Starting phenix.real_space_refine on Sat Sep 28 15:23:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6znm_11317/09_2024/6znm_11317.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6znm_11317/09_2024/6znm_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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6znm_11317/09_2024/6znm_11317.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6znm_11317/09_2024/6znm_11317.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6znm_11317/09_2024/6znm_11317.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6znm_11317/09_2024/6znm_11317.cif" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/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, 'ASN:plan1': 1, 'ASP:plan': 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: {'GLU:plan': 2, 'ASP:plan': 3, 'ASN:plan1': 1, 'HIS:plan': 1} 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: {'GLN:plan1': 1, 'ASN:plan1': 2, 'ASP:plan': 6, 'PHE:plan': 1, 'GLU:plan': 9, 'ARG:plan': 3} 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: {'GLN:plan1': 10, 'ASP:plan': 5, 'TYR:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 3, 'GLU:plan': 11, 'ARG:plan': 7} 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: {'GLN:plan1': 4, 'HIS:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 5, 'ASP:plan': 14, 'PHE:plan': 3, 'GLU:plan': 21, 'ARG:plan': 4} 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: {'GLN:plan1': 10, 'ASP:plan': 5, 'TYR:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 3, 'GLU:plan': 11, 'ARG:plan': 7} 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: 11.33, per 1000 atoms: 0.59 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: 4.89 Conformation dependent library (CDL) restraints added in 2.2 seconds 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: 2.80 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: 6.04 Time building geometry restraints manager: 5.70 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: 11594 30.85 - 61.69: 275 61.69 - 92.54: 11 92.54 - 123.38: 4 123.38 - 154.23: 3 Dihedral angle restraints: 11887 sinusoidal: 4336 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 11884 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 376 or resid 800 \ )) selection = chain 'I' } ncs_group { reference = chain 'X' selection = (chain 'x' and (resid 251 through 325 or resid 326 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: 1.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.750 Check model and map are aligned: 0.140 Set scattering table: 0.190 Process input model: 46.640 Find NCS groups from input model: 0.770 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 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 : 0.013 0.118 19630 Z= 0.896 Angle : 1.751 12.947 26706 Z= 1.285 Chirality : 0.087 0.234 3086 Planarity : 0.003 0.029 3454 Dihedral : 13.500 154.227 6999 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.080 0.003 TRP G 357 HIS 0.017 0.002 HIS G 372 PHE 0.016 0.002 PHE M 71 TYR 0.019 0.002 TYR I 38 ARG 0.017 0.001 ARG G 329 *********************** 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 fitting. rotamer outliers: 0 poor density : 511 time to evaluate : 2.163 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: 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: 0.9461 (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: 0.8780 (p) REVERT: G 181 MET cc_start: 0.8232 (mmm) cc_final: 0.7686 (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: 0.7887 (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: 0.8706 (pt0) REVERT: G 280 VAL cc_start: 0.9571 (m) cc_final: 0.9364 (p) REVERT: G 284 GLN cc_start: 0.9256 (mt0) cc_final: 0.8790 (pt0) REVERT: G 286 SER cc_start: 0.8740 (m) cc_final: 0.8344 (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: 0.8832 (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: 0.8904 (mp) REVERT: H 184 ASP cc_start: 0.9066 (m-30) cc_final: 0.8836 (m-30) REVERT: H 195 GLU cc_start: 0.9143 (mt-10) cc_final: 0.8729 (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: 0.7619 (p) REVERT: H 283 MET cc_start: 0.9032 (mmm) cc_final: 0.8813 (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: 0.8879 (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 112 GLU cc_start: 0.9386 (mm-30) cc_final: 0.8533 (tt0) REVERT: I 116 ASN cc_start: 0.7665 (m-40) cc_final: 0.6137 (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: 0.7764 (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: 0.8856 (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: 0.6925 (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: 0.9033 (mt0) REVERT: J 231 PHE cc_start: 0.8545 (m-10) cc_final: 0.8188 (m-10) REVERT: J 289 MET cc_start: 0.8858 (ttp) cc_final: 0.8623 (ttm) REVERT: J 301 GLU cc_start: 0.8695 (mt-10) cc_final: 0.8264 (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: 0.8803 (tp30) REVERT: J 326 LEU cc_start: 0.9110 (mt) cc_final: 0.8603 (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: 0.7434 (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: 0.8873 (m90) REVERT: U 57 GLU cc_start: 0.8769 (mt-10) cc_final: 0.8523 (pt0) 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: 0.7229 (m-80) REVERT: U 95 TYR cc_start: 0.7907 (t80) cc_final: 0.7322 (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: 0.8464 (tp) REVERT: U 139 GLU cc_start: 0.8873 (tp30) cc_final: 0.8224 (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: 0.9268 (mm-40) REVERT: U 168 MET cc_start: 0.9039 (mmt) cc_final: 0.8797 (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: 0.8420 (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: 0.8746 (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: 0.8922 (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: 0.8527 (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: 0.7443 (tt) REVERT: Y 224 GLU cc_start: 0.9373 (pt0) cc_final: 0.9020 (pm20) REVERT: Y 242 ARG cc_start: 0.9297 (ttt180) cc_final: 0.9016 (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: 0.6900 (t-90) outliers start: 0 outliers final: 0 residues processed: 511 average time/residue: 0.3242 time to fit residues: 244.9153 Evaluate side-chains 293 residues out of total 2158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 293 time to evaluate : 2.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 215 optimal weight: 2.9990 chunk 193 optimal weight: 50.0000 chunk 107 optimal weight: 0.9980 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 5.9990 chunk 103 optimal weight: 0.8980 chunk 199 optimal weight: 20.0000 chunk 77 optimal weight: 3.9990 chunk 121 optimal weight: 1.9990 chunk 148 optimal weight: 2.9990 chunk 231 optimal weight: 0.8980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 120 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.2598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 19630 Z= 0.204 Angle : 0.640 10.375 26706 Z= 0.326 Chirality : 0.043 0.159 3086 Planarity : 0.004 0.044 3454 Dihedral : 8.998 166.108 2858 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.60 % Favored : 96.32 % Rotamer: Outliers : 0.16 % Allowed : 2.75 % Favored : 97.