Starting phenix.real_space_refine on Sun Dec 10 17:36:17 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u1o_41819/12_2023/8u1o_41819.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u1o_41819/12_2023/8u1o_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_41819/12_2023/8u1o_41819.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u1o_41819/12_2023/8u1o_41819.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u1o_41819/12_2023/8u1o_41819.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u1o_41819/12_2023/8u1o_41819.pdb" } 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-1.21rc1-5172/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: 8.22, per 1000 atoms: 0.54 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: 5.76 Conformation dependent library (CDL) restraints added in 3.0 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: 2.22 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: 5.97 Time building geometry restraints manager: 6.23 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 2.440 nonbonded pdb=" OG1 THR p 209 " pdb=" OE1 GLN p 213 " model vdw 2.226 2.440 nonbonded pdb=" O GLN o 513 " pdb=" NH2 ARG o 535 " model vdw 2.229 2.520 nonbonded pdb=" O GLY o 495 " pdb=" OG SER o 522 " model vdw 2.239 2.440 nonbonded pdb=" O GLY p 495 " pdb=" OG SER p 522 " model vdw 2.251 2.440 ... (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 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: 3.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 17.390 Check model and map are aligned: 0.230 Set scattering table: 0.140 Process input model: 43.350 Find NCS groups from input model: 0.950 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.250 ------------------------------------------------------------------------------- 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 : 1.648 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 outliers start: 15 outliers final: 8 residues processed: 360 average time/residue: 0.3233 time to fit residues: 163.0006 Evaluate side-chains 344 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 336 time to evaluate : 1.634 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1365 time to fit residues: 4.2814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 167 optimal weight: 7.9990 chunk 150 optimal weight: 4.9990 chunk 83 optimal weight: 10.0000 chunk 51 optimal weight: 3.9990 chunk 101 optimal weight: 9.9990 chunk 80 optimal weight: 3.9990 chunk 155 optimal weight: 4.9990 chunk 60 optimal weight: 20.0000 chunk 94 optimal weight: 6.9990 chunk 115 optimal weight: 20.0000 chunk 179 optimal weight: 2.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- 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** p 7 ASN ** p 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 566 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 537 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7256 moved from start: 0.1258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.069 15405 Z= 0.435 Angle : 0.770 13.923 20934 Z= 0.406 Chirality : 0.051 0.191 2352 Planarity : 0.005 0.079 2745 Dihedral : 6.385 37.387 2139 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 21.60 Ramachandran Plot: Outliers : 0.25 % Allowed : 9.98 % Favored : 89.76 % Rotamer: Outliers : 5.88 % Allowed : 27.02 % Favored : 67.10 % 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: -2.59 (0.17), residues: 1983 helix: -1.59 (0.49), residues: 93 sheet: -1.54 (0.22), residues: 470 loop : -1.91 (0.15), residues: 1420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP p 392 HIS 0.006 0.002 HIS o 58 PHE 0.015 0.002 PHE o 283 TYR 0.021 0.002 TYR q 32 ARG 0.014 0.001 ARG q 339 *********************** 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 449 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 353 time to evaluate : 1.721 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 outliers start: 96 outliers final: 55 residues processed: 416 average time/residue: 0.3136 time to fit residues: 185.4848 Evaluate side-chains 396 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 341 time to evaluate : 1.895 Switching outliers to nearest non-outliers outliers start: 55 outliers final: 0 residues processed: 55 average time/residue: 0.1589 time to fit residues: 17.5652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 99 optimal weight: 9.9990 chunk 55 optimal weight: 30.0000 chunk 149 optimal weight: 4.9990 chunk 122 optimal weight: 8.9990 chunk 49 optimal weight: 5.9990 chunk 180 optimal weight: 0.0010 chunk 194 optimal weight: 6.9990 chunk 160 optimal weight: 1.9990 chunk 178 optimal weight: 0.9990 chunk 61 optimal weight: 0.7980 chunk 144 optimal weight: 3.9990 overall best weight: 1.