Starting phenix.real_space_refine on Sun Sep 13 00:41:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6znm_11317/09_2026/6znm_11317.cif Found real_map, /net/cci-nas-00/data/ceres_data/6znm_11317/09_2026/6znm_11317.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/6znm_11317/09_2026/6znm_11317.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6znm_11317/09_2026/6znm_11317.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6znm_11317/09_2026/6znm_11317.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6znm_11317/09_2026/6znm_11317.map" model { file = "/net/cci-nas-00/data/ceres_data/6znm_11317/09_2026/6znm_11317.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6znm_11317/09_2026/6znm_11317.cif" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 3 6.06 5 P 9 5.49 5 S 97 5.16 5 C 12189 2.51 5 N 3377 2.21 5 O 3578 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 47 residue(s): 0.02s 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: 19253 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: "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: 373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 373 Classifications: {'peptide': 75} Incomplete info: {'truncation_to_alanine': 71} Link IDs: {'TRANS': 74} Unresolved non-hydrogen bonds: 257 Unresolved non-hydrogen angles: 324 Unresolved non-hydrogen dihedrals: 199 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'GLU:plan': 11, 'GLN:plan1': 10, 'ASP:plan': 5, 'ARG:plan': 7, 'HIS:plan': 3, 'ASN:plan1': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 159 Chain: "X" Number of atoms: 320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 320 Classifications: {'peptide': 64} Incomplete info: {'truncation_to_alanine': 64} Link IDs: {'TRANS': 63} Unresolved non-hydrogen bonds: 128 Unresolved non-hydrogen angles: 192 Unresolved non-hydrogen dihedrals: 64 Planarities with less than four sites: {'UNK:plan-1': 64} Unresolved non-hydrogen planarities: 64 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: 373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 373 Classifications: {'peptide': 75} Incomplete info: {'truncation_to_alanine': 71} Link IDs: {'TRANS': 74} Unresolved non-hydrogen bonds: 257 Unresolved non-hydrogen angles: 324 Unresolved non-hydrogen dihedrals: 199 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'GLU:plan': 11, 'GLN:plan1': 10, 'ASP:plan': 5, 'ARG:plan': 7, 'HIS:plan': 3, 'ASN:plan1': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 159 Chain: "x" Number of atoms: 335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 335 Classifications: {'peptide': 67} Incomplete info: {'truncation_to_alanine': 67} Link IDs: {'TRANS': 66} Unresolved non-hydrogen bonds: 134 Unresolved non-hydrogen angles: 201 Unresolved non-hydrogen dihedrals: 67 Planarities with less than four sites: {'UNK:plan-1': 67} Unresolved non-hydrogen planarities: 67 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 15737 SG CYS Y 33 72.733 59.691 78.362 1.00306.96 S ATOM 17294 SG CYS Y 287 72.128 56.100 78.822 1.00267.58 S ATOM 15872 SG CYS Y 51 92.579 27.815 81.460 1.00244.54 S ATOM 16016 SG CYS Y 70 90.642 24.158 82.493 1.00231.81 S ATOM 16057 SG CYS Y 76 104.743 27.852 86.501 1.00252.50 S ATOM 16212 SG CYS Y 114 109.394 27.453 86.629 1.00262.38 S Time building chain proxies: 4.10, per 1000 atoms: 0.21 Number of scatterers: 19253 At special positions: 0 Unit cell: (160.8, 99.16, 222.44, 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 3578 8.00 N 3377 7.00 C 12189 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 Links applied TRANS " UNK X 326 " - " GLN X 325 " " UNK x 326 " - " GLN x 325 " Time building additional restraints: 1.34 Conformation dependent library (CDL) restraints added in 768.7 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 " 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4882 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 38 sheets defined 44.5% alpha, 12.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.62 Creating SS restraints... Processing helix chain 'G' and resid 59 through 65 Processing helix chain 'G' and resid 82 through 95 removed outlier: 3.579A 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: 3.867A pdb=" N LEU G 145 " --> pdb=" O MET G 141 " (cutoff:3.500A) removed outlier: 3.687A 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: 3.822A pdb=" N ILE G 213 " --> pdb=" O SER G 209 " (cutoff:3.500A) Processing helix chain 'G' and resid 227 through 234 removed outlier: 3.611A 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: 4.365A 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: 3.704A 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: 3.732A 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: 3.501A 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: 3.529A 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: 3.692A 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: 3.841A pdb=" N ILE I 213 " --> pdb=" O SER I 209 " (cutoff:3.500A) removed outlier: 3.565A 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: 3.553A 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: 5.019A pdb=" N THR I 293 " --> pdb=" O ASP I 289 " (cutoff:3.500A) Processing helix chain 'I' and resid 309 through 322 removed outlier: 3.506A 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: 3.802A pdb=" N LEU I 321 " --> pdb=" O GLU I 317 " (cutoff:3.500A) Processing helix chain 'I' and resid 338 through 350 removed outlier: 3.505A 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: 3.569A 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: 3.518A 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: 3.770A 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: 4.116A 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: 3.631A 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: 3.849A pdb=" N GLU J 328 " --> pdb=" O ARG J 324 " (cutoff:3.500A) removed outlier: 3.546A 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: 3.635A pdb=" N GLY J 358 " --> pdb=" O ALA J 354 " (cutoff:3.500A) Processing helix chain 'J' and resid 364 through 372 removed outlier: 4.041A 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: 3.970A 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 'U' and resid 65 through 70 Processing helix chain 'U' and resid 161 through 171 removed outlier: 3.928A pdb=" N MET U 168 " --> pdb=" O LEU U 164 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N LYS U 169 " --> pdb=" O ASP U 165 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ILE U 170 " --> pdb=" O PHE U 166 " (cutoff:3.500A) Processing helix chain 'V' and resid 161 through 175 removed outlier: 4.140A 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 252 through 388 Processing helix chain 'Y' and resid 59 through 67 removed outlier: 3.500A pdb=" N LEU Y 65 " --> pdb=" O ALA Y 61 " (cutoff:3.500A) 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: 3.516A 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 252 through 390 removed outlier: 4.021A pdb=" N ALA x 256 " --> pdb=" O GLU x 252 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N GLU x 257 " --> pdb=" O SER x 253 " (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: 6.319A pdb=" N ILE G 298 " --> pdb=" O SER G 331 " (cutoff:3.500A) removed outlier: 7.629A 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: 3.678A 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: 3.718A 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: 3.654A 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: 6.744A pdb=" N ILE H 151 " --> pdb=" O VAL H 298 " (cutoff:3.500A) removed outlier: 6.683A 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: 3.846A 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: 3.761A 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: 6.230A pdb=" N VAL I 156 " --> pdb=" O VAL I 299 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N SER I 301 " --> pdb=" O VAL I 156 " (cutoff:3.500A) removed outlier: 6.299A 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: 6.980A pdb=" N VAL J 16 " --> pdb=" O VAL J 90 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N ILE J 92 " --> pdb=" O VAL J 16 " (cutoff:3.500A) removed outlier: 6.510A 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: 3.511A 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: 6.393A pdb=" N PHE V 92 " --> pdb=" O VAL V 110 " (cutoff:3.500A) removed outlier: 6.591A 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: 7.754A 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: 6.918A 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: 7.779A 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: 5.082A 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: 3.953A 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: 6.716A 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 317 770 hydrogen bonds defined for protein. 2124 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: 3.58 Time building geometry restraints manager: 1.