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.16), residues: 2444 helix: 1.20 (0.17), residues: 838 sheet: -1.49 (0.25), residues: 357 loop : -1.75 (0.16), residues: 1249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.003 TRP G 357 HIS 0.005 0.001 HIS H 173 PHE 0.035 0.002 PHE G 353 TYR 0.022 0.002 TYR M 20 ARG 0.005 0.001 ARG V 70 *********************** 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 329 residues out of total 2158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 326 time to evaluate : 2.300 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 10 GLN cc_start: 0.9506 (mm-40) cc_final: 0.9069 (tp40) REVERT: G 44 HIS cc_start: 0.8496 (m-70) cc_final: 0.8066 (m-70) REVERT: G 86 MET cc_start: 0.9648 (tpp) cc_final: 0.9260 (tpp) REVERT: G 112 GLU cc_start: 0.8801 (tt0) cc_final: 0.7776 (tt0) REVERT: G 141 MET cc_start: 0.7059 (mmm) cc_final: 0.6567 (mmp) REVERT: G 142 GLN cc_start: 0.8628 (mt0) cc_final: 0.7712 (mp10) REVERT: G 146 SER cc_start: 0.9718 (t) cc_final: 0.9400 (p) REVERT: G 181 MET cc_start: 0.7611 (mmm) cc_final: 0.7194 (tpp) REVERT: G 184 ASP cc_start: 0.8136 (m-30) cc_final: 0.7765 (m-30) REVERT: G 227 ASN cc_start: 0.8290 (m-40) cc_final: 0.8034 (t0) REVERT: G 271 GLU cc_start: 0.9304 (mm-30) cc_final: 0.8826 (pt0) REVERT: G 284 GLN cc_start: 0.9303 (mt0) cc_final: 0.8967 (pt0) REVERT: G 346 ILE cc_start: 0.9641 (OUTLIER) cc_final: 0.9414 (tp) REVERT: G 350 LEU cc_start: 0.9168 (mt) cc_final: 0.8790 (mm) REVERT: H 44 MET cc_start: 0.9047 (ptm) cc_final: 0.8533 (ppp) REVERT: H 47 MET cc_start: 0.8474 (mmm) cc_final: 0.8110 (mmp) REVERT: H 72 GLU cc_start: 0.8510 (mt-10) cc_final: 0.8084 (mp0) REVERT: H 78 ASN cc_start: 0.8479 (t0) cc_final: 0.8156 (t0) REVERT: H 82 MET cc_start: 0.9527 (tpt) cc_final: 0.8912 (tpp) REVERT: H 103 VAL cc_start: 0.9239 (t) cc_final: 0.8888 (p) REVERT: H 153 MET cc_start: 0.9064 (tmm) cc_final: 0.8310 (tmm) REVERT: H 184 ASP cc_start: 0.9239 (m-30) cc_final: 0.8978 (m-30) REVERT: H 195 GLU cc_start: 0.9304 (mt-10) cc_final: 0.8946 (tt0) REVERT: H 215 LYS cc_start: 0.9139 (mmtm) cc_final: 0.8932 (mppt) REVERT: H 217 CYS cc_start: 0.9606 (m) cc_final: 0.9267 (m) REVERT: H 272 CYS cc_start: 0.8337 (p) cc_final: 0.7534 (p) REVERT: H 291 LYS cc_start: 0.9283 (tttt) cc_final: 0.8961 (mptt) REVERT: H 325 MET cc_start: 0.9029 (mmm) cc_final: 0.8578 (mmt) REVERT: H 355 MET cc_start: 0.9050 (mtp) cc_final: 0.8824 (mpp) REVERT: I 100 GLN cc_start: 0.9328 (tt0) cc_final: 0.9036 (tp40) REVERT: I 112 GLU cc_start: 0.9356 (mm-30) cc_final: 0.8431 (tt0) REVERT: I 116 ASN cc_start: 0.7138 (m-40) cc_final: 0.5910 (m-40) REVERT: I 141 MET cc_start: 0.7215 (mmm) cc_final: 0.6584 (mmm) REVERT: I 159 ASP cc_start: 0.9073 (t0) cc_final: 0.8330 (t70) REVERT: I 189 ASP cc_start: 0.9309 (m-30) cc_final: 0.8779 (m-30) REVERT: I 268 ILE cc_start: 0.9574 (tp) cc_final: 0.9344 (tp) REVERT: I 334 GLN cc_start: 0.8871 (tt0) cc_final: 0.8349 (tp-100) REVERT: J 19 ASP cc_start: 0.8074 (t0) cc_final: 0.7720 (t0) REVERT: J 137 MET cc_start: 0.7249 (tpp) cc_final: 0.6629 (tpp) REVERT: J 141 CYS cc_start: 0.9022 (m) cc_final: 0.8792 (p) REVERT: J 145 GLU cc_start: 0.8712 (pt0) cc_final: 0.8177 (mm-30) REVERT: J 178 GLN cc_start: 0.9333 (mm-40) cc_final: 0.9080 (mm-40) REVERT: J 179 LEU cc_start: 0.9428 (mt) cc_final: 0.9177 (pp) REVERT: J 214 THR cc_start: 0.9284 (p) cc_final: 0.8801 (t) REVERT: J 298 GLN cc_start: 0.8650 (tp-100) cc_final: 0.8139 (mm-40) REVERT: J 301 GLU cc_start: 0.8708 (mt-10) cc_final: 0.8443 (mm-30) REVERT: J 311 MET cc_start: 0.9474 (tpp) cc_final: 0.8827 (mtm) REVERT: J 322 GLU cc_start: 0.9467 (tp30) cc_final: 0.8934 (tp30) REVERT: J 326 LEU cc_start: 0.9197 (mt) cc_final: 0.8854 (mt) REVERT: J 352 CYS cc_start: 0.8907 (m) cc_final: 0.7908 (p) REVERT: J 387 TRP cc_start: 0.8438 (p-90) cc_final: 0.7980 (p-90) REVERT: M 21 GLU cc_start: 0.9547 (pt0) cc_final: 0.9001 (mp0) REVERT: M 38 GLU cc_start: 0.9182 (mm-30) cc_final: 0.8872 (pm20) REVERT: M 39 GLU cc_start: 0.8378 (tp30) cc_final: 0.7635 (tp30) REVERT: M 46 GLU cc_start: 0.8567 (tm-30) cc_final: 0.8207 (tm-30) REVERT: M 58 LYS cc_start: 0.9603 (ttpt) cc_final: 0.9294 (ttpt) REVERT: M 62 LYS cc_start: 0.8756 (mmtp) cc_final: 0.7164 (tttt) REVERT: M 77 LYS cc_start: 0.8619 (mmmt) cc_final: 0.8194 (mmtm) REVERT: U 36 HIS cc_start: 0.9390 (m-70) cc_final: 0.8906 (m90) REVERT: U 38 LYS cc_start: 0.9014 (mmtt) cc_final: 0.8751 (mmmt) REVERT: U 57 GLU cc_start: 0.9095 (mt-10) cc_final: 0.8834 (pt0) REVERT: U 90 PHE cc_start: 0.8337 (m-80) cc_final: 0.7450 (m-80) REVERT: U 95 TYR cc_start: 0.7923 (t80) cc_final: 0.7415 (t80) REVERT: U 101 MET cc_start: 0.9523 (mtm) cc_final: 0.9144 (mtt) REVERT: U 112 TYR cc_start: 0.9185 (t80) cc_final: 0.8594 (t80) REVERT: V 8 TYR cc_start: 0.8702 (m-80) cc_final: 0.8362 (m-80) REVERT: V 25 GLN cc_start: 0.9234 (tp-100) cc_final: 0.8630 (tm-30) REVERT: V 40 THR cc_start: 0.8753 (m) cc_final: 0.8447 (p) REVERT: V 90 HIS cc_start: 0.8859 (m-70) cc_final: 0.8392 (m170) REVERT: V 100 ASN cc_start: 0.9013 (m-40) cc_final: 0.8494 (t0) REVERT: V 114 CYS cc_start: 0.8522 (p) cc_final: 0.8228 (p) REVERT: V 120 CYS cc_start: 0.8959 (t) cc_final: 0.8567 (m) REVERT: V 125 CYS cc_start: 0.8906 (m) cc_final: 0.8304 (p) REVERT: V 161 THR cc_start: 0.9261 (m) cc_final: 0.8978 (p) REVERT: V 176 PHE cc_start: 0.9195 (t80) cc_final: 0.8829 (t80) REVERT: Y 27 LEU cc_start: 0.9306 (mt) cc_final: 0.9020 (mt) REVERT: Y 58 MET cc_start: 0.8681 (mtp) cc_final: 0.8246 (ttm) REVERT: Y 123 MET cc_start: 0.8135 (mtp) cc_final: 0.7808 (mtp) REVERT: Y 163 ASP cc_start: 0.9442 (m-30) cc_final: 0.9207 (m-30) REVERT: Y 221 ILE cc_start: 0.8189 (mt) cc_final: 0.7929 (tt) REVERT: Y 289 HIS cc_start: 0.7470 (t70) cc_final: 0.7000 (t-90) REVERT: Y 319 MET cc_start: 0.8604 (tpt) cc_final: 0.8400 (ptt) outliers start: 3 outliers final: 0 residues processed: 329 average time/residue: 0.2974 time to fit residues: 151.8573 Evaluate side-chains 228 residues out of total 2158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 227 time to evaluate : 2.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 128 optimal weight: 10.0000 chunk 71 optimal weight: 0.9980 chunk 192 optimal weight: 30.0000 chunk 157 optimal weight: 10.0000 chunk 63 optimal weight: 3.9990 chunk 231 optimal weight: 20.0000 chunk 250 optimal weight: 50.0000 chunk 206 optimal weight: 10.0000 chunk 230 optimal weight: 30.0000 chunk 79 optimal weight: 0.0870 chunk 186 optimal weight: 2.9990 overall best weight: 3.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 166 HIS G 276 HIS ** H 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 178 HIS ** I 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 87 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.3635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 19630 Z= 0.388 Angle : 0.680 10.241 26706 Z= 0.342 Chirality : 0.044 0.152 3086 Planarity : 0.005 0.052 3454 Dihedral : 8.920 179.637 2858 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.42 % Favored : 95.50 % Rotamer: Outliers : 0.16 % Allowed : 2.80 % Favored : 97.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.17), residues: 2444 helix: 1.55 (0.18), residues: 831 sheet: -1.21 (0.26), residues: 344 loop : -1.28 (0.16), residues: 1269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.067 0.003 TRP G 357 HIS 0.006 0.001 HIS G 276 PHE 0.036 0.002 PHE G 193 TYR 0.021 0.002 TYR G 197 ARG 0.008 0.001 ARG V 70 *********************** 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 260 residues out of total 2158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 257 time to evaluate : 2.149 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: G 75 MET cc_start: 0.8300 (tmm) cc_final: 0.7315 (tmm) REVERT: G 112 GLU cc_start: 0.8827 (tt0) cc_final: 0.7843 (tt0) REVERT: G 142 GLN cc_start: 0.8837 (mt0) cc_final: 0.7914 (mp10) REVERT: G 176 MET cc_start: 0.5593 (mmm) cc_final: 0.5148 (mmm) REVERT: G 181 MET cc_start: 0.7629 (mmm) cc_final: 0.7346 (tpp) REVERT: G 184 ASP cc_start: 0.7891 (m-30) cc_final: 0.7345 (m-30) REVERT: G 227 ASN cc_start: 0.8273 (m-40) cc_final: 0.7941 (t0) REVERT: G 350 LEU cc_start: 0.9325 (mt) cc_final: 0.9079 (mm) REVERT: G 353 PHE cc_start: 0.9507 (t80) cc_final: 0.9246 (t80) REVERT: H 44 MET cc_start: 0.8839 (ptm) cc_final: 0.8355 (ppp) REVERT: H 47 MET cc_start: 0.8621 (mmm) cc_final: 0.8254 (mmp) REVERT: H 72 GLU cc_start: 0.8661 (mt-10) cc_final: 0.8226 (mp0) REVERT: H 78 ASN cc_start: 0.8430 (t0) cc_final: 0.8214 (t0) REVERT: H 82 MET cc_start: 0.9573 (tpt) cc_final: 0.8746 (tpp) REVERT: H 153 MET cc_start: 0.9136 (tmm) cc_final: 0.7812 (tmm) REVERT: H 184 ASP cc_start: 0.9279 (m-30) cc_final: 0.9018 (m-30) REVERT: H 195 GLU cc_start: 0.9329 (mt-10) cc_final: 0.8939 (tt0) REVERT: H 217 CYS cc_start: 0.9491 (m) cc_final: 0.9217 (m) REVERT: H 227 MET cc_start: 0.9129 (mmm) cc_final: 0.8721 (mmm) REVERT: H 272 CYS cc_start: 0.8400 (p) cc_final: 0.7881 (p) REVERT: H 291 LYS cc_start: 0.9244 (tttt) cc_final: 0.8897 (mptt) REVERT: H 325 MET cc_start: 0.9077 (mmm) cc_final: 0.8448 (mmt) REVERT: I 100 GLN cc_start: 0.9329 (tt0) cc_final: 0.9058 (tm-30) REVERT: I 112 GLU cc_start: 0.9245 (mm-30) cc_final: 0.8364 (tt0) REVERT: I 116 ASN cc_start: 0.7603 (m-40) cc_final: 