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: o 135 GLN ** o 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 7 ASN ** p 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 566 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 297 ASN ** q 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7190 moved from start: 0.1389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 15405 Z= 0.218 Angle : 0.691 12.879 20934 Z= 0.358 Chirality : 0.049 0.177 2352 Planarity : 0.005 0.102 2745 Dihedral : 5.916 35.494 2139 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 19.19 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.56 % Favored : 92.18 % Rotamer: Outliers : 2.27 % Allowed : 29.35 % Favored : 68.38 % 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: -2.44 (0.17), residues: 1983 helix: -1.24 (0.53), residues: 88 sheet: -1.29 (0.24), residues: 440 loop : -1.87 (0.15), residues: 1455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP o 316 HIS 0.008 0.001 HIS o 421 PHE 0.018 0.001 PHE q 442 TYR 0.029 0.002 TYR q 465 ARG 0.014 0.001 ARG o 535 *********************** 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 394 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 357 time to evaluate : 1.677 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 37 outliers final: 14 residues processed: 386 average time/residue: 0.3433 time to fit residues: 190.3071 Evaluate side-chains 358 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 344 time to evaluate : 1.737 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.1479 time to fit residues: 6.4613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.1980 chunk 93 optimal weight: 10.0000 chunk 19 optimal weight: 0.1980 chunk 85 optimal weight: 4.9990 chunk 120 optimal weight: 0.8980 chunk 180 optimal weight: 0.5980 chunk 191 optimal weight: 3.9990 chunk 94 optimal weight: 4.9990 chunk 171 optimal weight: 10.0000 chunk 51 optimal weight: 7.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- 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 537 ASN ** 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 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7169 moved from start: 0.1569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 15405 Z= 0.192 Angle : 0.668 14.846 20934 Z= 0.342 Chirality : 0.048 0.256 2352 Planarity : 0.004 0.043 2745 Dihedral : 5.601 34.822 2139 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 17.89 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.26 % Favored : 92.49 % Rotamer: Outliers : 2.94 % Allowed : 30.15 % Favored : 66.91 % 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: -2.32 (0.18), residues: 1983 helix: -1.15 (0.54), residues: 84 sheet: -1.23 (0.24), residues: 436 loop : -1.78 (0.15), residues: 1463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP o 208 HIS 0.007 0.001 HIS o 421 PHE 0.024 0.001 PHE p 353 TYR 0.029 0.001 TYR q 465 ARG 0.006 0.000 ARG p 14 *********************** 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 396 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 348 time to evaluate : 1.766 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 48 outliers final: 30 residues processed: 373 average time/residue: 0.3215 time to fit residues: 170.1274 Evaluate side-chains 372 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 342 time to evaluate : 1.662 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 0 residues processed: 30 average time/residue: 0.1522 time to fit residues: 10.6757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 5.9990 chunk 2 optimal weight: 0.5980 chunk 142 optimal weight: 0.7980 chunk 78 optimal weight: 5.9990 chunk 163 optimal weight: 8.9990 chunk 132 optimal weight: 0.0270 chunk 0 optimal weight: 7.9990 chunk 97 optimal weight: 0.9980 chunk 171 optimal weight: 9.9990 chunk 48 optimal weight: 9.9990 overall best weight: 1.6840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: o 135 GLN o 234 GLN ** o 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 593 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 566 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7184 moved from start: 0.1779 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= 0.218 Angle : 0.670 14.944 20934 Z= 0.344 Chirality : 0.048 0.201 2352 Planarity : 0.004 0.042 2745 Dihedral : 5.556 34.316 2139 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 18.93 Ramachandran Plot: Outliers : 0.30 % Allowed : 7.82 % Favored : 91.88 % Rotamer: Outliers : 2.14 % Allowed : 31.13 % Favored : 66.73 % 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: -2.24 (0.18), residues: 1983 helix: -1.17 (0.54), residues: 84 sheet: -1.04 (0.24), residues: 452 loop : -1.78 (0.15), residues: 1447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP p 392 HIS 0.004 0.001 HIS o 421 PHE 0.025 0.001 PHE p 353 TYR 0.025 0.002 TYR q 465 ARG 0.009 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 395 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 360 time to evaluate : 2.247 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 35 outliers final: 17 residues processed: 384 average time/residue: 0.3121 time to fit residues: 170.2307 Evaluate side-chains 361 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 344 time to evaluate : 1.786 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.1509 time to fit residues: 7.1637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 64 optimal weight: 50.0000 chunk 172 optimal weight: 6.9990 chunk 37 optimal weight: 9.9990 chunk 112 optimal weight: 5.9990 chunk 47 optimal weight: 9.9990 chunk 191 optimal weight: 6.9990 chunk 159 optimal weight: 10.0000 chunk 88 optimal weight: 0.9990 chunk 15 optimal weight: 4.9990 chunk 63 optimal weight: 5.9990 chunk 100 optimal weight: 8.