Starting phenix.real_space_refine on Tue Aug 6 04:24:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u1o_41819/08_2024/8u1o_41819.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u1o_41819/08_2024/8u1o_41819.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u1o_41819/08_2024/8u1o_41819.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u1o_41819/08_2024/8u1o_41819.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u1o_41819/08_2024/8u1o_41819.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u1o_41819/08_2024/8u1o_41819.cif" } resolution = 3.4 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= 0.005 sd= 0.044 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: 4 Type Number sf(0) Gaussians S 48 5.16 5 C 9519 2.51 5 N 2568 2.21 5 O 2961 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "o GLU 264": "OE1" <-> "OE2" Residue "o GLU 543": "OE1" <-> "OE2" Residue "p GLU 543": "OE1" <-> "OE2" Residue "q TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q GLU 157": "OE1" <-> "OE2" Residue "q GLU 310": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 15096 Number of models: 1 Model: "" Number of chains: 3 Chain: "o" Number of atoms: 5032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 663, 5032 Classifications: {'peptide': 663} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 28, 'TRANS': 634} Chain: "p" Number of atoms: 5032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 663, 5032 Classifications: {'peptide': 663} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 28, 'TRANS': 634} Chain: "q" Number of atoms: 5032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 663, 5032 Classifications: {'peptide': 663} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 28, 'TRANS': 634} Time building chain proxies: 8.76, per 1000 atoms: 0.58 Number of scatterers: 15096 At special positions: 0 Unit cell: (103.758, 95.5971, 184.199, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 48 16.00 O 2961 8.00 N 2568 7.00 C 9519 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.66 Conformation dependent library (CDL) restraints added in 2.7 seconds 3966 Ramachandran restraints generated. 1983 Oldfield, 0 Emsley, 1983 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3552 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 35 sheets defined 7.0% alpha, 28.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.61 Creating SS restraints... Processing helix chain 'o' and resid 110 through 122 removed outlier: 4.033A pdb=" N ILE o 116 " --> pdb=" O ASP o 112 " (cutoff:3.500A) Processing helix chain 'o' and resid 134 through 141 Processing helix chain 'o' and resid 217 through 223 Processing helix chain 'o' and resid 237 through 243 removed outlier: 4.052A pdb=" N VAL o 241 " --> pdb=" O VAL o 237 " (cutoff:3.500A) Processing helix chain 'o' and resid 245 through 250 removed outlier: 3.954A pdb=" N LEU o 249 " --> pdb=" O GLY o 245 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N LEU o 250 " --> pdb=" O ILE o 246 " (cutoff:3.500A) No H-bonds generated for 'chain 'o' and resid 245 through 250' Processing helix chain 'o' and resid 610 through 614 Processing helix chain 'p' and resid 42 through 46 removed outlier: 3.507A pdb=" N GLN p 46 " --> pdb=" O PRO p 43 " (cutoff:3.500A) Processing helix chain 'p' and resid 105 through 110 removed outlier: 3.673A pdb=" N ASP p 110 " --> pdb=" O LEU p 107 " (cutoff:3.500A) Processing helix chain 'p' and resid 113 through 120 removed outlier: 4.758A pdb=" N GLU p 117 " --> pdb=" O GLN p 113 " (cutoff:3.500A) Processing helix chain 'p' and resid 129 through 131 No H-bonds generated for 'chain 'p' and resid 129 through 131' Processing helix chain 'p' and resid 133 through 141 Processing helix chain 'p' and resid 217 through 224 Processing helix chain 'p' and resid 236 through 243 removed outlier: 3.646A pdb=" N VAL p 241 " --> pdb=" O VAL p 237 " (cutoff:3.500A) Processing helix chain 'p' and resid 245 through 250 Processing helix chain 'p' and resid 251 through 255 Processing helix chain 'p' and resid 532 through 534 No H-bonds generated for 'chain 'p' and resid 532 through 534' Processing helix chain 'q' and resid 113 through 122 removed outlier: 3.854A pdb=" N GLU q 117 " --> pdb=" O GLN q 113 " (cutoff:3.500A) Processing helix chain 'q' and resid 129 through 131 No H-bonds generated for 'chain 'q' and resid 129 through 131' Processing helix chain 'q' and resid 133 through 141 removed outlier: 3.586A pdb=" N ALA q 137 " --> pdb=" O THR q 133 " (cutoff:3.500A) Processing helix chain 'q' and resid 218 through 224 Processing helix chain 'q' and resid 611 through 614 Processing sheet with id=AA1, first strand: chain 'o' and resid 8 through 9 Processing sheet with id=AA2, first strand: chain 'o' and resid 73 through 74 removed outlier: 4.227A pdb=" N ILE o 66 " --> pdb=" O VAL o 74 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'o' and resid 58 through 61 removed outlier: 4.519A pdb=" N VAL o 49 " --> pdb=" O ILE o 61 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'o' and resid 126 through 127 removed outlier: 6.557A pdb=" N VAL o 126 " --> pdb=" O LEU o 146 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'o' and resid 151 through 154 removed outlier: 3.812A pdb=" N ASP o 177 " --> pdb=" O PHE o 153 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLU o 197 " --> pdb=" O PHE o 174 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'o' and resid 158 through 159 removed outlier: 5.640A pdb=" N THR o 262 " --> pdb=" O GLY o 176 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N GLY o 178 " --> pdb=" O THR o 262 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N GLU o 264 " --> pdb=" O GLY o 178 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N LEU o 180 " --> pdb=" O GLU o 264 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N ARG o 266 " --> pdb=" O LEU o 180 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N PHE o 182 " --> pdb=" O ARG o 266 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N LEU o 284 " --> pdb=" O SER o 261 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N LEU o 263 " --> pdb=" O LEU o 284 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N ARG o 286 " --> pdb=" O LEU o 263 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N ILE o 265 " --> pdb=" O ARG o 286 " (cutoff:3.500A) removed outlier: 5.762A pdb=" N PHE o 285 " --> pdb=" O GLU o 310 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N ILE o 307 " --> pdb=" O GLN o 336 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N LEU o 338 " --> pdb=" O ILE o 307 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N PHE o 309 " --> pdb=" O LEU o 338 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N ALA o 335 " --> pdb=" O LYS o 364 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N VAL o 363 " --> pdb=" O ASP o 396 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'o' and resid 167 through 169 removed outlier: 6.256A pdb=" N ILE o 191 " --> pdb=" O HIS o 274 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'o' and resid 203 through 205 Processing sheet with id=AA9, first strand: chain 'o' and resid 322 through 323 removed outlier: 6.279A pdb=" N VAL o 322 " --> pdb=" O ILE o 351 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N VAL o 350 " --> pdb=" O ARG o 383 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N ILE o 429 " --> pdb=" O SER o 452 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N PHE o 473 " --> pdb=" O ASN o 500 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N LEU o 502 " --> pdb=" O PHE o 473 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ILE o 527 " --> pdb=" O GLY o 501 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N ARG o 503 " --> pdb=" O ILE o 527 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ILE o 491 " --> pdb=" O ASP o 518 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'o' and resid 322 through 323 removed outlier: 6.279A pdb=" N VAL o 322 " --> pdb=" O ILE o 351 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N VAL o 350 " --> pdb=" O ARG o 383 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N ILE o 429 " --> pdb=" O SER o 452 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N PHE o 473 " --> pdb=" O ASN o 500 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N LEU o 502 " --> pdb=" O PHE o 473 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ILE o 527 " --> pdb=" O GLY o 501 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N ARG o 503 " --> pdb=" O ILE o 527 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N VAL o 538 " --> pdb=" O PRO o 520 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N SER o 522 " --> pdb=" O VAL o 538 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ASN o 540 " --> pdb=" O SER o 522 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ALA o 542 " --> pdb=" O VAL o 524 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N GLY o 526 " --> pdb=" O ALA o 542 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ASN p 548 " --> pdb=" O LEU o 541 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLU o 543 " --> pdb=" O ASN p 548 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N ARG p 550 " --> pdb=" O GLU o 543 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ILE p 549 " --> pdb=" O ALA q 560 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N VAL q 605 " --> pdb=" O ALA q 596 " (cutoff:3.500A) removed outlier: 8.482A pdb=" N SER q 606 " --> pdb=" O PRO q 620 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N ALA q 617 " --> pdb=" O PRO o 639 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N ILE q 619 " --> pdb=" O PHE o 637 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N PHE o 637 " --> pdb=" O ILE q 619 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N LEU o 648 " --> pdb=" O LEU o 664 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'o' and resid 354 through 356 removed outlier: 3.714A pdb=" N ARG o 435 " --> pdb=" O VAL o 387 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N VAL o 434 " --> pdb=" O GLU o 457 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'o' and resid 369 through 370 removed outlier: 4.212A pdb=" N THR o 373 " --> pdb=" O VAL o 370 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'o' and resid 550 through 553 removed outlier: 3.719A pdb=" N VAL p 605 " --> pdb=" O ALA p 596 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'o' and resid 605 through 609 removed outlier: 3.770A pdb=" N VAL o 605 " --> pdb=" O ALA o 596 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'o' and resid 619 through 620 removed outlier: 3.911A pdb=" N ILE o 619 " --> pdb=" O PHE p 637 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLU p 642 " --> pdb=" O SER p 647 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N SER p 647 " --> pdb=" O GLU p 642 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'q' and resid 59 through 61 removed outlier: 4.640A pdb=" N VAL q 49 " --> pdb=" O ILE q 61 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N LYS q 108 " --> pdb=" O VAL p 9 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'p' and resid 73 through 74 removed outlier: 4.204A pdb=" N ILE p 66 " --> pdb=" O VAL p 74 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'p' and resid 126 through 127 removed outlier: 6.528A pdb=" N VAL p 126 " --> pdb=" O LEU p 146 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N LEU p 145 " --> pdb=" O GLU p 169 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N SER p 189 " --> pdb=" O GLU p 272 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N HIS p 274 " --> pdb=" O SER p 189 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N ILE p 191 " --> pdb=" O HIS p 274 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N VAL p 271 " --> pdb=" O LYS p 292 " (cutoff:3.500A) removed outlier: 7.898A pdb=" N VAL p 294 " --> pdb=" O VAL p 271 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N VAL p 273 " --> pdb=" O VAL p 294 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N MET p 293 " --> pdb=" O ILE p 323 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N VAL p 322 " --> pdb=" O ILE p 351 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ARG p 383 " --> pdb=" O VAL p 350 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N ILE p 429 " --> pdb=" O SER p 452 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR p 474 " --> pdb=" O VAL p 451 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N SER p 471 " --> pdb=" O ARG p 498 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N ASN p 500 " --> pdb=" O SER p 471 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N PHE p 473 " --> pdb=" O ASN p 500 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N CYS p 497 " --> pdb=" O THR p 523 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N SER p 525 " --> pdb=" O CYS p 497 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N VAL p 499 " --> pdb=" O SER p 525 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ASN p 537 " --> pdb=" O ASP p 518 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N SER p 522 " --> pdb=" O ALA p 539 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'p' and resid 151 through 152 removed outlier: 5.962A pdb=" N TYR p 151 " --> pdb=" O ILE p 175 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'p' and resid 158 through 160 removed outlier: 6.431A pdb=" N VAL p 159 " --> pdb=" O THR p 183 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N SER p 261 " --> pdb=" O GLY p 282 " (cutoff:3.500A) removed outlier: 8.161A pdb=" N LEU p 284 " --> pdb=" O SER p 261 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N LEU p 263 " --> pdb=" O LEU p 284 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N ARG p 286 " --> pdb=" O LEU p 263 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ILE p 265 " --> pdb=" O ARG p 286 " (cutoff:3.500A) removed outlier: 8.947A pdb=" N THR p 308 " --> pdb=" O ALA p 281 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N PHE p 283 " --> pdb=" O THR p 308 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N GLU p 310 " --> pdb=" O PHE p 283 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N PHE p 285 " --> pdb=" O GLU p 310 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ILE p 307 " --> pdb=" O GLN p 336 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N LEU p 338 " --> pdb=" O ILE p 307 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N PHE p 309 " --> pdb=" O LEU p 338 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ALA p 335 " --> pdb=" O LYS p 364 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N VAL p 363 " --> pdb=" O ASP p 396 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N PHE p 442 " --> pdb=" O TYR p 465 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N ALA p 464 " --> pdb=" O TYR p 492 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'p' and resid 203 through 204 Processing sheet with id=AC4, first strand: chain 'p' and resid 297 through 301 removed outlier: 4.330A pdb=" N ASN p 297 " --> pdb=" O ARG p 326 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N SER p 328 " --> pdb=" O ASN p 297 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N SER p 355 " --> pdb=" O ILE p 388 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N VAL p 434 " --> pdb=" O GLU p 457 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'p' and resid 340 through 341 removed outlier: 6.650A pdb=" N ASN p 340 " --> pdb=" O TYR p 378 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'p' and resid 369 through 370 removed outlier: 3.855A pdb=" N THR p 373 " --> pdb=" O VAL p 370 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'p' and resid 619 through 620 removed outlier: 3.717A pdb=" N ILE p 619 " --> pdb=" O PHE q 637 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N LEU q 648 " --> pdb=" O LEU q 664 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'q' and resid 78 through 79 removed outlier: 4.537A pdb=" N ILE q 66 " --> pdb=" O VAL q 74 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N HIS q 88 " --> pdb=" O ASN q 105 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ASN q 105 " --> pdb=" O HIS q 88 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'q' and resid 126 through 127 removed outlier: 6.491A pdb=" N VAL q 126 " --> pdb=" O LEU q 146 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU q 145 " --> pdb=" O THR q 167 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N ILE q 191 " --> pdb=" O HIS q 274 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N ALA q 276 " --> pdb=" O ILE q 191 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N MET q 196 " --> pdb=" O LEU q 279 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N PHE q 174 " --> pdb=" O GLU q 197 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N TYR q 151 " --> pdb=" O ILE q 175 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'q' and resid 126 through 127 removed outlier: 6.491A pdb=" N VAL q 126 " --> pdb=" O LEU q 146 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU q 145 " --> pdb=" O THR q 167 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N ILE q 191 " --> pdb=" O HIS q 274 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N ALA q 276 " --> pdb=" O ILE q 191 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N ALA q 296 " --> pdb=" O ARG q 275 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N SER q 277 " --> pdb=" O ALA q 296 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'q' and resid 157 through 160 removed outlier: 6.269A pdb=" N GLU q 157 " --> pdb=" O ILE q 181 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N THR q 183 " --> pdb=" O GLU q 157 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N VAL q 159 " --> pdb=" O THR q 183 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N GLY q 178 " --> pdb=" O THR q 262 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N GLU q 264 " --> pdb=" O GLY q 178 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N LEU q 180 " --> pdb=" O GLU q 264 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N ARG q 266 " --> pdb=" O LEU q 180 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N PHE q 182 " --> pdb=" O ARG q 266 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N SER q 261 " --> pdb=" O GLY q 282 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N LEU q 284 " --> pdb=" O SER q 261 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N LEU q 263 " --> pdb=" O LEU q 284 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ARG q 286 " --> pdb=" O LEU q 263 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N ILE q 265 " --> pdb=" O ARG q 286 " (cutoff:3.500A) removed outlier: 8.822A pdb=" N THR q 308 " --> pdb=" O ALA q 281 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N PHE q 283 " --> pdb=" O THR q 308 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N GLU q 310 " --> pdb=" O PHE q 283 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N PHE q 285 " --> pdb=" O GLU q 310 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N ALA q 335 " --> pdb=" O LYS q 364 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N VAL q 363 " --> pdb=" O ASP q 396 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'q' and resid 203 through 204 Processing sheet with id=AD4, first strand: chain 'q' and resid 320 through 323 removed outlier: 6.620A pdb=" N ASN q 320 " --> pdb=" O GLY q 349 " (cutoff:3.500A) removed outlier: 7.922A pdb=" N ILE q 351 " --> pdb=" O ASN q 320 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N VAL q 322 " --> pdb=" O ILE q 351 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N PHE q 353 " --> pdb=" O VAL q 322 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'q' and resid 320 through 323 removed outlier: 6.620A pdb=" N ASN q 320 " --> pdb=" O GLY q 349 " (cutoff:3.500A) removed outlier: 7.922A pdb=" N ILE q 351 " --> pdb=" O ASN q 320 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N VAL q 322 " --> pdb=" O ILE q 351 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N PHE q 353 " --> pdb=" O VAL q 322 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N SER q 385 " --> pdb=" O GLY q 352 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N THR q 354 " --> pdb=" O SER q 385 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N VAL q 387 " --> pdb=" O THR q 354 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N TYR q 356 " --> pdb=" O VAL q 387 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N LEU q 432 " --> pdb=" O ASP q 384 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N VAL q 386 " --> pdb=" O LEU q 432 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N VAL q 434 " --> pdb=" O VAL q 386 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N ILE q 388 " --> pdb=" O VAL q 434 " (cutoff:3.500A) removed outlier: 8.019A pdb=" N GLU q 457 " --> pdb=" O LEU q 432 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N VAL q 434 " --> pdb=" O GLU q 457 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N VAL q 456 " --> pdb=" O ILE q 479 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ASN q 475 " --> pdb=" O ASN q 500 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N LEU q 502 " --> pdb=" O ASN q 475 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N ALA q 477 " --> pdb=" O LEU q 502 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'q' and resid 369 through 370 Processing sheet with id=AD7, first strand: chain 'q' and resid 443 through 444 removed outlier: 3.604A pdb=" N MET q 444 " --> pdb=" O TYR q 465 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'q' and resid 517 through 519 305 hydrogen bonds defined for protein. 810 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: 6.15 Time building geometry restraints manager: 6.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2789 1.32 - 1.45: 3926 1.45 - 1.57: 8617 1.57 - 1.69: 1 1.69 - 1.82: 72 Bond restraints: 15405 Sorted by residual: bond pdb=" CA ASN o 258 " pdb=" CB ASN o 258 " ideal model delta sigma weight residual 1.526 1.593 -0.067 1.70e-02 3.46e+03 1.54e+01 bond pdb=" C ARG o 409 " pdb=" N PRO o 410 " ideal model delta sigma weight residual 1.335 1.367 -0.032 8.70e-03 1.32e+04 1.39e+01 bond pdb=" N LEU o 180 " pdb=" CA LEU o 180 " ideal model delta sigma weight residual 1.456 1.491 -0.035 1.21e-02 6.83e+03 8.22e+00 bond pdb=" C PRO o 410 " pdb=" O PRO o 410 " ideal model delta sigma weight residual 1.233 1.208 0.025 9.60e-03 1.09e+04 6.81e+00 bond pdb=" C PRO o 419 " pdb=" O PRO o 419 " ideal model delta sigma weight residual 1.235 1.201 0.034 1.30e-02 5.92e+03 6.74e+00 ... (remaining 15400 not shown) Histogram of bond angle deviations from ideal: 98.73 - 105.84: 317 105.84 - 112.95: 8062 112.95 - 120.06: 5322 120.06 - 127.17: 7079 127.17 - 134.28: 154 Bond angle restraints: 20934 Sorted by residual: angle pdb=" C PRO o 410 " pdb=" CA PRO o 410 " pdb=" CB PRO o 410 " ideal model delta sigma weight residual 111.40 104.49 6.91 9.10e-01 1.21e+00 5.77e+01 angle pdb=" C PRO p 419 " pdb=" CA PRO p 419 " pdb=" CB PRO p 419 " ideal model delta sigma weight residual 111.22 102.56 8.66 1.51e+00 4.39e-01 3.29e+01 angle pdb=" CA LYS o 206 " pdb=" CB LYS o 206 " pdb=" CG LYS o 206 " ideal model delta sigma weight residual 114.10 124.25 -10.15 2.00e+00 2.50e-01 2.58e+01 angle pdb=" C ASP o 143 " pdb=" N GLY o 144 " pdb=" CA GLY o 144 " ideal model delta sigma weight residual 121.58 117.30 4.28 8.60e-01 1.35e+00 2.48e+01 angle pdb=" CA TYR q 389 " pdb=" C TYR q 389 " pdb=" N PRO q 390 " ideal model delta sigma weight residual 118.16 121.61 -3.45 7.00e-01 2.04e+00 2.42e+01 ... (remaining 20929 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 7843 17.98 - 35.96: 981 35.96 - 53.94: 199 53.94 - 71.93: 46 71.93 - 89.91: 15 Dihedral angle restraints: 9084 sinusoidal: 3465 harmonic: 5619 Sorted by residual: dihedral pdb=" CA ASP q 511 " pdb=" C ASP q 511 " pdb=" N GLY q 512 " pdb=" CA GLY q 512 " ideal model delta harmonic sigma weight residual -180.00 -141.89 -38.11 0 5.00e+00 4.00e-02 5.81e+01 dihedral pdb=" CA GLN q 513 " pdb=" C GLN q 513 " pdb=" N GLY q 514 " pdb=" CA GLY q 514 " ideal model delta harmonic sigma weight residual -180.00 -143.52 -36.48 0 5.00e+00 4.00e-02 5.32e+01 dihedral pdb=" CA CYS o 170 " pdb=" C CYS o 170 " pdb=" N LYS o 171 " pdb=" CA LYS o 171 " ideal model delta harmonic sigma weight residual -180.00 -150.55 -29.45 0 5.00e+00 4.00e-02 3.47e+01 ... (remaining 9081 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 1729 0.058 - 0.116: 510 0.116 - 0.174: 97 0.174 - 0.232: 13 0.232 - 0.289: 3 Chirality restraints: 2352 Sorted by residual: chirality pdb=" CG LEU p 284 " pdb=" CB LEU p 284 " pdb=" CD1 LEU p 284 " pdb=" CD2 LEU p 284 " both_signs ideal model delta sigma weight residual False -2.59 -2.88 0.29 2.00e-01 2.50e+01 2.09e+00 chirality pdb=" CB ILE q 175 " pdb=" CA ILE q 175 " pdb=" CG1 ILE q 175 " pdb=" CG2 ILE q 175 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.27 2.00e-01 2.50e+01 1.88e+00 chirality pdb=" CG LEU o 263 " pdb=" CB LEU o 263 " pdb=" CD1 LEU o 263 " pdb=" CD2 LEU o 263 " both_signs ideal model delta sigma weight residual False -2.59 -2.35 -0.24 2.00e-01 2.50e+01 1.47e+00 ... (remaining 2349 not shown) Planarity restraints: 2745 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR p 418 " -0.019 2.00e-02 2.50e+03 3.80e-02 1.44e+01 pdb=" C TYR p 418 " 0.066 2.00e-02 2.50e+03 pdb=" O TYR p 418 " -0.025 2.00e-02 2.50e+03 pdb=" N PRO p 419 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR q 114 " 0.010 2.00e-02 2.50e+03 1.98e-02 7.81e+00 pdb=" CG TYR q 114 " -0.047 2.00e-02 2.50e+03 pdb=" CD1 TYR q 114 " 0.020 2.00e-02 2.50e+03 pdb=" CD2 TYR q 