0.6136 (m-40) REVERT: I 141 MET cc_start: 0.7341 (mmp) cc_final: 0.7125 (mmm) REVERT: I 159 ASP cc_start: 0.8943 (t0) cc_final: 0.8355 (t70) REVERT: I 176 MET cc_start: 0.8484 (mpp) cc_final: 0.7360 (mpp) REVERT: I 189 ASP cc_start: 0.9329 (m-30) cc_final: 0.8764 (m-30) REVERT: I 271 GLU cc_start: 0.9157 (tp30) cc_final: 0.8243 (tt0) REVERT: I 334 GLN cc_start: 0.9071 (tt0) cc_final: 0.8579 (tp-100) REVERT: J 37 CYS cc_start: 0.7862 (t) cc_final: 0.6015 (t) REVERT: J 137 MET cc_start: 0.7402 (tpp) cc_final: 0.6787 (tpt) REVERT: J 145 GLU cc_start: 0.8808 (pt0) cc_final: 0.8171 (mm-30) REVERT: J 178 GLN cc_start: 0.9311 (mm-40) cc_final: 0.8976 (mm-40) REVERT: J 289 MET cc_start: 0.8798 (ttm) cc_final: 0.8429 (ttm) REVERT: J 298 GLN cc_start: 0.8666 (tp-100) cc_final: 0.8320 (mm-40) REVERT: J 301 GLU cc_start: 0.8878 (mt-10) cc_final: 0.8552 (mm-30) REVERT: J 311 MET cc_start: 0.9445 (tpp) cc_final: 0.8872 (mtm) REVERT: J 322 GLU cc_start: 0.9491 (tp30) cc_final: 0.8954 (tp30) REVERT: J 326 LEU cc_start: 0.9284 (mt) cc_final: 0.9075 (mt) REVERT: J 352 CYS cc_start: 0.8911 (m) cc_final: 0.8116 (p) REVERT: J 387 TRP cc_start: 0.8816 (p-90) cc_final: 0.8562 (p-90) REVERT: M 21 GLU cc_start: 0.9444 (pt0) cc_final: 0.8799 (pm20) REVERT: M 38 GLU cc_start: 0.9308 (mm-30) cc_final: 0.8889 (pm20) REVERT: M 46 GLU cc_start: 0.8460 (tm-30) cc_final: 0.8081 (tm-30) REVERT: M 51 ASN cc_start: 0.9624 (t0) cc_final: 0.9063 (t0) REVERT: M 58 LYS cc_start: 0.9582 (ttpt) cc_final: 0.9248 (tttt) REVERT: M 62 LYS cc_start: 0.8974 (mmtp) cc_final: 0.7963 (tttt) REVERT: M 77 LYS cc_start: 0.8757 (mmmt) cc_final: 0.8428 (mmtm) REVERT: U 38 LYS cc_start: 0.8930 (mmtt) cc_final: 0.8709 (mmmt) REVERT: U 57 GLU cc_start: 0.9259 (mt-10) cc_final: 0.8728 (pt0) REVERT: U 90 PHE cc_start: 0.8431 (m-80) cc_final: 0.7729 (m-80) REVERT: U 95 TYR cc_start: 0.7891 (t80) cc_final: 0.7358 (t80) REVERT: U 101 MET cc_start: 0.9643 (mtm) cc_final: 0.9185 (mtm) REVERT: U 112 TYR cc_start: 0.9138 (t80) cc_final: 0.8401 (t80) REVERT: U 150 ARG cc_start: 0.8293 (mtm180) cc_final: 0.7821 (mtt90) REVERT: V 8 TYR cc_start: 0.8746 (m-80) cc_final: 0.8299 (m-80) REVERT: V 25 GLN cc_start: 0.9432 (tp-100) cc_final: 0.8788 (tm-30) REVERT: V 100 ASN cc_start: 0.8719 (m-40) cc_final: 0.8339 (t0) REVERT: V 103 GLN cc_start: 0.9188 (tp-100) cc_final: 0.8892 (tp-100) REVERT: V 114 CYS cc_start: 0.8579 (p) cc_final: 0.8333 (p) REVERT: V 120 CYS cc_start: 0.9016 (t) cc_final: 0.8598 (m) REVERT: V 125 CYS cc_start: 0.8834 (m) cc_final: 0.7919 (p) REVERT: V 126 CYS cc_start: 0.9179 (p) cc_final: 0.8965 (p) REVERT: V 154 SER cc_start: 0.9605 (t) cc_final: 0.9377 (p) REVERT: V 157 LEU cc_start: 0.8592 (mt) cc_final: 0.7896 (mt) REVERT: V 165 MET cc_start: 0.9648 (mmm) cc_final: 0.9096 (mtp) REVERT: V 176 PHE cc_start: 0.9246 (t80) cc_final: 0.8893 (t80) REVERT: Y 27 LEU cc_start: 0.9301 (mt) cc_final: 0.8978 (mt) REVERT: Y 123 MET cc_start: 0.8266 (mtp) cc_final: 0.7981 (mtp) REVERT: Y 163 ASP cc_start: 0.9501 (m-30) cc_final: 0.9255 (m-30) REVERT: Y 319 MET cc_start: 0.8632 (tpt) cc_final: 0.8376 (ptp) outliers start: 3 outliers final: 2 residues processed: 260 average time/residue: 0.2908 time to fit residues: 118.1886 Evaluate side-chains 207 residues out of total 2158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 205 time to evaluate : 2.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 229 optimal weight: 10.0000 chunk 174 optimal weight: 9.9990 chunk 120 optimal weight: 0.9980 chunk 25 optimal weight: 0.9990 chunk 110 optimal weight: 5.9990 chunk 155 optimal weight: 10.0000 chunk 232 optimal weight: 4.9990 chunk 246 optimal weight: 30.0000 chunk 121 optimal weight: 6.9990 chunk 220 optimal weight: 5.9990 chunk 66 optimal weight: 0.6980 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 284 GLN H 59 GLN ** H 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 344 HIS Y 273 HIS ** Y 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.3991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 19630 Z= 0.292 Angle : 0.607 11.877 26706 Z= 0.304 Chirality : 0.043 0.144 3086 Planarity : 0.004 0.045 3454 Dihedral : 8.570 171.542 2858 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.01 % Favored : 95.91 % Rotamer: Outliers : 0.05 % Allowed : 3.02 % Favored : 96.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.17), residues: 2444 helix: 1.70 (0.18), residues: 832 sheet: -1.19 (0.27), residues: 348 loop : -1.08 (0.17), residues: 1264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.070 0.003 TRP G 357 HIS 0.005 0.001 HIS J 79 PHE 0.026 0.002 PHE G 295 TYR 0.015 0.002 TYR U 144 ARG 0.004 0.000 ARG M 63 *********************** 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 252 residues out of total 2158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 251 time to evaluate : 2.306 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 10 GLN cc_start: 0.9400 (mm-40) cc_final: 0.9195 (mm-40) REVERT: G 75 MET cc_start: 0.8130 (tmm) cc_final: 0.7234 (tmm) REVERT: G 106 HIS cc_start: 0.9701 (m-70) cc_final: 0.9427 (m-70) REVERT: G 112 GLU cc_start: 0.8873 (tt0) cc_final: 0.7873 (tt0) REVERT: G 142 GLN cc_start: 0.8820 (mt0) cc_final: 0.7932 (mp10) REVERT: G 176 MET cc_start: 0.6344 (mmm) cc_final: 0.5952 (mmm) REVERT: G 181 MET cc_start: 0.7650 (mmm) cc_final: 0.7418 (tpp) REVERT: G 184 ASP cc_start: 0.7954 (m-30) cc_final: 0.7579 (p0) REVERT: G 189 ASP cc_start: 0.9421 (m-30) cc_final: 0.8827 (m-30) REVERT: G 284 GLN cc_start: 0.9454 (mt0) cc_final: 0.9158 (mt0) REVERT: H 44 MET cc_start: 0.8757 (ptm) cc_final: 0.8339 (ppp) REVERT: H 47 MET cc_start: 0.8703 (mmm) cc_final: 0.8385 (mmp) REVERT: H 72 GLU cc_start: 0.8638 (mt-10) cc_final: 0.8172 (mp0) REVERT: H 82 MET cc_start: 0.9562 (tpt) cc_final: 0.9228 (tpt) REVERT: H 153 MET cc_start: 0.9348 (tmm) cc_final: 0.8296 (tmm) REVERT: H 184 ASP cc_start: 0.9157 (m-30) cc_final: 0.8825 (m-30) REVERT: H 195 GLU cc_start: 0.9335 (mt-10) cc_final: 0.8932 (tt0) REVERT: H 217 CYS cc_start: 0.9440 (m) cc_final: 0.9222 (m) REVERT: H 227 MET cc_start: 0.9196 (mmm) cc_final: 0.8729 (mmm) REVERT: H 272 CYS cc_start: 0.8351 (p) cc_final: 0.7847 (p) REVERT: H 291 LYS cc_start: 0.9252 (tttt) cc_final: 0.8917 (mptt) REVERT: H 306 TYR cc_start: 0.8911 (m-80) cc_final: 0.8697 (m-10) REVERT: H 325 MET cc_start: 0.9036 (mmm) cc_final: 0.8491 (mmt) REVERT: H 355 MET cc_start: 0.9362 (mmp) cc_final: 0.8988 (mmp) REVERT: I 13 VAL cc_start: 0.9374 (t) cc_final: 0.9131 (m) REVERT: I 75 MET cc_start: 0.8764 (ttp) cc_final: 0.8020 (ptm) REVERT: I 100 GLN cc_start: 0.9306 (tt0) cc_final: 0.9048 (tm-30) REVERT: I 112 GLU cc_start: 0.9279 (mm-30) cc_final: 0.8413 (tt0) REVERT: I 116 ASN cc_start: 0.7654 (m-40) cc_final: 0.6267 (m-40) REVERT: I 159 ASP cc_start: 0.8964 (t0) cc_final: 0.8317 (t70) REVERT: I 176 MET cc_start: 0.8378 (mpp) cc_final: 0.7319 (mpp) REVERT: I 189 ASP cc_start: 0.9325 (m-30) cc_final: 0.8732 (m-30) REVERT: I 268 ILE cc_start: 0.9538 (tp) cc_final: 0.8877 (tp) REVERT: I 270 GLU cc_start: 0.8003 (mm-30) cc_final: 0.7279 (mm-30) REVERT: I 271 GLU cc_start: 0.9086 (tp30) cc_final: 0.8228 (tt0) REVERT: I 356 MET cc_start: 0.8780 (mpp) cc_final: 0.8212 (mtt) REVERT: J 37 CYS cc_start: 0.7539 (t) cc_final: 0.6933 (t) REVERT: J 48 MET cc_start: 0.9187 (mpp) cc_final: 0.8975 (mpp) REVERT: J 56 GLN cc_start: 0.8714 (mt0) cc_final: 0.8479 (mt0) REVERT: J 137 MET cc_start: 0.7386 (tpp) cc_final: 0.6807 (tpp) REVERT: J 178 GLN cc_start: 0.9198 (mm-40) cc_final: 0.8902 (mm-40) REVERT: J 289 MET cc_start: 0.8791 (ttm) cc_final: 0.8425 (ttm) REVERT: J 298 GLN cc_start: 0.8603 (tp-100) cc_final: 0.8223 (mm-40) REVERT: J 311 MET cc_start: 0.9410 (tpp) cc_final: 0.8779 (mtm) REVERT: J 322 GLU cc_start: 0.9484 (tp30) cc_final: 0.8919 (tp30) REVERT: J 326 LEU cc_start: 0.9289 (mt) cc_final: 0.9001 (mt) REVERT: J 352 CYS cc_start: 0.8902 (m) cc_final: 0.8380 (p) REVERT: J 387 TRP cc_start: 0.8845 (p-90) cc_final: 0.8570 (p-90) REVERT: M 21 GLU cc_start: 0.9400 (pt0) cc_final: 0.8831 (pm20) REVERT: M 38 GLU cc_start: 0.9288 (mm-30) cc_final: 0.8930 (pm20) REVERT: M 46 GLU cc_start: 0.8484 (tm-30) cc_final: 0.8024 (tm-30) REVERT: M 51 ASN cc_start: 0.9556 (t0) cc_final: 0.9248 (t0) REVERT: M 58 LYS cc_start: 0.9624 (ttpt) cc_final: 0.9205 (pttt) REVERT: M 62 LYS cc_start: 0.8933 (mmtp) cc_final: 0.7901 (tttt) REVERT: M 77 LYS cc_start: 0.8799 (mmmt) cc_final: 0.8492 (mmtm) REVERT: U 84 ILE cc_start: 0.9398 (mt) cc_final: 0.9053 (tp) REVERT: U 91 GLU cc_start: 0.8770 (mt-10) cc_final: 0.8523 (mt-10) REVERT: U 95 TYR cc_start: 0.7904 (t80) cc_final: 0.7335 (t80) REVERT: U 101 MET cc_start: 0.9671 (mtm) cc_final: 0.9194 (mtm) REVERT: U 112 TYR cc_start: 0.9127 (t80) cc_final: 0.8512 (t80) REVERT: U 148 CYS cc_start: 0.8860 (m) cc_final: 0.8575 (m) REVERT: U 150 ARG cc_start: 0.8316 (mtm180) cc_final: 0.7718 (mtt90) REVERT: V 8 TYR cc_start: 0.8733 (m-80) cc_final: 0.8098 (m-80) REVERT: V 25 GLN cc_start: 0.9449 (tp-100) cc_final: 0.8761 (tm-30) REVERT: V 100 ASN cc_start: 0.8759 (m-40) cc_final: 0.8171 (t0) REVERT: V 103 GLN cc_start: 0.9190 (tp-100) cc_final: 0.8829 (tp-100) REVERT: V 114 CYS cc_start: 0.8522 (p) cc_final: 0.8224 (p) REVERT: V 120 CYS cc_start: 0.9016 (t) cc_final: 0.8588 (m) REVERT: V 126 CYS cc_start: 0.8974 (p) cc_final: 0.8734 (p) REVERT: V 154 SER cc_start: 0.9584 (t) cc_final: 0.9383 (p) REVERT: V 157 LEU cc_start: 0.8734 (mt) cc_final: 0.8130 (mt) REVERT: V 176 PHE cc_start: 0.9256 (t80) cc_final: 0.8890 (t80) REVERT: Y 27 LEU cc_start: 0.9274 (mt) cc_final: 0.9027 (mt) REVERT: Y 163 ASP cc_start: 0.9470 (m-30) cc_final: 0.9182 (m-30) outliers start: 1 outliers final: 0 residues processed: 252 average time/residue: 0.3026 time to fit residues: 118.8082 Evaluate side-chains 203 residues out of total 2158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 203 time to evaluate : 2.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 205 optimal weight: 7.9990 chunk 139 optimal weight: 0.9980 chunk 3 optimal weight: 0.0370 chunk 183 optimal weight: 0.7980 chunk 101 optimal weight: 0.8980 chunk 210 optimal weight: 7.9990 chunk 170 optimal weight: 7.9990 chunk 0 optimal weight: 8.9990 chunk 125 optimal weight: 0.8980 chunk 221 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 overall best weight: 0.7258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 16 ASN H 371 HIS U 163 GLN ** Y 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 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 : 0.002 0.024 19630 Z= 0.147 Angle : 0.566 11.841 26706 Z= 0.280 Chirality : 0.042 0.187 3086 Planarity : 0.004 0.044 3454 Dihedral : 8.060 169.215 2858 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.76 % Favored : 96.15 % Rotamer: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.17), residues: 2444 helix: 1.78 (0.18), residues: 830 sheet: -1.07 (0.27), residues: 346 loop : -0.93 (0.17), residues: 1268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.076 0.003 TRP G 357 HIS 0.009 0.001 HIS V 109 PHE 0.039 0.001 PHE G 193 TYR 0.022 0.001 TYR J 76 ARG 0.003 0.000 ARG Y 242 *********************** 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 270 residues out of total 2158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 270 time to evaluate : 2.330 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: 0.7972 (tmm) cc_final: 0.7120 (tmm) REVERT: G 106 HIS cc_start: 0.9691 (m-70) cc_final: 0.9436 (m-70) REVERT: G 112 GLU cc_start: 0.8885 (tt0) cc_final: 0.7654 (tt0) REVERT: G 142 GLN cc_start: 0.8703 (mt0) cc_final: 0.7945 (mp10) REVERT: G 176 MET cc_start: 0.6257 (mmm) cc_final: 0.5880 (mmm) REVERT: G 181 MET cc_start: 0.7485 (mmm) cc_final: 0.7265 (tpp) REVERT: G 184 ASP cc_start: 0.7940 (m-30) cc_final: 0.7580 (p0) REVERT: G 189 ASP cc_start: 0.9449 (m-30) cc_final: 0.8842 (m-30) REVERT: G 227 ASN cc_start: 0.8217 (t0) cc_final: 0.7644 (t0) REVERT: G 240 GLN cc_start: 0.8348 (tt0) cc_final: 0.8108 (tt0) REVERT: G 284 GLN cc_start: 0.9447 (mt0) cc_final: 0.9131 (mt0) REVERT: H 44 MET cc_start: 0.8851 (ptm) cc_final: 0.8520 (ppp) REVERT: H 47 MET cc_start: 0.8718 (mmm) cc_final: 0.8212 (mmp) REVERT: H 72 GLU cc_start: 0.8610 (mt-10) cc_final: 0.8155 (mp0) REVERT: H 78 ASN cc_start: 0.8386 (t0) cc_final: 0.7960 (t0) REVERT: H 82 MET cc_start: 0.9472 (tpt) cc_final: 0.8869 (tpp) REVERT: H 142 LEU cc_start: 0.9428 (tp) cc_final: 0.9224 (tp) REVERT: H 153 MET cc_start: 0.9382 (tmm) cc_final: 0.8481 (tmm) REVERT: H 184 ASP cc_start: 0.9118 (m-30) cc_final: 0.8816 (m-30) REVERT: H 195 GLU cc_start: 0.9329 (mt-10) cc_final: 0.8950 (tt0) REVERT: H 217 CYS cc_start: 0.9462 (m) cc_final: 0.9111 (m) REVERT: H 272 CYS cc_start: 0.8283 (p) cc_final: 0.7783 (p) REVERT: H 291 LYS cc_start: 0.9249 (tttt) cc_final: 0.8953 (mptt) REVERT: H 325 MET cc_start: 0.8960 (mmm) cc_final: 0.8442 (mmt) REVERT: H 355 MET cc_start: 0.9340 (mmp) cc_final: 0.9045 (mmp) REVERT: I 75 MET cc_start: 0.8649 (ttp) cc_final: 0.8000 (ptm) REVERT: I 100 GLN cc_start: 0.9350 (tt0) cc_final: 0.9120 (tm-30) REVERT: I 112 GLU cc_start: 0.9174 (mm-30) cc_final: 0.8311 (tt0) REVERT: I 116 ASN cc_start: 0.7775 (m-40) cc_final: 0.6431 (m-40) REVERT: I 159 ASP cc_start: 0.8971 (t0) cc_final: 0.8316 (t70) REVERT: I 176 MET cc_start: 0.8513 (mpp) cc_final: 0.7309 (mpp) REVERT: I 189 ASP cc_start: 0.9086 (m-30) cc_final: 0.8453 (m-30) REVERT: I 268 ILE cc_start: 0.9523 (tp) cc_final: 0.8066 (tp) REVERT: I 270 GLU cc_start: 0.8078 (mm-30) cc_final: 0.7144 (mp0) REVERT: I 271 GLU cc_start: 0.9046 (tp30) cc_final: 0.8194 (tt0) REVERT: I 356 MET cc_start: 0.8757 (mpp) cc_final: 0.8332 (mtm) REVERT: I 357 TRP cc_start: 0.8847 (p-90) cc_final: 0.8350 (p-90) REVERT: J 37 CYS cc_start: 0.7437 (t) cc_final: 0.6849 (t) REVERT: J 56 GLN cc_start: 0.8656 (mt0) cc_final: 0.8381 (mt0) REVERT: J 137 MET cc_start: 0.7505 (tpp) cc_final: 0.6908 (tpp) REVERT: J 178 GLN cc_start: 0.9221 (mm-40) cc_final: 0.8922 (mm-40) REVERT: J 289 MET cc_start: 0.8825 (ttm) cc_final: 0.8508 (ttm) REVERT: J 311 MET cc_start: 0.9381 (tpp) cc_final: 0.8758 (mtm) REVERT: J 322 GLU cc_start: 0.9463 (tp30) cc_final: 0.8871 (tp30) REVERT: J 326 LEU cc_start: 0.9269 (mt) cc_final: 0.8907 (mt) REVERT: J 352 CYS cc_start: 0.8904 (m) cc_final: 0.8325 (p) REVERT: J 387 TRP cc_start: 0.8700 (p-90) cc_final: 0.8302 (p-90) REVERT: M 21 GLU cc_start: 0.9449 (pt0) cc_final: 0.8833 (pm20) REVERT: M 38 GLU cc_start: 0.9296 (mm-30) cc_final: 0.8857 (pm20) REVERT: M 46 GLU cc_start: 0.8433 (tm-30) cc_final: 0.7943 (tm-30) REVERT: M 48 ILE cc_start: 0.9271 (tp) cc_final: 0.9052 (tp) REVERT: M 51 ASN cc_start: 0.9595 (t0) cc_final: 0.9201 (t0) REVERT: M 58 LYS cc_start: 0.9636 (ttpt) cc_final: 0.9182 (pttt) REVERT: M 62 LYS cc_start: 0.8991 (mmtp) cc_final: 0.8009 (tttt) REVERT: M 67 LYS cc_start: 0.9568 (tppp) cc_final: 0.9332 (tppp) REVERT: M 77 LYS cc_start: 0.8774 (mmmt) cc_final: 0.8480 (mmtm) REVERT: U 10 LYS cc_start: 0.9578 (tptp) cc_final: 0.9327 (mmtm) REVERT: U 90 PHE cc_start: 0.8204 (m-80) cc_final: 0.7898 (m-80) REVERT: U 95 TYR cc_start: 0.7891 (t80) cc_final: 0.7362 (t80) REVERT: U 112 TYR cc_start: 0.9101 (t80) cc_final: 0.8483 (t80) REVERT: U 131 LEU cc_start: 0.8628 (pp) cc_final: 0.8349 (pp) REVERT: U 144 TYR cc_start: 0.8575 (p90) cc_final: 0.8374 (p90) REVERT: U 148 CYS cc_start: 0.8826 (m) cc_final: 0.8562 (m) REVERT: U 150 ARG cc_start: 0.8395 (mtm180) cc_final: 0.7815 (mtt90) REVERT: V 8 TYR cc_start: 0.8706 (m-80) cc_final: 0.8061 (m-80) REVERT: V 25 GLN cc_start: 0.9465 (tp-100) cc_final: 0.8780 (tm-30) REVERT: V 100 ASN cc_start: 0.8792 (m-40) cc_final: 0.8129 (t0) REVERT: V 103 GLN cc_start: 0.9206 (tp-100) cc_final: 0.8939 (tp-100) REVERT: V 120 CYS cc_start: 0.9095 (t) cc_final: 0.8610 (m) REVERT: V 126 CYS cc_start: 0.8939 (p) cc_final: 0.8371 (m) REVERT: V 157 LEU cc_start: 0.8746 (mt) cc_final: 0.8173 (mt) REVERT: V 165 MET cc_start: 0.9660 (mmm) cc_final: 0.9108 (mtp) REVERT: V 176 PHE cc_start: 0.9236 (t80) cc_final: 0.8851 (t80) REVERT: Y 27 LEU cc_start: 0.9325 (mt) cc_final: 0.9085 (mt) REVERT: Y 58 MET cc_start: 0.7803 (ttt) cc_final: 0.7471 (tmm) REVERT: Y 123 MET cc_start: 0.8608 (mtp) cc_final: 0.8396 (mtp) REVERT: Y 163 ASP cc_start: 0.9453 (m-30) cc_final: 0.9154 (m-30) REVERT: Y 289 HIS cc_start: 0.7657 (t-90) cc_final: 0.7282 (t-90) outliers start: 0 outliers final: 0 residues processed: 270 average time/residue: 0.2935 time to fit residues: 123.9701 Evaluate side-chains 205 residues out of total 2158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 205 time to evaluate : 2.