT: V 123 LYS cc_start: 0.9320 (mmtt) cc_final: 0.8898 (mmtm) REVERT: V 138 THR cc_start: 0.9752 (t) cc_final: 0.9415 (m) REVERT: V 143 PHE cc_start: 0.9565 (m-80) cc_final: 0.9203 (m-80) REVERT: V 161 THR cc_start: 0.9739 (m) cc_final: 0.9349 (m) REVERT: V 165 MET cc_start: 0.9619 (mmp) cc_final: 0.9251 (mmm) REVERT: Y 123 MET cc_start: 0.8315 (mmm) cc_final: 0.8098 (mmp) REVERT: Y 230 ASP cc_start: 0.9321 (m-30) cc_final: 0.8533 (p0) REVERT: Y 257 LEU cc_start: 0.9748 (mt) cc_final: 0.9436 (mt) REVERT: Y 260 ASP cc_start: 0.8984 (p0) cc_final: 0.8613 (p0) REVERT: Y 261 PHE cc_start: 0.9382 (p90) cc_final: 0.8816 (p90) REVERT: Y 276 LEU cc_start: 0.9736 (mt) cc_final: 0.9469 (mt) REVERT: Y 289 HIS cc_start: 0.8301 (t70) cc_final: 0.7973 (t-90) REVERT: Y 290 ASN cc_start: 0.8806 (t0) cc_final: 0.8442 (t0) outliers start: 2 outliers final: 0 residues processed: 358 average time/residue: 0.1216 time to fit residues: 69.0411 Evaluate side-chains 263 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 262 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 42 optimal weight: 8.9990 chunk 27 optimal weight: 0.8980 chunk 188 optimal weight: 7.9990 chunk 80 optimal weight: 7.9990 chunk 235 optimal weight: 5.9990 chunk 59 optimal weight: 3.9990 chunk 36 optimal weight: 10.0000 chunk 150 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 52.6549 > 50:) chunk 141 optimal weight: 9.9990 chunk 124 optimal weight: 4.9990 chunk 174 optimal weight: 10.0000 overall best weight: 4.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 372 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 371 HIS ** I 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 297 ASN J 56 GLN ** J 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 344 HIS J 379 ASN J 380 GLN ** U 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 162 GLN V 174 GLN ** Y 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 140 HIS Y 268 GLN ** Y 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.045719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2534 r_free = 0.2534 target = 0.030797 restraints weight = 130071.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2575 r_free = 0.2575 target = 0.032046 restraints weight = 74825.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2605 r_free = 0.2605 target = 0.032958 restraints weight = 50599.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2627 r_free = 0.2627 target = 0.033640 restraints weight = 37544.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2642 r_free = 0.2642 target = 0.034131 restraints weight = 29635.285| |-----------------------------------------------------------------------------| r_work (final): 0.2610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.4849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.101 19840 Z= 0.307 Angle : 0.779 12.661 26994 Z= 0.389 Chirality : 0.044 0.207 3130 Planarity : 0.005 0.051 3494 Dihedral : 8.287 179.829 2898 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 15.88 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.31 % Favored : 94.60 % Rotamer: Outliers : 0.11 % Allowed : 3.99 % Favored : 95.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.80 (0.17), residues: 2298 helix: 0.43 (0.19), residues: 713 sheet: -1.09 (0.27), residues: 331 loop : -0.90 (0.17), residues: 1254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG I 336 TYR 0.020 0.002 TYR G 33 PHE 0.039 0.003 PHE M 59 TRP 0.073 0.004 TRP G 357 HIS 0.010 0.002 HIS G 276 Details of bonding type rmsd/Z covalent geometry : bond 0.00622 / 0.31 (19834) covalent geometry : angle 0.77857 / 0.39 (26994) hydrogen bonds : bond 0.04506 / 3.06 ( 920) hydrogen bonds : angle 5.11833 / 3.67 ( 2592) metal coordination : bond 0.00304 / 0.16 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 292 time to evaluate : 0.594 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: G 15 ASP cc_start: 0.9156 (t70) cc_final: 0.8859 (t0) REVERT: G 37 ASN cc_start: 0.9642 (t0) cc_final: 0.9353 (t0) REVERT: G 75 MET cc_start: 0.9445 (ptp) cc_final: 0.9191 (ptp) REVERT: G 86 MET cc_start: 0.9753 (tpp) cc_final: 0.9393 (tpp) REVERT: G 227 ASN cc_start: 0.8508 (t0) cc_final: 0.8089 (t0) REVERT: H 16 MET cc_start: 0.9387 (mmm) cc_final: 0.8823 (mmm) REVERT: H 81 ASP cc_start: 0.9575 (m-30) cc_final: 0.9160 (t0) REVERT: H 82 MET cc_start: 0.9695 (tpt) cc_final: 0.9472 (tpp) REVERT: H 85 ILE cc_start: 0.9841 (mt) cc_final: 0.9536 (mt) REVERT: H 90 PHE cc_start: 0.9613 (m-80) cc_final: 0.9313 (m-10) REVERT: H 115 ASN cc_start: 0.9427 (t0) cc_final: 0.9027 (t0) REVERT: H 119 MET cc_start: 0.9517 (ptt) cc_final: 0.9015 (ptt) REVERT: H 123 MET cc_start: 0.9103 (tpp) cc_final: 0.8855 (tpp) REVERT: H 154 ASP cc_start: 0.9579 (t0) cc_final: 0.9232 (t0) REVERT: H 184 ASP cc_start: 0.9414 (m-30) cc_final: 0.9145 (m-30) REVERT: H 190 MET cc_start: 0.9407 (mmm) cc_final: 0.9174 (mmm) REVERT: H 192 ILE cc_start: 0.9584 (pt) cc_final: 0.9239 (mm) REVERT: H 195 GLU cc_start: 0.9633 (tt0) cc_final: 0.9093 (mt-10) REVERT: H 217 CYS cc_start: 0.9564 (m) cc_final: 0.9199 (m) REVERT: H 272 CYS cc_start: 0.8624 (p) cc_final: 0.8308 (p) REVERT: H 292 ASP cc_start: 0.9544 (m-30) cc_final: 0.8868 (p0) REVERT: H 305 MET cc_start: 0.9261 (mmt) cc_final: 0.8808 (mmm) REVERT: H 313 MET cc_start: 0.9706 (mmp) cc_final: 0.9368 (mmm) REVERT: H 355 MET cc_start: 0.9756 (mmp) cc_final: 0.9506 (mmm) REVERT: I 44 HIS cc_start: 0.9106 (t-90) cc_final: 0.8906 (t-90) REVERT: I 86 MET cc_start: 0.9745 (tpt) cc_final: 0.9339 (tpt) REVERT: I 91 GLN cc_start: 0.9785 (tt0) cc_final: 0.9510 (tp-100) REVERT: I 160 SER cc_start: 0.9632 (m) cc_final: 0.9372 (p) REVERT: I 181 MET cc_start: 0.9319 (mmm) cc_final: 0.9013 (tpp) REVERT: I 189 ASP cc_start: 0.9358 (m-30) cc_final: 0.8914 (m-30) REVERT: I 262 LEU cc_start: 0.9884 (tp) cc_final: 0.9604 (tp) REVERT: I 290 LEU cc_start: 0.9730 (mt) cc_final: 0.9432 (mt) REVERT: I 300 LEU cc_start: 0.9909 (mt) cc_final: 0.9696 (mm) REVERT: J 19 ASP cc_start: 0.9170 (t0) cc_final: 0.8955 (t70) REVERT: J 64 LEU