114 " 0.020 2.00e-02 2.50e+03 pdb=" CE1 TYR q 114 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR q 114 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR q 114 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR q 114 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR p 329 " 0.019 2.00e-02 2.50e+03 1.75e-02 6.15e+00 pdb=" CG TYR p 329 " -0.041 2.00e-02 2.50e+03 pdb=" CD1 TYR p 329 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 TYR p 329 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR p 329 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR p 329 " 0.014 2.00e-02 2.50e+03 pdb=" CZ TYR p 329 " -0.005 2.00e-02 2.50e+03 pdb=" OH TYR p 329 " 0.002 2.00e-02 2.50e+03 ... (remaining 2742 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 2395 2.76 - 3.30: 15198 3.30 - 3.83: 27222 3.83 - 4.37: 31816 4.37 - 4.90: 53969 Nonbonded interactions: 130600 Sorted by model distance: nonbonded pdb=" OH TYR p 378 " pdb=" OD1 ASP p 412 " model vdw 2.225 3.040 nonbonded pdb=" OG1 THR p 209 " pdb=" OE1 GLN p 213 " model vdw 2.226 3.040 nonbonded pdb=" O GLN o 513 " pdb=" NH2 ARG o 535 " model vdw 2.229 3.120 nonbonded pdb=" O GLY o 495 " pdb=" OG SER o 522 " model vdw 2.239 3.040 nonbonded pdb=" O GLY p 495 " pdb=" OG SER p 522 " model vdw 2.251 3.040 ... (remaining 130595 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 'o' selection = chain 'p' selection = chain 'q' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.550 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 43.510 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7137 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 : 0.005 0.070 15405 Z= 0.310 Angle : 0.999 14.484 20934 Z= 0.547 Chirality : 0.057 0.289 2352 Planarity : 0.006 0.075 2745 Dihedral : 16.712 89.907 5532 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.35 % Allowed : 7.67 % Favored : 91.98 % Rotamer: Outliers : 0.92 % Allowed : 30.82 % Favored : 68.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -2.51 (0.17), residues: 1983 helix: -2.01 (0.50), residues: 89 sheet: -1.40 (0.22), residues: 490 loop : -1.84 (0.16), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.003 TRP p 392 HIS 0.013 0.002 HIS o 421 PHE 0.031 0.002 PHE o 182 TYR 0.047 0.002 TYR q 114 ARG 0.017 0.001 ARG q 266 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3966 Ramachandran restraints generated. 1983 Oldfield, 0 Emsley, 1983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3966 Ramachandran restraints generated. 1983 Oldfield, 0 Emsley, 1983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 352 time to evaluate : 1.591 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: o 336 GLN cc_start: 0.7019 (mp10) cc_final: 0.6769 (mp10) REVERT: p 19 GLU cc_start: 0.8209 (mm-30) cc_final: 0.7979 (mm-30) REVERT: p 54 GLU cc_start: 0.6879 (tm-30) cc_final: 0.6409 (tm-30) REVERT: p 206 LYS cc_start: 0.8294 (tptp) cc_final: 0.7959 (tppt) REVERT: p 386 VAL cc_start: 0.7323 (t) cc_final: 0.6826 (m) REVERT: p 467 LEU cc_start: 0.7693 (tp) cc_final: 0.7367 (tt) REVERT: p 530 MET cc_start: 0.5603 (ptp) cc_final: 0.5253 (ptp) REVERT: q 177 ASP cc_start: 0.7150 (m-30) cc_final: 0.6913 (m-30) REVERT: q 320 ASN cc_start: 0.8352 (OUTLIER) cc_final: 0.8076 (t0) REVERT: q 339 ARG cc_start: 0.7702 (ttt-90) cc_final: 0.7428 (ttt-90) outliers start: 15 outliers final: 8 residues processed: 360 average time/residue: 0.3082 time to fit residues: 156.0281 Evaluate side-chains 342 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 333 time to evaluate : 1.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain o residue 284 LEU Chi-restraints excluded: chain o residue 333 SER Chi-restraints excluded: chain o residue 420 LEU Chi-restraints excluded: chain p residue 42 ASN Chi-restraints excluded: chain p residue 336 GLN Chi-restraints excluded: chain q residue 130 ASP Chi-restraints excluded: chain q residue 209 THR Chi-restraints excluded: chain q residue 320 ASN Chi-restraints excluded: chain q residue 509 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 167 optimal weight: 5.9990 chunk 150 optimal weight: 1.9990 chunk 83 optimal weight: 10.0000 chunk 51 optimal weight: 7.9990 chunk 101 optimal weight: 7.9990 chunk 80 optimal weight: 1.9990 chunk 155 optimal weight: 0.7980 chunk 60 optimal weight: 20.0000 chunk 94 optimal weight: 6.9990 chunk 115 optimal weight: 0.0270 chunk 179 optimal weight: 10.0000 overall best weight: 2.1644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** o 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 610 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 566 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 320 ASN q 537 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7187 moved from start: 0.0993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 15405 Z= 0.260 Angle : 0.693 9.230 20934 Z= 0.364 Chirality : 0.049 0.178 2352 Planarity : 0.005 0.055 2745 Dihedral : 6.411 57.519 2155 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 13.48 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.82 % Favored : 91.93 % Rotamer: Outliers : 4.66 % Allowed : 27.21 % Favored : 68.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -2.35 (0.18), residues: 1983 helix: -1.07 (0.54), residues: 86 sheet: -1.27 (0.23), residues: 482 loop : -1.81 (0.15), residues: 1415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP p 392 HIS 0.005 0.001 HIS o 421 PHE 0.016 0.001 PHE o 182 TYR 0.022 0.002 TYR o 378 ARG 0.010 0.001 ARG q 266 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3966 Ramachandran restraints generated. 1983 Oldfield, 0 Emsley, 1983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3966 Ramachandran restraints generated. 1983 Oldfield, 0 Emsley, 1983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 343 time to evaluate : 1.594 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: o 151 TYR cc_start: 0.7853 (t80) cc_final: 0.7608 (t80) REVERT: o 226 LYS cc_start: 0.7531 (mmtt) cc_final: 0.7025 (mmtt) REVERT: o 258 ASN cc_start: 0.8265 (p0) cc_final: 0.7961 (p0) REVERT: o 280 MET cc_start: 0.7923 (tmm) cc_final: 0.7499 (tmm) REVERT: o 318 LYS cc_start: 0.7498 (tptt) cc_final: 0.7272 (tptt) REVERT: o 336 GLN cc_start: 0.7202 (mp10) cc_final: 0.6773 (mp10) REVERT: o 535 ARG cc_start: 0.7360 (OUTLIER) cc_final: 0.6305 (mmm160) REVERT: o 608 LYS cc_start: 0.5425 (OUTLIER) cc_final: 0.5115 (ttmm) REVERT: p 54 GLU cc_start: 0.7068 (tm-30) cc_final: 0.6614 (tm-30) REVERT: p 171 LYS cc_start: 0.8528 (mttm) cc_final: 0.8277 (mttm) REVERT: p 187 LYS cc_start: 0.8382 (tptt) cc_final: 0.8178 (tptt) REVERT: p 196 MET cc_start: 0.7738 (mmm) cc_final: 0.7508 (mmm) REVERT: p 213 GLN cc_start: 0.7446 (pm20) cc_final: 0.7175 (pm20) REVERT: p 230 THR cc_start: 0.6651 (OUTLIER) cc_final: 0.6346 (t) REVERT: p 329 TYR cc_start: 0.6375 (m-80) cc_final: 0.5963 (m-80) REVERT: p 378 TYR cc_start: 0.6700 (m-80) cc_final: 0.6498 (m-80) REVERT: p 386 VAL cc_start: 0.7451 (t) cc_final: 0.6964 (m) REVERT: p 402 ASP cc_start: 0.2980 (OUTLIER) cc_final: 0.2441 (p0) REVERT: p 467 LEU cc_start: 0.7640 (tp) cc_final: 0.7209 (tt) REVERT: q 150 ASP cc_start: 0.7602 (m-30) cc_final: 0.7160 (m-30) REVERT: q 161 PHE cc_start: 0.8456 (m-10) cc_final: 0.8157 (m-10) REVERT: q 169 GLU cc_start: 0.7712 (OUTLIER) cc_final: 0.7120 (tm-30) REVERT: q 242 LYS cc_start: 0.8926 (mmtp) cc_final: 0.8719 (mmmm) REVERT: q 266 ARG cc_start: 0.8206 (ttm-80) cc_final: 0.7931 (ttm-80) REVERT: q 346 ARG cc_start: 0.7075 (mmt90) cc_final: 0.6684 (mmt90) REVERT: q 378 TYR cc_start: 0.7501 (m-80) cc_final: 0.7211 (m-80) REVERT: q 381 GLN cc_start: 0.7554 (pm20) cc_final: 0.7050 (pm20) REVERT: q 444 MET cc_start: 0.6554 (ppp) cc_final: 0.6224 (ppp) outliers start: 76 outliers final: 37 residues processed: 389 average time/residue: 0.2988 time to fit residues: 166.0501 Evaluate side-chains 382 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 340 time to evaluate : 1.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain o residue 31 ILE Chi-restraints excluded: chain o residue 92 ILE Chi-restraints excluded: chain o residue 98 SER Chi-restraints excluded: chain o residue 158 THR Chi-restraints excluded: chain o residue 165 VAL Chi-restraints excluded: chain o residue 180 LEU Chi-restraints excluded: chain o residue 264 GLU Chi-restraints excluded: chain o residue 300 SER Chi-restraints excluded: chain o residue 338 LEU Chi-restraints excluded: chain o residue 421 HIS Chi-restraints excluded: chain o residue 451 VAL Chi-restraints excluded: chain o residue 523 THR Chi-restraints excluded: chain o residue 535 ARG Chi-restraints excluded: chain o residue 540 ASN Chi-restraints excluded: chain o residue 546 LEU Chi-restraints excluded: chain o residue 608 LYS Chi-restraints excluded: chain p residue 49 VAL Chi-restraints excluded: chain p residue 67 ILE Chi-restraints excluded: chain p residue 100 VAL Chi-restraints excluded: chain p residue 133 THR Chi-restraints excluded: chain p residue 230 THR Chi-restraints excluded: chain p residue 383 ARG Chi-restraints excluded: chain p residue 402 ASP Chi-restraints excluded: chain p residue 440 VAL Chi-restraints excluded: chain p residue 469 HIS Chi-restraints excluded: chain p residue 480 ASP Chi-restraints excluded: chain p residue 491 ILE Chi-restraints excluded: chain q residue 8 VAL Chi-restraints excluded: chain q residue 26 VAL Chi-restraints excluded: chain q residue 47 ILE Chi-restraints excluded: chain q residue 59 VAL Chi-restraints excluded: chain q residue 83 VAL Chi-restraints excluded: chain q residue 133 THR Chi-restraints excluded: chain q residue 169 GLU Chi-restraints excluded: chain q residue 212 ASN Chi-restraints excluded: chain q residue 230 THR Chi-restraints excluded: chain q residue 265 ILE Chi-restraints excluded: chain q residue 308 THR Chi-restraints excluded: chain q residue 492 TYR Chi-restraints excluded: chain q residue 509 SER Chi-restraints excluded: chain q residue 566 HIS Chi-restraints excluded: chain q residue 571 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 99 optimal weight: 10.0000 chunk 55 optimal weight: 30.0000 chunk 149 optimal weight: 0.8980 chunk 122 optimal weight: 5.9990 chunk 49 optimal weight: 8.9990 chunk 180 optimal weight: 0.9990 chunk 194 optimal weight: 30.0000 chunk 160 optimal weight: 0.8980 chunk 178 optimal weight: 2.9990 chunk 61 optimal weight: 20.0000 chunk 144 optimal weight: 3.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** o 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 610 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 566 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7189 moved from start: 0.1337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 15405 Z= 0.236 Angle : 0.673 14.362 20934 Z= 0.349 Chirality : 0.049 0.246 2352 Planarity : 0.004 0.052 2745 Dihedral : 5.814 43.836 2140 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 13.94 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.61 % Favored : 92.13 % Rotamer: Outliers : 4.96 % Allowed : 26.53 % Favored : 68.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -2.36 (0.17), residues: 1983 helix: -1.36 (0.51), residues: 90 sheet: -1.23 (0.24), residues: 441 loop : -1.81 (0.15), residues: 1452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP p 392 HIS 0.004 0.001 HIS o 421 PHE 0.020 0.002 PHE q 290 TYR 0.016 0.002 TYR q 32 ARG 0.012 0.001 ARG p 266 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3966 Ramachandran restraints generated. 1983 Oldfield, 0 Emsley, 1983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3966 Ramachandran restraints generated. 