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 82 optimal weight: 0.7980 chunk 221 optimal weight: 5.9990 chunk 48 optimal weight: 0.9990 chunk 144 optimal weight: 4.9990 chunk 60 optimal weight: 6.9990 chunk 246 optimal weight: 30.0000 chunk 204 optimal weight: 7.9990 chunk 114 optimal weight: 6.9990 chunk 20 optimal weight: 4.9990 chunk 81 optimal weight: 1.9990 chunk 129 optimal weight: 9.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 161 HIS ** J 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.4482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 19630 Z= 0.314 Angle : 0.612 11.939 26706 Z= 0.303 Chirality : 0.042 0.153 3086 Planarity : 0.004 0.041 3454 Dihedral : 8.038 164.025 2858 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.58 % Favored : 95.34 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.17), residues: 2444 helix: 1.85 (0.18), residues: 822 sheet: -0.97 (0.27), residues: 346 loop : -0.80 (0.17), residues: 1276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.076 0.003 TRP G 357 HIS 0.007 0.001 HIS V 109 PHE 0.036 0.002 PHE I 295 TYR 0.015 0.001 TYR M 83 ARG 0.003 0.000 ARG H 206 *********************** 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 243 residues out of total 2158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 243 time to evaluate : 2.147 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: G 75 MET cc_start: 0.8161 (tmm) cc_final: 0.7097 (tmm) REVERT: G 112 GLU cc_start: 0.8765 (tt0) cc_final: 0.7530 (tt0) REVERT: G 142 GLN cc_start: 0.8741 (mt0) cc_final: 0.8041 (mp10) REVERT: G 176 MET cc_start: 0.6637 (mmm) cc_final: 0.6198 (mmm) REVERT: G 184 ASP cc_start: 0.7940 (m-30) cc_final: 0.7591 (p0) REVERT: G 189 ASP cc_start: 0.9392 (m-30) cc_final: 0.8785 (m-30) REVERT: G 227 ASN cc_start: 0.8244 (t0) cc_final: 0.7753 (t0) REVERT: G 284 GLN cc_start: 0.9470 (mt0) cc_final: 0.9131 (mt0) REVERT: H 44 MET cc_start: 0.8711 (ptm) cc_final: 0.8353 (ppp) REVERT: H 47 MET cc_start: 0.8739 (mmm) cc_final: 0.8426 (mmp) REVERT: H 72 GLU cc_start: 0.8673 (mt-10) cc_final: 0.8185 (mp0) REVERT: H 78 ASN cc_start: 0.8343 (t0) cc_final: 0.8011 (t0) REVERT: H 82 MET cc_start: 0.9561 (tpt) cc_final: 0.9304 (tpt) REVERT: H 153 MET cc_start: 0.9351 (tmm) cc_final: 0.8517 (tmm) REVERT: H 184 ASP cc_start: 0.9110 (m-30) cc_final: 0.8810 (m-30) REVERT: H 195 GLU cc_start: 0.9333 (mt-10) cc_final: 0.8947 (tt0) REVERT: H 272 CYS cc_start: 0.8267 (p) cc_final: 0.7759 (p) REVERT: H 291 LYS cc_start: 0.9251 (tttt) cc_final: 0.8919 (mptt) REVERT: H 325 MET cc_start: 0.8985 (mmm) cc_final: 0.8429 (mmt) REVERT: H 355 MET cc_start: 0.9288 (mmp) cc_final: 0.8854 (mmm) REVERT: I 100 GLN cc_start: 0.9269 (tt0) cc_final: 0.9043 (tm-30) REVERT: I 159 ASP cc_start: 0.8978 (t0) cc_final: 0.8317 (t70) REVERT: I 176 MET cc_start: 0.8344 (mpp) cc_final: 0.7322 (mpp) REVERT: I 189 ASP cc_start: 0.9000 (m-30) cc_final: 0.8433 (m-30) REVERT: I 229 GLN cc_start: 0.9346 (mp10) cc_final: 0.9111 (mp10) REVERT: I 268 ILE cc_start: 0.9536 (tp) cc_final: 0.8862 (tp) REVERT: I 270 GLU cc_start: 0.8034 (mm-30) cc_final: 0.7517 (mm-30) REVERT: I 271 GLU cc_start: 0.9029 (tp30) cc_final: 0.8164 (tt0) REVERT: I 357 TRP cc_start: 0.8868 (p-90) cc_final: 0.8538 (p-90) REVERT: J 37 CYS cc_start: 0.7528 (t) cc_final: 0.6879 (t) REVERT: J 48 MET cc_start: 0.9195 (mpp) cc_final: 0.8979 (mpp) REVERT: J 56 GLN cc_start: 0.8664 (mt0) cc_final: 0.8448 (mt0) REVERT: J 137 MET cc_start: 0.7550 (tpp) cc_final: 0.6952 (tpp) REVERT: J 178 GLN cc_start: 0.9158 (mm-40) cc_final: 0.8904 (mm-40) REVERT: J 231 PHE cc_start: 0.8412 (m-80) cc_final: 0.8095 (m-80) REVERT: J 289 MET cc_start: 0.8817 (ttm) cc_final: 0.8514 (ttm) REVERT: J 298 GLN cc_start: 0.8490 (tp40) cc_final: 0.8117 (mm-40) REVERT: J 311 MET cc_start: 0.9406 (tpp) cc_final: 0.8916 (mmm) REVERT: J 322 GLU cc_start: 0.9472 (tp30) cc_final: 0.8927 (tp30) REVERT: J 326 LEU cc_start: 0.9319 (mt) cc_final: 0.9048 (mt) REVERT: M 21 GLU cc_start: 0.9372 (pt0) cc_final: 0.8856 (pm20) REVERT: M 38 GLU cc_start: 0.9307 (mm-30) cc_final: 0.8937 (pm20) REVERT: M 46 GLU cc_start: 0.8429 (tm-30) cc_final: 0.8009 (tm-30) REVERT: M 51 ASN cc_start: 0.9591 (t0) cc_final: 0.9153 (t0) REVERT: M 58 LYS cc_start: 0.9625 (ttpt) cc_final: 0.9196 (pttt) REVERT: M 62 LYS cc_start: 0.8990 (mmtp) cc_final: 0.8004 (tttt) REVERT: M 67 LYS cc_start: 0.9622 (tppp) cc_final: 0.9372 (tppp) REVERT: M 77 LYS cc_start: 0.8880 (mmmt) cc_final: 0.8592 (mmtm) REVERT: U 90 PHE cc_start: 0.8130 (m-80) cc_final: 0.7707 (m-80) REVERT: U 95 TYR cc_start: 0.7835 (t80) cc_final: 0.7295 (t80) REVERT: U 112 TYR cc_start: 0.9073 (t80) cc_final: 0.8437 (t80) REVERT: U 131 LEU cc_start: 0.8609 (pp) cc_final: 0.8295 (pp) REVERT: U 148 CYS cc_start: 0.8850 (m) cc_final: 0.8600 (m) REVERT: U 150 ARG cc_start: 0.8336 (mtm180) cc_final: 0.7734 (mtt90) REVERT: V 25 GLN cc_start: 0.9488 (tp-100) cc_final: 0.8777 (tm-30) REVERT: V 52 LEU cc_start: 0.8359 (tp) cc_final: 0.8116 (tp) REVERT: V 103 GLN cc_start: 0.9255 (tp-100) cc_final: 0.8892 (tp-100) REVERT: V 114 CYS cc_start: 0.8853 (p) cc_final: 0.8568 (p) REVERT: V 120 CYS cc_start: 0.9122 (t) cc_final: 0.8670 (m) REVERT: V 126 CYS cc_start: 0.8869 (p) cc_final: 0.8663 (p) REVERT: V 154 SER cc_start: 0.9583 (t) cc_final: 0.9381 (p) REVERT: V 157 LEU cc_start: 0.8730 (mt) cc_final: 0.8177 (mt) REVERT: V 165 MET cc_start: 0.9676 (mmm) cc_final: 0.9292 (mtp) REVERT: V 176 PHE cc_start: 0.9285 (t80) cc_final: 0.8942 (t80) REVERT: Y 27 LEU cc_start: 0.9191 (mt) cc_final: 0.8923 (mt) REVERT: Y 58 MET cc_start: 0.7980 (ttt) cc_final: 0.7628 (tmm) REVERT: Y 123 MET cc_start: 0.8594 (mtp) cc_final: 0.8382 (mtp) REVERT: Y 163 ASP cc_start: 0.9466 (m-30) cc_final: 0.9173 (m-30) outliers start: 0 outliers final: 0 residues processed: 243 average time/residue: 0.2869 time to fit residues: 109.0252 Evaluate side-chains 194 residues out of total 2158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 194 time to evaluate : 2.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 237 optimal weight: 0.0170 chunk 27 optimal weight: 3.9990 chunk 140 optimal weight: 0.0000 chunk 180 optimal weight: 7.9990 chunk 139 optimal weight: 0.0870 chunk 207 optimal weight: 4.9990 chunk 137 optimal weight: 0.9990 chunk 245 optimal weight: 30.0000 chunk 153 optimal weight: 0.0170 chunk 149 optimal weight: 3.9990 chunk 113 optimal weight: 5.9990 overall best weight: 0.2240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 37 ASN G 240 GLN J 56 GLN J 344 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 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.4535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 19630 Z= 0.141 Angle : 0.575 10.796 26706 Z= 0.282 Chirality : 0.042 0.144 3086 Planarity : 0.004 0.041 3454 Dihedral : 7.600 160.580 2858 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.85 % Favored : 96.07 % Rotamer: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.17), residues: 2444 helix: 1.77 (0.18), residues: 830 sheet: -0.88 (0.27), residues: 346 loop : -0.76 (0.17), residues: 1268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.076 0.003 TRP G 357 HIS 0.005 0.001 HIS V 109 PHE 0.036 0.001 PHE G 193 TYR 0.017 0.001 TYR G 197 ARG 0.011 0.000 ARG M 14 *********************** 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 269 residues out of total 2158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 269 time to evaluate : 2.262 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: G 75 MET cc_start: 0.8086 (tmm) cc_final: 0.7328 (tmm) REVERT: G 112 GLU cc_start: 0.8506 (tt0) cc_final: 0.8057 (tp30) REVERT: G 142 GLN cc_start: 0.8426 (mt0) cc_final: 0.8027 (mp10) REVERT: G 176 MET cc_start: 0.6464 (mmm) cc_final: 0.6246 (mmm) REVERT: G 184 ASP cc_start: 0.7863 (m-30) cc_final: 0.7549 (p0) REVERT: G 189 ASP cc_start: 0.9453 (m-30) cc_final: 0.8828 (m-30) REVERT: G 227 ASN cc_start: 0.8081 (t0) cc_final: 0.7561 (t0) REVERT: G 284 GLN cc_start: 0.9451 (mt0) cc_final: 0.9099 (mt0) REVERT: H 44 MET cc_start: 0.8879 (ptm) cc_final: 0.8504 (ppp) REVERT: H 78 ASN cc_start: 