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 3663 1.33 - 1.45: 4488 1.45 - 1.57: 11320 1.57 - 1.70: 14 1.70 - 1.82: 145 Bond restraints: 19630 Sorted by residual: bond pdb=" C4 ADP G 800 " pdb=" C5 ADP G 800 " ideal model delta sigma weight residual 1.490 1.382 0.108 2.00e-02 2.50e+03 2.91e+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 2.87e+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 2.86e+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 2.09e+01 bond pdb=" N LEU V 177 " pdb=" CA LEU V 177 " ideal model delta sigma weight residual 1.453 1.490 -0.037 8.30e-03 1.45e+04 1.97e+01 ... (remaining 19625 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.59: 22864 2.59 - 5.18: 3676 5.18 - 7.77: 152 7.77 - 10.36: 12 10.36 - 12.95: 2 Bond angle restraints: 26706 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 103.30 110.08 -6.78 8.00e-01 1.56e+00 7.19e+01 angle pdb=" PB ATP H 401 " pdb=" O3B ATP H 401 " pdb=" PG ATP H 401 " ideal model delta sigma weight residual 139.87 132.15 7.72 1.00e+00 1.00e+00 5.96e+01 angle pdb=" PA ATP H 401 " pdb=" O3A ATP H 401 " pdb=" PB ATP H 401 " ideal model delta sigma weight residual 136.83 129.78 7.05 1.00e+00 1.00e+00 4.97e+01 angle pdb=" N PRO Y 447 " pdb=" CA PRO Y 447 " pdb=" CB PRO Y 447 " ideal model delta sigma weight residual 103.25 110.12 -6.87 1.05e+00 9.07e-01 4.28e+01 angle pdb=" N PRO Y 441 " pdb=" CA PRO Y 441 " pdb=" CB PRO Y 441 " ideal model delta sigma weight residual 103.25 110.06 -6.81 1.05e+00 9.07e-01 4.20e+01 ... (remaining 26701 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.85: 11580 30.85 - 61.69: 261 61.69 - 92.54: 8 92.54 - 123.38: 4 123.38 - 154.23: 3 Dihedral angle restraints: 11856 sinusoidal: 4305 harmonic: 7551 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 94.23 -154.23 1 2.00e+01 2.50e-03 4.56e+01 dihedral pdb=" C5' ADP I 800 " pdb=" O5' ADP I 800 " pdb=" PA ADP I 800 " pdb=" O2A ADP I 800 " ideal model delta sinusoidal sigma weight residual -60.00 87.27 -147.27 1 2.00e+01 2.50e-03 4.42e+01 dihedral pdb=" O2A ADP I 800 " pdb=" O3A ADP I 800 " pdb=" PA ADP I 800 " pdb=" PB ADP I 800 " ideal model delta sinusoidal sigma weight residual -60.00 70.65 -130.65 1 2.00e+01 2.50e-03 3.96e+01 ... (remaining 11853 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 1146 0.047 - 0.093: 948 0.093 - 0.140: 668 0.140 - 0.187: 266 0.187 - 0.234: 58 Chirality restraints: 3086 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 1.36e+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 1.24e+00 chirality pdb=" CA VAL J 17 " pdb=" N VAL J 17 " pdb=" C VAL J 17 " pdb=" CB VAL J 17 " both_signs ideal model delta sigma weight residual False 2.44 2.66 -0.22 2.00e-01 2.50e+01 1.22e+00 ... (remaining 3083 not shown) Planarity restraints: 3456 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP G 357 " 0.036 2.00e-02 2.50e+03 2.87e-02 2.05e+01 pdb=" CG TRP G 357 " -0.080 2.00e-02 2.50e+03 pdb=" CD1 TRP G 357 " 0.019 2.00e-02 2.50e+03 pdb=" CD2 TRP G 357 " 0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP G 357 " 0.007 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 " -0.001 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 UNK X 348 " 0.012 2.00e-02 2.50e+03 2.47e-02 6.08e+00 pdb=" C UNK X 348 " -0.043 2.00e-02 2.50e+03 pdb=" O UNK X 348 " 0.016 2.00e-02 2.50e+03 pdb=" N UNK X 349 " 0.014 2.00e-02 2.50e+03 ... (remaining 3453 not shown) Histogram of nonbonded interaction distances: 1.79 - 2.41: 9 2.41 - 3.03: 9688 3.03 - 3.66: 29275 3.66 - 4.28: 41352 4.28 - 4.90: 69347 Nonbonded interactions: 149671 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 2.214 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 149666 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 'X' selection = (chain 'x' and resid 251 through 389) } 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: 1.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.280 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 19.440 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.070 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:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7471 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 : 0.014 0.515 19638 Z= 1.039 Angle : 1.750 12.947 26712 Z= 1.285 Chirality : 0.087 0.234 3086 Planarity : 0.003 0.029 3454 Dihedral : 13.251 154.227 6968 Min Nonbonded Distance : 1.790 Molprobity Statistics. All-atom Clashscore : 1.80 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.24 % Favored : 92.64 % Rotamer: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % 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: -2.56 (0.15), residues: 2444 helix: -0.58 (0.16), residues: 813 sheet: -2.29 (0.28), residues: 283 loop : -2.35 (0.14), residues: 1348 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 0.016 0.002 PHE M 71 TRP 0.080 0.003 TRP G 357 HIS 0.017 0.002 HIS G 372 Details of bonding type rmsd/Z covalent geometry : bond 0.01346 / 1.03 (19630) covalent geometry : angle 1.75058 / 1.29 (26706) hydrogen bonds : bond 0.26382 / 17.79 ( 764) hydrogen bonds : angle 8.11797 / 5.84 ( 2124) metal coordination : bond 0.29071 / 16.71 ( 6) link_TRANS : bond 0.00206 / 0.11 ( 2) link_TRANS : angle 0.59095 / 0.30 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 511 residues out of total 2158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 511 time to evaluate : 0.558 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: G 10 GLN cc_start: 0.9333 (mm-40) cc_final: 0.9108 (tp40) REVERT: G 34 CYS cc_start: 0.9100 (p) cc_final: 0.8733 (p) REVERT: G 37 ASN cc_start: 0.9001 (t0) cc_final: 0.8739 (t0) REVERT: G 86 MET cc_start: 0.9670 (tpp) cc_final: 0.9465 (tpp) REVERT: G 95 SER cc_start: 0.9429 (t) cc_final: 0.9200 (p) REVERT: G 98 GLN cc_start: 0.9059 (mm-40) cc_final: 0.8640 (mp10) REVERT: G 100 GLN cc_start: 0.9300 (tt0) cc_final: 0.8947 (mt0) REVERT: G 146 SER cc_start: 0.9766 (t) cc_final: 0.9493 (p) REVERT: G 160 SER cc_start: 0.9096 (m) cc_final: 0.8781 (p) REVERT: G 181 MET cc_start: 0.8232 (mmm) cc_final: 0.7683 (tpp) REVERT: G 184 ASP cc_start: 0.8367 (m-30) cc_final: 0.7518 (m-30) REVERT: G 227 ASN cc_start: 0.8802 (m-40) cc_final: 0.8010 (t0) REVERT: G 240 GLN cc_start: 0.9027 (pt0) cc_final: 0.8792 (pt0) REVERT: G 271 GLU cc_start: 0.9160 (mm-30) cc_final: 0.8705 (pt0) REVERT: G 284 GLN cc_start: 0.9256 (mt0) cc_final: 0.8911 (pt0) REVERT: G 286 SER cc_start: 0.8740 (m) cc_final: 0.8343 (p) REVERT: G 306 LEU cc_start: 0.9327 (mt) cc_final: 0.8970 (mt) REVERT: G 338 TYR cc_start: 0.9111 (m-80) cc_final: 0.8714 (m-80) REVERT: G 352 THR cc_start: 0.9137 (t) cc_final: 0.8440 (m) REVERT: G 356 MET cc_start: 0.9104 (mtp) cc_final: 0.8831 (mtp) REVERT: H 44 MET cc_start: 0.8858 (ptm) cc_final: 0.8422 (ppp) REVERT: H 47 MET cc_start: 0.8606 (mmm) cc_final: 0.8302 (mmp) REVERT: H 78 ASN cc_start: 0.8886 (t0) cc_final: 0.8532 (t0) REVERT: H 82 MET cc_start: 0.9436 (tpt) cc_final: 0.8830 (tpp) REVERT: H 103 VAL cc_start: 0.9350 (t) cc_final: 0.8900 (p) REVERT: H 132 MET cc_start: 0.8557 (tpt) cc_final: 0.8091 (tpt) REVERT: H 153 MET cc_start: 0.8401 (tmm) cc_final: 0.7799 (tpt) REVERT: H 165 ILE cc_start: 0.9139 (mt) cc_final: 0.8903 (mp) REVERT: H 184 ASP cc_start: 0.9066 (m-30) cc_final: 0.8837 (m-30) REVERT: H 195 GLU cc_start: 0.9143 (mt-10) cc_final: 0.8730 (mt-10) REVERT: H 227 MET cc_start: 0.9203 (mtp) cc_final: 0.8962 (mmm) REVERT: H 272 CYS cc_start: 0.8260 (p) cc_final: 0.7618 (p) REVERT: H 283 MET cc_start: 0.9032 (mmm) cc_final: 0.8814 (mmm) REVERT: H 291 LYS cc_start: 0.9263 (tttt) cc_final: 0.8939 (mptt) REVERT: H 325 MET cc_start: 0.8766 (mmm) cc_final: 0.8463 (mmt) REVERT: H 355 MET cc_start: 0.9106 (mtp) cc_final: 0.8793 (mpp) REVERT: I 100 GLN cc_start: 0.9110 (tt0) cc_final: 0.8880 (tt0) REVERT: I 105 GLU cc_start: 0.8714 (mm-30) cc_final: 0.8212 (tm-30) REVERT: I 106 HIS cc_start: 0.9051 (m-70) cc_final: 0.8453 (m90) REVERT: I 110 LEU cc_start: 0.9104 (mt) cc_final: 0.8900 (mm) REVERT: I 112 GLU cc_start: 0.9386 (mm-30) cc_final: 0.8409 (tt0) REVERT: I 116 ASN cc_start: 0.7665 (m-40) cc_final: 0.5947 (m-40) REVERT: I 159 ASP cc_start: 0.9139 (t0) cc_final: 0.8563 (t70) REVERT: I 181 MET cc_start: 0.8290 (tpp) cc_final: 0.7768 (mmt) REVERT: I 189 ASP cc_start: 0.9262 (m-30) cc_final: 0.8692 (m-30) REVERT: I 268 ILE cc_start: 0.9471 (tp) cc_final: 0.9252 (tp) REVERT: I 334 GLN cc_start: 0.8796 (tt0) cc_final: 0.8405 (tp40) REVERT: I 356 MET cc_start: 0.8768 (mtt) cc_final: 0.8386 (mtt) REVERT: I 357 TRP cc_start: 0.9082 (p-90) cc_final: 0.8855 (p-90) REVERT: J 27 CYS cc_start: 0.9003 (m) cc_final: 0.8674 (m) REVERT: J 91 VAL cc_start: 0.8766 (t) cc_final: 0.8549 (t) REVERT: J 137 MET cc_start: 0.7304 (tpp) cc_final: 0.6924 (tpt) REVERT: J 141 CYS cc_start: 0.8872 (m) cc_final: 0.8621 (p) REVERT: J 145 GLU cc_start: 0.8620 (pt0) cc_final: 0.8171 (mm-30) REVERT: J 178 GLN cc_start: 0.9227 (mm-40) cc_final: 0.8987 (mm-40) REVERT: J 179 LEU cc_start: 0.9321 (mt) cc_final: 0.9089 (pp) REVERT: J 227 GLN cc_start: 0.9324 (mt0) cc_final: 0.9032 (mt0) REVERT: J 231 PHE cc_start: 0.8545 (m-10) cc_final: 0.8189 (m-10) REVERT: J 289 MET cc_start: 0.8858 (ttp) cc_final: 0.8624 (ttm) REVERT: J 301 GLU cc_start: 0.8695 (mt-10) cc_final: 0.8199 (pt0) REVERT: J 311 MET cc_start: 0.9425 (tpp) cc_final: 0.8796 (mtm) REVERT: J 322 GLU cc_start: 0.9527 (tp30) cc_final: 0.8801 (tp30) REVERT: J 326 LEU cc_start: 0.9110 (mt) cc_final: 0.8639 (mt) REVERT: J 352 CYS cc_start: 0.9009 (m) cc_final: 0.7895 (p) REVERT: J 387 TRP cc_start: 0.8428 (p-90) cc_final: 0.7917 (p-90) REVERT: M 38 GLU cc_start: 0.9053 (mm-30) cc_final: 0.8774 (pm20) REVERT: M 39 GLU cc_start: 0.7926 (tp30) cc_final: 0.7435 (tp30) REVERT: M 62 LYS cc_start: 0.8136 (mmtp) cc_final: 0.6573 (tttt) REVERT: M 64 VAL cc_start: 0.7808 (m) cc_final: 0.7345 (m) REVERT: M 77 LYS cc_start: 0.8783 (mmmt) cc_final: 0.8252 (mmtm) REVERT: U 24 ARG cc_start: 0.8955 (mtp-110) cc_final: 0.7824 (ttp80) REVERT: U 36 HIS cc_start: 0.9327 (m-70) cc_final: 0.8719 (m90) REVERT: U 84 ILE cc_start: 0.9353 (mt) cc_final: 0.7770 (mt) REVERT: U 90 PHE cc_start: 0.8409 (m-80) cc_final: 0.8048 (m-80) REVERT: U 95 TYR cc_start: 0.7907 (t80) cc_final: 0.7323 (t80) REVERT: U 112 TYR cc_start: 0.9201 (t80) cc_final: 0.8387 (t80) REVERT: U 125 ILE cc_start: 0.8723 (mm) cc_final: 0.8465 (tp) REVERT: U 139 GLU cc_start: 