cc_start: 0.9861 (tp) cc_final: 0.9606 (tp) REVERT: J 70 GLU cc_start: 0.9755 (mm-30) cc_final: 0.9213 (mt-10) REVERT: J 145 GLU cc_start: 0.9657 (pt0) cc_final: 0.9008 (tt0) REVERT: J 149 LEU cc_start: 0.9792 (tp) cc_final: 0.9578 (tp) REVERT: J 174 GLU cc_start: 0.9591 (tp30) cc_final: 0.8698 (tm-30) REVERT: J 178 GLN cc_start: 0.9712 (mm-40) cc_final: 0.9352 (mm-40) REVERT: J 311 MET cc_start: 0.9095 (mmt) cc_final: 0.8290 (mmm) REVERT: J 322 GLU cc_start: 0.9547 (tt0) cc_final: 0.8903 (mt-10) REVERT: J 387 TRP cc_start: 0.9500 (p-90) cc_final: 0.9022 (p-90) REVERT: U 36 HIS cc_start: 0.9189 (m170) cc_final: 0.8847 (m170) REVERT: U 38 LYS cc_start: 0.9092 (ttpp) cc_final: 0.8891 (tmtt) REVERT: U 90 PHE cc_start: 0.9116 (m-80) cc_final: 0.8739 (m-80) REVERT: U 99 MET cc_start: 0.9291 (tpp) cc_final: 0.8847 (tpt) REVERT: U 144 TYR cc_start: 0.9093 (p90) cc_final: 0.8174 (p90) REVERT: U 151 ARG cc_start: 0.8812 (ttm170) cc_final: 0.7825 (tpp80) REVERT: V 39 LYS cc_start: 0.9200 (mmtt) cc_final: 0.8994 (mmtp) REVERT: V 103 GLN cc_start: 0.8829 (tm-30) cc_final: 0.8432 (tm-30) REVERT: V 123 LYS cc_start: 0.9389 (mmtt) cc_final: 0.9133 (mmmt) REVERT: V 143 PHE cc_start: 0.9599 (m-80) cc_final: 0.8991 (m-80) REVERT: V 161 THR cc_start: 0.9726 (m) cc_final: 0.9482 (m) REVERT: V 165 MET cc_start: 0.9558 (mmp) cc_final: 0.9230 (mmm) REVERT: Y 230 ASP cc_start: 0.9288 (m-30) cc_final: 0.8583 (p0) REVERT: Y 260 ASP cc_start: 0.8989 (p0) cc_final: 0.8674 (p0) REVERT: Y 261 PHE cc_start: 0.9403 (p90) cc_final: 0.8857 (p90) outliers start: 2 outliers final: 0 residues processed: 294 average time/residue: 0.1286 time to fit residues: 59.2931 Evaluate side-chains 221 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 221 time to evaluate : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 74 optimal weight: 10.0000 chunk 6 optimal weight: 6.9990 chunk 55 optimal weight: 6.9990 chunk 129 optimal weight: 0.0050 chunk 70 optimal weight: 5.9990 chunk 204 optimal weight: 40.0000 chunk 164 optimal weight: 20.0000 chunk 103 optimal weight: 6.9990 chunk 187 optimal weight: 9.9990 chunk 72 optimal weight: 4.9990 chunk 62 optimal weight: 0.0040 overall best weight: 3.6012 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 372 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 101 HIS H 263 GLN ** I 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 56 GLN J 193 GLN U 97 GLN ** U 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 163 GLN V 60 HIS ** V 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 152 GLN ** Y 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.046145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2538 r_free = 0.2538 target = 0.031011 restraints weight = 129957.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2580 r_free = 0.2580 target = 0.032273 restraints weight = 74070.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2610 r_free = 0.2610 target = 0.033198 restraints weight = 49852.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2631 r_free = 0.2631 target = 0.033857 restraints weight = 36853.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.2648 r_free = 0.2648 target = 0.034379 restraints weight = 29201.772| |-----------------------------------------------------------------------------| r_work (final): 0.2610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.5174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 19840 Z= 0.219 Angle : 0.637 12.049 26994 Z= 0.321 Chirality : 0.043 0.197 3130 Planarity : 0.004 0.036 3494 Dihedral : 7.790 169.293 2898 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 13.04 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.18 % Favored : 94.73 % Rotamer: Outliers : 0.05 % Allowed : 2.59 % Favored : 97.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.63 (0.17), residues: 2298 helix: 0.56 (0.19), residues: 728 sheet: -1.03 (0.26), residues: 353 loop : -0.77 (0.17), residues: 1217 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 336 TYR 0.016 0.002 TYR G 33 PHE 0.032 0.002 PHE H 124 TRP 0.068 0.003 TRP G 357 HIS 0.019 0.002 HIS H 73 Details of bonding type rmsd/Z covalent geometry : bond 0.00447 / 0.22 (19834) covalent geometry : angle 0.63728 / 0.32 (26994) hydrogen bonds : bond 0.04045 / 2.74 ( 920) hydrogen bonds : angle 4.84565 / 3.47 ( 2592) metal coordination : bond 0.00286 / 0.14 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 285 time to evaluate : 0.602 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: G 15 ASP cc_start: 0.9068 (t70) cc_final: 0.8801 (t0) REVERT: G 37 ASN cc_start: 0.9635 (t0) cc_final: 0.9325 (t0) REVERT: G 75 MET cc_start: 0.9379 (ptp) cc_final: 0.9041 (ptp) REVERT: G 86 MET cc_start: 0.9774 (tpp) cc_final: 0.9297 (tpp) REVERT: G 94 TYR cc_start: 0.8999 (m-80) cc_final: 0.8732 (m-80) REVERT: G 181 MET cc_start: 0.9130 (mmp) cc_final: 0.8912 (mmm) REVERT: G 227 ASN cc_start: 0.8461 (t0) cc_final: 0.8077 (t0) REVERT: G 347 LEU cc_start: 0.9878 (tp) cc_final: 0.9519 (tp) REVERT: H 16 MET cc_start: 0.9410 (mmm) cc_final: 0.8921 (mmm) REVERT: H 78 ASN cc_start: 0.8960 (t0) cc_final: 0.8290 (t0) REVERT: H 81 ASP cc_start: 0.9617 (m-30) cc_final: 0.9333 (m-30) REVERT: H 90 PHE cc_start: 0.9667 (m-80) cc_final: 0.9360 (m-10) REVERT: H 115 ASN cc_start: 0.9370 (t0) cc_final: 0.9138 (t0) REVERT: H 117 GLU cc_start: 0.9473 (pt0) cc_final: 0.9184 (pp20) REVERT: H 119 MET cc_start: 0.9486 (ptt) cc_final: 0.8890 (ptt) REVERT: H 129 THR cc_start: 0.9223 (p) cc_final: 0.8828 (t) REVERT: H 154 ASP cc_start: 0.9375 (t0) cc_final: 0.9024 (t0) REVERT: H 184 ASP cc_start: 0.9311 (m-30) cc_final: 0.9080 (m-30) REVERT: H 195 GLU cc_start: 0.9587 (tt0) cc_final: 0.9203 (tp30) REVERT: H 217 CYS cc_start: 0.9526 (m) cc_final: 0.9122 (m) REVERT: H 272 CYS cc_start: 0.8616 (p) cc_final: 0.8234 (p) REVERT: H 292 ASP cc_start: 0.9545 (m-30) cc_final: 0.8895 (p0) REVERT: H 305 MET cc_start: 0.9298 (mmt) cc_final: 0.8722 (mmm) REVERT: H 311 ASP cc_start: 0.9689 (m-30) cc_final: 0.9172 (p0) REVERT: H 313 MET cc_start: 