0.8276 (t0) cc_final: 0.7758 (t0) REVERT: H 82 MET cc_start: 0.9523 (tpt) cc_final: 0.8701 (tpp) REVERT: H 153 MET cc_start: 0.9028 (tmm) cc_final: 0.8506 (tmm) REVERT: H 184 ASP cc_start: 0.9077 (m-30) cc_final: 0.8778 (m-30) REVERT: H 195 GLU cc_start: 0.9273 (mt-10) cc_final: 0.8832 (tt0) REVERT: H 217 CYS cc_start: 0.9401 (m) cc_final: 0.9114 (m) REVERT: H 272 CYS cc_start: 0.8296 (p) cc_final: 0.7766 (p) REVERT: H 291 LYS cc_start: 0.9264 (tttt) cc_final: 0.8979 (mptt) REVERT: H 325 MET cc_start: 0.8934 (mmm) cc_final: 0.8420 (mmt) REVERT: H 355 MET cc_start: 0.9326 (mmp) cc_final: 0.8605 (mtp) REVERT: I 75 MET cc_start: 0.8722 (ttp) cc_final: 0.8106 (ptm) REVERT: I 100 GLN cc_start: 0.9236 (tt0) cc_final: 0.8946 (tm-30) REVERT: I 116 ASN cc_start: 0.8718 (t0) cc_final: 0.8400 (t0) REVERT: I 146 SER cc_start: 0.9405 (t) cc_final: 0.9152 (m) REVERT: I 176 MET cc_start: 0.8318 (mpp) cc_final: 0.7212 (mpp) REVERT: I 189 ASP cc_start: 0.9005 (m-30) cc_final: 0.8402 (m-30) REVERT: I 229 GLN cc_start: 0.9347 (mp10) cc_final: 0.9085 (mp10) REVERT: I 271 GLU cc_start: 0.9069 (tp30) cc_final: 0.8342 (tt0) REVERT: I 356 MET cc_start: 0.8800 (mpp) cc_final: 0.8233 (mtt) REVERT: I 357 TRP cc_start: 0.8947 (p-90) cc_final: 0.8641 (p-90) REVERT: J 37 CYS cc_start: 0.7533 (t) cc_final: 0.6890 (t) REVERT: J 56 GLN cc_start: 0.8627 (mt0) cc_final: 0.8375 (mt0) REVERT: J 137 MET cc_start: 0.7765 (tpp) cc_final: 0.7429 (tpp) REVERT: J 178 GLN cc_start: 0.9257 (mm-40) cc_final: 0.8912 (mm-40) REVERT: J 215 CYS cc_start: 0.9375 (m) cc_final: 0.9154 (m) REVERT: J 231 PHE cc_start: 0.8312 (m-80) cc_final: 0.7978 (m-80) REVERT: J 289 MET cc_start: 0.8872 (ttm) cc_final: 0.8585 (ttm) REVERT: J 298 GLN cc_start: 0.8356 (tp40) cc_final: 0.7951 (mm-40) REVERT: J 311 MET cc_start: 0.9402 (tpp) cc_final: 0.8804 (mtm) REVERT: J 322 GLU cc_start: 0.9463 (tp30) cc_final: 0.8900 (tp30) REVERT: J 326 LEU cc_start: 0.9313 (mt) cc_final: 0.8948 (mt) REVERT: J 387 TRP cc_start: 0.8621 (p-90) cc_final: 0.8186 (p-90) REVERT: M 21 GLU cc_start: 0.9438 (pt0) cc_final: 0.8827 (pm20) REVERT: M 38 GLU cc_start: 0.9310 (mm-30) cc_final: 0.8822 (pm20) REVERT: M 39 GLU cc_start: 0.8966 (tp30) cc_final: 0.7658 (tp30) REVERT: M 46 GLU cc_start: 0.8445 (tm-30) cc_final: 0.7999 (tm-30) REVERT: M 51 ASN cc_start: 0.9557 (t0) cc_final: 0.9106 (t0) REVERT: M 58 LYS cc_start: 0.9649 (ttpt) cc_final: 0.9221 (pttt) REVERT: M 62 LYS cc_start: 0.9083 (mmtp) cc_final: 0.8191 (tttt) REVERT: M 67 LYS cc_start: 0.9595 (tppp) cc_final: 0.9345 (tppp) REVERT: M 77 LYS cc_start: 0.8864 (mmmt) cc_final: 0.8583 (mmtm) REVERT: U 36 HIS cc_start: 0.9285 (m-70) cc_final: 0.8637 (m-70) REVERT: U 91 GLU cc_start: 0.8596 (mt-10) cc_final: 0.8339 (mt-10) REVERT: U 95 TYR cc_start: 0.7941 (t80) cc_final: 0.7483 (t80) REVERT: U 101 MET cc_start: 0.9489 (mtt) cc_final: 0.9124 (mpp) REVERT: U 104 ASN cc_start: 0.9527 (m-40) cc_final: 0.9291 (m-40) REVERT: U 112 TYR cc_start: 0.9046 (t80) cc_final: 0.8462 (t80) REVERT: U 131 LEU cc_start: 0.8566 (pp) cc_final: 0.8315 (pp) REVERT: U 148 CYS cc_start: 0.8812 (m) cc_final: 0.8561 (m) REVERT: U 150 ARG cc_start: 0.8370 (mtm180) cc_final: 0.7729 (mtt90) REVERT: V 8 TYR cc_start: 0.8700 (m-80) cc_final: 0.8079 (m-80) REVERT: V 25 GLN cc_start: 0.9465 (tp-100) cc_final: 0.8737 (tm-30) REVERT: V 103 GLN cc_start: 0.9222 (tp-100) cc_final: 0.8915 (tp-100) REVERT: V 120 CYS cc_start: 0.9124 (t) cc_final: 0.8621 (m) REVERT: V 126 CYS cc_start: 0.9106 (p) cc_final: 0.8735 (p) REVERT: V 157 LEU cc_start: 0.8745 (mt) cc_final: 0.8192 (mt) REVERT: V 165 MET cc_start: 0.9677 (mmm) cc_final: 0.9237 (mtp) REVERT: V 176 PHE cc_start: 0.9267 (t80) cc_final: 0.8841 (t80) REVERT: Y 27 LEU cc_start: 0.9280 (mt) cc_final: 0.9021 (mt) REVERT: Y 58 MET cc_start: 0.7848 (ttt) cc_final: 0.7496 (tmm) REVERT: Y 113 PHE cc_start: 0.8558 (t80) cc_final: 0.8247 (t80) REVERT: Y 123 MET cc_start: 0.8629 (mtp) cc_final: 0.8411 (mtp) REVERT: Y 163 ASP cc_start: 0.9444 (m-30) cc_final: 0.9136 (m-30) REVERT: Y 289 HIS cc_start: 0.7741 (t-90) cc_final: 0.7314 (t-90) outliers start: 0 outliers final: 0 residues processed: 269 average time/residue: 0.2917 time to fit residues: 123.0982 Evaluate side-chains 202 residues out of total 2158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 202 time to evaluate : 2.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 152 optimal weight: 3.9990 chunk 98 optimal weight: 3.9990 chunk 146 optimal weight: 0.0010 chunk 74 optimal weight: 10.0000 chunk 48 optimal weight: 0.9980 chunk 47 optimal weight: 0.9980 chunk 156 optimal weight: 10.0000 chunk 167 optimal weight: 9.9990 chunk 121 optimal weight: 2.9990 chunk 22 optimal weight: 0.0030 chunk 193 optimal weight: 8.9990 overall best weight: 0.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 44 HIS ** G 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** V 90 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.4694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 19630 Z= 0.164 Angle : 0.570 11.151 26706 Z= 0.277 Chirality : 0.041 0.165 3086 Planarity : 0.004 0.039 3454 Dihedral : 7.341 156.272 2858 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.56 % Favored : 96.36 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.17), residues: 2444 helix: 1.84 (0.18), residues: 830 sheet: -0.86 (0.28), residues: 337 loop : -0.65 (0.17), residues: 1277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.086 0.003 TRP G 357 HIS 0.007 0.001 HIS V 90 PHE 0.025 0.001 PHE I 295 TYR 0.013 0.001 TYR V 13 ARG 0.003 0.000 ARG V 70 *********************** 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 256 residues out of total 2158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 256 time to evaluate : 3.618 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: 0.8029 (tmm) cc_final: 0.7034 (tmm) REVERT: G 91 GLN cc_start: 0.9557 (mm110) cc_final: 0.9348 (mm-40) REVERT: G 106 HIS cc_start: 0.9660 (m-70) cc_final: 0.9170 (m-70) REVERT: G 112 GLU cc_start: 0.8502 (tt0) cc_final: 0.8063 (tp30) REVERT: G 139 ILE cc_start: 0.9414 (mt) cc_final: 0.9170 (mm) REVERT: G 142 GLN cc_start: 0.8589 (mt0) cc_final: 0.8125 (mp10) REVERT: G 176 MET cc_start: 0.6596 (mmm) cc_final: 0.6246 (mmm) REVERT: G 181 MET cc_start: 0.7603 (tpp) cc_final: 0.7018 (tpp) REVERT: G 184 ASP cc_start: 0.7889 (m-30) cc_final: 0.7580 (p0) REVERT: G 189 ASP cc_start: 0.9434 (m-30) cc_final: 0.8816 (m-30) REVERT: G 227 ASN cc_start: 0.8110 (t0) cc_final: 0.7575 (t0) REVERT: G 240 GLN cc_start: 0.8676 (pp30) cc_final: 0.8231 (tm-30) REVERT: G 284 GLN cc_start: 0.9460 (mt0) cc_final: 0.9080 (mt0) REVERT: H 44 MET cc_start: 0.8786 (ptm) cc_final: 0.8469 (ppp) REVERT: H 72 GLU cc_start: 0.8652 (mt-10) cc_final: 0.8173 (mp0) REVERT: H 78 ASN cc_start: 0.8282 (t0) cc_final: 0.7777 (t0) REVERT: H 82 MET cc_start: 0.9545 (tpt) cc_final: 0.9337 (tpt) REVERT: H 153 MET cc_start: 0.9226 (tmm) cc_final: 0.8410 (tmm) REVERT: H 184 ASP cc_start: 0.9080 (m-30) cc_final: 0.8780 (m-30) REVERT: H 195 GLU cc_start: 0.9285 (mt-10) cc_final: 0.8846 (tt0) REVERT: H 217 CYS cc_start: 0.9450 (m) cc_final: 0.9174 (m) REVERT: H 272 CYS cc_start: 0.8306 (p) cc_final: 0.7779 (p) REVERT: H 291 LYS cc_start: 0.9263 (tttt) cc_final: 0.8957 (mptt) REVERT: H 325 MET cc_start: 0.8947 (mmm) cc_final: 0.8429 (mmt) REVERT: H 355 MET cc_start: 0.9281 (mmp) cc_final: 0.8560 (mtp) REVERT: I 75 MET cc_start: 0.8791 (ttp) cc_final: 0.7927 (ptm) REVERT: I 100 GLN cc_start: 0.9262 (tt0) cc_final: 0.8961 (tm-30) REVERT: I 116 ASN cc_start: 0.8628 (t0) cc_final: 0.8305 (t0) REVERT: I 146 SER cc_start: 0.9406 (t) cc_final: 0.9153 (m) REVERT: I 176 MET cc_start: 0.8249 (mpp) cc_final: 0.7149 (mpp) REVERT: I 189 ASP cc_start: 0.8965 (m-30) cc_final: 0.8415 (m-30) REVERT: I 229 GLN cc_start: 0.9354 (mp10) cc_final: 0.9092 (mp10) REVERT: I 240 GLN cc_start: 0.8308 (mm-40) cc_final: 0.7849 (tp-100) REVERT: I 271 GLU cc_start: 0.9228 (tp30) cc_final: 0.8327 (tt0) REVERT: I 356 MET cc_start: 0.8815 (mpp) cc_final: 0.8457 (mpp) REVERT: I 357 TRP cc_start: 0.9000 (p-90) cc_final: 0.8680 (p-90) REVERT: J 37 CYS cc_start: 0.7558 (t) cc_final: 0.6901 (t) REVERT: J 56 GLN cc_start: 0.8611 (mt0) cc_final: 0.8378 (mt0) REVERT: J 137 MET cc_start: 0.7319 (tpp) cc_final: 0.6634 (tpt) REVERT: J 178 GLN cc_start: 0.9236 (mm-40) cc_final: 0.8934 (mm-40) REVERT: J 215 CYS cc_start: 0.9384 (m) cc_final: 0.9167 (m) REVERT: J 231 PHE cc_start: 0.8360 (m-80) cc_final: 0.7972 (m-80) REVERT: J 289 MET cc_start: 0.8948 (ttm) cc_final: 0.8567 (mtp) REVERT: J 298 GLN cc_start: 0.8417 (tp40) cc_final: 0.7962 (mm-40) REVERT: J 311 MET cc_start: 0.9397 (tpp) cc_final: 0.8888 (mmm) REVERT: J 322 GLU cc_start: 0.9463 (tp30) cc_final: 0.8925 (tp30) REVERT: J 326 LEU cc_start: 0.9347 (mt) cc_final: 0.9017 (mt) REVERT: J 387 TRP cc_start: 0.8667 (p-90) cc_final: 0.8236 (p-90) REVERT: M 21 GLU cc_start: 0.9334 (pt0) cc_final: 0.9008 (pm20) REVERT: M 38 GLU cc_start: 0.9304 (mm-30) cc_final: 0.8881 (pm20) REVERT: M 39 GLU cc_start: 0.8974 (tp30) cc_final: 0.7657 (tp30) REVERT: M 46 GLU cc_start: 0.8455 (tm-30) cc_final: 0.8016 (tm-30) REVERT: M 51 ASN cc_start: 0.9544 (t0) cc_final: 0.9079 (t0) REVERT: M 58 LYS cc_start: 0.9650 (ttpt) cc_final: 0.9230 (pttt) REVERT: M 62 LYS cc_start: 0.9079 (mmtp) cc_final: 0.8212 (tttt) REVERT: M 77 LYS cc_start: 0.8874 (mmmt) cc_final: 0.8593 (mmtm) REVERT: U 36 HIS cc_start: 0.9349 (m90) cc_final: 0.8993 (m170) REVERT: U 90 PHE cc_start: 0.7517 (m-80) cc_final: 0.7311 (m-80) REVERT: U 95 TYR cc_start: 0.8005 (t80) cc_final: 0.7500 (t80) REVERT: U 112 TYR cc_start: 0.9075 (t80) cc_final: 0.8455 (t80) REVERT: U 131 LEU cc_start: 0.8614 (pp) cc_final: 0.8254 (pp) REVERT: U 134 PHE cc_start: 0.8620 (p90) cc_final: 0.8405 (p90) REVERT: U 148 CYS cc_start: 0.8825 (m) cc_final: 0.8585 (m) REVERT: U 150 ARG cc_start: 0.8375 (mtm180) cc_final: 0.7753 (mtt90) REVERT: V 8 TYR cc_start: 0.8721 (m-80) cc_final: 0.8112 (m-80) REVERT: V 25 GLN cc_start: 0.9458 (tp-100) cc_final: 0.8765 (tm-30) REVERT: V 103 GLN cc_start: 0.9291 (tp-100) cc_final: 0.8930 (tp-100) REVERT: V 120 CYS cc_start: 0.9095 (t) cc_final: 0.8635 (m) REVERT: V 126 CYS cc_start: 0.9090 (p) cc_final: 0.8732 (p) REVERT: V 127 LYS cc_start: 0.8633 (tttp) cc_final: 0.8100 (ttpp) REVERT: V 157 LEU cc_start: 0.8759 (mt) cc_final: 0.8178 (mt) REVERT: V 165 MET cc_start: 0.9662 (mmm) cc_final: 0.9244 (mtp) REVERT: V 176 PHE cc_start: 0.9277 (t80) cc_final: 0.8865 (t80) REVERT: Y 27 LEU cc_start: 0.9272 (mt) cc_final: 0.9007 (mt) REVERT: Y 58 MET cc_start: 0.7883 (ttt) cc_final: 0.7450 (tmm) REVERT: Y 113 PHE cc_start: 0.8714 (t80) cc_final: 0.8362 (t80) REVERT: Y 123 MET cc_start: 0.8660 (mtp) cc_final: 0.8437 (mtp) REVERT: Y 163 ASP cc_start: 0.9446 (m-30) cc_final: 0.9154 (m-30) REVERT: Y 273 HIS cc_start: 0.9201 (m-70) cc_final: 0.8859 (m-70) REVERT: Y 289 HIS cc_start: 0.7774 (t-90) cc_final: 0.7338 (t-90) outliers start: 0 outliers final: 0 residues processed: 256 average time/residue: 0.3239 time to fit residues: 132.0693 Evaluate side-chains 207 residues out of total 2158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 207 time to evaluate : 2.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 223 optimal weight: 5.9990 chunk 235 optimal weight: 10.0000 chunk 214 optimal weight: 0.9980 chunk 229 optimal weight: 7.9990 chunk 137 optimal weight: 4.9990 chunk 99 optimal weight: 4.9990 chunk 179 optimal weight: 6.9990 chunk 70 optimal weight: 6.9990 chunk 206 optimal weight: 4.9990 chunk 216 optimal weight: 20.0000 chunk 228 optimal weight: 6.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 137 GLN ** I 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 56 GLN ** J 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 54 ASN ** U 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 44 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.5133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.117 19630 Z= 0.469 Angle : 0.746 13.669 26706 Z= 0.369 Chirality : 0.044 0.193 3086 Planarity : 0.005 0.043 3454 Dihedral : 7.872 151.382 2858 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.16 % Favored : 94.76 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.17), residues: 2444 helix: 1.49 (0.18), residues: 840 sheet: -0.84 (0.28), residues: 335 loop : -0.71 (0.17), residues: 1269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.094 0.004 TRP G 357 HIS 0.008 0.002 HIS Y 273 PHE 0.032 0.002 PHE G 193 TYR 0.019 0.002 TYR G 338 ARG 0.009 0.001 ARG I 264 *********************** 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 fitting. rotamer outliers: 0 poor density : 224 time to evaluate : 2.471 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: 0.8190 (tmm) cc_final: 0.7073 (tmm) REVERT: G 142 GLN cc_start: 0.8725 (mt0) cc_final: 0.7919 (mp10) REVERT: G 176 MET cc_start: 0.6872 (mmm) cc_final: 0.6359 (mmm) REVERT: G 181 MET cc_start: 0.7585 (tpp) cc_final: 0.6984 (tpp) REVERT: G 184 ASP cc_start: 0.7789 (m-30) cc_final: 0.7450 (p0) REVERT: G 189 ASP cc_start: 0.9360 (m-30) cc_final: 0.8786 (m-30) REVERT: G 227 ASN cc_start: 0.8147 (t0) cc_final: 0.7680 (t0) REVERT: G 240 GLN cc_start: 0.8524 (pp30) cc_final: 0.8162 (tm-30) REVERT: G 284 GLN cc_start: 0.9468 (mt0) cc_final: 0.9103 (mt0) REVERT: G 350 LEU cc_start: 0.9454 (mt) cc_final: 0.9195 (mt) REVERT: H 44 MET cc_start: 0.8557 (ptm) cc_final: 0.8116 (ppp) REVERT: H 72 GLU cc_start: 0.8784 (mt-10) cc_final: 0.8297 (mp0) REVERT: H 78 ASN cc_start: 0.8368 (t0) cc_final: 0.7980 (t0) REVERT: H 82 MET cc_start: 0.9587 (tpt) cc_final: 0.9278 (tpt) REVERT: H 153 MET cc_start: 0.9087 (tmm) cc_final: 0.8534 (tmm) REVERT: H 184 ASP cc_start: 0.9056 (m-30) cc_final: 0.8774 (m-30) REVERT: H 195 GLU cc_start: 0.9345 (mt-10) cc_final: 0.8943 (tt0) REVERT: H 217 CYS cc_start: 0.9428 (m) cc_final: 0.9227 (m) REVERT: H 272 CYS cc_start: 0.8286 (p) cc_final: 0.7782 (p) REVERT: H 291 LYS cc_start: 0.9229 (tttt) cc_final: 0.8885 (mptt) REVERT: H 325 MET cc_start: 0.8992 (mmm) cc_final: 0.8348 (mmt) REVERT: H 355 MET cc_start: 0.9234 (mmp) cc_final: 0.8755 (mmp) REVERT: I 75 MET cc_start: 0.8904 (ttp) cc_final: 0.7807 (ptm) REVERT: I 100 GLN cc_start: 0.9244 (tt0) cc_final: 0.8933 (tm-30) REVERT: I 116 ASN cc_start: 0.8549 (t0) cc_final: 0.8213 (t0) REVERT: I 189 ASP cc_start: 0.8988 (m-30) cc_final: 0.8457 (m-30) REVERT: I 271 GLU cc_start: 0.9322 (tp30) cc_final: 0.8431 (tt0) REVERT: I 357 TRP cc_start: 0.8889 (p-90) cc_final: 0.8617 (p-90) REVERT: J 37 CYS cc_start: 0.7682 (t) cc_final: 0.7103 (t) REVERT: J 48 MET cc_start: 0.9225 (mpp) cc_final: 0.8958 (mpp) REVERT: J 137 MET cc_start: 0.7557 (tpp) cc_final: 0.6844 (tpt) REVERT: J 178 GLN cc_start: 0.9221 (mm-40) cc_final: 0.8919 (mm-40) REVERT: J 231 PHE cc_start: 0.8470 (m-80) cc_final: 0.8049 (m-80) REVERT: J 289 MET cc_start: 0.8947 (ttm) cc_final: 0.8729 (ttm) REVERT: J 298 GLN cc_start: 0.8521 (tp40) cc_final: 0.8103 (mm-40) REVERT: J 311 MET cc_start: 0.9473 (tpp) cc_final: 0.8938 (tpp) REVERT: M 21 GLU cc_start: 0.9235 (pt0) cc_final: 0.8918 (mp0) REVERT: M 38 GLU cc_start: 0.9398 (mm-30) cc_final: 0.8992 (pm20) REVERT: M 39 GLU cc_start: 0.9011 (tp30) cc_final: 0.7558 (tp30) REVERT: M 46 GLU cc_start: 0.8307 (tm-30) cc_final: 0.7921 (tm-30) REVERT: M 51 ASN cc_start: 0.9561 (t0) cc_final: 0.9082 (t0) REVERT: M 58 LYS cc_start: 0.9628 (ttpt) cc_final: 0.9266 (tttt) REVERT: M 62 LYS cc_start: 0.9013 (mmtp) cc_final: 0.8212 (tttt) REVERT: M 77 LYS cc_start: 0.9039 (mmmt) cc_final: 0.8704 (mmtm) REVERT: U 95 TYR cc_start: 0.8179 (t80) cc_final: 0.7683 (t80) REVERT: U 112 TYR cc_start: 0.9015 (t80) cc_final: 0.8389 (t80) REVERT: U 148 CYS cc_start: 0.8913 (m) cc_final: 0.8633 (m) REVERT: U 150 ARG cc_start: 0.8174 (mtm180) cc_final: 0.7563 (mtt90) REVERT: U 168 MET cc_start: 0.9138 (mmp) cc_final: 0.8839 (mmp) REVERT: V 6 LEU cc_start: 0.9125 (mt) cc_final: 0.8356 (tp) REVERT: V 8 TYR cc_start: 0.8708 (m-80) cc_final: 0.7964 (m-80) REVERT: V 25 GLN cc_start: 0.9510 (tp-100) cc_final: 0.8801 (tm-30) REVERT: V 52 LEU cc_start: 0.8454 (tp) cc_final: 0.8184 (tp) REVERT: V 103 GLN cc_start: 0.9211 (tp-100) cc_final: 0.8925 (tp-100) REVERT: V 120 CYS cc_start: 0.9141 (t) cc_final: 0.8648 (m) REVERT: V 126 CYS cc_start: 0.9052 (p) cc_final: 0.8624 (p) REVERT: V 157 LEU cc_start: 0.8745 (mt) cc_final: 0.8239 (mt) REVERT: V 165 MET cc_start: 0.9692 (mmm) cc_final: 0.9287 (mtp) REVERT: V 176 PHE cc_start: 0.9279 (t80) cc_final: 0.8719 (t80) REVERT: Y 27 LEU cc_start: 0.9086 (mt) cc_final: 0.8692 (mt) REVERT: Y 113 PHE cc_start: 0.8630 (t80) cc_final: 0.7908 (t80) REVERT: Y 163 ASP cc_start: 0.9470 (m-30) cc_final: 0.9176 (m-30) REVERT: Y 273 HIS cc_start: 0.9193 (m90) cc_final: 0.8783 (m170) REVERT: Y 319 MET cc_start: 0.8795 (tpt) cc_final: 0.8475 (ptp) outliers start: 0 outliers final: 0 residues processed: 224 average time/residue: 0.3201 time to fit residues: 111.6337 Evaluate side-chains 181 residues out of total 2158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 181 time to evaluate : 2.