0.8873 (tp30) cc_final: 0.8061 (tp30) REVERT: U 150 ARG cc_start: 0.8591 (mtm180) cc_final: 0.8016 (mtt90) REVERT: U 153 GLN cc_start: 0.9520 (tt0) cc_final: 0.9266 (mm-40) REVERT: U 168 MET cc_start: 0.9039 (mmt) cc_final: 0.8798 (mmp) REVERT: V 8 TYR cc_start: 0.8615 (m-80) cc_final: 0.8333 (m-80) REVERT: V 25 GLN cc_start: 0.9148 (tp-100) cc_final: 0.8637 (tm-30) REVERT: V 92 PHE cc_start: 0.8010 (t80) cc_final: 0.7785 (t80) REVERT: V 100 ASN cc_start: 0.9070 (m-40) cc_final: 0.8426 (t0) REVERT: V 114 CYS cc_start: 0.7336 (p) cc_final: 0.6729 (p) REVERT: V 120 CYS cc_start: 0.8888 (t) cc_final: 0.8643 (m) REVERT: V 125 CYS cc_start: 0.8865 (m) cc_final: 0.7736 (p) REVERT: V 161 THR cc_start: 0.9191 (m) cc_final: 0.8942 (p) REVERT: Y 27 LEU cc_start: 0.9473 (mt) cc_final: 0.9164 (tt) REVERT: Y 36 LEU cc_start: 0.9163 (pt) cc_final: 0.8747 (pp) REVERT: Y 45 GLU cc_start: 0.7366 (mm-30) cc_final: 0.6652 (mp0) REVERT: Y 56 GLU cc_start: 0.9223 (mm-30) cc_final: 0.8921 (mp0) REVERT: Y 58 MET cc_start: 0.8553 (mtp) cc_final: 0.8075 (ttm) REVERT: Y 62 GLU cc_start: 0.8826 (tt0) cc_final: 0.8528 (tp30) REVERT: Y 80 MET cc_start: 0.8765 (mpp) cc_final: 0.8410 (mtm) REVERT: Y 158 GLU cc_start: 0.8890 (tm-30) cc_final: 0.8651 (tm-30) REVERT: Y 221 ILE cc_start: 0.7843 (mt) cc_final: 0.7442 (tt) REVERT: Y 224 GLU cc_start: 0.9373 (pt0) cc_final: 0.9019 (pm20) REVERT: Y 242 ARG cc_start: 0.9297 (ttt180) cc_final: 0.8832 (ptm-80) REVERT: Y 257 LEU cc_start: 0.9229 (mt) cc_final: 0.8731 (mm) REVERT: Y 289 HIS cc_start: 0.7478 (t70) cc_final: 0.6901 (t-90) outliers start: 0 outliers final: 0 residues processed: 511 average time/residue: 0.1420 time to fit residues: 109.2011 Evaluate side-chains 294 residues out of total 2158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 294 time to evaluate : 0.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 216 optimal weight: 9.9990 chunk 98 optimal weight: 7.9990 chunk 194 optimal weight: 30.0000 chunk 227 optimal weight: 1.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 247 optimal weight: 20.0000 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.8980 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 120 ASN G 227 ASN G 297 ASN ** H 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 152 GLN Y 268 GLN ** Y 297 ASN ** 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 = 0.3355 r_free = 0.3355 target = 0.067851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.047336 restraints weight = 89919.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.049012 restraints weight = 46224.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 62)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.050204 restraints weight = 29173.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.051014 restraints weight = 20966.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.051583 restraints weight = 16572.975| |-----------------------------------------------------------------------------| r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.2651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 19638 Z= 0.153 Angle : 0.643 10.481 26712 Z= 0.327 Chirality : 0.043 0.160 3086 Planarity : 0.004 0.042 3454 Dihedral : 8.039 166.005 2827 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.60 % Favored : 96.32 % Rotamer: Outliers : 0.22 % Allowed : 2.64 % Favored : 97.14 % 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: -0.97 (0.16), residues: 2444 helix: 1.21 (0.17), residues: 839 sheet: -1.48 (0.25), residues: 357 loop : -1.73 (0.16), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG M 14 TYR 0.023 0.002 TYR Y 12 PHE 0.032 0.002 PHE G 353 TRP 0.044 0.002 TRP G 357 HIS 0.005 0.001 HIS H 173 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.15 (19630) covalent geometry : angle 0.64269 / 0.33 (26706) hydrogen bonds : bond 0.04990 / 3.32 ( 764) hydrogen bonds : angle 5.16841 / 3.74 ( 2124) metal coordination : bond 0.01053 / 0.66 ( 6) link_TRANS : bond 0.00022 / 0.01 ( 2) link_TRANS : angle 0.24084 / 0.11 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 2158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 321 time to evaluate : 0.730 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 120 ASN cc_start: 0.8410 (OUTLIER) cc_final: 0.8124 (t0) REVERT: G 142 GLN cc_start: 0.8663 (mt0) cc_final: 0.8243 (mp10) REVERT: G 181 MET cc_start: 0.9210 (mmm) cc_final: 0.8968 (tpp) REVERT: G 184 ASP cc_start: 0.8740 (m-30) cc_final: 0.8414 (m-30) REVERT: G 346 ILE cc_start: 0.9720 (OUTLIER) cc_final: 0.9446 (tp) REVERT: H 44 MET cc_start: 0.9240 (ptm) cc_final: 0.8910 (ppp) REVERT: H 47 MET cc_start: 0.8315 (mmm) cc_final: 0.8070 (mmp) REVERT: H 78 ASN cc_start: 0.8659 (t0) cc_final: 0.8374 (t0) REVERT: H 82 MET cc_start: 0.9507 (tpt) cc_final: 0.9086 (tpp) REVERT: H 153 MET cc_start: 0.8866 (tmm) cc_final: 0.8108 (tmm) REVERT: H 272 CYS cc_start: 0.9012 (p) cc_final: 0.8500 (p) REVERT: H 291 LYS cc_start: 0.9437 (tttt) cc_final: 0.9165 (mptt) REVERT: H 305 MET cc_start: 0.9341 (mtt) cc_final: 0.9094 (mtt) REVERT: H 325 MET cc_start: 0.8982 (mmm) cc_final: 0.8468 (mmt) REVERT: I 141 MET cc_start: 0.7871 (mmm) cc_final: 0.7629 (mmm) REVERT: I 159 ASP cc_start: 0.8787 (t0) cc_final: 0.8538 (t70) REVERT: I 181 MET cc_start: 0.8661 (tpp) cc_final: 0.8432 (mmm) REVERT: I 189 ASP cc_start: 0.9070 (m-30) cc_final: 0.8615 (m-30) REVERT: I 334 GLN cc_start: 0.8913 (tt0) cc_final: 0.8575 (tp-100) REVERT: J 19 ASP cc_start: 0.8691 (t0) cc_final: 0.8268 (t0) REVERT: J 137 MET cc_start: 0.8963 (tpp) cc_final: 0.8249 (tpp) REVERT: J 178 GLN cc_start: 0.9294 (mm-40) cc_final: 0.9064 (mm-40) REVERT: J 179 LEU cc_start: 0.9589 (mt) cc_final: 0.9296 (pp) REVERT: J 214 THR cc_start: 0.9469 (p) cc_final: 0.9057 (t) REVERT: J 298 GLN cc_start: 0.9226 (tp-100) cc_final: 0.8658 (mm-40) REVERT: J 322 GLU cc_start: 0.9154 (tp30) cc_final: 0.8592 (tp30) REVERT: J 326 LEU cc_start: 0.9528 (mt) cc_final: 0.9019 (mt) REVERT: J 352 CYS cc_start: 0.9126 (m) cc_final: 0.8351 (p) REVERT: J 387 TRP cc_start: 0.8636 (p-90) cc_final: 0.8295 (p-90) REVERT: M 39 GLU cc_start: 0.8007 (tp30) cc_final: 0.7784 (tp30) REVERT: M 48 ILE cc_start: 0.9209 (tp) cc_final: 0.8959 (tp) REVERT: M 62 LYS cc_start: 0.9255 (mmtp) cc_final: 0.7306 (tttt) REVERT: M 77 LYS cc_start: 0.8421 (mmmt) cc_final: 0.8143 (mmtm) REVERT: U 36 HIS cc_start: 0.9220 (m-70) cc_final: 0.8867 (m90) REVERT: U 38 LYS cc_start: 0.9349 (mmtt) cc_final: 0.8973 (mmmt) REVERT: U 90 PHE cc_start: 0.8410 (m-80) cc_final: 0.7772 (m-80) REVERT: U 95 TYR cc_start: 0.7703 (t80) cc_final: 0.7481 (t80) REVERT: U 112 TYR cc_start: 0.9034 (t80) cc_final: 0.8557 (t80) REVERT: V 25 GLN cc_start: 0.8853 (tp-100) cc_final: 0.8472 (tm-30) REVERT: V 40 THR cc_start: 0.9134 (m) cc_final: 0.8753 (p) REVERT: V 125 CYS cc_start: 0.8678 (m) cc_final: 0.8446 (p) REVERT: V 161 THR cc_start: 0.9349 (m) cc_final: 0.9085 (p) REVERT: V 165 MET cc_start: 0.9627 (mmm) cc_final: 0.9066 (mtp) REVERT: V 176 PHE cc_start: 0.8793 (t80) cc_final: 0.8413 (t80) REVERT: Y 27 LEU cc_start: 0.9645 (mt) cc_final: 0.9309 (mt) REVERT: Y 123 MET cc_start: 0.8389 (mtp) cc_final: 0.8091 (mtp) REVERT: Y 163 ASP cc_start: 0.9434 (m-30) cc_final: 0.9113 (m-30) REVERT: Y 289 HIS cc_start: 0.6885 (t70) cc_final: 0.6466 (t-90) outliers start: 4 outliers final: 0 residues processed: 325 average time/residue: 0.1283 time to fit residues: 65.5520 Evaluate side-chains 214 residues out of total 2158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 212 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 133 optimal weight: 20.0000 chunk 90 optimal weight: 0.7980 chunk 107 optimal weight: 7.9990 chunk 95 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 181 optimal weight: 4.9990 chunk 164 optimal weight: 9.9990 chunk 248 optimal weight: 50.0000 chunk 42 optimal weight: 4.9990 chunk 202 optimal weight: 4.9990 chunk 119 optimal weight: 3.9990 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 44 HIS G 166 HIS G 276 HIS ** H 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 161 HIS ** H 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 100 GLN ** I 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 178 HIS ** I 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 297 ASN ** J 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 87 ASN ** Y 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 405 ASN ** 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 = 0.3221 r_free = 0.3221 target = 0.062372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2736 r_free = 0.2736 target = 0.043052 restraints weight = 92222.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.2780 r_free = 0.2780 target = 0.044550 restraints weight = 48611.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.045618 restraints weight = 31157.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.046381 restraints weight = 22632.