1983 Oldfield, 0 Emsley, 1983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 348 time to evaluate : 1.602 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: o 135 GLN cc_start: 0.8222 (tp40) cc_final: 0.7983 (tp-100) REVERT: o 151 TYR cc_start: 0.7863 (t80) cc_final: 0.7600 (t80) REVERT: o 197 GLU cc_start: 0.6681 (OUTLIER) cc_final: 0.5784 (pm20) REVERT: o 234 GLN cc_start: 0.8059 (OUTLIER) cc_final: 0.6915 (tt0) REVERT: o 258 ASN cc_start: 0.8368 (p0) cc_final: 0.8008 (p0) REVERT: o 266 ARG cc_start: 0.8568 (ttm-80) cc_final: 0.8059 (ttm-80) REVERT: o 279 LEU cc_start: 0.8510 (mm) cc_final: 0.8231 (mm) REVERT: o 280 MET cc_start: 0.7905 (tmm) cc_final: 0.7416 (tmm) REVERT: o 318 LYS cc_start: 0.7591 (tptt) cc_final: 0.7337 (tptt) REVERT: o 336 GLN cc_start: 0.7415 (mp10) cc_final: 0.6959 (mp10) REVERT: o 535 ARG cc_start: 0.7481 (OUTLIER) cc_final: 0.6425 (mmm160) REVERT: o 608 LYS cc_start: 0.5571 (OUTLIER) cc_final: 0.5226 (ttmm) REVERT: p 54 GLU cc_start: 0.6394 (tm-30) cc_final: 0.5882 (tm-30) REVERT: p 169 GLU cc_start: 0.7233 (tm-30) cc_final: 0.6570 (tm-30) REVERT: p 171 LYS cc_start: 0.8565 (mttm) cc_final: 0.8168 (mttt) REVERT: p 190 ARG cc_start: 0.8282 (mtp85) cc_final: 0.8032 (mtp85) REVERT: p 196 MET cc_start: 0.7626 (mmm) cc_final: 0.7377 (mmm) REVERT: p 213 GLN cc_start: 0.7399 (pm20) cc_final: 0.7163 (mp10) REVERT: p 230 THR cc_start: 0.6642 (OUTLIER) cc_final: 0.6339 (t) REVERT: p 280 MET cc_start: 0.6439 (ppp) cc_final: 0.6018 (ppp) REVERT: p 329 TYR cc_start: 0.6516 (m-80) cc_final: 0.5588 (m-80) REVERT: p 386 VAL cc_start: 0.7484 (t) cc_final: 0.6952 (m) REVERT: p 402 ASP cc_start: 0.3014 (OUTLIER) cc_final: 0.2513 (p0) REVERT: p 467 LEU cc_start: 0.7604 (tp) cc_final: 0.7021 (tt) REVERT: q 49 VAL cc_start: 0.8747 (OUTLIER) cc_final: 0.8451 (m) REVERT: q 161 PHE cc_start: 0.8272 (m-10) cc_final: 0.8041 (m-10) REVERT: q 169 GLU cc_start: 0.7690 (OUTLIER) cc_final: 0.7109 (tm-30) REVERT: q 174 PHE cc_start: 0.8016 (OUTLIER) cc_final: 0.7739 (m-10) REVERT: q 226 LYS cc_start: 0.7917 (tptp) cc_final: 0.7646 (tptp) REVERT: q 266 ARG cc_start: 0.8133 (ttm-80) cc_final: 0.7882 (ttm-80) REVERT: q 345 GLU cc_start: 0.8040 (mp0) cc_final: 0.7539 (mp0) REVERT: q 378 TYR cc_start: 0.7519 (m-80) cc_final: 0.7136 (m-80) REVERT: q 381 GLN cc_start: 0.7573 (pm20) cc_final: 0.6868 (pm20) REVERT: q 444 MET cc_start: 0.6402 (ppp) cc_final: 0.6044 (ppp) outliers start: 81 outliers final: 47 residues processed: 399 average time/residue: 0.3022 time to fit residues: 170.2435 Evaluate side-chains 388 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 332 time to evaluate : 1.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain o residue 31 ILE Chi-restraints excluded: chain o residue 158 THR Chi-restraints excluded: chain o residue 180 LEU Chi-restraints excluded: chain o residue 197 GLU Chi-restraints excluded: chain o residue 234 GLN Chi-restraints excluded: chain o residue 264 GLU Chi-restraints excluded: chain o residue 300 SER Chi-restraints excluded: chain o residue 333 SER Chi-restraints excluded: chain o residue 497 CYS Chi-restraints excluded: chain o residue 523 THR Chi-restraints excluded: chain o residue 535 ARG Chi-restraints excluded: chain o residue 540 ASN Chi-restraints excluded: chain o residue 546 LEU Chi-restraints excluded: chain o residue 608 LYS Chi-restraints excluded: chain p residue 42 ASN Chi-restraints excluded: chain p residue 49 VAL Chi-restraints excluded: chain p residue 67 ILE Chi-restraints excluded: chain p residue 85 VAL Chi-restraints excluded: chain p residue 133 THR Chi-restraints excluded: chain p residue 183 THR Chi-restraints excluded: chain p residue 230 THR Chi-restraints excluded: chain p residue 263 LEU Chi-restraints excluded: chain p residue 336 GLN Chi-restraints excluded: chain p residue 383 ARG Chi-restraints excluded: chain p residue 402 ASP Chi-restraints excluded: chain p residue 413 TYR Chi-restraints excluded: chain p residue 440 VAL Chi-restraints excluded: chain p residue 469 HIS Chi-restraints excluded: chain q residue 16 ILE Chi-restraints excluded: chain q residue 47 ILE Chi-restraints excluded: chain q residue 49 VAL Chi-restraints excluded: chain q residue 83 VAL Chi-restraints excluded: chain q residue 133 THR Chi-restraints excluded: chain q residue 165 VAL Chi-restraints excluded: chain q residue 169 GLU Chi-restraints excluded: chain q residue 174 PHE Chi-restraints excluded: chain q residue 183 THR Chi-restraints excluded: chain q residue 199 THR Chi-restraints excluded: chain q residue 212 ASN Chi-restraints excluded: chain q residue 230 THR Chi-restraints excluded: chain q residue 240 TYR Chi-restraints excluded: chain q residue 265 ILE Chi-restraints excluded: chain q residue 308 THR Chi-restraints excluded: chain q residue 326 ARG Chi-restraints excluded: chain q residue 379 ASN Chi-restraints excluded: chain q residue 385 SER Chi-restraints excluded: chain q residue 425 LEU Chi-restraints excluded: chain q residue 428 LEU Chi-restraints excluded: chain q residue 449 MET Chi-restraints excluded: chain q residue 451 VAL Chi-restraints excluded: chain q residue 459 CYS Chi-restraints excluded: chain q residue 492 TYR Chi-restraints excluded: chain q residue 509 SER Chi-restraints excluded: chain q residue 566 HIS Chi-restraints excluded: chain q residue 571 THR Chi-restraints excluded: chain q residue 631 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 177 optimal weight: 10.0000 chunk 135 optimal weight: 0.6980 chunk 93 optimal weight: 0.3980 chunk 19 optimal weight: 7.9990 chunk 85 optimal weight: 2.9990 chunk 120 optimal weight: 10.0000 chunk 180 optimal weight: 0.6980 chunk 191 optimal weight: 0.0020 chunk 94 optimal weight: 7.9990 chunk 171 optimal weight: 0.4980 chunk 51 optimal weight: 9.9990 overall best weight: 0.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: o 298 ASN o 537 ASN o 610 ASN p 234 GLN ** p 566 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7130 moved from start: 0.1567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 15405 Z= 0.162 Angle : 0.631 13.119 20934 Z= 0.326 Chirality : 0.048 0.179 2352 Planarity : 0.004 0.038 2745 Dihedral : 5.455 49.634 2140 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.25 % Favored : 93.49 % Rotamer: Outliers : 5.02 % Allowed : 26.96 % Favored : 68.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -2.21 (0.18), residues: 1983 helix: -1.14 (0.52), residues: 91 sheet: -1.08 (0.24), residues: 446 loop : -1.73 (0.15), residues: 1446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP o 208 HIS 0.003 0.001 HIS p 427 PHE 0.014 0.001 PHE q 290 TYR 0.020 0.001 TYR o 356 ARG 0.008 0.001 ARG o 376 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3966 Ramachandran restraints generated. 1983 Oldfield, 0 Emsley, 1983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3966 Ramachandran restraints generated. 1983 Oldfield, 0 Emsley, 1983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 356 time to evaluate : 1.663 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: o 135 GLN cc_start: 0.8281 (tp40) cc_final: 0.7916 (tp-100) REVERT: o 151 TYR cc_start: 0.7847 (t80) cc_final: 0.7626 (t80) REVERT: o 195 PHE cc_start: 0.8497 (t80) cc_final: 0.8023 (t80) REVERT: o 197 GLU cc_start: 0.6664 (OUTLIER) cc_final: 0.5760 (pm20) REVERT: o 213 GLN cc_start: 0.7358 (pp30) cc_final: 0.7124 (pp30) REVERT: o 234 GLN cc_start: 0.7952 (OUTLIER) cc_final: 0.6895 (tp-100) REVERT: o 258 ASN cc_start: 0.8344 (p0) cc_final: 0.7955 (p0) REVERT: o 266 ARG cc_start: 0.8523 (ttm-80) cc_final: 0.8033 (ttm-80) REVERT: o 279 LEU cc_start: 0.8483 (mm) cc_final: 0.8147 (mm) REVERT: o 280 MET cc_start: 0.7897 (tmm) cc_final: 0.7248 (tmm) REVERT: o 318 LYS cc_start: 0.7532 (tptt) cc_final: 0.7215 (tptt) REVERT: o 333 SER cc_start: 0.7971 (OUTLIER) cc_final: 0.7234 (m) REVERT: o 346 ARG cc_start: 0.6581 (OUTLIER) cc_final: 0.6320 (mtt-85) REVERT: o 388 ILE cc_start: 0.8312 (mt) cc_final: 0.8070 (mm) REVERT: o 535 ARG cc_start: 0.7364 (OUTLIER) cc_final: 0.6436 (mmm160) REVERT: o 608 LYS cc_start: 0.5432 (OUTLIER) cc_final: 0.5140 (ttmm) REVERT: p 46 GLN cc_start: 0.8584 (mt0) cc_final: 0.8261 (mt0) REVERT: p 54 GLU cc_start: 0.7009 (tm-30) cc_final: 0.6546 (tm-30) REVERT: p 112 ASP cc_start: 0.8039 (t0) cc_final: 0.7570 (t0) REVERT: p 113 GLN cc_start: 0.8372 (mm-40) cc_final: 0.8142 (mm-40) REVERT: p 169 GLU cc_start: 0.7215 (tm-30) cc_final: 0.6577 (tm-30) REVERT: p 171 LYS cc_start: 0.8535 (mttm) cc_final: 0.8177 (mttt) REVERT: p 190 ARG cc_start: 0.8261 (mtp85) cc_final: 0.7971 (mtp85) REVERT: p 195 PHE cc_start: 0.6921 (OUTLIER) cc_final: 0.5978 (t80) REVERT: p 196 MET cc_start: 0.7634 (mmm) cc_final: 0.7433 (mmm) REVERT: p 230 THR cc_start: 0.6584 (OUTLIER) cc_final: 0.6295 (t) REVERT: p 280 MET cc_start: 0.6264 (ppp) cc_final: 0.6024 (ppp) REVERT: p 329 TYR cc_start: 0.6572 (m-80) cc_final: 0.5637 (m-80) REVERT: p 386 VAL cc_start: 0.7407 (t) cc_final: 0.6899 (m) REVERT: p 402 ASP cc_start: 0.3021 (OUTLIER) cc_final: 0.2229 (p0) REVERT: p 449 MET cc_start: 0.5900 (OUTLIER) cc_final: 0.5435 (pmm) REVERT: p 467 LEU cc_start: 0.7494 (tp) cc_final: 0.6883 (tt) REVERT: q 49 VAL cc_start: 0.8724 (OUTLIER) cc_final: 0.8480 (m) REVERT: q 169 GLU cc_start: 0.7612 (OUTLIER) cc_final: 0.7015 (tm-30) REVERT: q 174 PHE cc_start: 0.7917 (OUTLIER) cc_final: 0.7555 (m-10) REVERT: q 190 ARG cc_start: 0.8430 (mmm-85) cc_final: 0.8036 (mmm-85) REVERT: q 226 LYS cc_start: 0.7915 (tptp) cc_final: 0.7638 (tptp) REVERT: q 238 SER cc_start: 0.8861 (m) cc_final: 0.8247 (p) REVERT: q 266 ARG cc_start: 0.8045 (ttm-80) cc_final: 0.7766 (ttm-80) REVERT: q 269 ILE cc_start: 0.9083 (mp) cc_final: 0.8795 (mt) REVERT: q 341 ASN cc_start: 0.7655 (m-40) cc_final: 0.7301 (m-40) REVERT: q 345 GLU cc_start: 0.8017 (mp0) cc_final: 0.7366 (mp0) REVERT: q 346 ARG cc_start: 0.7121 (mmt90) cc_final: 0.6907 (mmt90) REVERT: q 381 GLN cc_start: 0.7490 (pm20) cc_final: 0.6755 (pm20) REVERT: q 444 MET cc_start: 0.6346 (ppp) cc_final: 0.5792 (ppp) outliers start: 82 outliers final: 43 residues processed: 408 average time/residue: 0.3316 time to fit residues: 193.6776 Evaluate side-chains 392 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 336 time to evaluate : 1.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain o residue 8 VAL Chi-restraints excluded: chain o residue 92 ILE Chi-restraints excluded: chain o residue 103 ILE Chi-restraints excluded: chain o residue 149 ARG Chi-restraints excluded: chain o residue 158 THR Chi-restraints excluded: chain o residue 165 VAL Chi-restraints excluded: chain o residue 166 LEU Chi-restraints excluded: chain o residue 180 LEU Chi-restraints excluded: chain o residue 197 GLU Chi-restraints excluded: chain o residue 234 GLN Chi-restraints excluded: chain o residue 264 GLU Chi-restraints excluded: chain o residue 300 SER Chi-restraints excluded: chain o residue 333 SER Chi-restraints excluded: chain o residue 345 GLU Chi-restraints excluded: chain o residue 346 ARG Chi-restraints excluded: chain o residue 403 MET Chi-restraints excluded: chain o residue 421 HIS Chi-restraints excluded: chain o residue 497 CYS Chi-restraints excluded: chain o residue 523 THR Chi-restraints excluded: chain o residue 535 ARG Chi-restraints excluded: chain o residue 540 ASN Chi-restraints excluded: chain o residue 546 LEU Chi-restraints excluded: chain o residue 608 LYS Chi-restraints excluded: chain p residue 49 VAL Chi-restraints excluded: chain p residue 67 ILE Chi-restraints excluded: chain p residue 133 THR Chi-restraints excluded: chain p residue 195 PHE Chi-restraints excluded: chain p residue 230 THR Chi-restraints excluded: chain p residue 383 ARG Chi-restraints excluded: chain p residue 402 ASP Chi-restraints excluded: chain p residue 413 TYR Chi-restraints excluded: chain p residue 440 VAL Chi-restraints excluded: chain p residue 449 MET Chi-restraints excluded: chain p residue 469 HIS Chi-restraints excluded: chain p residue 491 ILE Chi-restraints excluded: chain q residue 8 VAL Chi-restraints excluded: chain q residue 16 ILE Chi-restraints excluded: chain q residue 26 VAL Chi-restraints excluded: chain q residue 47 ILE Chi-restraints excluded: chain q residue 49 VAL Chi-restraints excluded: chain q residue 59 VAL Chi-restraints excluded: chain q residue 83 VAL Chi-restraints excluded: chain q residue 165 VAL Chi-restraints excluded: chain q residue 169 GLU Chi-restraints excluded: chain q residue 174 PHE Chi-restraints excluded: chain q residue 212 ASN Chi-restraints excluded: chain q residue 230 THR Chi-restraints excluded: chain q residue 265 ILE Chi-restraints excluded: chain q residue 425 LEU Chi-restraints excluded: chain q residue 428 LEU Chi-restraints excluded: chain q residue 449 MET Chi-restraints excluded: chain q residue 492 TYR Chi-restraints excluded: chain q residue 509 SER Chi-restraints excluded: chain q residue 566 HIS Chi-restraints excluded: chain q residue 571 THR Chi-restraints excluded: chain q residue 631 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 159 optimal weight: 10.0000 chunk 108 optimal weight: 9.9990 chunk 2 optimal weight: 0.9980 chunk 142 optimal weight: 3.9990 chunk 78 optimal weight: 5.9990 chunk 163 optimal weight: 1.9990 chunk 132 optimal weight: 0.5980 chunk 0 optimal weight: 6.9990 chunk 97 optimal weight: 6.9990 chunk 171 optimal weight: 0.7980 chunk 48 optimal weight: 9.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** o 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 566 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 297 ASN q 320 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7173 moved from start: 0.1749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 15405 Z= 0.222 Angle : 0.646 12.440 20934 Z= 0.336 Chirality : 0.048 0.170 2352 Planarity : 0.004 0.052 2745 Dihedral : 5.512 52.398 2140 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 14.08 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.31 % Favored : 92.44 % Rotamer: Outliers : 5.33 % Allowed : 27.39 % Favored : 67.