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 150 optimal weight: 2.9990 chunk 242 optimal weight: 30.0000 chunk 147 optimal weight: 2.9990 chunk 114 optimal weight: 5.9990 chunk 168 optimal weight: 10.0000 chunk 254 optimal weight: 50.0000 chunk 233 optimal weight: 0.2980 chunk 202 optimal weight: 4.9990 chunk 21 optimal weight: 1.9990 chunk 156 optimal weight: 9.9990 chunk 124 optimal weight: 2.9990 overall best weight: 2.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 97 GLN ** 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.5206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 19630 Z= 0.260 Angle : 0.616 13.302 26706 Z= 0.303 Chirality : 0.042 0.152 3086 Planarity : 0.004 0.064 3454 Dihedral : 7.508 144.884 2858 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.54 % Favored : 95.38 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.17), residues: 2444 helix: 1.68 (0.18), residues: 839 sheet: -0.85 (0.28), residues: 339 loop : -0.71 (0.17), residues: 1266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.093 0.003 TRP G 357 HIS 0.008 0.001 HIS Y 138 PHE 0.022 0.001 PHE I 295 TYR 0.014 0.001 TYR V 13 ARG 0.004 0.000 ARG H 183 ********************** 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 223 residues out of total 2158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 223 time to evaluate : 2.267 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: 0.8161 (tmm) cc_final: 0.7275 (tmm) REVERT: G 142 GLN cc_start: 0.8611 (mt0) cc_final: 0.8170 (mp10) REVERT: G 176 MET cc_start: 0.7028 (mmm) cc_final: 0.6494 (mmm) REVERT: G 181 MET cc_start: 0.7542 (tpp) cc_final: 0.6910 (tpp) REVERT: G 184 ASP cc_start: 0.7864 (m-30) cc_final: 0.7532 (p0) REVERT: G 189 ASP cc_start: 0.9437 (m-30) cc_final: 0.8856 (m-30) REVERT: G 227 ASN cc_start: 0.8246 (t0) cc_final: 0.7777 (t0) REVERT: G 240 GLN cc_start: 0.8520 (pp30) cc_final: 0.8164 (tm-30) REVERT: G 284 GLN cc_start: 0.9479 (mt0) cc_final: 0.9100 (mt0) REVERT: H 44 MET cc_start: 0.8621 (ptm) cc_final: 0.8268 (ppp) REVERT: H 78 ASN cc_start: 0.8248 (t0) cc_final: 0.7772 (t0) REVERT: H 82 MET cc_start: 0.9559 (tpt) cc_final: 0.9267 (tpt) REVERT: H 153 MET cc_start: 0.9230 (tmm) cc_final: 0.8457 (tmm) REVERT: H 184 ASP cc_start: 0.9079 (m-30) cc_final: 0.8781 (m-30) REVERT: H 195 GLU cc_start: 0.9290 (mt-10) cc_final: 0.8874 (tt0) REVERT: H 217 CYS cc_start: 0.9472 (m) cc_final: 0.9232 (m) REVERT: H 291 LYS cc_start: 0.9235 (tttt) cc_final: 0.8929 (mptt) REVERT: H 325 MET cc_start: 0.8958 (mmm) cc_final: 0.8413 (mmt) REVERT: H 355 MET cc_start: 0.9251 (mmp) cc_final: 0.8472 (mtp) REVERT: I 75 MET cc_start: 0.8836 (ttp) cc_final: 0.7855 (ptm) REVERT: I 100 GLN cc_start: 0.9238 (tt0) cc_final: 0.8955 (tm-30) REVERT: I 116 ASN cc_start: 0.8689 (t0) cc_final: 0.8394 (t0) REVERT: I 189 ASP cc_start: 0.8951 (m-30) cc_final: 0.8418 (m-30) REVERT: I 240 GLN cc_start: 0.8541 (mm-40) cc_final: 0.8316 (tp-100) REVERT: I 271 GLU cc_start: 0.9310 (tp30) cc_final: 0.8399 (tt0) REVERT: I 357 TRP cc_start: 0.8971 (p-90) cc_final: 0.8756 (p-90) REVERT: J 37 CYS cc_start: 0.7721 (t) cc_final: 0.7105 (t) REVERT: J 126 MET cc_start: 0.9259 (mmm) cc_final: 0.8105 (mmm) REVERT: J 137 MET cc_start: 0.7476 (tpp) cc_final: 0.6762 (tpt) REVERT: J 178 GLN cc_start: 0.9238 (mm-40) cc_final: 0.8914 (mm-40) REVERT: J 231 PHE cc_start: 0.8402 (m-80) cc_final: 0.8043 (m-80) REVERT: J 289 MET cc_start: 0.8917 (ttm) cc_final: 0.8685 (tpp) REVERT: J 298 GLN cc_start: 0.8520 (tp40) cc_final: 0.8079 (mm-40) REVERT: J 311 MET cc_start: 0.9415 (tpp) cc_final: 0.8900 (mmm) REVERT: M 21 GLU cc_start: 0.9290 (pt0) cc_final: 0.8902 (mp0) REVERT: M 38 GLU cc_start: 0.9349 (mm-30) cc_final: 0.8998 (pm20) REVERT: M 46 GLU cc_start: 0.8330 (tm-30) cc_final: 0.7912 (tm-30) REVERT: M 51 ASN cc_start: 0.9517 (t0) cc_final: 0.9078 (t0) REVERT: M 58 LYS cc_start: 0.9638 (ttpt) cc_final: 0.9278 (tttt) REVERT: M 62 LYS cc_start: 0.9044 (mmtp) cc_final: 0.8240 (tttt) REVERT: M 77 LYS cc_start: 0.9077 (mmmt) cc_final: 0.8747 (mmtm) REVERT: U 36 HIS cc_start: 0.9486 (m90) cc_final: 0.8673 (m170) REVERT: U 95 TYR cc_start: 0.8116 (t80) cc_final: 0.7656 (t80) REVERT: U 112 TYR cc_start: 0.8986 (t80) cc_final: 0.8416 (t80) REVERT: U 131 LEU cc_start: 0.8722 (pp) cc_final: 0.8343 (pp) REVERT: U 148 CYS cc_start: 0.8920 (m) cc_final: 0.8627 (m) REVERT: U 150 ARG cc_start: 0.8166 (mtm180) cc_final: 0.7496 (mtt90) REVERT: V 6 LEU cc_start: 0.9124 (mt) cc_final: 0.7737 (tp) REVERT: V 8 TYR cc_start: 0.8708 (m-80) cc_final: 0.8121 (m-10) REVERT: V 25 GLN cc_start: 0.9494 (tp-100) cc_final: 0.8730 (tm-30) REVERT: V 52 LEU cc_start: 0.8211 (tp) cc_final: 0.7975 (tp) REVERT: V 103 GLN cc_start: 0.9205 (tp-100) cc_final: 0.8890 (tp-100) REVERT: V 120 CYS cc_start: 0.9169 (t) cc_final: 0.8683 (m) REVERT: V 126 CYS cc_start: 0.9079 (p) cc_final: 0.8640 (p) REVERT: V 127 LYS cc_start: 0.8577 (tttp) cc_final: 0.8327 (ttpp) REVERT: V 165 MET cc_start: 0.9672 (mmm) cc_final: 0.9210 (mtp) REVERT: V 176 PHE cc_start: 0.9285 (t80) cc_final: 0.8825 (t80) REVERT: Y 27 LEU cc_start: 0.9144 (mt) cc_final: 0.8856 (mt) REVERT: Y 113 PHE cc_start: 0.8803 (t80) cc_final: 0.8527 (t80) REVERT: Y 123 MET cc_start: 0.8537 (mtp) cc_final: 0.8232 (mtm) REVERT: Y 273 HIS cc_start: 0.9158 (m90) cc_final: 0.8770 (m90) REVERT: Y 289 HIS cc_start: 0.8054 (t-90) cc_final: 0.7473 (t70) REVERT: Y 319 MET cc_start: 0.8876 (tpt) cc_final: 0.8503 (ptp) outliers start: 0 outliers final: 0 residues processed: 223 average time/residue: 0.2966 time to fit residues: 103.6884 Evaluate side-chains 188 residues out of total 2158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 188 time to evaluate : 2.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 160 optimal weight: 7.9990 chunk 215 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 186 optimal weight: 8.9990 chunk 29 optimal weight: 4.9990 chunk 56 optimal weight: 1.9990 chunk 202 optimal weight: 5.9990 chunk 84 optimal weight: 0.9980 chunk 208 optimal weight: 6.9990 chunk 25 optimal weight: 0.7980 chunk 37 optimal weight: 10.0000 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 137 GLN H 263 GLN ** I 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 298 GLN ** 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 = 0.3170 r_free = 0.3170 target = 0.060757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2672 r_free = 0.2672 target = 0.041261 restraints weight = 91127.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.2716 r_free = 0.2716 target = 0.042775 restraints weight = 47940.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.2747 r_free = 0.2747 target = 0.043827 restraints weight = 30755.167| |-----------------------------------------------------------------------------| r_work (final): 0.2703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.5347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 19630 Z= 0.274 Angle : 0.625 13.036 26706 Z= 0.308 Chirality : 0.042 0.173 3086 Planarity : 0.004 0.062 3454 Dihedral : 7.439 141.018 2858 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.99 % Favored : 94.93 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.17), residues: 2444 helix: 1.59 (0.18), residues: 838 sheet: -0.87 (0.28), residues: 341 loop : -0.68 (0.17), residues: 1265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.100 0.003 TRP G 357 HIS 0.007 0.001 HIS Y 138 PHE 0.022 0.002 PHE I 295 TYR 0.023 0.001 TYR G 197 ARG 0.005 0.000 ARG H 183 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3632.90 seconds wall clock time: 65 minutes 43.16 seconds (3943.16 seconds total)