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 54)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.046910 restraints weight = 17932.172| |-----------------------------------------------------------------------------| r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.3905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.088 19638 Z= 0.292 Angle : 0.720 11.336 26712 Z= 0.365 Chirality : 0.045 0.152 3086 Planarity : 0.005 0.054 3454 Dihedral : 8.128 177.424 2827 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.71 % Favored : 95.21 % Rotamer: Outliers : 0.16 % Allowed : 3.83 % Favored : 96.01 % 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: -0.45 (0.17), residues: 2444 helix: 1.48 (0.18), residues: 830 sheet: -1.19 (0.26), residues: 355 loop : -1.27 (0.16), residues: 1259 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG V 70 TYR 0.020 0.002 TYR Y 326 PHE 0.027 0.002 PHE I 295 TRP 0.074 0.003 TRP G 357 HIS 0.007 0.001 HIS G 276 Details of bonding type rmsd/Z covalent geometry : bond 0.00630 / 0.29 (19630) covalent geometry : angle 0.72034 / 0.37 (26706) hydrogen bonds : bond 0.04861 / 3.28 ( 764) hydrogen bonds : angle 5.13694 / 3.71 ( 2124) metal coordination : bond 0.00330 / 0.16 ( 6) link_TRANS : bond 0.00070 / 0.04 ( 2) link_TRANS : angle 0.39972 / 0.19 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 2158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 246 time to evaluate : 0.574 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: G 75 MET cc_start: 0.8776 (tmm) cc_final: 0.7969 (tmm) REVERT: G 106 HIS cc_start: 0.9361 (m-70) cc_final: 0.9088 (m-70) REVERT: G 112 GLU cc_start: 0.8252 (tt0) cc_final: 0.7981 (tt0) REVERT: G 142 GLN cc_start: 0.8620 (mt0) cc_final: 0.8172 (mp10) REVERT: G 176 MET cc_start: 0.6781 (mmm) cc_final: 0.6284 (mmm) REVERT: G 184 ASP cc_start: 0.8541 (m-30) cc_final: 0.7791 (m-30) REVERT: G 189 ASP cc_start: 0.9137 (m-30) cc_final: 0.8862 (m-30) REVERT: G 350 LEU cc_start: 0.9364 (mm) cc_final: 0.9133 (mm) REVERT: H 44 MET cc_start: 0.9257 (ptm) cc_final: 0.8923 (ppp) REVERT: H 47 MET cc_start: 0.8529 (mmm) cc_final: 0.8281 (mmp) REVERT: H 82 MET cc_start: 0.9595 (tpt) cc_final: 0.8957 (tpp) REVERT: H 153 MET cc_start: 0.9055 (tmm) cc_final: 0.7811 (tmm) REVERT: H 195 GLU cc_start: 0.8986 (pt0) cc_final: 0.8703 (pp20) REVERT: H 227 MET cc_start: 0.9430 (mmm) cc_final: 0.9010 (mmm) REVERT: H 272 CYS cc_start: 0.8924 (p) cc_final: 0.8710 (p) REVERT: H 291 LYS cc_start: 0.9432 (tttt) cc_final: 0.9148 (mptt) REVERT: H 325 MET cc_start: 0.8923 (mmm) cc_final: 0.8438 (mmt) REVERT: I 87 GLU cc_start: 0.9492 (OUTLIER) cc_final: 0.8974 (pm20) REVERT: I 176 MET cc_start: 0.8952 (mpp) cc_final: 0.8222 (mpp) REVERT: I 189 ASP cc_start: 0.9067 (m-30) cc_final: 0.8579 (m-30) REVERT: I 271 GLU cc_start: 0.8684 (tp30) cc_final: 0.8342 (tt0) REVERT: J 19 ASP cc_start: 0.8672 (t0) cc_final: 0.8459 (t0) REVERT: J 37 CYS cc_start: 0.8529 (t) cc_final: 0.7364 (t) REVERT: J 137 MET cc_start: 0.9093 (tpp) cc_final: 0.8393 (tpt) REVERT: J 178 GLN cc_start: 0.9289 (mm-40) cc_final: 0.8963 (mm-40) REVERT: J 215 CYS cc_start: 0.9511 (m) cc_final: 0.9305 (m) REVERT: J 322 GLU cc_start: 0.9217 (tp30) cc_final: 0.8656 (tp30) REVERT: J 326 LEU cc_start: 0.9572 (mt) cc_final: 0.9180 (mt) REVERT: M 38 GLU cc_start: 0.8409 (pm20) cc_final: 0.8106 (pm20) REVERT: M 46 GLU cc_start: 0.8485 (tm-30) cc_final: 0.8259 (tm-30) REVERT: M 51 ASN cc_start: 0.9643 (t0) cc_final: 0.9107 (t0) REVERT: M 62 LYS cc_start: 0.9211 (mmtp) cc_final: 0.7903 (tttt) REVERT: U 38 LYS cc_start: 0.9296 (mmtt) cc_final: 0.8955 (mmmt) REVERT: U 84 ILE cc_start: 0.9522 (OUTLIER) cc_final: 0.9252 (tp) REVERT: U 95 TYR cc_start: 0.7651 (t80) cc_final: 0.7302 (t80) REVERT: U 108 GLU cc_start: 0.9347 (mm-30) cc_final: 0.9044 (mm-30) REVERT: U 112 TYR cc_start: 0.8928 (t80) cc_final: 0.8465 (t80) REVERT: U 150 ARG cc_start: 0.8547 (mtm180) cc_final: 0.8000 (mtt90) REVERT: V 6 LEU cc_start: 0.8678 (mt) cc_final: 0.8391 (tp) REVERT: V 25 GLN cc_start: 0.9124 (tp-100) cc_final: 0.8653 (tm-30) REVERT: V 100 ASN cc_start: 0.8035 (t0) cc_final: 0.7689 (t0) REVERT: V 123 LYS cc_start: 0.9402 (mmmm) cc_final: 0.9147 (mmmm) REVERT: V 125 CYS cc_start: 0.8898 (m) cc_final: 0.8576 (p) REVERT: V 157 LEU cc_start: 0.9356 (mt) cc_final: 0.8889 (mt) REVERT: V 176 PHE cc_start: 0.8830 (t80) cc_final: 0.8433 (t80) REVERT: Y 27 LEU cc_start: 0.9702 (mt) cc_final: 0.9367 (mt) REVERT: Y 163 ASP cc_start: 0.9486 (m-30) cc_final: 0.9126 (m-30) outliers start: 3 outliers final: 0 residues processed: 249 average time/residue: 0.1312 time to fit residues: 50.8598 Evaluate side-chains 187 residues out of total 2158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 185 time to evaluate : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 206 optimal weight: 1.9990 chunk 93 optimal weight: 5.9990 chunk 161 optimal weight: 4.9990 chunk 41 optimal weight: 3.9990 chunk 128 optimal weight: 10.0000 chunk 32 optimal weight: 5.9990 chunk 81 optimal weight: 1.9990 chunk 117 optimal weight: 2.9990 chunk 63 optimal weight: 0.9990 chunk 97 optimal weight: 1.9990 chunk 76 optimal weight: 5.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 59 GLN H 371 HIS ** I 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 60 HIS ** 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 = 0.3248 r_free = 0.3248 target = 0.063303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2768 r_free = 0.2768 target = 0.044089 restraints weight = 88601.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.2813 r_free = 0.2813 target = 0.045654 restraints weight = 46245.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.046761 restraints weight = 29345.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.047531 restraints weight = 21126.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.048098 restraints weight = 16593.344| |-----------------------------------------------------------------------------| r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.4153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 19638 Z= 0.165 Angle : 0.598 10.799 26712 Z= 0.300 Chirality : 0.043 0.156 3086 Planarity : 0.004 0.046 3454 Dihedral : 7.641 172.088 2827 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.13 % Favored : 95.79 % Rotamer: Outliers : 0.05 % Allowed : 2.48 % Favored : 97.46 % 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: -0.20 (0.17), residues: 2444 helix: 1.67 (0.18), residues: 838 sheet: -1.14 (0.27), residues: 347 loop : -1.10 (0.17), residues: 1259 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG Y 242 TYR 0.013 0.001 TYR V 13 PHE 0.026 0.001 PHE U 90 TRP 0.072 0.003 TRP G 357 HIS 0.005 0.001 HIS G 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.16 (19630) covalent geometry : angle 0.59821 / 0.30 (26706) hydrogen bonds : bond 0.04072 / 2.72 ( 764) hydrogen bonds : angle 4.77074 / 3.43 ( 2124) metal coordination : bond 0.00250 / 0.15 ( 6) link_TRANS : bond 0.00036 / 0.02 ( 2) link_TRANS : angle 0.37633 / 0.18 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 2158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 252 time to evaluate : 0.790 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 75 MET cc_start: 0.8537 (tmm) cc_final: 0.7785 (tmm) REVERT: G 112 GLU cc_start: 0.8520 (tt0) cc_final: 0.7871 (tt0) REVERT: G 176 MET cc_start: 0.7110 (mmm) cc_final: 0.6636 (mmm) REVERT: G 184 ASP cc_start: 0.8577 (m-30) cc_final: 0.8005 (p0) REVERT: G 189 ASP cc_start: 0.9191 (m-30) cc_final: 0.8793 (m-30) REVERT: G 285 LYS cc_start: 0.9564 (mttm) cc_final: 0.9345 (mttp) REVERT: H 44 MET cc_start: 0.9255 (ptm) cc_final: 0.8957 (ppp) REVERT: H 78 ASN cc_start: 0.8602 (t0) cc_final: 0.8170 (t0) REVERT: H 142 LEU cc_start: 0.9674 (tp) cc_final: 0.9251 (tp) REVERT: H 153 MET cc_start: 0.9022 (tmm) cc_final: 0.7983 (tmm) REVERT: H 195 GLU cc_start: 0.9020 (pt0) cc_final: 0.8641 (pp20) REVERT: H 227 MET cc_start: 0.9404 (mmm) cc_final: 0.8863 (mmm) REVERT: H 283 MET cc_start: 0.9323 (mmm) cc_final: 0.9104 (mmm) REVERT: H 291 LYS cc_start: 0.9436 (tttt) cc_final: 0.9160 (mptt) REVERT: H 306 TYR cc_start: 0.9138 (m-80) cc_final: 0.8911 (m-10) REVERT: H 313 MET cc_start: 0.9786 (tpt) cc_final: 0.9510 (mmm) REVERT: H 325 MET cc_start: 0.8925 (mmm) cc_final: 0.8447 (mmt) REVERT: I 66 ARG cc_start: 0.7534 (mtm110) cc_final: 0.6578 (ttp-110) REVERT: I 141 MET cc_start: 0.8458 (mmm) cc_final: 0.7829 (mmm) REVERT: I 159 ASP cc_start: 0.8721 (t70) cc_final: 0.8406 (t70) REVERT: I 176 MET cc_start: 0.9124 (mpp) cc_final: 0.8046 (mpp) REVERT: I 189 ASP cc_start: 0.8854 (m-30) cc_final: 0.8388 (m-30) REVERT: J 19 ASP cc_start: 0.8651 (t0) cc_final: 0.8449 (t0) REVERT: J 37 CYS cc_start: 0.8514 (t) cc_final: 0.7970 (t) REVERT: J 137 MET cc_start: 0.9036 (tpp) cc_final: 0.8322 (tpp) REVERT: J 178 GLN cc_start: 0.9209 (mm-40) cc_final: 0.8892 (mm-40) REVERT: J 215 CYS cc_start: 0.9498 (m) cc_final: 0.9295 (m) REVERT: J 298 GLN cc_start: 0.9095 (tp40) cc_final: 0.8601 (mm-40) REVERT: J 322 GLU cc_start: 0.9181 (tp30) cc_final: 0.8588 (tp30) REVERT: J 326 LEU cc_start: 0.9541 (mt) cc_final: 0.9000 (mt) REVERT: M 38 GLU cc_start: 0.8463 (pm20) cc_final: 0.8171 (pm20) REVERT: M 46 GLU cc_start: 0.8485 (tm-30) cc_final: 0.8237 (tm-30) REVERT: M 51 ASN cc_start: 0.9547 (t0) cc_final: 0.9306 (t0) REVERT: M 62 LYS cc_start: 0.9274 (mmtp) cc_final: 0.8071 (tttt) REVERT: U 38 LYS cc_start: 0.9276 (mmtt) cc_final: 0.8936 (mmmt) REVERT: U 90 PHE cc_start: 0.8184 (m-80) cc_final: 0.7824 (m-80) REVERT: U 95 TYR cc_start: 0.7726 (t80) cc_final: 0.7354 (t80) REVERT: U 108 GLU cc_start: 0.9245 (mm-30) cc_final: 0.9022 (mm-30) REVERT: U 112 TYR cc_start: 0.8923 (t80) cc_final: 0.8517 (t80) REVERT: U 148 CYS cc_start: 0.8264 (m) cc_final: 0.7753 (m) REVERT: U 150 ARG cc_start: 0.8570 (mtm180) cc_final: 0.7900 (mtt90) REVERT: V 6 LEU cc_start: 0.8790 (mt) cc_final: 0.8523 (tp) REVERT: V 25 GLN cc_start: 0.9097 (tp-100) cc_final: 0.8611 (tm-30) REVERT: V 40 THR cc_start: 0.9415 (m) cc_final: 0.9123 (p) REVERT: V 100 ASN cc_start: 0.8277 (t0) cc_final: 0.7689 (t0) REVERT: V 157 LEU cc_start: 0.9415 (mt) cc_final: 0.8926 (mt) REVERT: V 176 PHE cc_start: 0.8792 (t80) cc_final: 0.8403 (t80) REVERT: Y 27 LEU cc_start: 0.9703 (mt) cc_final: 0.9434 (mt) REVERT: Y 163 ASP cc_start: 0.9478 (m-30) cc_final: 0.9085 (m-30) REVERT: Y 319 MET cc_start: 0.8075 (ptp) cc_final: 0.7692 (ptt) outliers start: 1 outliers final: 0 residues processed: 253 average time/residue: 0.1375 time to fit residues: 54.5995 Evaluate side-chains 193 residues out of total 2158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 193 time to evaluate : 0.