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -2.23 (0.18), residues: 1983 helix: -1.10 (0.52), residues: 91 sheet: -1.11 (0.23), residues: 458 loop : -1.74 (0.16), residues: 1434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP p 392 HIS 0.004 0.001 HIS p 566 PHE 0.020 0.001 PHE q 290 TYR 0.025 0.001 TYR o 356 ARG 0.005 0.001 ARG p 14 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3966 Ramachandran restraints generated. 1983 Oldfield, 0 Emsley, 1983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3966 Ramachandran restraints generated. 1983 Oldfield, 0 Emsley, 1983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 440 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 353 time to evaluate : 1.530 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: o 151 TYR cc_start: 0.7872 (t80) cc_final: 0.7657 (t80) REVERT: o 182 PHE cc_start: 0.8279 (m-10) cc_final: 0.8035 (m-10) REVERT: o 195 PHE cc_start: 0.8514 (t80) cc_final: 0.7920 (t80) REVERT: o 197 GLU cc_start: 0.6690 (OUTLIER) cc_final: 0.5587 (pm20) REVERT: o 208 TRP cc_start: 0.7248 (p90) cc_final: 0.6911 (p90) REVERT: o 234 GLN cc_start: 0.8026 (OUTLIER) cc_final: 0.7023 (tp-100) REVERT: o 266 ARG cc_start: 0.8518 (ttm-80) cc_final: 0.8069 (ttm-80) REVERT: o 318 LYS cc_start: 0.7651 (tptt) cc_final: 0.7291 (tptt) REVERT: o 333 SER cc_start: 0.7761 (OUTLIER) cc_final: 0.7000 (m) REVERT: o 346 ARG cc_start: 0.6412 (OUTLIER) cc_final: 0.6161 (mtt-85) REVERT: o 502 LEU cc_start: 0.5985 (OUTLIER) cc_final: 0.5675 (mt) REVERT: o 535 ARG cc_start: 0.7362 (OUTLIER) cc_final: 0.6487 (mmm160) REVERT: o 608 LYS cc_start: 0.5671 (OUTLIER) cc_final: 0.5311 (ttmm) REVERT: p 54 GLU cc_start: 0.6440 (tm-30) cc_final: 0.5997 (tm-30) REVERT: p 112 ASP cc_start: 0.8043 (t0) cc_final: 0.7556 (t0) REVERT: p 113 GLN cc_start: 0.8440 (mm-40) cc_final: 0.8179 (mm-40) REVERT: p 169 GLU cc_start: 0.7238 (tm-30) cc_final: 0.6610 (tm-30) REVERT: p 171 LYS cc_start: 0.8533 (mttm) cc_final: 0.8137 (mttt) REVERT: p 196 MET cc_start: 0.7568 (mmm) cc_final: 0.7329 (mmm) REVERT: p 230 THR cc_start: 0.6685 (OUTLIER) cc_final: 0.6378 (t) REVERT: p 329 TYR cc_start: 0.6613 (m-80) cc_final: 0.5654 (m-10) REVERT: p 386 VAL cc_start: 0.7457 (t) cc_final: 0.6967 (m) REVERT: p 402 ASP cc_start: 0.3083 (OUTLIER) cc_final: 0.2548 (p0) REVERT: p 429 ILE cc_start: 0.7923 (mm) cc_final: 0.7692 (mm) REVERT: p 467 LEU cc_start: 0.7605 (tp) cc_final: 0.6935 (tt) REVERT: q 49 VAL cc_start: 0.8648 (OUTLIER) cc_final: 0.8373 (m) REVERT: q 174 PHE cc_start: 0.7957 (OUTLIER) cc_final: 0.7497 (m-10) REVERT: q 226 LYS cc_start: 0.7942 (tptp) cc_final: 0.7661 (tptp) REVERT: q 238 SER cc_start: 0.8873 (m) cc_final: 0.8282 (p) REVERT: q 266 ARG cc_start: 0.8049 (ttm-80) cc_final: 0.7761 (ttm-80) REVERT: q 269 ILE cc_start: 0.9065 (mp) cc_final: 0.8819 (mt) REVERT: q 345 GLU cc_start: 0.8055 (mp0) cc_final: 0.7535 (mp0) REVERT: q 346 ARG cc_start: 0.7183 (mmt90) cc_final: 0.6979 (mmt90) REVERT: q 381 GLN cc_start: 0.7529 (pm20) cc_final: 0.6753 (pm20) REVERT: q 386 VAL cc_start: 0.8232 (t) cc_final: 0.7937 (m) REVERT: q 444 MET cc_start: 0.6357 (ppp) cc_final: 0.5897 (ppp) outliers start: 87 outliers final: 58 residues processed: 411 average time/residue: 0.3085 time to fit residues: 179.2949 Evaluate side-chains 409 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 340 time to evaluate : 1.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain o residue 8 VAL Chi-restraints excluded: chain o residue 31 ILE Chi-restraints excluded: chain o residue 92 ILE Chi-restraints excluded: chain o residue 149 ARG Chi-restraints excluded: chain o residue 158 THR Chi-restraints excluded: chain o residue 165 VAL Chi-restraints excluded: chain o residue 180 LEU Chi-restraints excluded: chain o residue 194 VAL Chi-restraints excluded: chain o residue 197 GLU Chi-restraints excluded: chain o residue 234 GLN Chi-restraints excluded: chain o residue 264 GLU Chi-restraints excluded: chain o residue 265 ILE Chi-restraints excluded: chain o residue 333 SER Chi-restraints excluded: chain o residue 346 ARG Chi-restraints excluded: chain o residue 363 VAL Chi-restraints excluded: chain o residue 378 TYR Chi-restraints excluded: chain o residue 403 MET Chi-restraints excluded: chain o residue 497 CYS Chi-restraints excluded: chain o residue 502 LEU Chi-restraints excluded: chain o residue 523 THR Chi-restraints excluded: chain o residue 535 ARG Chi-restraints excluded: chain o residue 546 LEU Chi-restraints excluded: chain o residue 608 LYS Chi-restraints excluded: chain p residue 49 VAL Chi-restraints excluded: chain p residue 67 ILE Chi-restraints excluded: chain p residue 133 THR Chi-restraints excluded: chain p residue 142 VAL Chi-restraints excluded: chain p residue 183 THR Chi-restraints excluded: chain p residue 230 THR Chi-restraints excluded: chain p residue 336 GLN Chi-restraints excluded: chain p residue 383 ARG Chi-restraints excluded: chain p residue 402 ASP Chi-restraints excluded: chain p residue 413 TYR Chi-restraints excluded: chain p residue 440 VAL Chi-restraints excluded: chain p residue 469 HIS Chi-restraints excluded: chain p residue 491 ILE Chi-restraints excluded: chain p residue 517 ILE Chi-restraints excluded: chain p residue 660 VAL Chi-restraints excluded: chain q residue 8 VAL Chi-restraints excluded: chain q residue 16 ILE Chi-restraints excluded: chain q residue 26 VAL Chi-restraints excluded: chain q residue 47 ILE Chi-restraints excluded: chain q residue 49 VAL Chi-restraints excluded: chain q residue 59 VAL Chi-restraints excluded: chain q residue 67 ILE Chi-restraints excluded: chain q residue 83 VAL Chi-restraints excluded: chain q residue 108 LYS Chi-restraints excluded: chain q residue 128 LEU Chi-restraints excluded: chain q residue 133 THR Chi-restraints excluded: chain q residue 165 VAL Chi-restraints excluded: chain q residue 174 PHE Chi-restraints excluded: chain q residue 183 THR Chi-restraints excluded: chain q residue 187 LYS Chi-restraints excluded: chain q residue 212 ASN Chi-restraints excluded: chain q residue 230 THR Chi-restraints excluded: chain q residue 237 VAL Chi-restraints excluded: chain q residue 240 TYR Chi-restraints excluded: chain q residue 265 ILE Chi-restraints excluded: chain q residue 283 PHE Chi-restraints excluded: chain q residue 385 SER Chi-restraints excluded: chain q residue 392 TRP Chi-restraints excluded: chain q residue 425 LEU Chi-restraints excluded: chain q residue 449 MET Chi-restraints excluded: chain q residue 462 SER Chi-restraints excluded: chain q residue 492 TYR Chi-restraints excluded: chain q residue 509 SER Chi-restraints excluded: chain q residue 566 HIS Chi-restraints excluded: chain q residue 571 THR Chi-restraints excluded: chain q residue 631 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 64 optimal weight: 6.9990 chunk 172 optimal weight: 3.9990 chunk 37 optimal weight: 9.9990 chunk 112 optimal weight: 8.9990 chunk 47 optimal weight: 9.9990 chunk 191 optimal weight: 0.8980 chunk 159 optimal weight: 10.0000 chunk 88 optimal weight: 9.9990 chunk 15 optimal weight: 5.9990 chunk 63 optimal weight: 9.9990 chunk 100 optimal weight: 9.9990 overall best weight: 5.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: o 45 ASN ** o 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 421 HIS ** o 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 521 ASN ** p 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 566 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 320 ASN ** q 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 611 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7310 moved from start: 0.2373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.138 15405 Z= 0.557 Angle : 0.827 11.177 20934 Z= 0.440 Chirality : 0.053 0.200 2352 Planarity : 0.006 0.084 2745 Dihedral : 6.415 45.666 2140 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 21.23 Ramachandran Plot: Outliers : 0.25 % Allowed : 10.89 % Favored : 88.86 % Rotamer: Outliers : 7.17 % Allowed : 27.21 % Favored : 65.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -2.71 (0.17), residues: 1983 helix: -1.84 (0.49), residues: 84 sheet: -1.55 (0.23), residues: 492 loop : -2.02 (0.15), residues: 1407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP o 366 HIS 0.008 0.002 HIS p 566 PHE 0.024 0.003 PHE o 283 TYR 0.032 0.003 TYR q 233 ARG 0.010 0.001 ARG o 14 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3966 Ramachandran restraints generated. 1983 Oldfield, 0 Emsley, 1983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3966 Ramachandran restraints generated. 1983 Oldfield, 0 Emsley, 1983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 473 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 356 time to evaluate : 1.555 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: o 98 SER cc_start: 0.8784 (OUTLIER) cc_final: 0.8339 (p) REVERT: o 151 TYR cc_start: 0.7983 (t80) cc_final: 0.7715 (t80) REVERT: o 213 GLN cc_start: 0.7461 (pp30) cc_final: 0.7236 (pp30) REVERT: o 234 GLN cc_start: 0.8169 (OUTLIER) cc_final: 0.7241 (tt0) REVERT: o 280 MET cc_start: 0.7911 (tmm) cc_final: 0.7637 (tmm) REVERT: o 318 LYS cc_start: 0.7962 (tptt) cc_final: 0.7622 (tptt) REVERT: o 339 ARG cc_start: 0.6315 (ttt180) cc_final: 0.6079 (ttt-90) REVERT: o 474 THR cc_start: 0.7863 (m) cc_final: 0.7550 (p) REVERT: o 502 LEU cc_start: 0.5970 (OUTLIER) cc_final: 0.5611 (mt) REVERT: o 535 ARG cc_start: 0.7534 (OUTLIER) cc_final: 0.6318 (mmm160) REVERT: o 546 LEU cc_start: 0.5876 (OUTLIER) cc_final: 0.5287 (pt) REVERT: o 607 LEU cc_start: 0.4693 (OUTLIER) cc_final: 0.4439 (pp) REVERT: o 608 LYS cc_start: 0.6362 (OUTLIER) cc_final: 0.5841 (ttmt) REVERT: p 54 GLU cc_start: 0.6520 (tm-30) cc_final: 0.5736 (tm-30) REVERT: p 90 MET cc_start: 0.8460 (ttm) cc_final: 0.8258 (ttp) REVERT: p 169 GLU cc_start: 0.7314 (tm-30) cc_final: 0.6654 (tm-30) REVERT: p 171 LYS cc_start: 0.8615 (mttm) cc_final: 0.8164 (mttt) REVERT: p 196 MET cc_start: 0.7421 (mmm) cc_final: 0.7108 (mmm) REVERT: p 213 GLN cc_start: 0.7533 (pm20) cc_final: 0.7243 (mp10) REVERT: p 230 THR cc_start: 0.6715 (OUTLIER) cc_final: 0.6425 (t) REVERT: p 337 PHE cc_start: 0.7581 (m-80) cc_final: 0.6984 (m-10) REVERT: p 402 ASP cc_start: 0.3375 (OUTLIER) cc_final: 0.2636 (p0) REVERT: p 429 ILE cc_start: 0.8152 (mm) cc_final: 0.7934 (mm) REVERT: p 445 ASP cc_start: 0.5306 (OUTLIER) cc_final: 0.4509 (p0) REVERT: p 467 LEU cc_start: 0.8071 (tp) cc_final: 0.7373 (tt) REVERT: p 530 MET cc_start: 0.6115 (ptp) cc_final: 0.5426 (ptp) REVERT: p 550 ARG cc_start: 0.7529 (ptm-80) cc_final: 0.6917 (ptm-80) REVERT: q 49 VAL cc_start: 0.8792 (OUTLIER) cc_final: 0.8522 (m) REVERT: q 174 PHE cc_start: 0.8092 (OUTLIER) cc_final: 0.7576 (m-10) REVERT: q 217 ASP cc_start: 0.7664 (OUTLIER) cc_final: 0.7304 (p0) REVERT: q 238 SER cc_start: 0.8893 (m) cc_final: 0.8396 (p) REVERT: q 266 ARG cc_start: 0.8220 (ttm-80) cc_final: 0.7953 (ttm-80) REVERT: q 269 ILE cc_start: 0.9068 (mp) cc_final: 0.8825 (mt) REVERT: q 312 LEU cc_start: 0.8551 (pp) cc_final: 0.8346 (pt) REVERT: q 345 GLU cc_start: 0.8136 (mp0) cc_final: 0.7787 (mp0) REVERT: q 346 ARG cc_start: 0.7412 (mmt90) cc_final: 0.7106 (mmt90) REVERT: q 366 TRP cc_start: 0.6539 (m-10) cc_final: 0.6336 (m-10) REVERT: q 381 GLN cc_start: 0.7610 (pm20) cc_final: 0.6838 (pm20) REVERT: q 418 TYR cc_start: 0.7485 (m-80) cc_final: 0.7077 (m-80) REVERT: q 444 MET cc_start: 0.6489 (ppp) cc_final: 0.6275 (ppp) REVERT: q 487 GLN cc_start: 0.7725 (mm-40) cc_final: 0.7514 (mm-40) outliers start: 117 outliers final: 77 residues processed: 434 average time/residue: 0.3048 time to fit residues: 190.6316 Evaluate side-chains 442 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 352 time to evaluate : 1.