0.9725 (mmp) cc_final: 0.9460 (mmm) REVERT: H 355 MET cc_start: 0.9740 (mmp) cc_final: 0.9486 (mmm) REVERT: H 374 CYS cc_start: 0.7995 (p) cc_final: 0.7474 (t) REVERT: I 37 ASN cc_start: 0.9257 (t0) cc_final: 0.9039 (t0) REVERT: I 44 HIS cc_start: 0.9137 (t-90) cc_final: 0.8927 (t70) REVERT: I 75 MET cc_start: 0.8544 (ttp) cc_final: 0.7359 (tmm) REVERT: I 86 MET cc_start: 0.9713 (tpt) cc_final: 0.9280 (tpt) REVERT: I 91 GLN cc_start: 0.9751 (tt0) cc_final: 0.9476 (tp-100) REVERT: I 160 SER cc_start: 0.9602 (m) cc_final: 0.9350 (p) REVERT: I 181 MET cc_start: 0.9306 (mmm) cc_final: 0.8950 (tpp) REVERT: I 189 ASP cc_start: 0.9442 (m-30) cc_final: 0.9102 (m-30) REVERT: I 290 LEU cc_start: 0.9762 (mt) cc_final: 0.9448 (mt) REVERT: J 19 ASP cc_start: 0.9261 (t0) cc_final: 0.8917 (t0) REVERT: J 64 LEU cc_start: 0.9852 (tp) cc_final: 0.9596 (tp) REVERT: J 70 GLU cc_start: 0.9764 (mm-30) cc_final: 0.9317 (mm-30) REVERT: J 145 GLU cc_start: 0.9623 (pt0) cc_final: 0.8959 (tt0) REVERT: J 174 GLU cc_start: 0.9574 (tp30) cc_final: 0.8721 (tm-30) REVERT: J 178 GLN cc_start: 0.9721 (mm-40) cc_final: 0.9259 (mm-40) REVERT: J 311 MET cc_start: 0.9357 (mmt) cc_final: 0.8790 (mmm) REVERT: J 319 LEU cc_start: 0.9818 (tp) cc_final: 0.9577 (mm) REVERT: J 322 GLU cc_start: 0.9578 (tt0) cc_final: 0.9020 (mt-10) REVERT: J 387 TRP cc_start: 0.9527 (p-90) cc_final: 0.9201 (p-90) REVERT: U 36 HIS cc_start: 0.9214 (m170) cc_final: 0.8878 (m170) REVERT: U 38 LYS cc_start: 0.9049 (ttpp) cc_final: 0.8835 (tmtt) REVERT: U 90 PHE cc_start: 0.9045 (m-80) cc_final: 0.8737 (m-80) REVERT: U 144 TYR cc_start: 0.9013 (p90) cc_final: 0.8366 (p90) REVERT: U 151 ARG cc_start: 0.8711 (ttm170) cc_final: 0.7871 (tpp80) REVERT: U 156 ARG cc_start: 0.9323 (ttp80) cc_final: 0.9077 (ttp80) REVERT: V 60 HIS cc_start: 0.8975 (m-70) cc_final: 0.8765 (m170) REVERT: V 123 LYS cc_start: 0.9498 (mmtt) cc_final: 0.9016 (mmtm) REVERT: V 143 PHE cc_start: 0.9595 (m-80) cc_final: 0.8871 (m-80) REVERT: V 160 CYS cc_start: 0.9481 (t) cc_final: 0.8174 (p) REVERT: V 161 THR cc_start: 0.9695 (m) cc_final: 0.9401 (p) REVERT: V 172 TYR cc_start: 0.9725 (t80) cc_final: 0.9403 (t80) REVERT: Y 163 ASP cc_start: 0.9401 (m-30) cc_final: 0.9193 (m-30) REVERT: Y 230 ASP cc_start: 0.9273 (m-30) cc_final: 0.8577 (p0) REVERT: Y 257 LEU cc_start: 0.9712 (mt) cc_final: 0.9357 (mt) REVERT: Y 260 ASP cc_start: 0.8996 (p0) cc_final: 0.8690 (p0) REVERT: Y 261 PHE cc_start: 0.9397 (p90) cc_final: 0.8876 (p90) REVERT: Y 290 ASN cc_start: 0.8869 (t0) cc_final: 0.8631 (t0) outliers start: 1 outliers final: 0 residues processed: 286 average time/residue: 0.1279 time to fit residues: 57.7264 Evaluate side-chains 217 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 217 time to evaluate : 0.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 98 optimal weight: 9.9990 chunk 177 optimal weight: 10.0000 chunk 60 optimal weight: 8.9990 chunk 27 optimal weight: 5.9990 chunk 136 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 168 optimal weight: 7.9990 chunk 4 optimal weight: 7.9990 chunk 207 optimal weight: 40.0000 chunk 132 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 372 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 12 ASN I 16 ASN ** I 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 174 GLN ** Y 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.045980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2536 r_free = 0.2536 target = 0.030783 restraints weight = 129356.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2579 r_free = 0.2579 target = 0.032075 restraints weight = 73529.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2609 r_free = 0.2609 target = 0.032986 restraints weight = 49336.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2630 r_free = 0.2630 target = 0.033644 restraints weight = 36603.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.2647 r_free = 0.2647 target = 0.034170 restraints weight = 29088.264| |-----------------------------------------------------------------------------| r_work (final): 0.2610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.5480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 19840 Z= 0.193 Angle : 0.635 12.733 26994 Z= 0.314 Chirality : 0.042 0.189 3130 Planarity : 0.004 0.036 3494 Dihedral : 7.505 164.456 2898 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 13.36 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.96 % Favored : 94.95 % Rotamer: Outliers : 0.05 % Allowed : 1.40 % Favored : 98.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.17), residues: 2298 helix: 0.74 (0.19), residues: 730 sheet: -0.92 (0.26), residues: 360 loop : -0.65 (0.18), residues: 1208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG Y 69 TYR 0.014 0.001 TYR G 33 PHE 0.037 0.002 PHE I 193 TRP 0.076 0.003 TRP G 357 HIS 0.015 0.002 HIS H 73 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.19 (19834) covalent geometry : angle 0.63536 / 0.31 (26994) hydrogen bonds : bond 0.03893 / 2.63 ( 920) hydrogen bonds : angle 4.72564 / 3.37 ( 2592) metal coordination : bond 0.00513 / 0.22 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 277 time to evaluate : 0.650 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: G 37 ASN cc_start: 0.9620 (t0) cc_final: 0.9267 (t0) REVERT: G 75 MET cc_start: 0.9418 (ptp) cc_final: 0.9064 (ptp) REVERT: G 86 MET cc_start: 0.9737 (tpp) cc_final: 0.9307 (tpp) REVERT: G 89 ILE cc_start: 0.9781 (pt) cc_final: 0.9532 (pt) REVERT: G 94 TYR cc_start: 0.9114 (m-80) cc_final: 0.8818 (m-80) REVERT: G 181 MET cc_start: 0.9119 (mmp) cc_final: 0.8864 (mmm) REVERT: G 227 ASN cc_start: 0.8570 (t0) cc_final: 0.8159 (t0) REVERT: G 314 LEU cc_start: 0.9864 (tt) cc_final: 0.9606 (pp) REVERT: G 347 LEU cc_start: 0.9877 (tp) cc_final: 0.9482 (tp) REVERT: H 16 MET cc_start: 0.9408 (mmm) cc_final: 0.8977 (mmm) REVERT: H 81 ASP cc_start: 0.9590 (m-30) cc_final: 0.9071 (t0) REVERT: H 82 MET cc_start: 0.9675 (tpt) cc_final: 0.9290 (tpp) REVERT: H 85 ILE cc_start: 0.9798 (mt) cc_final: 0.9445 (mt) REVERT: H 