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 36 optimal weight: 7.9990 chunk 123 optimal weight: 7.9990 chunk 73 optimal weight: 0.0970 chunk 78 optimal weight: 0.0870 chunk 33 optimal weight: 3.9990 chunk 116 optimal weight: 4.9990 chunk 107 optimal weight: 7.9990 chunk 16 optimal weight: 0.9990 chunk 220 optimal weight: 4.9990 chunk 120 optimal weight: 4.9990 chunk 127 optimal weight: 3.9990 overall best weight: 1.8362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 284 GLN ** H 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 163 GLN ** V 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 273 HIS ** Y 297 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 = 0.3256 r_free = 0.3256 target = 0.063457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2757 r_free = 0.2757 target = 0.043490 restraints weight = 92089.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2803 r_free = 0.2803 target = 0.045089 restraints weight = 47705.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.046209 restraints weight = 30341.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 56)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.046991 restraints weight = 21883.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.047495 restraints weight = 17347.209| |-----------------------------------------------------------------------------| r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.4432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 19638 Z= 0.156 Angle : 0.591 12.404 26712 Z= 0.296 Chirality : 0.043 0.183 3086 Planarity : 0.004 0.044 3454 Dihedral : 7.228 168.849 2827 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.34 % Favored : 95.58 % Rotamer: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % 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: -0.09 (0.17), residues: 2444 helix: 1.67 (0.18), residues: 835 sheet: -1.02 (0.28), residues: 343 loop : -0.97 (0.17), residues: 1266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG V 70 TYR 0.020 0.001 TYR G 197 PHE 0.042 0.001 PHE G 193 TRP 0.070 0.003 TRP G 357 HIS 0.009 0.001 HIS V 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.16 (19630) covalent geometry : angle 0.59116 / 0.30 (26706) hydrogen bonds : bond 0.03941 / 2.62 ( 764) hydrogen bonds : angle 4.67276 / 3.36 ( 2124) metal coordination : bond 0.00202 / 0.12 ( 6) link_TRANS : bond 0.00030 / 0.02 ( 2) link_TRANS : angle 0.37957 / 0.19 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 2158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 247 time to evaluate : 0.891 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 75 MET cc_start: 0.8533 (tmm) cc_final: 0.7717 (tmm) REVERT: G 106 HIS cc_start: 0.9203 (m-70) cc_final: 0.8862 (m-70) REVERT: G 141 MET cc_start: 0.7400 (mmp) cc_final: 0.7110 (mmp) REVERT: G 176 MET cc_start: 0.7149 (mmm) cc_final: 0.6719 (mmm) REVERT: G 184 ASP cc_start: 0.8559 (m-30) cc_final: 0.8008 (p0) REVERT: G 189 ASP cc_start: 0.9175 (m-30) cc_final: 0.8746 (m-30) REVERT: G 240 GLN cc_start: 0.8678 (tt0) cc_final: 0.8334 (tt0) REVERT: G 284 GLN cc_start: 0.8858 (pt0) cc_final: 0.8623 (pt0) REVERT: G 285 LYS cc_start: 0.9541 (mttm) cc_final: 0.9299 (mttp) REVERT: H 44 MET cc_start: 0.9244 (ptm) cc_final: 0.8964 (ppp) REVERT: H 78 ASN cc_start: 0.8198 (t0) cc_final: 0.7762 (t0) REVERT: H 153 MET cc_start: 0.9061 (tmm) cc_final: 0.8291 (tmm) REVERT: H 195 GLU cc_start: 0.9026 (pt0) cc_final: 0.8596 (pp20) REVERT: H 272 CYS cc_start: 0.8655 (p) cc_final: 0.8397 (p) REVERT: H 283 MET cc_start: 0.9320 (mmm) cc_final: 0.9105 (mmm) REVERT: H 291 LYS cc_start: 0.9447 (tttt) cc_final: 0.9171 (mptt) REVERT: H 313 MET cc_start: 0.9769 (tpt) cc_final: 0.9469 (mmm) REVERT: H 325 MET cc_start: 0.8906 (mmm) cc_final: 0.8429 (mmt) REVERT: I 66 ARG cc_start: 0.7752 (mtm110) cc_final: 0.6822 (ttp-110) REVERT: I 141 MET cc_start: 0.8450 (mmm) cc_final: 0.8015 (mmm) REVERT: I 159 ASP cc_start: 0.8830 (t70) cc_final: 0.8459 (t70) REVERT: I 176 MET cc_start: 0.9211 (mpp) cc_final: 0.8041 (mpp) REVERT: I 189 ASP cc_start: 0.8886 (m-30) cc_final: 0.8437 (m-30) REVERT: I 229 GLN cc_start: 0.9343 (mp10) cc_final: 0.9047 (mp10) REVERT: I 357 TRP cc_start: 0.9020 (p-90) cc_final: 0.8516 (p-90) REVERT: J 37 CYS cc_start: 0.8398 (t) cc_final: 0.7850 (t) REVERT: J 137 MET cc_start: 0.9064 (tpp) cc_final: 0.8400 (tpp) REVERT: J 178 GLN cc_start: 0.9180 (mm-40) cc_final: 0.8853 (mm-40) REVERT: J 215 CYS cc_start: 0.9481 (m) cc_final: 0.9255 (m) REVERT: J 322 GLU cc_start: 0.9138 (tp30) cc_final: 0.8535 (tp30) REVERT: J 326 LEU cc_start: 0.9549 (mt) cc_final: 0.8967 (mt) REVERT: M 21 GLU cc_start: 0.8897 (pm20) cc_final: 0.8576 (pm20) REVERT: M 38 GLU cc_start: 0.8439 (pm20) cc_final: 0.8225 (pm20) REVERT: M 46 GLU cc_start: 0.8479 (tm-30) cc_final: 0.8231 (tm-30) REVERT: M 51 ASN cc_start: 0.9493 (t0) cc_final: 0.9169 (t0) REVERT: M 62 LYS cc_start: 0.9400 (mmtp) cc_final: 0.8223 (tttt) REVERT: U 38 LYS cc_start: 0.9292 (mmtt) cc_final: 0.8945 (mmmt) REVERT: U 95 TYR cc_start: 0.7695 (t80) cc_final: 0.7301 (t80) REVERT: U 112 TYR cc_start: 0.8907 (t80) cc_final: 0.8480 (t80) REVERT: U 148 CYS cc_start: 0.8336 (m) cc_final: 0.7834 (m) REVERT: U 150 ARG cc_start: 0.8523 (mtm180) cc_final: 0.7863 (mtt90) REVERT: V 6 LEU cc_start: 0.8925 (mt) cc_final: 0.8665 (tp) REVERT: V 25 GLN cc_start: 0.9158 (tp-100) cc_final: 0.8623 (tm-30) REVERT: V 52 LEU cc_start: 0.8466 (tp) cc_final: 0.8254 (tp) REVERT: V 100 ASN cc_start: 0.8286 (t0) cc_final: 0.7864 (t0) REVERT: V 157 LEU cc_start: 0.9402 (mt) cc_final: 0.8973 (mt) REVERT: V 176 PHE cc_start: 0.8794 (t80) cc_final: 0.8406 (t80) REVERT: Y 27 LEU cc_start: 0.9688 (mt) cc_final: 0.9404 (mt) REVERT: Y 163 ASP cc_start: 0.9482 (m-30) cc_final: 0.9089 (m-30) REVERT: Y 319 MET cc_start: 0.7972 (ptp) cc_final: 0.7569 (ptt) outliers start: 0 outliers final: 0 residues processed: 247 average time/residue: 0.1420 time to fit residues: 55.0525 Evaluate side-chains 191 residues out of total 2158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 191 time to evaluate : 0.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 115 optimal weight: 0.1980 chunk 3 optimal weight: 0.9980 chunk 32 optimal weight: 3.9990 chunk 41 optimal weight: 4.9990 chunk 15 optimal weight: 7.9990 chunk 204 optimal weight: 10.0000 chunk 64 optimal weight: 4.9990 chunk 202 optimal weight: 4.9990 chunk 57 optimal weight: 0.8980 chunk 39 optimal weight: 5.9990 chunk 6 optimal weight: 3.9990 overall best weight: 2.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 16 ASN ** H 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 100 GLN ** U 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 49 HIS Y 273 HIS ** Y 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.063060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2758 r_free = 0.2758 target = 0.043979 restraints weight = 89767.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.2803 r_free = 0.2803 target = 0.045529 restraints weight = 46914.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.046637 restraints weight = 29937.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.047404 restraints weight = 21562.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.047955 restraints weight = 16981.361| |-----------------------------------------------------------------------------| r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.4646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 19638 Z= 0.166 Angle : 0.597 11.591 26712 Z= 0.296 Chirality : 0.042 0.153 3086 Planarity : 0.004 0.043 3454 Dihedral : 7.068 163.711 2827 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.34 % Favored : 95.58 % Rotamer: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % 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: 0.03 (0.17), residues: 2444 helix: 1.71 (0.18), residues: 832 sheet: -1.02 (0.27), residues: 343 loop : -0.82 (0.17), residues: 1269 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG V 70 TYR 0.019 0.001 TYR J 76 PHE 0.023 0.001 PHE U 90 TRP 0.079 0.003 TRP G 357 HIS 0.007 0.001 HIS V 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.17 (19630) covalent geometry : angle 0.59659 / 0.30 (26706) hydrogen bonds : bond 0.03861 / 2.57 ( 764) hydrogen bonds : angle 4.61455 / 3.31 ( 2124) metal coordination : bond 0.00281 / 0.17 ( 6) link_TRANS : bond 0.00033 / 0.02 ( 2) link_TRANS : angle 0.40189 / 0.20 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 2158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 238 time to evaluate : 0.734 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 75 MET cc_start: 0.8519 (tmm) cc_final: 0.7853 (tmm) REVERT: G 176 MET cc_start: 0.7257 (mmm) cc_final: 0.6788 (mmm) REVERT: G 184 ASP cc_start: 0.8573 (m-30) cc_final: 0.7996 (p0) REVERT: G 189 ASP cc_start: 0.9153 (m-30) cc_final: 0.8724 (m-30) REVERT: G 227 ASN cc_start: 0.8688 (t0) cc_final: 0.8324 (t0) REVERT: G 240 GLN cc_start: 0.8751 (tt0) cc_final: 0.8549 (tm-30) REVERT: H 44 MET cc_start: 0.9241 (ptm) cc_final: 0.8948 (ppp) REVERT: H 78 ASN cc_start: 0.8230 (t0) cc_final: 0.7757 (t0) REVERT: H 153 MET cc_start: 0.9022 (tmm) cc_final: 0.8257 (tmm) REVERT: H 195 GLU cc_start: 0.9048 (pt0) cc_final: 0.8595 (pp20) REVERT: H 272 CYS cc_start: 0.8689 (p) cc_final: 0.8485 (p) REVERT: H 291 LYS cc_start: 0.9464 (tttt) cc_final: 0.9165 (mptt) REVERT: H 313 MET cc_start: 0.9762 (tpt) cc_final: 0.9451 (mmm) REVERT: H 325 MET cc_start: 0.8918 (mmm) cc_final: 0.8421 (mmt) REVERT: I 66 ARG cc_start: 0.7808 (mtm110) cc_final: 