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain o residue 8 VAL Chi-restraints excluded: chain o residue 19 GLU Chi-restraints excluded: chain o residue 31 ILE Chi-restraints excluded: chain o residue 41 VAL Chi-restraints excluded: chain o residue 83 VAL Chi-restraints excluded: chain o residue 98 SER Chi-restraints excluded: chain o residue 148 ASP Chi-restraints excluded: chain o residue 158 THR Chi-restraints excluded: chain o residue 165 VAL Chi-restraints excluded: chain o residue 180 LEU Chi-restraints excluded: chain o residue 194 VAL Chi-restraints excluded: chain o residue 234 GLN Chi-restraints excluded: chain o residue 264 GLU Chi-restraints excluded: chain o residue 265 ILE Chi-restraints excluded: chain o residue 333 SER Chi-restraints excluded: chain o residue 341 ASN Chi-restraints excluded: chain o residue 345 GLU Chi-restraints excluded: chain o residue 350 VAL Chi-restraints excluded: chain o residue 365 THR Chi-restraints excluded: chain o residue 369 THR Chi-restraints excluded: chain o residue 421 HIS Chi-restraints excluded: chain o residue 444 MET Chi-restraints excluded: chain o residue 451 VAL Chi-restraints excluded: chain o residue 493 ILE Chi-restraints excluded: chain o residue 497 CYS Chi-restraints excluded: chain o residue 502 LEU Chi-restraints excluded: chain o residue 523 THR Chi-restraints excluded: chain o residue 535 ARG Chi-restraints excluded: chain o residue 537 ASN Chi-restraints excluded: chain o residue 540 ASN Chi-restraints excluded: chain o residue 546 LEU Chi-restraints excluded: chain o residue 607 LEU Chi-restraints excluded: chain o residue 608 LYS Chi-restraints excluded: chain p residue 42 ASN Chi-restraints excluded: chain p residue 49 VAL Chi-restraints excluded: chain p residue 67 ILE Chi-restraints excluded: chain p residue 85 VAL Chi-restraints excluded: chain p residue 100 VAL Chi-restraints excluded: chain p residue 115 SER Chi-restraints excluded: chain p residue 133 THR Chi-restraints excluded: chain p residue 146 LEU Chi-restraints excluded: chain p residue 183 THR Chi-restraints excluded: chain p residue 230 THR Chi-restraints excluded: chain p residue 286 ARG Chi-restraints excluded: chain p residue 300 SER Chi-restraints excluded: chain p residue 336 GLN Chi-restraints excluded: chain p residue 383 ARG Chi-restraints excluded: chain p residue 402 ASP Chi-restraints excluded: chain p residue 413 TYR Chi-restraints excluded: chain p residue 440 VAL Chi-restraints excluded: chain p residue 445 ASP Chi-restraints excluded: chain p residue 469 HIS Chi-restraints excluded: chain p residue 471 SER Chi-restraints excluded: chain p residue 491 ILE Chi-restraints excluded: chain p residue 517 ILE Chi-restraints excluded: chain p residue 538 VAL Chi-restraints excluded: chain p residue 660 VAL Chi-restraints excluded: chain q residue 8 VAL Chi-restraints excluded: chain q residue 16 ILE Chi-restraints excluded: chain q residue 26 VAL Chi-restraints excluded: chain q residue 47 ILE Chi-restraints excluded: chain q residue 49 VAL Chi-restraints excluded: chain q residue 59 VAL Chi-restraints excluded: chain q residue 83 VAL Chi-restraints excluded: chain q residue 128 LEU Chi-restraints excluded: chain q residue 133 THR Chi-restraints excluded: chain q residue 165 VAL Chi-restraints excluded: chain q residue 174 PHE Chi-restraints excluded: chain q residue 183 THR Chi-restraints excluded: chain q residue 212 ASN Chi-restraints excluded: chain q residue 217 ASP Chi-restraints excluded: chain q residue 230 THR Chi-restraints excluded: chain q residue 237 VAL Chi-restraints excluded: chain q residue 240 TYR Chi-restraints excluded: chain q residue 265 ILE Chi-restraints excluded: chain q residue 283 PHE Chi-restraints excluded: chain q residue 289 HIS Chi-restraints excluded: chain q residue 326 ARG Chi-restraints excluded: chain q residue 379 ASN Chi-restraints excluded: chain q residue 385 SER Chi-restraints excluded: chain q residue 423 LEU Chi-restraints excluded: chain q residue 425 LEU Chi-restraints excluded: chain q residue 449 MET Chi-restraints excluded: chain q residue 459 CYS Chi-restraints excluded: chain q residue 492 TYR Chi-restraints excluded: chain q residue 509 SER Chi-restraints excluded: chain q residue 521 ASN Chi-restraints excluded: chain q residue 566 HIS Chi-restraints excluded: chain q residue 571 THR Chi-restraints excluded: chain q residue 631 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 184 optimal weight: 9.9990 chunk 21 optimal weight: 0.6980 chunk 109 optimal weight: 0.9980 chunk 139 optimal weight: 0.7980 chunk 108 optimal weight: 0.9980 chunk 161 optimal weight: 4.9990 chunk 106 optimal weight: 5.9990 chunk 190 optimal weight: 10.0000 chunk 119 optimal weight: 0.0970 chunk 116 optimal weight: 9.9990 chunk 88 optimal weight: 0.0470 overall best weight: 0.5276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** o 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 421 HIS ** o 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 234 GLN ** p 566 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 7 ASN q 537 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7185 moved from start: 0.2293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 15405 Z= 0.196 Angle : 0.701 10.707 20934 Z= 0.363 Chirality : 0.049 0.187 2352 Planarity : 0.004 0.045 2745 Dihedral : 5.683 49.953 2140 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 15.41 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.25 % Favored : 93.49 % Rotamer: Outliers : 5.02 % Allowed : 29.84 % Favored : 65.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -2.41 (0.18), residues: 1983 helix: -1.09 (0.55), residues: 82 sheet: -1.37 (0.23), residues: 513 loop : -1.82 (0.16), residues: 1388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP p 208 HIS 0.016 0.001 HIS o 421 PHE 0.033 0.002 PHE q 153 TYR 0.026 0.002 TYR q 465 ARG 0.006 0.001 ARG q 190 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3966 Ramachandran restraints generated. 1983 Oldfield, 0 Emsley, 1983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3966 Ramachandran restraints generated. 1983 Oldfield, 0 Emsley, 1983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 448 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 366 time to evaluate : 1.625 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: o 135 GLN cc_start: 0.8266 (tp40) cc_final: 0.8026 (tp-100) REVERT: o 151 TYR cc_start: 0.7904 (t80) cc_final: 0.7668 (t80) REVERT: o 208 TRP cc_start: 0.7130 (p90) cc_final: 0.6906 (p90) REVERT: o 258 ASN cc_start: 0.8443 (p0) cc_final: 0.8128 (p0) REVERT: o 266 ARG cc_start: 0.8502 (ttm-80) cc_final: 0.8085 (ttm-80) REVERT: o 280 MET cc_start: 0.7813 (tmm) cc_final: 0.7491 (tmm) REVERT: o 318 LYS cc_start: 0.7624 (tptt) cc_final: 0.7201 (tptt) REVERT: o 322 VAL cc_start: 0.8979 (t) cc_final: 0.8639 (m) REVERT: o 339 ARG cc_start: 0.6265 (ttt180) cc_final: 0.5943 (ttp80) REVERT: o 388 ILE cc_start: 0.8363 (mt) cc_final: 0.8115 (mm) REVERT: o 502 LEU cc_start: 0.5895 (OUTLIER) cc_final: 0.5602 (mt) REVERT: o 535 ARG cc_start: 0.7192 (OUTLIER) cc_final: 0.6421 (mmm160) REVERT: o 607 LEU cc_start: 0.4553 (OUTLIER) cc_final: 0.4208 (pp) REVERT: o 608 LYS cc_start: 0.5952 (OUTLIER) cc_final: 0.5463 (ttmt) REVERT: p 46 GLN cc_start: 0.8618 (mt0) cc_final: 0.8298 (mt0) REVERT: p 54 GLU cc_start: 0.6206 (tm-30) cc_final: 0.5445 (tm-30) REVERT: p 112 ASP cc_start: 0.8025 (t0) cc_final: 0.7626 (t0) REVERT: p 113 GLN cc_start: 0.8471 (mm-40) cc_final: 0.8245 (mm-40) REVERT: p 157 GLU cc_start: 0.7717 (mp0) cc_final: 0.7461 (mp0) REVERT: p 169 GLU cc_start: 0.7234 (tm-30) cc_final: 0.6779 (tm-30) REVERT: p 171 LYS cc_start: 0.8574 (mttm) cc_final: 0.8015 (mttt) REVERT: p 195 PHE cc_start: 0.6906 (OUTLIER) cc_final: 0.5507 (t80) REVERT: p 230 THR cc_start: 0.6773 (OUTLIER) cc_final: 0.6463 (t) REVERT: p 266 ARG cc_start: 0.7672 (ttm170) cc_final: 0.7343 (ttm170) REVERT: p 329 TYR cc_start: 0.6616 (m-10) cc_final: 0.6091 (m-10) REVERT: p 337 PHE cc_start: 0.7373 (m-80) cc_final: 0.6815 (m-10) REVERT: p 353 PHE cc_start: 0.7658 (t80) cc_final: 0.7427 (t80) REVERT: p 356 TYR cc_start: 0.6911 (t80) cc_final: 0.6511 (t80) REVERT: p 382 PHE cc_start: 0.7120 (m-80) cc_final: 0.6900 (m-80) REVERT: p 402 ASP cc_start: 0.3132 (OUTLIER) cc_final: 0.2288 (p0) REVERT: p 429 ILE cc_start: 0.8017 (mm) cc_final: 0.7787 (mm) REVERT: p 467 LEU cc_start: 0.7781 (tp) cc_final: 0.7014 (tt) REVERT: p 530 MET cc_start: 0.5411 (ptp) cc_final: 0.4850 (ptp) REVERT: p 550 ARG cc_start: 0.7295 (ptm-80) cc_final: 0.6863 (ptm-80) REVERT: q 49 VAL cc_start: 0.8620 (OUTLIER) cc_final: 0.8336 (m) REVERT: q 238 SER cc_start: 0.8899 (m) cc_final: 0.8302 (p) REVERT: q 266 ARG cc_start: 0.8172 (ttm-80) cc_final: 0.7855 (ttm-80) REVERT: q 269 ILE cc_start: 0.9071 (mp) cc_final: 0.8852 (mt) REVERT: q 312 LEU cc_start: 0.8478 (pp) cc_final: 0.8269 (pt) REVERT: q 345 GLU cc_start: 0.7876 (mp0) cc_final: 0.7378 (mp0) REVERT: q 381 GLN cc_start: 0.7553 (pm20) cc_final: 0.6750 (pm20) REVERT: q 392 TRP cc_start: 0.7439 (m100) cc_final: 0.7057 (m-10) REVERT: q 418 TYR cc_start: 0.7335 (m-80) cc_final: 0.6988 (m-80) REVERT: q 444 MET cc_start: 0.6361 (ppp) cc_final: 0.6016 (ppp) REVERT: q 467 LEU cc_start: 0.8010 (mt) cc_final: 0.7234 (tt) REVERT: q 487 GLN cc_start: 0.7597 (mm-40) cc_final: 0.7366 (mm-40) outliers start: 82 outliers final: 58 residues processed: 420 average time/residue: 0.2986 time to fit residues: 178.1355 Evaluate side-chains 417 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 351 time to evaluate : 1.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain o residue 8 VAL Chi-restraints excluded: chain o residue 31 ILE Chi-restraints excluded: chain o residue 83 VAL Chi-restraints excluded: chain o residue 103 ILE Chi-restraints excluded: chain o residue 158 THR Chi-restraints excluded: chain o residue 165 VAL Chi-restraints excluded: chain o residue 180 LEU Chi-restraints excluded: chain o residue 194 VAL Chi-restraints excluded: chain o residue 264 GLU Chi-restraints excluded: chain o residue 265 ILE Chi-restraints excluded: chain o residue 333 SER Chi-restraints excluded: chain o residue 341 ASN Chi-restraints excluded: chain o residue 395 PHE Chi-restraints excluded: chain o residue 403 MET Chi-restraints excluded: chain o residue 497 CYS Chi-restraints excluded: chain o residue 502 LEU Chi-restraints excluded: chain o residue 523 THR Chi-restraints excluded: chain o residue 535 ARG Chi-restraints excluded: chain o residue 540 ASN Chi-restraints excluded: chain o residue 546 LEU Chi-restraints excluded: chain o residue 607 LEU Chi-restraints excluded: chain o residue 608 LYS Chi-restraints excluded: chain p residue 49 VAL Chi-restraints excluded: chain p residue 67 ILE Chi-restraints excluded: chain p residue 115 SER Chi-restraints excluded: chain p residue 133 THR Chi-restraints excluded: chain p residue 173 LYS Chi-restraints excluded: chain p residue 183 THR Chi-restraints excluded: chain p residue 195 PHE Chi-restraints excluded: chain p residue 203 TRP Chi-restraints excluded: chain p residue 230 THR Chi-restraints excluded: chain p residue 263 LEU Chi-restraints excluded: chain p residue 265 ILE Chi-restraints excluded: chain p residue 336 GLN Chi-restraints excluded: chain p residue 383 ARG Chi-restraints excluded: chain p residue 402 ASP Chi-restraints excluded: chain p residue 413 TYR Chi-restraints excluded: chain p residue 440 VAL Chi-restraints excluded: chain p residue 469 HIS Chi-restraints excluded: chain p residue 491 ILE Chi-restraints excluded: chain p residue 517 ILE Chi-restraints excluded: chain p residue 660 VAL Chi-restraints excluded: chain q residue 8 VAL Chi-restraints excluded: chain q residue 16 ILE Chi-restraints excluded: chain q residue 26 VAL Chi-restraints excluded: chain q residue 49 VAL Chi-restraints excluded: chain q residue 59 VAL Chi-restraints excluded: chain q residue 83 VAL Chi-restraints excluded: chain q residue 128 LEU Chi-restraints excluded: chain q residue 133 THR Chi-restraints excluded: chain q residue 165 VAL Chi-restraints excluded: chain q residue 183 THR Chi-restraints excluded: chain q residue 212 ASN Chi-restraints excluded: chain q residue 230 THR Chi-restraints excluded: chain q residue 237 VAL Chi-restraints excluded: chain q residue 240 TYR Chi-restraints excluded: chain q residue 265 ILE Chi-restraints excluded: chain q residue 283 PHE Chi-restraints excluded: chain q residue 326 ARG Chi-restraints excluded: chain q residue 385 SER Chi-restraints excluded: chain q residue 449 MET Chi-restraints excluded: chain q residue 459 CYS Chi-restraints excluded: chain q residue 492 TYR Chi-restraints excluded: chain q residue 566 HIS Chi-restraints excluded: chain q residue 571 THR Chi-restraints excluded: chain q residue 631 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 118 optimal weight: 10.0000 chunk 76 optimal weight: 5.9990 chunk 113 optimal weight: 9.9990 chunk 57 optimal weight: 20.0000 chunk 37 optimal weight: 9.9990 chunk 36 optimal weight: 3.9990 chunk 121 optimal weight: 10.0000 chunk 130 optimal weight: 30.0000 chunk 94 optimal weight: 6.9990 chunk 17 optimal weight: 3.9990 chunk 150 optimal weight: 7.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: o 274 HIS ** o 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 566 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 404 ASN q 487 GLN ** q 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 611 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7325 moved from start: 0.2822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.145 15405 Z= 0.586 Angle : 0.849 11.748 20934 Z= 0.452 Chirality : 0.055 0.259 2352 Planarity : 0.006 0.085 2745 Dihedral : 6.367 33.148 2139 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 22.54 Ramachandran Plot: Outliers : 0.25 % Allowed : 11.30 % Favored : 88.45 % Rotamer: Outliers : 6.25 % Allowed : 29.84 % Favored : 63.