115 ASN cc_start: 0.9288 (t0) cc_final: 0.8871 (t0) REVERT: H 119 MET cc_start: 0.9457 (ptt) cc_final: 0.8813 (ptt) REVERT: H 123 MET cc_start: 0.9391 (tpp) cc_final: 0.9190 (tpp) REVERT: H 154 ASP cc_start: 0.9428 (t0) cc_final: 0.9048 (t0) REVERT: H 184 ASP cc_start: 0.9260 (m-30) cc_final: 0.8999 (m-30) REVERT: H 195 GLU cc_start: 0.9620 (tt0) cc_final: 0.9227 (tp30) REVERT: H 217 CYS cc_start: 0.9489 (m) cc_final: 0.9191 (m) REVERT: H 272 CYS cc_start: 0.8398 (p) cc_final: 0.8073 (p) REVERT: H 292 ASP cc_start: 0.9557 (m-30) cc_final: 0.8951 (p0) REVERT: H 305 MET cc_start: 0.9281 (mmt) cc_final: 0.8691 (mmm) REVERT: H 311 ASP cc_start: 0.9690 (m-30) cc_final: 0.9174 (p0) REVERT: H 313 MET cc_start: 0.9700 (mmp) cc_final: 0.9434 (mmm) REVERT: H 355 MET cc_start: 0.9748 (mmp) cc_final: 0.9501 (mmm) REVERT: H 374 CYS cc_start: 0.7925 (p) cc_final: 0.7361 (t) REVERT: I 75 MET cc_start: 0.8560 (ttp) cc_final: 0.7449 (tmm) REVERT: I 86 MET cc_start: 0.9705 (tpt) cc_final: 0.9252 (tpt) REVERT: I 91 GLN cc_start: 0.9746 (tt0) cc_final: 0.9431 (tp-100) REVERT: I 181 MET cc_start: 0.9296 (mmm) cc_final: 0.8939 (tpp) REVERT: I 189 ASP cc_start: 0.9382 (m-30) cc_final: 0.8967 (m-30) REVERT: I 290 LEU cc_start: 0.9766 (mt) cc_final: 0.9465 (mt) REVERT: J 19 ASP cc_start: 0.9165 (t0) cc_final: 0.8958 (t70) REVERT: J 64 LEU cc_start: 0.9857 (tp) cc_final: 0.9602 (tp) REVERT: J 70 GLU cc_start: 0.9768 (mm-30) cc_final: 0.9316 (mm-30) REVERT: J 174 GLU cc_start: 0.9577 (tp30) cc_final: 0.8730 (tm-30) REVERT: J 178 GLN cc_start: 0.9713 (mm-40) cc_final: 0.9361 (mm-40) REVERT: J 311 MET cc_start: 0.9257 (mmt) cc_final: 0.8639 (mmm) REVERT: J 322 GLU cc_start: 0.9556 (tt0) cc_final: 0.9011 (mt-10) REVERT: J 387 TRP cc_start: 0.9507 (p-90) cc_final: 0.9173 (p-90) REVERT: U 36 HIS cc_start: 0.9238 (m170) cc_final: 0.8928 (m170) REVERT: U 38 LYS cc_start: 0.9066 (ttpp) cc_final: 0.8590 (tmmt) REVERT: U 90 PHE cc_start: 0.9053 (m-80) cc_final: 0.8743 (m-80) REVERT: U 99 MET cc_start: 0.9160 (tpt) cc_final: 0.8878 (tpp) REVERT: U 144 TYR cc_start: 0.9159 (p90) cc_final: 0.8377 (p90) REVERT: U 151 ARG cc_start: 0.8727 (ttm170) cc_final: 0.7886 (tpp80) REVERT: U 162 LEU cc_start: 0.9497 (pt) cc_final: 0.9277 (tp) REVERT: V 123 LYS cc_start: 0.9479 (mmtt) cc_final: 0.8974 (mmtm) REVERT: V 143 PHE cc_start: 0.9562 (m-80) cc_final: 0.8812 (m-80) REVERT: V 160 CYS cc_start: 0.9411 (t) cc_final: 0.8108 (p) REVERT: V 161 THR cc_start: 0.9701 (m) cc_final: 0.9317 (p) REVERT: Y 163 ASP cc_start: 0.9374 (m-30) cc_final: 0.9166 (m-30) REVERT: Y 230 ASP cc_start: 0.9274 (m-30) cc_final: 0.8581 (p0) REVERT: Y 260 ASP cc_start: 0.8992 (p0) cc_final: 0.8681 (p0) REVERT: Y 261 PHE cc_start: 0.9393 (p90) cc_final: 0.8877 (p90) outliers start: 1 outliers final: 0 residues processed: 278 average time/residue: 0.1285 time to fit residues: 56.7779 Evaluate side-chains 200 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 200 time to evaluate : 0.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 218 optimal weight: 5.9990 chunk 152 optimal weight: 0.3980 chunk 14 optimal weight: 10.0000 chunk 69 optimal weight: 6.9990 chunk 131 optimal weight: 10.0000 chunk 182 optimal weight: 9.9990 chunk 158 optimal weight: 20.0000 chunk 178 optimal weight: 7.9990 chunk 103 optimal weight: 7.9990 chunk 77 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 overall best weight: 3.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 372 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 354 GLN ** I 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 65 HIS I 178 HIS ** I 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 49 HIS Y 81 HIS ** Y 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.045118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2523 r_free = 0.2523 target = 0.030341 restraints weight = 130252.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.2565 r_free = 0.2565 target = 0.031592 restraints weight = 74994.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2595 r_free = 0.2595 target = 0.032486 restraints weight = 50581.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2616 r_free = 0.2616 target = 0.033146 restraints weight = 37570.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2632 r_free = 0.2632 target = 0.033652 restraints weight = 29776.190| |-----------------------------------------------------------------------------| r_work (final): 0.2595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.5788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 19840 Z= 0.230 Angle : 0.657 11.741 26994 Z= 0.327 Chirality : 0.042 0.219 3130 Planarity : 0.004 0.037 3494 Dihedral : 7.435 158.088 2898 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 14.54 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.57 % Favored : 94.34 % Rotamer: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.46 (0.17), residues: 2298 helix: 0.63 (0.19), residues: 734 sheet: -0.83 (0.26), residues: 371 loop : -0.66 (0.18), residues: 1193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG U 115 TYR 0.019 0.002 TYR G 197 PHE 0.025 0.002 PHE H 90 TRP 0.080 0.003 TRP G 357 HIS 0.014 0.002 HIS H 73 Details of bonding type rmsd/Z covalent geometry : bond 0.00469 / 0.23 (19834) covalent geometry : angle 0.65661 / 0.33 (26994) hydrogen bonds : bond 0.03944 / 2.68 ( 920) hydrogen bonds : angle 4.84054 / 3.44 ( 2592) metal coordination : bond 0.00450 / 0.22 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 257 time to evaluate : 0.570 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: G 15 ASP cc_start: 0.9223 (t0) cc_final: 0.8768 (t0) REVERT: G 37 ASN cc_start: 0.9648 (t0) cc_final: 0.9332 (t0) REVERT: G 75 MET cc_start: 0.9406 (ptp) cc_final: 0.9136 (ptp) REVERT: G 86 MET cc_start: 0.9788 (tpp) cc_final: 0.9427 (tpp) REVERT: G 166 HIS cc_start: 0.9082 (p90) cc_final: 0.8791 (p90) REVERT: G 181 MET cc_start: 0.9130 (mmp) cc_final: 0.8857 (mmm) REVERT: G 227 ASN cc_start: 0.8600 (t0) cc_final: 0.8188 (t0) REVERT: G 314 LEU cc_start: 0.9871 (tt) cc_final: 0.9613 (pp) REVERT: G 347 LEU cc_start: 0.9879 (tp) cc_final: 0.9491 (tp) REVERT: H 16 MET cc_start: 0.9416 (mmm) cc_final: 0.9009 (mmm) REVERT: H 78 ASN cc_start: 0.9038 (t0) cc_final: 0.8408 (t0) REVERT: H 81 ASP cc_start: 0.9616 (m-30) cc_final: 0.9371 (m-30) REVERT: H 82 MET cc_start: 0.9695 (tpt) cc_final: 0.9365 (tpp) REVERT: H 115 ASN cc_start: 0.9313 (t0) cc_final: 0.8899 (t0) REVERT: H 119 MET cc_start: 0.9495 (ptt) cc_final: 0.8947 (ptt) REVERT: H 123 MET cc_start: 0.9228 (tpp) cc_final: 0.8987 (tpp) REVERT: H 154 ASP cc_start: 0.9383 (t0) cc_final: 0.9034 (t0) REVERT: H 184 ASP cc_start: 0.9210 (m-30) cc_final: 0.8961 (m-30) REVERT: H 190 MET cc_start: 0.9367 (mmm) cc_final: 0.8959 (mmm) REVERT: H 195 GLU cc_start: 0.9619 (tt0) cc_final: 0.9231 (tp30) REVERT: H 217 CYS cc_start: 0.9562 (m) cc_final: 0.9230 (m) REVERT: H 272 CYS cc_start: 0.8438 (p) cc_final: 0.8124 (p) REVERT: H 292 ASP cc_start: 0.9582 (m-30) cc_final: 0.8998 (p0) REVERT: H 305 MET cc_start: 0.9254 (mmt) cc_final: 0.8681 (mmm) REVERT: H 311 ASP cc_start: 0.9708 (m-30) cc_final: 0.9191 (p0) REVERT: H 313 MET cc_start: 0.9705 (mmp) cc_final: 0.9404 (mmm) REVERT: H 355 MET cc_start: 0.9797 (mmp) cc_final: 0.9547 (mmm) REVERT: H 374 CYS cc_start: 0.8179 (p) cc_final: 0.7563 (t) REVERT: I 44 HIS cc_start: 0.9398 (t70) cc_final: 0.9146 (t70) REVERT: I 86 MET cc_start: 0.9704 (tpt) cc_final: 0.9264 (tpt) REVERT: I 91 GLN cc_start: 0.9774 (tt0) cc_final: 0.9440 (tp-100) REVERT: I 189 ASP cc_start: 0.9351 (m-30) cc_final: 0.8948 (m-30) REVERT: J 19 ASP cc_start: 0.9235 (t0) cc_final: 0.9032 (t70) REVERT: J 64 LEU cc_start: 0.9863 (tp) cc_final: 0.9614 (tp) REVERT: J 70 GLU cc_start: 0.9775 (mm-30) cc_final: 0.9326 (mm-30) REVERT: J 174 GLU cc_start: 0.9539 (tp30) cc_final: 0.8699 (tm-30) REVERT: J 178 GLN cc_start: 0.9686 (mm-40) cc_final: 0.9273 (mm-40) REVERT: J 311 MET cc_start: 0.9390 (mmt) cc_final: 0.8789 (mmm) REVERT: J 322 GLU cc_start: 0.9575 (tt0) cc_final: 0.9034 (mt-10) REVERT: J 387 TRP cc_start: 0.9536 (p-90) cc_final: 0.9241 (p-90) REVERT: U 36 HIS cc_start: 0.9212 (m170) cc_final: 0.8828 (m170) REVERT: U 90 PHE cc_start: 0.8949 (m-80) cc_final: 0.8633 (m-80) REVERT: U 168 MET cc_start: 0.9685 (mmp) cc_final: 0.9481 (mmm) REVERT: V 123 LYS cc_start: 0.9496 (mmtt) cc_final: 0.9031 (mmtm) REVERT: V 143 PHE cc_start: 0.9519 (m-80) cc_final: 0.8750 (m-80) REVERT: V 160 CYS cc_start: 0.9321 (t) cc_final: 0.8078 (p) REVERT: V 161 THR cc_start: 0.9689 (m) cc_final: 0.9338 (p) REVERT: Y 163 ASP cc_start: 0.9371 (m-30) cc_final: 0.9163 (m-30) REVERT: Y 230 ASP cc_start: 0.9279 (m-30) cc_final: 0.8587 (p0) REVERT: Y 260 ASP cc_start: 0.9050 (p0) cc_final: 0.8770 (p0) REVERT: Y 261 PHE cc_start: 0.9410 (p90) cc_final: 0.8948 (p90) outliers start: 0 outliers final: 0 residues processed: 257 average time/residue: 0.1294 time to fit residues: 52.3786 Evaluate side-chains 189 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 189 time to evaluate : 0.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 37 optimal weight: 9.9990 chunk 16 optimal weight: 4.9990 chunk 225 optimal weight: 0.8980 chunk 29 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 189 optimal weight: 0.9980 chunk 137 optimal weight: 0.9990 chunk 135 optimal weight: 9.9990 chunk 155 optimal weight: 40.0000 chunk 180 optimal weight: 0.0980 chunk 230 optimal weight: 2.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 16 ASN H 59 GLN I 16 ASN I 65 HIS ** I 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 174 GLN Y 49 HIS ** Y 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.046398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2556 r_free = 0.2556 target = 0.031090 restraints weight = 125450.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2599 r_free = 0.2599 target = 0.032388 restraints weight = 70435.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2630 r_free = 0.2630 target = 0.033343 restraints weight = 47249.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2652 r_free = 0.2652 target = 0.034035 restraints weight = 34829.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2669 r_free = 0.2669 target = 0.034553 restraints weight = 27487.216| |-----------------------------------------------------------------------------| r_work (final): 0.2630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.5807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 19840 Z= 0.124 Angle : 0.600 11.240 26994 Z= 0.295 Chirality : 0.042 0.150 3130 Planarity : 0.004 0.040 3494 Dihedral : 7.022 150.758 2898 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.70 % Favored : 95.21 % Rotamer: Outliers : 0.05 % Allowed : 0.43 % Favored : 99.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.17), residues: 2298 helix: 0.96 (0.19), residues: 720 sheet: -0.61 (0.28), residues: 337 loop : -0.47 (0.18), residues: 1241 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG U 24 TYR 0.014 0.001 TYR V 107 PHE 0.016 0.001 PHE G 193 TRP 0.089 0.003 TRP G 357 HIS 0.009 0.001 HIS H 73 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 (19834) covalent geometry : angle 0.59964 / 0.30 (26994) hydrogen bonds : bond 0.03662 / 2.46 ( 920) hydrogen bonds : angle 4.50826 / 3.20 ( 2592) metal coordination : bond 0.00167 / 0.08 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 276 time to evaluate : 0.746 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: G 15 ASP cc_start: 0.9290 (t0) cc_final: 0.8901 (t0) REVERT: G 37 ASN cc_start: 0.9625 (t0) cc_final: 0.9271 (t0) REVERT: G 75 MET cc_start: 0.9424 (ptp) cc_final: 0.8648 (tmm) REVERT: G 86 MET cc_start: 0.9788 (tpp) cc_final: 0.9423 (tpp) REVERT: G 94 TYR cc_start: 0.9206 (m-80) cc_final: 0.8868 (m-80) REVERT: G 141 MET cc_start: 0.9292 (ppp) cc_final: 0.9046 (ppp) REVERT: G 166 HIS cc_start: 0.9065 (p90) cc_final: 0.8627 (p90) REVERT: G 181 MET cc_start: 0.9100 (mmp) cc_final: 0.8791 (mmm) REVERT: G 227 ASN cc_start: 0.8627 (t0) cc_final: 0.8254 (t0) REVERT: G 314 LEU cc_start: 0.9873 (tt) cc_final: 0.9613 (pp) REVERT: G 347 LEU cc_start: 0.9873 (tp) cc_final: 0.9440 (tp) REVERT: H 16 MET cc_start: 0.9329 (mmm) cc_final: 0.8824 (mmm) REVERT: H 78 ASN cc_start: 0.9058 (t0) cc_final: 0.8334 (t0) REVERT: H 81 ASP cc_start: 0.9616 (m-30) cc_final: 0.9355 (m-30) REVERT: H 82 MET cc_start: 0.9710 (tpt) cc_final: 0.9424 (tpp) REVERT: H 115 ASN cc_start: 0.9120 (t0) cc_final: 0.8756 (t0) REVERT: H 119 MET cc_start: 0.9447 (ptt) cc_final: 0.8816 (ptt) REVERT: H 123 MET cc_start: 0.9232 (tpp) cc_final: 0.8886 (tpp) REVERT: H 129 THR cc_start: 0.9190 (p) cc_final: 0.8957 (t) REVERT: H 154 ASP cc_start: 0.9415 (t0) cc_final: 0.8997 (t0) REVERT: H 190 MET cc_start: 0.9327 (mmm) cc_final: 0.9032 (mmm) REVERT: H 195 GLU cc_start: 0.9659 (tt0) cc_final: 0.9271 (tp30) REVERT: H 217 CYS cc_start: 0.9509 (m) cc_final: 0.9184 (m) REVERT: H 272 CYS cc_start: 0.8358 (p) cc_final: 0.8055 (p) REVERT: H 292 ASP cc_start: 0.9573 (m-30) cc_final: 0.8876 (p0) REVERT: H 305 MET cc_start: 0.9320 (mmt) cc_final: 0.8723 (mmm) REVERT: H 311 ASP cc_start: 0.9702 (m-30) cc_final: 0.9176 (p0) REVERT: H 313 MET cc_start: 0.9719 (mmp) cc_final: 0.9431 (mmm) REVERT: H 355 MET cc_start: 0.9777 (mmp) cc_final: 0.9476 (mmm) REVERT: H 374 CYS cc_start: 0.8084 (p) cc_final: 0.7520 (t) REVERT: I 75 MET cc_start: 0.8226 (ttp) cc_final: 0.7029 (tmm) REVERT: I 86 MET cc_start: 0.9708 (tpt) cc_final: 0.9332 (tpt) REVERT: I 91 GLN cc_start: 0.9739 (tt0) cc_final: 0.9393 (tp-100) REVERT: I 181 MET cc_start: 0.9230 (tpp) cc_final: 0.7532 (mtt) REVERT: I 290 LEU cc_start: 0.9756 (mt) cc_final: 0.9487 (mt) REVERT: J 19 ASP cc_start: 0.9259 (t0) cc_final: 0.8835 (t0) REVERT: J 64 LEU cc_start: 0.9848 (tp) cc_final: 0.9610 (tp) REVERT: J 70 GLU cc_start: 0.9771 (mm-30) cc_final: 0.9326 (mm-30) REVERT: J 174 GLU cc_start: 0.9497 (tp30) cc_final: 0.8641 (tm-30) REVERT: J 178 GLN cc_start: 0.9679 (mm-40) cc_final: 0.9339 (mm-40) REVERT: J 311 MET cc_start: 0.9429 (mmt) cc_final: 0.8767 (mmm) REVERT: J 319 LEU cc_start: 0.9810 (tp) cc_final: 0.9538 (mm) REVERT: J 322 GLU cc_start: 0.9608 (tt0) cc_final: 0.8984 (mt-10) REVERT: J 387 TRP cc_start: 0.9409 (p-90) cc_final: 0.9081 (p-90) REVERT: U 36 HIS cc_start: 0.9191 (m170) cc_final: 0.8879 (m170) REVERT: U 38 LYS cc_start: 0.9160 (ttpp) cc_final: 0.8741 (tmmt) REVERT: U 90 PHE cc_start: 0.9193 (m-80) cc_final: 0.8956 (m-80) REVERT: U 151 ARG cc_start: 0.8628 (ttm170) cc_final: 0.7804 (tpp80) REVERT: V 123 LYS cc_start: 0.9415 (mmtt) cc_final: 0.8893 (mmtm) REVERT: V 143 PHE cc_start: 0.9513 (m-80) cc_final: 0.8836 (m-80) REVERT: V 161 THR cc_start: 0.9699 (m) cc_final: 0.9361 (p) REVERT: Y 230 ASP cc_start: 0.9283 (m-30) cc_final: 0.8605 (p0) REVERT: Y 260 ASP cc_start: 0.8976 (p0) cc_final: 0.8658 (p0) REVERT: Y 261 PHE cc_start: 0.9357 (p90) cc_final: 0.8845 (p90) REVERT: Y 319 MET cc_start: 0.9624 (tpt) cc_final: 0.8890 (ptt) outliers start: 1 outliers final: 0 residues processed: 277 average time/residue: 0.1301 time to fit residues: 57.2114 Evaluate side-chains 201 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 201 time to evaluate : 0.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 232 optimal weight: 6.9990 chunk 255 optimal weight: 30.0000 chunk 233 optimal weight: 6.9990 chunk 231 optimal weight: 9.9990 chunk 15 optimal weight: 10.0000 chunk 37 optimal weight: 10.0000 chunk 63 optimal weight: 2.9990 chunk 180 optimal weight: 3.9990 chunk 59 optimal weight: 3.9990 chunk 26 optimal weight: 5.9990 chunk 141 optimal weight: 8.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 206 HIS ** G 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 372 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 174 GLN ** Y 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.044456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2509 r_free = 0.2509 target = 0.029865 restraints weight = 130913.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2550 r_free = 0.2550 target = 0.031070 restraints weight = 76093.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2579 r_free = 0.2579 target = 0.031933 restraints weight = 51793.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2603 r_free = 0.2603 target = 0.032624 restraints weight = 38671.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2619 r_free = 0.2619 target = 0.033123 restraints weight = 30538.673| |-----------------------------------------------------------------------------| r_work (final): 0.2584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.6232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 19840 Z= 0.272 Angle : 0.695 13.268 26994 Z= 0.346 Chirality : 0.043 0.259 3130 Planarity : 0.005 0.044 3494 Dihedral : 7.168 144.336 2898 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 16.66 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.87 % Favored : 94.04 % Rotamer: Outliers : 0.05 % Allowed : 0.59 % Favored : 99.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.50 (0.17), residues: 2298 helix: 0.49 (0.19), residues: 743 sheet: -0.92 (0.26), residues: 363 loop : -0.58 (0.18), residues: 1192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 336 TYR 0.017 0.002 TYR G 197 PHE 0.019 0.002 PHE H 90 TRP 0.089 0.004 TRP G 357 HIS 0.013 0.002 HIS G 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00551 / 0.27 (19834) covalent geometry : angle 0.69541 / 0.35 (26994) hydrogen bonds : bond 0.03947 / 2.70 ( 920) hydrogen bonds : angle 4.89539 / 3.48 ( 2592) metal coordination : bond 0.00607 / 0.30 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 241 time to evaluate : 0.674 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: G 15 ASP cc_start: 0.9274 (t0) cc_final: 0.8917 (t0) REVERT: G 37 ASN cc_start: 0.9635 (t0) cc_final: 0.9329 (t0) REVERT: G 75 MET cc_start: 0.9418 (ptp) cc_final: 0.9137 (ptp) REVERT: G 86 MET cc_start: 0.9794 (tpp) cc_final: 0.9448 (tpp) REVERT: G 141 MET cc_start: 0.9397 (ppp) cc_final: 0.9192 (ppp) REVERT: G 166 HIS cc_start: 0.9037 (p90) cc_final: 0.8783 (p90) REVERT: G 181 MET cc_start: 0.9218 (mmp) cc_final: 