0.7014 (ttp-110) REVERT: I 141 MET cc_start: 0.8364 (mmm) cc_final: 0.8012 (mmm) REVERT: I 159 ASP cc_start: 0.8856 (t70) cc_final: 0.8493 (t70) REVERT: I 176 MET cc_start: 0.9189 (mpp) cc_final: 0.8089 (mpp) REVERT: I 189 ASP cc_start: 0.8904 (m-30) cc_final: 0.8440 (m-30) REVERT: I 229 GLN cc_start: 0.9375 (mp10) cc_final: 0.9052 (mp10) REVERT: I 356 MET cc_start: 0.8822 (mpp) cc_final: 0.8473 (mtt) REVERT: I 357 TRP cc_start: 0.9082 (p-90) cc_final: 0.8753 (p-90) REVERT: J 37 CYS cc_start: 0.8494 (t) cc_final: 0.7995 (t) REVERT: J 126 MET cc_start: 0.9561 (mmp) cc_final: 0.9302 (mmm) REVERT: J 137 MET cc_start: 0.9071 (tpp) cc_final: 0.8681 (tpp) REVERT: J 178 GLN cc_start: 0.9219 (mm-40) cc_final: 0.8889 (mm-40) REVERT: J 215 CYS cc_start: 0.9467 (m) cc_final: 0.9244 (m) REVERT: J 298 GLN cc_start: 0.9083 (tp40) cc_final: 0.8633 (mm-40) REVERT: J 322 GLU cc_start: 0.9159 (tp30) cc_final: 0.8575 (tp30) REVERT: J 326 LEU cc_start: 0.9531 (mt) cc_final: 0.8982 (mt) REVERT: M 12 ILE cc_start: 0.9293 (mm) cc_final: 0.8880 (mm) REVERT: M 21 GLU cc_start: 0.8897 (pm20) cc_final: 0.8614 (mp0) REVERT: M 38 GLU cc_start: 0.8472 (pm20) cc_final: 0.8236 (pm20) REVERT: M 46 GLU cc_start: 0.8496 (tm-30) cc_final: 0.8255 (tm-30) REVERT: M 51 ASN cc_start: 0.9468 (t0) cc_final: 0.9120 (t0) REVERT: M 62 LYS cc_start: 0.9403 (mmtp) cc_final: 0.8393 (tttt) REVERT: U 38 LYS cc_start: 0.9261 (mmtt) cc_final: 0.8929 (mmmt) REVERT: U 90 PHE cc_start: 0.8135 (m-80) cc_final: 0.7831 (m-80) REVERT: U 95 TYR cc_start: 0.7805 (t80) cc_final: 0.7496 (t80) REVERT: U 108 GLU cc_start: 0.9291 (mm-30) cc_final: 0.9027 (mm-30) REVERT: U 112 TYR cc_start: 0.8902 (t80) cc_final: 0.8433 (t80) REVERT: U 148 CYS cc_start: 0.8362 (m) cc_final: 0.8118 (m) REVERT: V 6 LEU cc_start: 0.8928 (mt) cc_final: 0.8707 (tp) REVERT: V 25 GLN cc_start: 0.9178 (tp-100) cc_final: 0.8639 (tm-30) REVERT: V 52 LEU cc_start: 0.8402 (tp) cc_final: 0.8187 (tp) REVERT: V 100 ASN cc_start: 0.8022 (t0) cc_final: 0.7642 (t0) REVERT: V 103 GLN cc_start: 0.9318 (tp-100) cc_final: 0.9091 (tp-100) REVERT: V 157 LEU cc_start: 0.9438 (mt) cc_final: 0.9016 (mt) REVERT: V 165 MET cc_start: 0.9675 (mmm) cc_final: 0.9104 (mtp) REVERT: V 176 PHE cc_start: 0.8848 (t80) cc_final: 0.8463 (t80) REVERT: Y 27 LEU cc_start: 0.9674 (mt) cc_final: 0.9383 (mt) REVERT: Y 163 ASP cc_start: 0.9487 (m-30) cc_final: 0.9080 (m-30) REVERT: Y 319 MET cc_start: 0.8067 (ptp) cc_final: 0.7599 (ptt) outliers start: 0 outliers final: 0 residues processed: 238 average time/residue: 0.1432 time to fit residues: 53.3293 Evaluate side-chains 189 residues out of total 2158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 189 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 245 optimal weight: 40.0000 chunk 60 optimal weight: 5.9990 chunk 164 optimal weight: 10.0000 chunk 44 optimal weight: 2.9990 chunk 148 optimal weight: 9.9990 chunk 102 optimal weight: 0.9980 chunk 144 optimal weight: 0.7980 chunk 100 optimal weight: 2.9990 chunk 94 optimal weight: 3.9990 chunk 38 optimal weight: 10.0000 chunk 192 optimal weight: 10.0000 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 284 GLN H 296 ASN ** I 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 36 HIS ** U 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 273 HIS ** Y 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.062197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2745 r_free = 0.2745 target = 0.043076 restraints weight = 91923.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.2791 r_free = 0.2791 target = 0.044638 restraints weight = 47855.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2822 r_free = 0.2822 target = 0.045723 restraints weight = 30321.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.046500 restraints weight = 21829.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.047063 restraints weight = 17087.037| |-----------------------------------------------------------------------------| r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.4830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 19638 Z= 0.185 Angle : 0.602 12.810 26712 Z= 0.298 Chirality : 0.042 0.152 3086 Planarity : 0.004 0.042 3454 Dihedral : 6.994 159.356 2827 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.50 % Favored : 95.42 % Rotamer: Outliers : 0.00 % Allowed : 1.46 % 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: 0.07 (0.17), residues: 2444 helix: 1.71 (0.18), residues: 831 sheet: -0.93 (0.28), residues: 336 loop : -0.80 (0.17), residues: 1277 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG M 14 TYR 0.016 0.001 TYR G 197 PHE 0.023 0.001 PHE G 193 TRP 0.083 0.003 TRP G 357 HIS 0.006 0.001 HIS V 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.19 (19630) covalent geometry : angle 0.60212 / 0.30 (26706) hydrogen bonds : bond 0.03849 / 2.57 ( 764) hydrogen bonds : angle 4.63216 / 3.33 ( 2124) metal coordination : bond 0.00318 / 0.19 ( 6) link_TRANS : bond 0.00040 / 0.02 ( 2) link_TRANS : angle 0.41282 / 0.20 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 2158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 232 time to evaluate : 0.764 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: G 75 MET cc_start: 0.8571 (tmm) cc_final: 0.7994 (tmm) REVERT: G 176 MET cc_start: 0.7296 (mmm) cc_final: 0.6755 (mmm) REVERT: G 184 ASP cc_start: 0.8552 (m-30) cc_final: 0.8006 (p0) REVERT: G 189 ASP cc_start: 0.9174 (m-30) cc_final: 0.8746 (m-30) REVERT: G 227 ASN cc_start: 0.8784 (t0) cc_final: 0.8243 (t0) REVERT: H 44 MET cc_start: 0.9208 (ptm) cc_final: 0.8909 (ppp) REVERT: H 78 ASN cc_start: 0.8232 (t0) cc_final: 0.7762 (t0) REVERT: H 153 MET cc_start: 0.8788 (tmm) cc_final: 0.8055 (tmm) REVERT: H 195 GLU cc_start: 0.9061 (pt0) cc_final: 0.8595 (pp20) REVERT: H 272 CYS cc_start: 0.8716 (p) cc_final: 0.8502 (p) REVERT: H 283 MET cc_start: 0.9302 (mmm) cc_final: 0.9083 (mmm) REVERT: H 291 LYS cc_start: 0.9484 (tttt) cc_final: 0.9172 (mptt) REVERT: H 313 MET cc_start: 0.9760 (tpt) cc_final: 0.9442 (mmm) REVERT: H 325 MET cc_start: 0.8918 (mmm) cc_final: 0.8410 (mmt) REVERT: I 66 ARG cc_start: 0.7787 (mtm110) cc_final: 0.6919 (ttp-110) REVERT: I 141 MET cc_start: 0.8359 (mmm) cc_final: 0.8019 (mmm) REVERT: I 159 ASP cc_start: 0.8778 (t70) cc_final: 0.8422 (t70) REVERT: I 176 MET cc_start: 0.9192 (mpp) cc_final: 0.8104 (mpp) REVERT: I 189 ASP cc_start: 0.8898 (m-30) cc_final: 0.8426 (m-30) REVERT: I 356 MET cc_start: 0.8907 (mpp) cc_final: 0.8471 (mtt) REVERT: I 357 TRP cc_start: 0.9096 (p-90) cc_final: 0.8819 (p-90) REVERT: J 37 CYS cc_start: 0.8490 (t) cc_final: 0.7987 (t) REVERT: J 126 MET cc_start: 0.9572 (mmp) cc_final: 0.9360 (mmm) REVERT: J 137 MET cc_start: 0.9083 (tpp) cc_final: 0.8755 (tpp) REVERT: J 178 GLN cc_start: 0.9223 (mm-40) cc_final: 0.8872 (mm-40) REVERT: J 215 CYS cc_start: 0.9417 (m) cc_final: 0.9202 (m) REVERT: J 298 GLN cc_start: 0.9129 (tp40) cc_final: 0.8717 (mm-40) REVERT: J 322 GLU cc_start: 0.9170 (tp30) cc_final: 0.8585 (tp30) REVERT: J 326 LEU cc_start: 0.9551 (mt) cc_final: 0.9011 (mt) REVERT: M 46 GLU cc_start: 0.8520 (tm-30) cc_final: 0.8270 (tm-30) REVERT: M 51 ASN cc_start: 0.9466 (t0) cc_final: 0.9094 (t0) REVERT: M 62 LYS cc_start: 0.9398 (mmtp) cc_final: 0.8386 (tttt) REVERT: U 90 PHE cc_start: 0.8041 (m-80) cc_final: 0.7693 (m-80) REVERT: U 95 TYR cc_start: 0.7877 (t80) cc_final: 0.7558 (t80) REVERT: U 112 TYR cc_start: 0.8887 (t80) cc_final: 0.8410 (t80) REVERT: U 131 LEU cc_start: 0.8834 (pp) cc_final: 0.8625 (pp) REVERT: U 148 CYS cc_start: 0.8364 (m) cc_final: 0.7861 (m) REVERT: U 150 ARG cc_start: 0.8540 (mtm180) cc_final: 0.7817 (mtt90) REVERT: V 8 TYR cc_start: 0.7574 (m-80) cc_final: 0.7373 (m-80) REVERT: V 25 GLN cc_start: 0.9195 (tp-100) cc_final: 0.8625 (tm-30) REVERT: V 52 LEU cc_start: 0.8401 (tp) cc_final: 0.8180 (tp) REVERT: V 100 ASN cc_start: 0.8045 (t0) cc_final: 0.7635 (t0) REVERT: V 157 LEU cc_start: 0.9425 (mt) cc_final: 0.8997 (mt) REVERT: V 165 MET cc_start: 0.9674 (mmm) cc_final: 0.9049 (mtp) REVERT: V 176 PHE cc_start: 0.8872 (t80) cc_final: 0.8495 (t80) REVERT: Y 27 LEU cc_start: 0.9662 (mt) cc_final: 0.9368 (mt) REVERT: Y 163 ASP cc_start: 0.9483 (m-30) cc_final: 0.9070 (m-30) outliers start: 0 outliers final: 0 residues processed: 232 average time/residue: 0.1433 time to fit residues: 51.9923 Evaluate side-chains 182 residues out of total 2158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 182 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 139 optimal weight: 0.9980 chunk 249 optimal weight: 30.0000 chunk 77 optimal weight: 0.0050 chunk 82 optimal weight: 0.9980 chunk 202 optimal weight: 6.9990 chunk 61 optimal weight: 6.9990 chunk 28 optimal weight: 0.9980 chunk 126 optimal weight: 0.0270 chunk 86 optimal weight: 0.0170 chunk 44 optimal weight: 0.9980 chunk 214 optimal weight: 0.9990 overall best weight: 0.4090 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 37 ASN G 284 GLN ** I 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 405 ASN ** 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 = 0.3254 r_free = 0.3254 target = 0.063859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2750 r_free = 0.2750 target = 0.043643 restraints weight = 91510.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.2796 r_free = 0.2796 target = 0.045260 restraints weight = 47375.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.046417 restraints weight = 30028.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.047201 restraints weight = 21667.