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -2.79 (0.17), residues: 1983 helix: -1.95 (0.49), residues: 84 sheet: -1.59 (0.23), residues: 499 loop : -2.08 (0.15), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP p 214 HIS 0.008 0.002 HIS o 421 PHE 0.021 0.003 PHE q 290 TYR 0.028 0.003 TYR q 233 ARG 0.012 0.001 ARG o 14 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3966 Ramachandran restraints generated. 1983 Oldfield, 0 Emsley, 1983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3966 Ramachandran restraints generated. 1983 Oldfield, 0 Emsley, 1983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 465 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 363 time to evaluate : 1.460 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: o 46 GLN cc_start: 0.8498 (mt0) cc_final: 0.8237 (mt0) REVERT: o 94 ASP cc_start: 0.8298 (p0) cc_final: 0.8035 (p0) REVERT: o 98 SER cc_start: 0.8749 (t) cc_final: 0.8278 (p) REVERT: o 151 TYR cc_start: 0.7986 (t80) cc_final: 0.7702 (t80) REVERT: o 234 GLN cc_start: 0.8093 (OUTLIER) cc_final: 0.6782 (tt0) REVERT: o 257 GLN cc_start: 0.7604 (OUTLIER) cc_final: 0.4923 (pm20) REVERT: o 258 ASN cc_start: 0.8514 (p0) cc_final: 0.8258 (p0) REVERT: o 280 MET cc_start: 0.7887 (tmm) cc_final: 0.7549 (tmm) REVERT: o 312 LEU cc_start: 0.6516 (tp) cc_final: 0.6278 (tp) REVERT: o 318 LYS cc_start: 0.8089 (tptt) cc_final: 0.7669 (tptt) REVERT: o 322 VAL cc_start: 0.9082 (t) cc_final: 0.8745 (m) REVERT: o 383 ARG cc_start: 0.7945 (mpp80) cc_final: 0.7689 (mpp80) REVERT: o 474 THR cc_start: 0.7860 (m) cc_final: 0.7545 (p) REVERT: o 502 LEU cc_start: 0.5991 (OUTLIER) cc_final: 0.5727 (mt) REVERT: o 535 ARG cc_start: 0.7487 (OUTLIER) cc_final: 0.6376 (mmm160) REVERT: o 546 LEU cc_start: 0.5865 (OUTLIER) cc_final: 0.5259 (pt) REVERT: o 607 LEU cc_start: 0.4777 (OUTLIER) cc_final: 0.4430 (pp) REVERT: o 608 LYS cc_start: 0.6576 (OUTLIER) cc_final: 0.5928 (ttmt) REVERT: p 7 ASN cc_start: 0.8445 (t0) cc_final: 0.8239 (t0) REVERT: p 54 GLU cc_start: 0.6533 (tm-30) cc_final: 0.5457 (tm-30) REVERT: p 112 ASP cc_start: 0.8208 (t0) cc_final: 0.7701 (t0) REVERT: p 113 GLN cc_start: 0.8519 (mm-40) cc_final: 0.8311 (mm-40) REVERT: p 134 LEU cc_start: 0.8995 (tp) cc_final: 0.8676 (tt) REVERT: p 157 GLU cc_start: 0.7924 (mp0) cc_final: 0.7495 (mp0) REVERT: p 195 PHE cc_start: 0.6454 (OUTLIER) cc_final: 0.6238 (t80) REVERT: p 213 GLN cc_start: 0.7479 (pm20) cc_final: 0.7178 (pm20) REVERT: p 230 THR cc_start: 0.6817 (OUTLIER) cc_final: 0.6546 (t) REVERT: p 293 MET cc_start: 0.8328 (mtm) cc_final: 0.8121 (mtm) REVERT: p 337 PHE cc_start: 0.7511 (m-80) cc_final: 0.6947 (m-10) REVERT: p 356 TYR cc_start: 0.7242 (t80) cc_final: 0.6758 (t80) REVERT: p 402 ASP cc_start: 0.3472 (OUTLIER) cc_final: 0.2738 (p0) REVERT: p 429 ILE cc_start: 0.8244 (mm) cc_final: 0.8042 (mm) REVERT: p 445 ASP cc_start: 0.5280 (OUTLIER) cc_final: 0.4414 (p0) REVERT: p 467 LEU cc_start: 0.8054 (tp) cc_final: 0.7326 (tt) REVERT: p 550 ARG cc_start: 0.7541 (ptm-80) cc_final: 0.6989 (ptm-80) REVERT: q 101 ASP cc_start: 0.8499 (t0) cc_final: 0.8212 (t0) REVERT: q 161 PHE cc_start: 0.8418 (m-10) cc_final: 0.8206 (m-10) REVERT: q 238 SER cc_start: 0.8941 (m) cc_final: 0.8410 (p) REVERT: q 249 LEU cc_start: 0.3217 (OUTLIER) cc_final: 0.1896 (mt) REVERT: q 266 ARG cc_start: 0.8243 (ttm-80) cc_final: 0.7938 (ttm-80) REVERT: q 269 ILE cc_start: 0.9063 (mp) cc_final: 0.8837 (mt) REVERT: q 312 LEU cc_start: 0.8523 (pp) cc_final: 0.8313 (pt) REVERT: q 345 GLU cc_start: 0.7895 (mp0) cc_final: 0.7667 (mp0) REVERT: q 346 ARG cc_start: 0.7341 (mpt-90) cc_final: 0.7095 (mmt90) REVERT: q 381 GLN cc_start: 0.7653 (pm20) cc_final: 0.6871 (pm20) REVERT: q 418 TYR cc_start: 0.7496 (m-80) cc_final: 0.7232 (m-80) outliers start: 102 outliers final: 71 residues processed: 427 average time/residue: 0.2930 time to fit residues: 179.0394 Evaluate side-chains 444 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 361 time to evaluate : 1.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain o residue 8 VAL Chi-restraints excluded: chain o residue 31 ILE Chi-restraints excluded: chain o residue 83 VAL Chi-restraints excluded: chain o residue 158 THR Chi-restraints excluded: chain o residue 165 VAL Chi-restraints excluded: chain o residue 180 LEU Chi-restraints excluded: chain o residue 194 VAL Chi-restraints excluded: chain o residue 234 GLN Chi-restraints excluded: chain o residue 241 VAL Chi-restraints excluded: chain o residue 257 GLN Chi-restraints excluded: chain o residue 264 GLU Chi-restraints excluded: chain o residue 265 ILE Chi-restraints excluded: chain o residue 269 ILE Chi-restraints excluded: chain o residue 274 HIS Chi-restraints excluded: chain o residue 295 ASP Chi-restraints excluded: chain o residue 333 SER Chi-restraints excluded: chain o residue 341 ASN Chi-restraints excluded: chain o residue 444 MET Chi-restraints excluded: chain o residue 451 VAL Chi-restraints excluded: chain o residue 493 ILE Chi-restraints excluded: chain o residue 497 CYS Chi-restraints excluded: chain o residue 502 LEU Chi-restraints excluded: chain o residue 523 THR Chi-restraints excluded: chain o residue 535 ARG Chi-restraints excluded: chain o residue 540 ASN Chi-restraints excluded: chain o residue 546 LEU Chi-restraints excluded: chain o residue 607 LEU Chi-restraints excluded: chain o residue 608 LYS Chi-restraints excluded: chain p residue 42 ASN Chi-restraints excluded: chain p residue 49 VAL Chi-restraints excluded: chain p residue 57 SER Chi-restraints excluded: chain p residue 67 ILE Chi-restraints excluded: chain p residue 100 VAL Chi-restraints excluded: chain p residue 115 SER Chi-restraints excluded: chain p residue 133 THR Chi-restraints excluded: chain p residue 183 THR Chi-restraints excluded: chain p residue 195 PHE Chi-restraints excluded: chain p residue 200 THR Chi-restraints excluded: chain p residue 203 TRP Chi-restraints excluded: chain p residue 230 THR Chi-restraints excluded: chain p residue 286 ARG Chi-restraints excluded: chain p residue 300 SER Chi-restraints excluded: chain p residue 336 GLN Chi-restraints excluded: chain p residue 363 VAL Chi-restraints excluded: chain p residue 383 ARG Chi-restraints excluded: chain p residue 402 ASP Chi-restraints excluded: chain p residue 413 TYR Chi-restraints excluded: chain p residue 440 VAL Chi-restraints excluded: chain p residue 445 ASP Chi-restraints excluded: chain p residue 469 HIS Chi-restraints excluded: chain p residue 491 ILE Chi-restraints excluded: chain p residue 517 ILE Chi-restraints excluded: chain p residue 538 VAL Chi-restraints excluded: chain p residue 660 VAL Chi-restraints excluded: chain q residue 8 VAL Chi-restraints excluded: chain q residue 16 ILE Chi-restraints excluded: chain q residue 26 VAL Chi-restraints excluded: chain q residue 47 ILE Chi-restraints excluded: chain q residue 59 VAL Chi-restraints excluded: chain q residue 83 VAL Chi-restraints excluded: chain q residue 128 LEU Chi-restraints excluded: chain q residue 133 THR Chi-restraints excluded: chain q residue 165 VAL Chi-restraints excluded: chain q residue 183 THR Chi-restraints excluded: chain q residue 212 ASN Chi-restraints excluded: chain q residue 230 THR Chi-restraints excluded: chain q residue 237 VAL Chi-restraints excluded: chain q residue 240 TYR Chi-restraints excluded: chain q residue 249 LEU Chi-restraints excluded: chain q residue 265 ILE Chi-restraints excluded: chain q residue 283 PHE Chi-restraints excluded: chain q residue 289 HIS Chi-restraints excluded: chain q residue 326 ARG Chi-restraints excluded: chain q residue 340 ASN Chi-restraints excluded: chain q residue 379 ASN Chi-restraints excluded: chain q residue 431 ASN Chi-restraints excluded: chain q residue 449 MET Chi-restraints excluded: chain q residue 459 CYS Chi-restraints excluded: chain q residue 483 THR Chi-restraints excluded: chain q residue 492 TYR Chi-restraints excluded: chain q residue 521 ASN Chi-restraints excluded: chain q residue 566 HIS Chi-restraints excluded: chain q residue 631 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 173 optimal weight: 0.8980 chunk 182 optimal weight: 7.9990 chunk 166 optimal weight: 0.7980 chunk 177 optimal weight: 5.9990 chunk 107 optimal weight: 0.0870 chunk 77 optimal weight: 0.8980 chunk 139 optimal weight: 0.7980 chunk 54 optimal weight: 9.9990 chunk 160 optimal weight: 1.9990 chunk 168 optimal weight: 7.9990 chunk 116 optimal weight: 9.9990 overall best weight: 0.6958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: o 274 HIS ** o 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 152 ASN ** p 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 566 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 7 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7204 moved from start: 0.2720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 15405 Z= 0.206 Angle : 0.750 11.533 20934 Z= 0.390 Chirality : 0.050 0.204 2352 Planarity : 0.005 0.066 2745 Dihedral : 5.700 34.459 2139 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 16.89 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.56 % Favored : 93.19 % Rotamer: Outliers : 4.29 % Allowed : 32.41 % Favored : 63.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -2.51 (0.18), residues: 1983 helix: -1.18 (0.55), residues: 82 sheet: -1.41 (0.23), residues: 504 loop : -1.90 (0.15), residues: 1397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP o 316 HIS 0.009 0.001 HIS o 274 PHE 0.024 0.002 PHE q 153 TYR 0.028 0.002 TYR q 465 ARG 0.009 0.001 ARG q 615 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3966 Ramachandran restraints generated. 1983 Oldfield, 0 Emsley, 1983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3966 Ramachandran restraints generated. 1983 Oldfield, 0 Emsley, 1983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 363 time to evaluate : 1.821 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: o 28 ASN cc_start: 0.8467 (m110) cc_final: 0.8215 (m-40) REVERT: o 46 GLN cc_start: 0.8377 (mt0) cc_final: 0.8154 (mt0) REVERT: o 135 GLN cc_start: 0.8300 (tp40) cc_final: 0.8006 (tp-100) REVERT: o 151 TYR cc_start: 0.7901 (t80) cc_final: 0.7680 (t80) REVERT: o 258 ASN cc_start: 0.8451 (p0) cc_final: 0.8154 (p0) REVERT: o 266 ARG cc_start: 0.8538 (ttm-80) cc_final: 0.8165 (ttm-80) REVERT: o 280 MET cc_start: 0.7860 (tmm) cc_final: 0.7608 (tmm) REVERT: o 285 PHE cc_start: 0.7915 (m-10) cc_final: 0.7666 (m-10) REVERT: o 312 LEU cc_start: 0.6408 (tp) cc_final: 0.6085 (tp) REVERT: o 318 LYS cc_start: 0.7783 (tptt) cc_final: 0.7290 (tptt) REVERT: o 322 VAL cc_start: 0.8935 (t) cc_final: 0.8632 (m) REVERT: o 336 GLN cc_start: 0.7582 (mp10) cc_final: 0.7218 (mp10) REVERT: o 388 ILE cc_start: 0.8350 (mt) cc_final: 0.8096 (mm) REVERT: o 535 ARG cc_start: 0.7222 (OUTLIER) cc_final: 0.6486 (mmm160) REVERT: o 607 LEU cc_start: 0.4696 (OUTLIER) cc_final: 0.4324 (pp) REVERT: o 608 LYS cc_start: 0.6352 (OUTLIER) cc_final: 0.5826 (ttmt) REVERT: p 54 GLU cc_start: 0.6331 (tm-30) cc_final: 0.5466 (tm-30) REVERT: p 112 ASP cc_start: 0.8059 (t0) cc_final: 0.7632 (t0) REVERT: p 134 LEU cc_start: 0.8880 (tp) cc_final: 0.8514 (tt) REVERT: p 157 GLU cc_start: 0.7658 (mp0) cc_final: 0.7401 (mp0) REVERT: p 195 PHE cc_start: 0.6504 (OUTLIER) cc_final: 0.6271 (t80) REVERT: p 213 GLN cc_start: 0.7258 (pm20) cc_final: 0.7009 (pm20) REVERT: p 230 THR cc_start: 0.6867 (OUTLIER) cc_final: 0.6595 (t) REVERT: p 329 TYR cc_start: 0.6808 (m-10) cc_final: 0.6322 (m-80) REVERT: p 337 PHE cc_start: 0.7391 (m-80) cc_final: 0.6831 (m-10) REVERT: p 356 TYR cc_start: 0.6962 (t80) cc_final: 0.6462 (t80) REVERT: p 402 ASP cc_start: 0.3151 (OUTLIER) cc_final: 0.2351 (p0) REVERT: p 445 ASP cc_start: 0.5426 (OUTLIER) cc_final: 0.4639 (p0) REVERT: p 449 MET cc_start: 0.6060 (OUTLIER) cc_final: 0.5782 (pmm) REVERT: p 467 LEU cc_start: 0.7793 (tp) cc_final: 0.7024 (tt) REVERT: p 530 MET cc_start: 0.5949 (ptp) cc_final: 0.5718 (ptp) REVERT: p 550 ARG cc_start: 0.7483 (ptm-80) cc_final: 0.7062 (ptm-80) REVERT: q 238 SER cc_start: 0.8962 (m) cc_final: 0.8391 (p) REVERT: q 266 ARG cc_start: 0.8162 (ttm-80) cc_final: 0.7804 (ttm-80) REVERT: q 269 ILE cc_start: 0.9070 (mp) cc_final: 0.8859 (mt) REVERT: q 274 HIS cc_start: 0.8394 (m-70) cc_final: 0.8187 (m-70) REVERT: q 280 MET cc_start: 0.7645 (mpp) cc_final: 0.7257 (mmt) REVERT: q 320 ASN cc_start: 0.8087 (m-40) cc_final: 0.7605 (m-40) REVERT: q 345 GLU cc_start: 0.7774 (mp0) cc_final: 0.7347 (mp0) REVERT: q 380 LEU cc_start: 0.7670 (mt) cc_final: 0.7240 (mt) REVERT: q 381 GLN cc_start: 0.7536 (pm20) cc_final: 0.6740 (pm20) REVERT: q 392 TRP cc_start: 0.7437 (m100) cc_final: 0.7114 (m-10) REVERT: q 418 TYR cc_start: 0.7258 (m-80) cc_final: 0.7035 (m-80) REVERT: q 444 MET cc_start: 0.6943 (ppp) cc_final: 0.5922 (ppp) outliers start: 70 outliers final: 55 residues processed: 405 average time/residue: 0.3017 time to fit residues: 172.9053 Evaluate side-chains 416 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 353 time to evaluate : 1.