0.8851 (mmm) REVERT: G 227 ASN cc_start: 0.8589 (t0) cc_final: 0.8261 (t0) REVERT: G 314 LEU cc_start: 0.9874 (tt) cc_final: 0.9659 (pp) REVERT: G 347 LEU cc_start: 0.9871 (tp) cc_final: 0.9535 (tp) REVERT: H 78 ASN cc_start: 0.9246 (t0) cc_final: 0.8727 (t0) REVERT: H 81 ASP cc_start: 0.9594 (m-30) cc_final: 0.9350 (m-30) REVERT: H 82 MET cc_start: 0.9718 (tpt) cc_final: 0.9497 (tpt) REVERT: H 115 ASN cc_start: 0.9322 (t0) cc_final: 0.8874 (t0) REVERT: H 119 MET cc_start: 0.9404 (ptt) cc_final: 0.8789 (ptt) REVERT: H 132 MET cc_start: 0.9215 (tmm) cc_final: 0.8710 (tmm) REVERT: H 154 ASP cc_start: 0.9382 (t0) cc_final: 0.9036 (t0) REVERT: H 184 ASP cc_start: 0.9283 (m-30) cc_final: 0.9058 (m-30) REVERT: H 190 MET cc_start: 0.9375 (mmm) cc_final: 0.8999 (mmm) REVERT: H 195 GLU cc_start: 0.9670 (tt0) cc_final: 0.9257 (tp30) REVERT: H 217 CYS cc_start: 0.9501 (m) cc_final: 0.9211 (m) REVERT: H 272 CYS cc_start: 0.8407 (p) cc_final: 0.8145 (p) REVERT: H 292 ASP cc_start: 0.9592 (m-30) cc_final: 0.9128 (p0) REVERT: H 305 MET cc_start: 0.9266 (mmt) cc_final: 0.8796 (mmm) REVERT: H 311 ASP cc_start: 0.9702 (m-30) cc_final: 0.9206 (p0) REVERT: H 313 MET cc_start: 0.9707 (mmp) cc_final: 0.9430 (mmm) REVERT: H 355 MET cc_start: 0.9787 (mmp) cc_final: 0.9536 (mmm) REVERT: I 37 ASN cc_start: 0.9197 (t0) cc_final: 0.8974 (t0) REVERT: I 44 HIS cc_start: 0.9307 (t-90) cc_final: 0.9084 (t70) REVERT: I 86 MET cc_start: 0.9681 (tpt) cc_final: 0.9240 (tpt) REVERT: I 91 GLN cc_start: 0.9754 (tt0) cc_final: 0.9382 (tp-100) REVERT: I 181 MET cc_start: 0.9279 (tpp) cc_final: 0.8845 (mmm) REVERT: I 189 ASP cc_start: 0.9269 (m-30) cc_final: 0.9009 (m-30) REVERT: J 19 ASP cc_start: 0.9181 (t0) cc_final: 0.8932 (t70) REVERT: J 64 LEU cc_start: 0.9854 (tp) cc_final: 0.9620 (tp) REVERT: J 70 GLU cc_start: 0.9772 (mm-30) cc_final: 0.9367 (tm-30) REVERT: J 174 GLU cc_start: 0.9571 (tp30) cc_final: 0.8801 (tm-30) REVERT: J 178 GLN cc_start: 0.9693 (mm-40) cc_final: 0.9284 (mm-40) REVERT: J 311 MET cc_start: 0.9420 (mmt) cc_final: 0.8761 (mmm) REVERT: J 322 GLU cc_start: 0.9599 (tt0) cc_final: 0.9062 (mt-10) REVERT: J 387 TRP cc_start: 0.9539 (p-90) cc_final: 0.9250 (p-90) REVERT: U 36 HIS cc_start: 0.9224 (m170) cc_final: 0.8885 (m170) REVERT: U 90 PHE cc_start: 0.9015 (m-80) cc_final: 0.8809 (m-80) REVERT: U 108 GLU cc_start: 0.9636 (mt-10) cc_final: 0.9390 (mt-10) REVERT: U 112 TYR cc_start: 0.9229 (t80) cc_final: 0.8788 (t80) REVERT: U 125 ILE cc_start: 0.9206 (tp) cc_final: 0.8805 (tp) REVERT: V 123 LYS cc_start: 0.9511 (mmtt) cc_final: 0.9017 (mmtm) REVERT: V 143 PHE cc_start: 0.9398 (m-80) cc_final: 0.8865 (m-80) REVERT: V 161 THR cc_start: 0.9664 (m) cc_final: 0.9213 (m) REVERT: V 165 MET cc_start: 0.9441 (mmp) cc_final: 0.9157 (mmp) REVERT: Y 163 ASP cc_start: 0.9389 (m-30) cc_final: 0.9152 (m-30) REVERT: Y 230 ASP cc_start: 0.9399 (m-30) cc_final: 0.8479 (p0) REVERT: Y 260 ASP cc_start: 0.9038 (p0) cc_final: 0.8767 (p0) REVERT: Y 261 PHE cc_start: 0.9423 (p90) cc_final: 0.8960 (p90) REVERT: Y 319 MET cc_start: 0.9632 (tpt) cc_final: 0.9395 (tpp) outliers start: 1 outliers final: 0 residues processed: 242 average time/residue: 0.1297 time to fit residues: 49.6750 Evaluate side-chains 179 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 179 time to evaluate : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 34 optimal weight: 0.9990 chunk 222 optimal weight: 1.9990 chunk 229 optimal weight: 2.9990 chunk 237 optimal weight: 2.9990 chunk 59 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 217 optimal weight: 7.9990 chunk 258 optimal weight: 30.0000 chunk 241 optimal weight: 40.0000 chunk 189 optimal weight: 20.0000 chunk 23 optimal weight: 3.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 372 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 16 ASN I 65 HIS ** I 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.045398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2527 r_free = 0.2527 target = 0.030357 restraints weight = 130777.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2571 r_free = 0.2571 target = 0.031644 restraints weight = 73681.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2601 r_free = 0.2601 target = 0.032540 restraints weight = 49240.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2624 r_free = 0.2624 target = 0.033231 restraints weight = 36620.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2638 r_free = 0.2638 target = 0.033699 restraints weight = 28862.272| |-----------------------------------------------------------------------------| r_work (final): 0.2600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.6276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 19840 Z= 0.174 Angle : 0.627 11.429 26994 Z= 0.309 Chirality : 0.042 0.175 3130 Planarity : 0.004 0.046 3494 Dihedral : 6.842 134.483 2898 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 13.79 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.44 % Favored : 94.47 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.17), residues: 2298 helix: 0.66 (0.19), residues: 737 sheet: -0.87 (0.26), residues: 360 loop : -0.49 (0.18), residues: 1201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG J 87 TYR 0.018 0.001 TYR V 107 PHE 0.018 0.001 PHE H 90 TRP 0.099 0.003 TRP G 357 HIS 0.010 0.002 HIS H 73 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.17 (19834) covalent geometry : angle 0.62679 / 0.31 (26994) hydrogen bonds : bond 0.03739 / 2.54 ( 920) hydrogen bonds : angle 4.68934 / 3.33 ( 2592) metal coordination : bond 0.00344 / 0.16 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 254 time to evaluate : 0.689 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: G 15 ASP cc_start: 0.9293 (t0) cc_final: 0.9005 (t0) REVERT: G 37 ASN cc_start: 0.9628 (t0) cc_final: 0.9346 (t0) REVERT: G 75 MET cc_start: 0.9444 (ptp) cc_final: 0.8680 (tmm) REVERT: G 86 MET cc_start: 0.9786 (tpp) cc_final: 0.9349 (tpp) REVERT: G 94 TYR cc_start: 0.9381 (m-80) cc_final: 0.9091 (m-80) REVERT: G 166 HIS cc_start: 0.9070 (p90) cc_final: 0.8774 (p90) REVERT: G 181 MET cc_start: 0.9157 (mmp) cc_final: 0.8779 (mmm) REVERT: G 227 ASN cc_start: 0.8679 (t0) cc_final: 0.8389 (t0) REVERT: G 314 LEU cc_start: 0.9881 (tt) cc_final: 0.9661 (pp) REVERT: G 347 LEU cc_start: 0.9874 (tp) cc_final: 0.9649 (tp) REVERT: G 356 MET cc_start: 0.8722 (mmp) cc_final: 0.8510 (mmm) REVERT: H 44 MET cc_start: 0.8806 (ppp) cc_final: 0.8574 (ppp) REVERT: H 78 ASN cc_start: 0.9256 (t0) cc_final: 0.8610 (t0) REVERT: H 81 ASP cc_start: 0.9599 (m-30) cc_final: 0.9350 (m-30) REVERT: H 90 PHE cc_start: 0.9750 (m-80) cc_final: 0.9509 (m-10) REVERT: H 115 ASN cc_start: 0.9220 (t0) cc_final: 0.8828 (t0) REVERT: H 119 MET cc_start: 0.9402 (ptt) cc_final: 0.8846 (ptt) REVERT: H 132 MET cc_start: 0.9424 (tmm) cc_final: 0.8934 (tmm) REVERT: H 154 ASP cc_start: 0.9369 (t0) cc_final: 0.8981 (t0) REVERT: H 184 ASP cc_start: 0.9253 (m-30) cc_final: 0.9038 (m-30) REVERT: H 190 MET cc_start: 0.9354 (mmm) cc_final: 0.8987 (mmm) REVERT: H 195 GLU cc_start: 0.9635 (tt0) cc_final: 0.9252 (tp30) REVERT: H 217 CYS cc_start: 0.9536 (m) cc_final: 0.9218 (m) REVERT: H 272 CYS cc_start: 0.8390 (p) cc_final: 0.8138 (p) REVERT: H 292 ASP cc_start: 0.9602 (m-30) cc_final: 0.9025 (p0) REVERT: H 305 MET cc_start: 0.9278 (mmt) cc_final: 0.8667 (mmm) REVERT: H 311 ASP cc_start: 0.9712 (m-30) cc_final: 0.9187 (p0) REVERT: H 313 MET cc_start: 0.9728 (mmp) cc_final: 0.9438 (mmm) REVERT: H 355 MET cc_start: 0.9785 (mmp) cc_final: 0.9507 (mmm) REVERT: H 374 CYS cc_start: 0.8067 (p) cc_final: 0.7612 (t) REVERT: I 37 ASN cc_start: 0.9213 (t0) cc_final: 0.8958 (t0) REVERT: I 75 MET cc_start: 0.8360 (ttp) cc_final: 0.7077 (tmm) REVERT: I 86 MET cc_start: 0.9686 (tpt) cc_final: 0.9257 (tpt) REVERT: I 91 GLN cc_start: 0.9766 (tt0) cc_final: 0.9362 (tp-100) REVERT: I 181 MET cc_start: 0.9243 (tpp) cc_final: 0.7494 (mtt) REVERT: I 189 ASP cc_start: 0.9285 (m-30) cc_final: 0.9033 (m-30) REVERT: J 19 ASP cc_start: 0.9205 (t0) cc_final: 0.8752 (t0) REVERT: J 64 LEU cc_start: 0.9860 (tp) cc_final: 0.9631 (tp) REVERT: J 70 GLU cc_start: 0.9763 (mm-30) cc_final: 0.9379 (tm-30) REVERT: J 174 GLU cc_start: 0.9527 (tp30) cc_final: 0.8743 (tm-30) REVERT: J 178 GLN cc_start: 0.9698 (mm-40) cc_final: 0.9286 (mm-40) REVERT: J 301 GLU cc_start: 0.9402 (mt-10) cc_final: 0.9140 (mt-10) REVERT: J 311 MET cc_start: 0.9468 (mmt) cc_final: 0.8786 (mmm) REVERT: J 319 LEU cc_start: 0.9818 (tp) cc_final: 0.9511 (mm) REVERT: J 322 GLU cc_start: 0.9610 (tt0) cc_final: 0.9019 (mt-10) REVERT: J 387 TRP cc_start: 0.9486 (p-90) cc_final: 0.9219 (p-90) REVERT: U 36 HIS cc_start: 0.9255 (m170) cc_final: 0.8931 (m170) REVERT: U 90 PHE cc_start: 0.9120 (m-80) cc_final: 0.8876 (m-80) REVERT: U 108 GLU cc_start: 0.9653 (mt-10) cc_final: 0.9356 (mt-10) REVERT: U 125 ILE cc_start: 0.9281 (tp) cc_final: 0.8946 (tp) REVERT: V 123 LYS cc_start: 0.9444 (mmtt) cc_final: 0.8897 (mmtm) REVERT: V 143 PHE cc_start: 0.9396 (m-80) cc_final: 0.9022 (m-80) REVERT: V 165 MET cc_start: 0.9430 (mmp) cc_final: 0.9202 (mmp) REVERT: V 172 TYR cc_start: 0.9729 (t80) cc_final: 0.9339 (t80) REVERT: Y 163 ASP cc_start: 0.9397 (m-30) cc_final: 0.9177 (m-30) REVERT: Y 230 ASP cc_start: 0.9372 (m-30) cc_final: 0.8490 (p0) REVERT: Y 260 ASP cc_start: 0.9013 (p0) cc_final: 0.8742 (p0) REVERT: Y 261 PHE cc_start: 0.9379 (p90) cc_final: 0.8895 (p90) REVERT: Y 319 MET cc_start: 0.9646 (tpt) cc_final: 0.9384 (tpp) outliers start: 0 outliers final: 0 residues processed: 254 average time/residue: 0.1305 time to fit residues: 52.4930 Evaluate side-chains 186 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 186 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 35 optimal weight: 0.9980 chunk 252 optimal weight: 30.0000 chunk 183 optimal weight: 20.0000 chunk 59 optimal weight: 3.9990 chunk 101 optimal weight: 7.9990 chunk 10 optimal weight: 0.6980 chunk 198 optimal weight: 10.0000 chunk 60 optimal weight: 0.8980 chunk 12 optimal weight: 0.9980 chunk 151 optimal weight: 10.0000 chunk 47 optimal weight: 1.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 16 ASN I 65 HIS ** I 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 193 GLN U 140 ASN V 60 HIS V 174 GLN ** Y 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.046230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2556 r_free = 0.2556 target = 0.031010 restraints weight = 125006.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2599 r_free = 0.2599 target = 0.032294 restraints weight = 71585.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2630 r_free = 0.2630 target = 0.033244 restraints weight = 48287.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2652 r_free = 0.2652 target = 0.033928 restraints weight = 35730.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2669 r_free = 0.2669 target = 0.034452 restraints weight = 28311.906| |-----------------------------------------------------------------------------| r_work (final): 0.2634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.6276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 19840 Z= 0.123 Angle : 0.612 11.468 26994 Z= 0.299 Chirality : 0.042 0.151 3130 Planarity : 0.004 0.048 3494 Dihedral : 6.486 133.204 2898 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.83 % Favored : 95.08 % Rotamer: Outliers : 0.11 % Allowed : 0.32 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.18), residues: 2298 helix: 0.85 (0.19), residues: 724 sheet: -0.69 (0.27), residues: 349 loop : -0.43 (0.18), residues: 1225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG U 151 TYR 0.017 0.001 TYR V 107 PHE 0.016 0.001 PHE H 352 TRP 0.099 0.003 TRP G 357 HIS 0.009 0.001 HIS H 73 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.12 (19834) covalent geometry : angle 0.61228 / 0.30 (26994) hydrogen bonds : bond 0.03581 / 2.42 ( 920) hydrogen bonds : angle 4.48803 / 3.19 ( 2592) metal coordination : bond 0.00173 / 0.08 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2846.24 seconds wall clock time: 50 minutes 11.86 seconds (3011.86 seconds total)