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.047708 restraints weight = 17150.518| |-----------------------------------------------------------------------------| r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.4867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 19638 Z= 0.104 Angle : 0.582 12.232 26712 Z= 0.287 Chirality : 0.042 0.184 3086 Planarity : 0.004 0.041 3454 Dihedral : 6.637 155.825 2827 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.81 % Favored : 96.11 % Rotamer: Outliers : 0.05 % Allowed : 0.49 % Favored : 99.46 % 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: 0.13 (0.17), residues: 2444 helix: 1.76 (0.18), residues: 831 sheet: -0.90 (0.28), residues: 338 loop : -0.76 (0.17), residues: 1275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 46 TYR 0.018 0.001 TYR J 76 PHE 0.019 0.001 PHE G 353 TRP 0.088 0.003 TRP G 357 HIS 0.005 0.001 HIS J 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.10 (19630) covalent geometry : angle 0.58207 / 0.29 (26706) hydrogen bonds : bond 0.03609 / 2.39 ( 764) hydrogen bonds : angle 4.48071 / 3.22 ( 2124) metal coordination : bond 0.00057 / 0.03 ( 6) link_TRANS : bond 0.00018 / 0.01 ( 2) link_TRANS : angle 0.38756 / 0.20 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 2158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 250 time to evaluate : 0.854 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 75 MET cc_start: 0.8515 (tmm) cc_final: 0.7941 (tmm) REVERT: G 142 GLN cc_start: 0.8285 (mp10) cc_final: 0.7940 (mp-120) REVERT: G 176 MET cc_start: 0.7404 (mmm) cc_final: 0.6834 (mmm) REVERT: G 184 ASP cc_start: 0.8524 (m-30) cc_final: 0.7996 (p0) REVERT: G 189 ASP cc_start: 0.9162 (m-30) cc_final: 0.8767 (m-30) REVERT: G 227 ASN cc_start: 0.8675 (t0) cc_final: 0.8181 (t0) REVERT: H 44 MET cc_start: 0.9222 (ptm) cc_final: 0.8982 (ppp) REVERT: H 78 ASN cc_start: 0.8089 (t0) cc_final: 0.7582 (t0) REVERT: H 153 MET cc_start: 0.8770 (tmm) cc_final: 0.8258 (tmm) REVERT: H 195 GLU cc_start: 0.9019 (pt0) cc_final: 0.8373 (pp20) REVERT: H 227 MET cc_start: 0.9444 (mmm) cc_final: 0.9192 (mmm) REVERT: H 272 CYS cc_start: 0.8681 (p) cc_final: 0.8408 (p) REVERT: H 283 MET cc_start: 0.9299 (mmm) cc_final: 0.9093 (mmm) REVERT: H 291 LYS cc_start: 0.9471 (tttt) cc_final: 0.9191 (mptt) REVERT: H 313 MET cc_start: 0.9743 (tpt) cc_final: 0.9427 (mmm) REVERT: H 325 MET cc_start: 0.8907 (mmm) cc_final: 0.8431 (mmt) REVERT: H 356 TRP cc_start: 0.8156 (m100) cc_final: 0.7796 (m-10) REVERT: I 66 ARG cc_start: 0.7674 (mtm110) cc_final: 0.6818 (ttp-110) REVERT: I 141 MET cc_start: 0.8313 (mmm) cc_final: 0.8075 (mmm) REVERT: I 159 ASP cc_start: 0.8821 (t70) cc_final: 0.8420 (t70) REVERT: I 176 MET cc_start: 0.9203 (mpp) cc_final: 0.8063 (mpp) REVERT: I 189 ASP cc_start: 0.8851 (m-30) cc_final: 0.8400 (m-30) REVERT: I 240 GLN cc_start: 0.8582 (mm-40) cc_final: 0.8283 (tp-100) REVERT: I 357 TRP cc_start: 0.9105 (p-90) cc_final: 0.8823 (p-90) REVERT: J 37 CYS cc_start: 0.8499 (t) cc_final: 0.8010 (t) REVERT: J 137 MET cc_start: 0.9099 (tpp) cc_final: 0.8647 (tpp) REVERT: J 178 GLN cc_start: 0.9185 (mm-40) cc_final: 0.8824 (mm-40) REVERT: J 215 CYS cc_start: 0.9419 (m) cc_final: 0.9202 (m) REVERT: J 298 GLN cc_start: 0.9175 (tp40) cc_final: 0.8647 (mm-40) REVERT: J 322 GLU cc_start: 0.9127 (tp30) cc_final: 0.8538 (tp30) REVERT: J 326 LEU cc_start: 0.9553 (mt) cc_final: 0.8911 (mt) REVERT: M 21 GLU cc_start: 0.8861 (pm20) cc_final: 0.8618 (mp0) REVERT: M 46 GLU cc_start: 0.8518 (tm-30) cc_final: 0.8236 (tm-30) REVERT: M 51 ASN cc_start: 0.9451 (t0) cc_final: 0.9064 (t0) REVERT: M 62 LYS cc_start: 0.9449 (mmtp) cc_final: 0.8546 (tttt) REVERT: U 36 HIS cc_start: 0.8626 (m-70) cc_final: 0.8172 (m90) REVERT: U 90 PHE cc_start: 0.7981 (m-80) cc_final: 0.7602 (m-80) REVERT: U 95 TYR cc_start: 0.7796 (t80) cc_final: 0.7554 (t80) REVERT: U 108 GLU cc_start: 0.9297 (mm-30) cc_final: 0.9066 (mm-30) REVERT: U 112 TYR cc_start: 0.8853 (t80) cc_final: 0.8240 (t80) REVERT: U 148 CYS cc_start: 0.8670 (m) cc_final: 0.8181 (m) REVERT: U 150 ARG cc_start: 0.8548 (mtm180) cc_final: 0.7903 (mtt90) REVERT: V 25 GLN cc_start: 0.9180 (tp-100) cc_final: 0.8626 (tm-30) REVERT: V 70 ARG cc_start: 0.8326 (tmm-80) cc_final: 0.7438 (tmm-80) REVERT: V 100 ASN cc_start: 0.8100 (t0) cc_final: 0.5731 (t0) REVERT: V 157 LEU cc_start: 0.9429 (mt) cc_final: 0.9010 (mt) REVERT: V 165 MET cc_start: 0.9601 (mmm) cc_final: 0.9046 (mtp) REVERT: V 176 PHE cc_start: 0.8843 (t80) cc_final: 0.8471 (t80) REVERT: Y 27 LEU cc_start: 0.9651 (mt) cc_final: 0.9362 (mt) REVERT: Y 113 PHE cc_start: 0.9005 (t80) cc_final: 0.8448 (t80) REVERT: Y 163 ASP cc_start: 0.9474 (m-30) cc_final: 0.9058 (m-30) REVERT: Y 289 HIS cc_start: 0.7580 (t-90) cc_final: 0.7176 (t-90) outliers start: 1 outliers final: 0 residues processed: 251 average time/residue: 0.1447 time to fit residues: 56.8168 Evaluate side-chains 192 residues out of total 2158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 192 time to evaluate : 0.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 243 optimal weight: 6.9990 chunk 141 optimal weight: 4.9990 chunk 178 optimal weight: 9.9990 chunk 148 optimal weight: 4.9990 chunk 43 optimal weight: 4.9990 chunk 23 optimal weight: 0.0870 chunk 95 optimal weight: 6.9990 chunk 126 optimal weight: 1.9990 chunk 242 optimal weight: 8.9990 chunk 210 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 overall best weight: 2.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 263 GLN ** I 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 36 HIS ** U 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 273 HIS ** Y 297 ASN ** 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 = 0.3209 r_free = 0.3209 target = 0.061927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2703 r_free = 0.2703 target = 0.042065 restraints weight = 92068.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 62)----------------| | r_work = 0.2748 r_free = 0.2748 target = 0.043604 restraints weight = 48347.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 60)----------------| | r_work = 0.2780 r_free = 0.2780 target = 0.044701 restraints weight = 31007.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2802 r_free = 0.2802 target = 0.045419 restraints weight = 22498.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.045962 restraints weight = 17834.836| |-----------------------------------------------------------------------------| r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.5135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 19638 Z= 0.207 Angle : 0.643 12.888 26712 Z= 0.316 Chirality : 0.043 0.169 3086 Planarity : 0.004 0.039 3454 Dihedral : 6.776 151.498 2827 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.66 % Favored : 95.25 % Rotamer: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % 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: 0.16 (0.17), residues: 2444 helix: 1.67 (0.18), residues: 847 sheet: -0.93 (0.28), residues: 333 loop : -0.67 (0.17), residues: 1264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 264 TYR 0.013 0.001 TYR V 13 PHE 0.038 0.002 PHE G 193 TRP 0.094 0.003 TRP G 357 HIS 0.006 0.001 HIS V 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00450 / 0.21 (19630) covalent geometry : angle 0.64339 / 0.32 (26706) hydrogen bonds : bond 0.03828 / 2.57 ( 764) hydrogen bonds : angle 4.62721 / 3.32 ( 2124) metal coordination : bond 0.00372 / 0.23 ( 6) link_TRANS : bond 0.00042 / 0.02 ( 2) link_TRANS : angle 0.39659 / 0.20 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 2158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 224 time to evaluate : 0.810 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: G 75 MET cc_start: 0.8621 (tmm) cc_final: 0.7711 (tmm) REVERT: G 140 SER cc_start: 0.8960 (t) cc_final: 0.8651 (t) REVERT: G 176 MET cc_start: 0.7438 (mmm) cc_final: 0.6811 (mmm) REVERT: G 184 ASP cc_start: 0.8556 (m-30) cc_final: 0.8032 (p0) REVERT: G 189 ASP cc_start: 0.9147 (m-30) cc_final: 0.8727 (m-30) REVERT: G 227 ASN cc_start: 0.8707 (t0) cc_final: 0.8212 (t0) REVERT: H 44 MET cc_start: 0.9199 (ptm) cc_final: 0.8904 (ppp) REVERT: H 78 ASN cc_start: 0.8194 (t0) cc_final: 0.7691 (t0) REVERT: H 153 MET cc_start: 0.8844 (tmm) cc_final: 0.8372 (tmm) REVERT: H 195 GLU cc_start: 0.9021 (pt0) cc_final: 0.8620 (pp20) REVERT: H 227 MET cc_start: 0.9468 (mmm) cc_final: 0.9223 (mmm) REVERT: H 272 CYS cc_start: 0.8687 (p) cc_final: 0.8442 (p) REVERT: H 283 MET cc_start: 0.9297 (mmm) cc_final: 0.9091 (mmm) REVERT: H 291 LYS cc_start: 0.9481 (tttt) cc_final: 0.9166 (mptt) REVERT: H 325 MET cc_start: 0.8936 (mmm) cc_final: 0.8445 (mmt) REVERT: H 355 MET cc_start: 0.9090 (ptp) cc_final: 0.8870 (pmm) REVERT: H 356 TRP cc_start: 0.8273 (m100) cc_final: 0.8024 (m-10) REVERT: I 66 ARG cc_start: 0.7790 (mtm110) cc_final: 0.6925 (ttp-110) REVERT: I 116 ASN cc_start: 0.8784 (t0) cc_final: 0.8258 (t0) REVERT: I 141 MET cc_start: 0.8248 (mmm) cc_final: 0.8013 (mmm) REVERT: I 159 ASP cc_start: 0.8743 (t70) cc_final: 0.8329 (t0) REVERT: I 189 ASP cc_start: 0.8810 (m-30) cc_final: 0.8365 (m-30) REVERT: I 357 TRP cc_start: 0.9107 (p-90) cc_final: 0.8877 (p-90) REVERT: J 37 CYS cc_start: 0.8562 (t) cc_final: 0.8086 (t) REVERT: J 126 MET cc_start: 0.9547 (mmp) cc_final: 0.9278 (mmm) REVERT: J 137 MET cc_start: 0.9153 (tpp) cc_final: 0.8693 (tpp) REVERT: J 178 GLN cc_start: 0.9231 (mm-40) cc_final: 0.8931 (mm-40) REVERT: J 215 CYS cc_start: 0.9382 (m) cc_final: 0.9176 (m) REVERT: J 322 GLU cc_start: 0.9151 (tp30) cc_final: 0.8584 (tp30) REVERT: J 326 LEU cc_start: 0.9563 (mt) cc_final: 0.9039 (mt) REVERT: M 38 GLU cc_start: 0.8327 (pm20) cc_final: 0.7914 (pm20) REVERT: M 46 GLU cc_start: 0.8451 (tm-30) cc_final: 0.8214 (tm-30) REVERT: M 51 ASN cc_start: 0.9470 (t0) cc_final: 0.9090 (t0) REVERT: M 62 LYS cc_start: 0.9444 (mmtp) cc_final: 