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain o residue 8 VAL Chi-restraints excluded: chain o residue 31 ILE Chi-restraints excluded: chain o residue 83 VAL Chi-restraints excluded: chain o residue 92 ILE Chi-restraints excluded: chain o residue 103 ILE Chi-restraints excluded: chain o residue 158 THR Chi-restraints excluded: chain o residue 165 VAL Chi-restraints excluded: chain o residue 180 LEU Chi-restraints excluded: chain o residue 194 VAL Chi-restraints excluded: chain o residue 264 GLU Chi-restraints excluded: chain o residue 295 ASP Chi-restraints excluded: chain o residue 333 SER Chi-restraints excluded: chain o residue 341 ASN Chi-restraints excluded: chain o residue 395 PHE Chi-restraints excluded: chain o residue 403 MET Chi-restraints excluded: chain o residue 497 CYS Chi-restraints excluded: chain o residue 523 THR Chi-restraints excluded: chain o residue 535 ARG Chi-restraints excluded: chain o residue 540 ASN Chi-restraints excluded: chain o residue 546 LEU Chi-restraints excluded: chain o residue 607 LEU Chi-restraints excluded: chain o residue 608 LYS Chi-restraints excluded: chain p residue 49 VAL Chi-restraints excluded: chain p residue 67 ILE Chi-restraints excluded: chain p residue 133 THR Chi-restraints excluded: chain p residue 173 LYS Chi-restraints excluded: chain p residue 183 THR Chi-restraints excluded: chain p residue 195 PHE Chi-restraints excluded: chain p residue 200 THR Chi-restraints excluded: chain p residue 230 THR Chi-restraints excluded: chain p residue 336 GLN Chi-restraints excluded: chain p residue 383 ARG Chi-restraints excluded: chain p residue 402 ASP Chi-restraints excluded: chain p residue 413 TYR Chi-restraints excluded: chain p residue 440 VAL Chi-restraints excluded: chain p residue 445 ASP Chi-restraints excluded: chain p residue 449 MET Chi-restraints excluded: chain p residue 469 HIS Chi-restraints excluded: chain p residue 491 ILE Chi-restraints excluded: chain p residue 517 ILE Chi-restraints excluded: chain p residue 660 VAL Chi-restraints excluded: chain q residue 8 VAL Chi-restraints excluded: chain q residue 16 ILE Chi-restraints excluded: chain q residue 26 VAL Chi-restraints excluded: chain q residue 47 ILE Chi-restraints excluded: chain q residue 59 VAL Chi-restraints excluded: chain q residue 83 VAL Chi-restraints excluded: chain q residue 128 LEU Chi-restraints excluded: chain q residue 133 THR Chi-restraints excluded: chain q residue 165 VAL Chi-restraints excluded: chain q residue 212 ASN Chi-restraints excluded: chain q residue 230 THR Chi-restraints excluded: chain q residue 237 VAL Chi-restraints excluded: chain q residue 240 TYR Chi-restraints excluded: chain q residue 265 ILE Chi-restraints excluded: chain q residue 283 PHE Chi-restraints excluded: chain q residue 284 LEU Chi-restraints excluded: chain q residue 340 ASN Chi-restraints excluded: chain q residue 449 MET Chi-restraints excluded: chain q residue 483 THR Chi-restraints excluded: chain q residue 492 TYR Chi-restraints excluded: chain q residue 566 HIS Chi-restraints excluded: chain q residue 631 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 188 optimal weight: 0.8980 chunk 114 optimal weight: 0.0570 chunk 89 optimal weight: 5.9990 chunk 130 optimal weight: 20.0000 chunk 197 optimal weight: 0.7980 chunk 181 optimal weight: 0.9990 chunk 157 optimal weight: 9.9990 chunk 16 optimal weight: 7.9990 chunk 121 optimal weight: 9.9990 chunk 96 optimal weight: 6.9990 chunk 124 optimal weight: 10.0000 overall best weight: 1.7502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** o 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 422 GLN ** o 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 566 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7228 moved from start: 0.2865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 15405 Z= 0.247 Angle : 0.744 12.245 20934 Z= 0.386 Chirality : 0.050 0.202 2352 Planarity : 0.004 0.063 2745 Dihedral : 5.621 35.021 2139 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 17.25 Ramachandran Plot: Outliers : 0.25 % Allowed : 8.52 % Favored : 91.23 % Rotamer: Outliers : 4.04 % Allowed : 32.66 % Favored : 63.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -2.43 (0.18), residues: 1983 helix: -1.17 (0.55), residues: 82 sheet: -1.27 (0.23), residues: 476 loop : -1.88 (0.15), residues: 1425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP o 208 HIS 0.005 0.001 HIS o 421 PHE 0.029 0.002 PHE q 161 TYR 0.026 0.002 TYR o 356 ARG 0.007 0.001 ARG p 14 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3966 Ramachandran restraints generated. 1983 Oldfield, 0 Emsley, 1983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3966 Ramachandran restraints generated. 1983 Oldfield, 0 Emsley, 1983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 355 time to evaluate : 1.683 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: o 28 ASN cc_start: 0.8500 (m110) cc_final: 0.8241 (m-40) REVERT: o 46 GLN cc_start: 0.8364 (mt0) cc_final: 0.8130 (mt0) REVERT: o 135 GLN cc_start: 0.8238 (tp40) cc_final: 0.8038 (tp-100) REVERT: o 151 TYR cc_start: 0.7930 (t80) cc_final: 0.7681 (t80) REVERT: o 240 TYR cc_start: 0.7738 (m-80) cc_final: 0.7494 (m-80) REVERT: o 258 ASN cc_start: 0.8438 (p0) cc_final: 0.8036 (p0) REVERT: o 266 ARG cc_start: 0.8565 (ttm-80) cc_final: 0.8223 (ttm-80) REVERT: o 280 MET cc_start: 0.7875 (tmm) cc_final: 0.7530 (tmm) REVERT: o 285 PHE cc_start: 0.7992 (m-10) cc_final: 0.7729 (m-10) REVERT: o 318 LYS cc_start: 0.7943 (tptt) cc_final: 0.7409 (tptt) REVERT: o 322 VAL cc_start: 0.8971 (t) cc_final: 0.8696 (m) REVERT: o 336 GLN cc_start: 0.7625 (mp10) cc_final: 0.7241 (mp10) REVERT: o 388 ILE cc_start: 0.8327 (mt) cc_final: 0.8071 (mm) REVERT: o 502 LEU cc_start: 0.5811 (OUTLIER) cc_final: 0.5545 (mt) REVERT: o 535 ARG cc_start: 0.7149 (OUTLIER) cc_final: 0.6506 (mmm160) REVERT: o 607 LEU cc_start: 0.4729 (OUTLIER) cc_final: 0.4365 (pp) REVERT: o 608 LYS cc_start: 0.6343 (OUTLIER) cc_final: 0.5882 (ttmt) REVERT: p 54 GLU cc_start: 0.6602 (tm-30) cc_final: 0.5682 (tm-30) REVERT: p 112 ASP cc_start: 0.8164 (t0) cc_final: 0.7819 (t0) REVERT: p 134 LEU cc_start: 0.8918 (tp) cc_final: 0.8578 (tt) REVERT: p 157 GLU cc_start: 0.7753 (mp0) cc_final: 0.7548 (mp0) REVERT: p 213 GLN cc_start: 0.7320 (pm20) cc_final: 0.7119 (mp10) REVERT: p 230 THR cc_start: 0.6916 (OUTLIER) cc_final: 0.6647 (t) REVERT: p 329 TYR cc_start: 0.6807 (m-10) cc_final: 0.6233 (m-80) REVERT: p 336 GLN cc_start: 0.7612 (OUTLIER) cc_final: 0.6685 (mp10) REVERT: p 337 PHE cc_start: 0.7400 (m-80) cc_final: 0.6918 (m-10) REVERT: p 356 TYR cc_start: 0.7037 (t80) cc_final: 0.6761 (t80) REVERT: p 402 ASP cc_start: 0.3110 (OUTLIER) cc_final: 0.2344 (p0) REVERT: p 445 ASP cc_start: 0.5315 (OUTLIER) cc_final: 0.4578 (p0) REVERT: p 467 LEU cc_start: 0.7832 (tp) cc_final: 0.7022 (tt) REVERT: p 530 MET cc_start: 0.6036 (ptp) cc_final: 0.5782 (ptp) REVERT: p 550 ARG cc_start: 0.7528 (ptm-80) cc_final: 0.7096 (ptm-80) REVERT: q 238 SER cc_start: 0.8976 (m) cc_final: 0.8388 (p) REVERT: q 266 ARG cc_start: 0.8143 (ttm-80) cc_final: 0.7795 (ttm-80) REVERT: q 269 ILE cc_start: 0.9052 (mp) cc_final: 0.8851 (mt) REVERT: q 279 LEU cc_start: 0.8343 (mp) cc_final: 0.8133 (mt) REVERT: q 280 MET cc_start: 0.7694 (mpp) cc_final: 0.7319 (mmt) REVERT: q 364 LYS cc_start: 0.7905 (tttp) cc_final: 0.7661 (ptmm) REVERT: q 380 LEU cc_start: 0.7672 (mt) cc_final: 0.7223 (mt) REVERT: q 381 GLN cc_start: 0.7601 (pm20) cc_final: 0.6805 (pm20) REVERT: q 386 VAL cc_start: 0.8427 (t) cc_final: 0.7919 (p) REVERT: q 392 TRP cc_start: 0.7446 (m100) cc_final: 0.7146 (m-10) REVERT: q 444 MET cc_start: 0.7057 (ppp) cc_final: 0.5892 (ppp) outliers start: 66 outliers final: 51 residues processed: 399 average time/residue: 0.3025 time to fit residues: 172.3840 Evaluate side-chains 413 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 354 time to evaluate : 1.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain o residue 8 VAL Chi-restraints excluded: chain o residue 31 ILE Chi-restraints excluded: chain o residue 83 VAL Chi-restraints excluded: chain o residue 92 ILE Chi-restraints excluded: chain o residue 158 THR Chi-restraints excluded: chain o residue 165 VAL Chi-restraints excluded: chain o residue 180 LEU Chi-restraints excluded: chain o residue 194 VAL Chi-restraints excluded: chain o residue 264 GLU Chi-restraints excluded: chain o residue 333 SER Chi-restraints excluded: chain o residue 422 GLN Chi-restraints excluded: chain o residue 491 ILE Chi-restraints excluded: chain o residue 497 CYS Chi-restraints excluded: chain o residue 502 LEU Chi-restraints excluded: chain o residue 523 THR Chi-restraints excluded: chain o residue 535 ARG Chi-restraints excluded: chain o residue 540 ASN Chi-restraints excluded: chain o residue 546 LEU Chi-restraints excluded: chain o residue 607 LEU Chi-restraints excluded: chain o residue 608 LYS Chi-restraints excluded: chain p residue 49 VAL Chi-restraints excluded: chain p residue 67 ILE Chi-restraints excluded: chain p residue 133 THR Chi-restraints excluded: chain p residue 183 THR Chi-restraints excluded: chain p residue 200 THR Chi-restraints excluded: chain p residue 230 THR Chi-restraints excluded: chain p residue 265 ILE Chi-restraints excluded: chain p residue 336 GLN Chi-restraints excluded: chain p residue 363 VAL Chi-restraints excluded: chain p residue 383 ARG Chi-restraints excluded: chain p residue 402 ASP Chi-restraints excluded: chain p residue 413 TYR Chi-restraints excluded: chain p residue 440 VAL Chi-restraints excluded: chain p residue 445 ASP Chi-restraints excluded: chain p residue 469 HIS Chi-restraints excluded: chain p residue 491 ILE Chi-restraints excluded: chain p residue 517 ILE Chi-restraints excluded: chain p residue 660 VAL Chi-restraints excluded: chain q residue 8 VAL Chi-restraints excluded: chain q residue 16 ILE Chi-restraints excluded: chain q residue 26 VAL Chi-restraints excluded: chain q residue 47 ILE Chi-restraints excluded: chain q residue 59 VAL Chi-restraints excluded: chain q residue 83 VAL Chi-restraints excluded: chain q residue 133 THR Chi-restraints excluded: chain q residue 165 VAL Chi-restraints excluded: chain q residue 212 ASN Chi-restraints excluded: chain q residue 230 THR Chi-restraints excluded: chain q residue 237 VAL Chi-restraints excluded: chain q residue 240 TYR Chi-restraints excluded: chain q residue 265 ILE Chi-restraints excluded: chain q residue 283 PHE Chi-restraints excluded: chain q residue 284 LEU Chi-restraints excluded: chain q residue 340 ASN Chi-restraints excluded: chain q residue 449 MET Chi-restraints excluded: chain q residue 483 THR Chi-restraints excluded: chain q residue 492 TYR Chi-restraints excluded: chain q residue 566 HIS Chi-restraints excluded: chain q residue 631 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 167 optimal weight: 10.0000 chunk 48 optimal weight: 5.9990 chunk 144 optimal weight: 0.7980 chunk 23 optimal weight: 5.9990 chunk 43 optimal weight: 10.0000 chunk 157 optimal weight: 4.9990 chunk 65 optimal weight: 0.6980 chunk 161 optimal weight: 9.9990 chunk 19 optimal weight: 2.9990 chunk 28 optimal weight: 10.0000 chunk 138 optimal weight: 0.8980 overall best weight: 2.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** o 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 500 ASN ** p 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 234 GLN ** p 566 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.175933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.134747 restraints weight = 26465.294| |-----------------------------------------------------------------------------| r_work (start): 0.3793 rms_B_bonded: 3.63 r_work: 0.3651 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7249 moved from start: 0.2999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 15405 Z= 0.264 Angle : 0.757 12.532 20934 Z= 0.391 Chirality : 0.050 0.202 2352 Planarity : 0.005 0.126 2745 Dihedral : 5.656 34.950 2139 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 17.72 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.92 % Favored : 91.83 % Rotamer: Outliers : 3.98 % Allowed : 32.66 % Favored : 63.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -2.42 (0.18), residues: 1983 helix: -1.20 (0.55), residues: 82 sheet: -1.35 (0.22), residues: 519 loop : -1.84 (0.16), residues: 1382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP o 316 HIS 0.007 0.001 HIS o 469 PHE 0.026 0.002 PHE q 161 TYR 0.031 0.002 TYR o 356 ARG 0.022 0.001 ARG o 498 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4267.69 seconds wall clock time: 76 minutes 22.11 seconds (4582.11 seconds total)