0.8526 (tttt) REVERT: U 90 PHE cc_start: 0.7951 (m-80) cc_final: 0.7562 (m-80) REVERT: U 95 TYR cc_start: 0.7882 (t80) cc_final: 0.7620 (t80) REVERT: U 112 TYR cc_start: 0.8868 (t80) cc_final: 0.8398 (t80) REVERT: U 131 LEU cc_start: 0.8825 (pp) cc_final: 0.8592 (pp) REVERT: U 148 CYS cc_start: 0.8448 (m) cc_final: 0.7970 (m) REVERT: U 150 ARG cc_start: 0.8521 (mtm180) cc_final: 0.7709 (mtt90) REVERT: V 25 GLN cc_start: 0.9197 (tp-100) cc_final: 0.8675 (tm-30) REVERT: V 83 PHE cc_start: 0.9171 (t80) cc_final: 0.8954 (t80) REVERT: V 100 ASN cc_start: 0.8178 (t0) cc_final: 0.7835 (t0) REVERT: V 157 LEU cc_start: 0.9436 (mt) cc_final: 0.9005 (mt) REVERT: V 165 MET cc_start: 0.9646 (mmm) cc_final: 0.9086 (mtp) REVERT: V 176 PHE cc_start: 0.8721 (t80) cc_final: 0.8277 (t80) REVERT: Y 27 LEU cc_start: 0.9619 (mt) cc_final: 0.9318 (mt) REVERT: Y 113 PHE cc_start: 0.8953 (t80) cc_final: 0.8382 (t80) REVERT: Y 163 ASP cc_start: 0.9478 (m-30) cc_final: 0.9080 (m-30) REVERT: Y 289 HIS cc_start: 0.7721 (t-90) cc_final: 0.7179 (t70) outliers start: 0 outliers final: 0 residues processed: 224 average time/residue: 0.1409 time to fit residues: 49.8593 Evaluate side-chains 185 residues out of total 2158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 185 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 244 optimal weight: 8.9990 chunk 112 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 201 optimal weight: 4.9990 chunk 14 optimal weight: 4.9990 chunk 164 optimal weight: 10.0000 chunk 106 optimal weight: 0.9980 chunk 78 optimal weight: 10.0000 chunk 128 optimal weight: 3.9990 chunk 4 optimal weight: 6.9990 chunk 207 optimal weight: 5.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 44 HIS ** H 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 100 ASN Y 273 HIS ** Y 297 ASN ** 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 = 0.3200 r_free = 0.3200 target = 0.061733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2694 r_free = 0.2694 target = 0.041821 restraints weight = 92815.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.2740 r_free = 0.2740 target = 0.043374 restraints weight = 48688.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2771 r_free = 0.2771 target = 0.044429 restraints weight = 31221.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 67)----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.045215 restraints weight = 22766.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.045672 restraints weight = 18117.974| |-----------------------------------------------------------------------------| r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.5296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.090 19638 Z= 0.208 Angle : 0.647 12.763 26712 Z= 0.319 Chirality : 0.043 0.152 3086 Planarity : 0.004 0.052 3454 Dihedral : 6.810 148.776 2827 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.79 % Favored : 95.13 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % 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: 0.10 (0.17), residues: 2444 helix: 1.59 (0.18), residues: 846 sheet: -0.94 (0.28), residues: 336 loop : -0.68 (0.17), residues: 1262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG V 70 TYR 0.020 0.001 TYR G 197 PHE 0.017 0.001 PHE U 90 TRP 0.102 0.003 TRP G 357 HIS 0.006 0.001 HIS V 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00455 / 0.21 (19630) covalent geometry : angle 0.64714 / 0.32 (26706) hydrogen bonds : bond 0.03837 / 2.54 ( 764) hydrogen bonds : angle 4.67823 / 3.35 ( 2124) metal coordination : bond 0.00372 / 0.22 ( 6) link_TRANS : bond 0.00051 / 0.03 ( 2) link_TRANS : angle 0.43087 / 0.21 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 2158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 217 time to evaluate : 0.848 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: G 75 MET cc_start: 0.8614 (tmm) cc_final: 0.7734 (tmm) REVERT: G 106 HIS cc_start: 0.9202 (m-70) cc_final: 0.8936 (m-70) REVERT: G 176 MET cc_start: 0.7462 (mmm) cc_final: 0.6828 (mmm) REVERT: G 184 ASP cc_start: 0.8610 (m-30) cc_final: 0.8059 (p0) REVERT: G 189 ASP cc_start: 0.9159 (m-30) cc_final: 0.8752 (m-30) REVERT: G 227 ASN cc_start: 0.8656 (t0) cc_final: 0.8151 (t0) REVERT: H 44 MET cc_start: 0.9178 (ptm) cc_final: 0.8882 (ppp) REVERT: H 78 ASN cc_start: 0.8291 (t0) cc_final: 0.7793 (t0) REVERT: H 153 MET cc_start: 0.8870 (tmm) cc_final: 0.8382 (tmm) REVERT: H 195 GLU cc_start: 0.8996 (pt0) cc_final: 0.8613 (pp20) REVERT: H 227 MET cc_start: 0.9474 (mmm) cc_final: 0.9239 (mmm) REVERT: H 272 CYS cc_start: 0.8785 (p) cc_final: 0.8562 (p) REVERT: H 291 LYS cc_start: 0.9472 (tttt) cc_final: 0.9185 (mptt) REVERT: H 325 MET cc_start: 0.8913 (mmm) cc_final: 0.8365 (mmt) REVERT: H 356 TRP cc_start: 0.8396 (m100) cc_final: 0.8018 (m-10) REVERT: I 66 ARG cc_start: 0.7820 (mtm110) cc_final: 0.6991 (ttp-110) REVERT: I 116 ASN cc_start: 0.8791 (t0) cc_final: 0.8260 (t0) REVERT: I 141 MET cc_start: 0.8275 (mmm) cc_final: 0.8065 (mmm) REVERT: I 159 ASP cc_start: 0.8723 (t70) cc_final: 0.8338 (t0) REVERT: I 176 MET cc_start: 0.8789 (mpp) cc_final: 0.8128 (mpp) REVERT: I 189 ASP cc_start: 0.8817 (m-30) cc_final: 0.8369 (m-30) REVERT: I 357 TRP cc_start: 0.9094 (p-90) cc_final: 0.8841 (p-90) REVERT: J 37 CYS cc_start: 0.8563 (t) cc_final: 0.8071 (t) REVERT: J 126 MET cc_start: 0.9532 (mmp) cc_final: 0.9293 (mmm) REVERT: J 137 MET cc_start: 0.9152 (tpp) cc_final: 0.8635 (tpp) REVERT: J 178 GLN cc_start: 0.9200 (mm-40) cc_final: 0.8885 (mm-40) REVERT: J 298 GLN cc_start: 0.9096 (tp40) cc_final: 0.8669 (mm-40) REVERT: J 322 GLU cc_start: 0.9137 (tp30) cc_final: 0.8919 (tp30) REVERT: M 21 GLU cc_start: 0.8859 (pm20) cc_final: 0.8628 (mp0) REVERT: M 38 GLU cc_start: 0.8444 (pm20) cc_final: 0.7849 (pm20) REVERT: M 39 GLU cc_start: 0.8880 (tp30) cc_final: 0.8601 (tp30) REVERT: M 46 GLU cc_start: 0.8461 (tm-30) cc_final: 0.8209 (tm-30) REVERT: M 51 ASN cc_start: 0.9455 (t0) cc_final: 0.9064 (t0) REVERT: M 62 LYS cc_start: 0.9442 (mmtp) cc_final: 0.8523 (tttt) REVERT: U 36 HIS cc_start: 0.8893 (m90) cc_final: 0.8639 (m90) REVERT: U 90 PHE cc_start: 0.7905 (m-80) cc_final: 0.7502 (m-80) REVERT: U 95 TYR cc_start: 0.7969 (t80) cc_final: 0.7696 (t80) REVERT: U 112 TYR cc_start: 0.8847 (t80) cc_final: 0.8390 (t80) REVERT: U 131 LEU cc_start: 0.8872 (pp) cc_final: 0.8644 (pp) REVERT: U 148 CYS cc_start: 0.8433 (m) cc_final: 0.8181 (m) REVERT: V 25 GLN cc_start: 0.9189 (tp-100) cc_final: 0.8682 (tm-30) REVERT: V 83 PHE cc_start: 0.9182 (t80) cc_final: 0.8970 (t80) REVERT: V 100 ASN cc_start: 0.8271 (t160) cc_final: 0.7573 (t0) REVERT: V 157 LEU cc_start: 0.9505 (mt) cc_final: 0.9021 (mt) REVERT: V 176 PHE cc_start: 0.8765 (t80) cc_final: 0.8325 (t80) REVERT: Y 27 LEU cc_start: 0.9640 (mt) cc_final: 0.9355 (mt) REVERT: Y 113 PHE cc_start: 0.8966 (t80) cc_final: 0.8401 (t80) REVERT: Y 163 ASP cc_start: 0.9489 (m-30) cc_final: 0.9090 (m-30) REVERT: Y 319 MET cc_start: 0.8354 (pmm) cc_final: 0.8143 (pmm) outliers start: 0 outliers final: 0 residues processed: 217 average time/residue: 0.1474 time to fit residues: 49.9376 Evaluate side-chains 179 residues out of total 2158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 179 time to evaluate : 0.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 25 optimal weight: 0.9980 chunk 181 optimal weight: 6.9990 chunk 167 optimal weight: 3.9990 chunk 23 optimal weight: 0.4980 chunk 10 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 234 optimal weight: 20.0000 chunk 221 optimal weight: 4.9990 chunk 138 optimal weight: 0.7980 chunk 180 optimal weight: 3.9990 chunk 71 optimal weight: 0.7980 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 240 GLN H 296 ASN ** I 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 405 ASN ** 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 = 0.3228 r_free = 0.3228 target = 0.062688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2726 r_free = 0.2726 target = 0.042813 restraints weight = 92175.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2772 r_free = 0.2772 target = 0.044403 restraints weight = 48098.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 68)----------------| | r_work = 0.2804 r_free = 0.2804 target = 0.045506 restraints weight = 30525.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.046264 restraints weight = 22116.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.046732 restraints weight = 17555.073| |-----------------------------------------------------------------------------| r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.5325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 19638 Z= 0.126 Angle : 0.601 12.433 26712 Z= 0.296 Chirality : 0.042 0.143 3086 Planarity : 0.004 0.041 3454 Dihedral : 6.543 143.460 2827 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.30 % Favored : 95.62 % Rotamer: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % 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: 0.18 (0.17), residues: 2444 helix: 1.65 (0.18), residues: 845 sheet: -0.80 (0.27), residues: 355 loop : -0.65 (0.17), residues: 1244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG J 78 TYR 0.014 0.001 TYR V 13 PHE 0.011 0.001 PHE G 353 TRP 0.102 0.003 TRP G 357 HIS 0.007 0.001 HIS J 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.13 (19630) covalent geometry : angle 0.60104 / 0.30 (26706) hydrogen bonds : bond 0.03672 / 2.43 ( 764) hydrogen bonds : angle 4.53001 / 3.25 ( 2124) metal coordination : bond 0.00139 / 0.08 ( 6) link_TRANS : bond 0.00029 / 0.01 ( 2) link_TRANS : angle 0.39899 / 0.20 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3320.64 seconds wall clock time: 58 minutes 15.84 seconds (3495.84 seconds total)