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** o 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 421 HIS ** o 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 521 ASN ** o 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 593 GLN p 63 GLN ** p 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 566 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 257 GLN ** q 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 404 ASN ** q 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 537 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7301 moved from start: 0.2441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.107 15405 Z= 0.507 Angle : 0.812 12.677 20934 Z= 0.429 Chirality : 0.053 0.187 2352 Planarity : 0.005 0.057 2745 Dihedral : 6.396 34.070 2139 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 27.59 Ramachandran Plot: Outliers : 0.30 % Allowed : 11.25 % Favored : 88.45 % Rotamer: Outliers : 4.60 % Allowed : 30.88 % Favored : 64.52 % 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: -2.69 (0.17), residues: 1983 helix: -2.05 (0.46), residues: 96 sheet: -1.37 (0.23), residues: 485 loop : -2.05 (0.15), residues: 1402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP p 214 HIS 0.009 0.002 HIS o 421 PHE 0.033 0.003 PHE p 353 TYR 0.030 0.003 TYR q 32 ARG 0.010 0.001 ARG q 266 *********************** 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 437 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 362 time to evaluate : 1.755 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 75 outliers final: 47 residues processed: 400 average time/residue: 0.3131 time to fit residues: 179.4082 Evaluate side-chains 401 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 354 time to evaluate : 1.655 Switching outliers to nearest non-outliers outliers start: 47 outliers final: 0 residues processed: 47 average time/residue: 0.1810 time to fit residues: 16.9738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 184 optimal weight: 6.9990 chunk 21 optimal weight: 8.9990 chunk 109 optimal weight: 10.0000 chunk 139 optimal weight: 0.5980 chunk 108 optimal weight: 3.9990 chunk 161 optimal weight: 9.9990 chunk 106 optimal weight: 4.9990 chunk 190 optimal weight: 10.0000 chunk 119 optimal weight: 10.0000 chunk 116 optimal weight: 0.0570 chunk 88 optimal weight: 6.9990 overall best weight: 3.3304 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: o 213 GLN ** o 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 566 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7269 moved from start: 0.2554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 15405 Z= 0.355 Angle : 0.765 13.175 20934 Z= 0.397 Chirality : 0.051 0.199 2352 Planarity : 0.005 0.046 2745 Dihedral : 6.143 33.135 2139 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 24.78 Ramachandran Plot: Outliers : 0.30 % Allowed : 8.83 % Favored : 90.87 % Rotamer: Outliers : 2.51 % Allowed : 31.99 % Favored : 65.50 % 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: -2.56 (0.18), residues: 1983 helix: -1.79 (0.50), residues: 88 sheet: -1.24 (0.24), residues: 472 loop : -1.99 (0.15), residues: 1423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP q 366 HIS 0.007 0.001 HIS p 566 PHE 0.034 0.002 PHE q 153 TYR 0.025 0.002 TYR o 356 ARG 0.010 0.001 ARG o 535 *********************** 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 393 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 352 time to evaluate : 1.781 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 41 outliers final: 27 residues processed: 380 average time/residue: 0.3131 time to fit residues: 168.4657 Evaluate side-chains 366 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 339 time to evaluate : 1.765 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 0 residues processed: 27 average time/residue: 0.1544 time to fit residues: 9.8445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 118 optimal weight: 0.8980 chunk 76 optimal weight: 3.9990 chunk 113 optimal weight: 6.9990 chunk 57 optimal weight: 30.0000 chunk 37 optimal weight: 9.9990 chunk 36 optimal weight: 0.0060 chunk 121 optimal weight: 4.9990 chunk 130 optimal weight: 20.0000 chunk 94 optimal weight: 6.9990 chunk 17 optimal weight: 0.9990 chunk 150 optimal weight: 3.9990 overall best weight: 1.9802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: o 213 GLN ** o 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 566 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7238 moved from start: 0.2589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 15405 Z= 0.253 Angle : 0.750 16.430 20934 Z= 0.383 Chirality : 0.050 0.218 2352 Planarity : 0.004 0.048 2745 Dihedral : 5.892 33.266 2139 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 22.54 Ramachandran Plot: Outliers : 0.30 % Allowed : 9.23 % Favored : 90.47 % Rotamer: Outliers : 1.29 % Allowed : 33.82 % Favored : 64.89 % 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: -2.42 (0.18), residues: 1983 helix: -1.52 (0.54), residues: 82 sheet: -1.38 (0.24), residues: 440 loop : -1.81 (0.16), residues: 1461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP o 203 HIS 0.009 0.001 HIS o 469 PHE 0.022 0.002 PHE p 195 TYR 0.025 0.002 TYR q 465 ARG 0.009 0.001 ARG o 346 *********************** 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 373 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 352 time to evaluate : 1.685 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 14 residues processed: 360 average time/residue: 0.3297 time to fit residues: 167.6370 Evaluate side-chains 358 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 344 time to evaluate : 1.659 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.1629 time to fit residues: 6.5903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 173 optimal weight: 0.0870 chunk 182 optimal weight: 10.0000 chunk 166 optimal weight: 0.9980 chunk 177 optimal weight: 10.0000 chunk 107 optimal weight: 20.0000 chunk 77 optimal weight: 3.9990 chunk 139 optimal weight: 0.9990 chunk 54 optimal weight: 9.9990 chunk 160 optimal weight: 6.9990 chunk 168 optimal weight: 2.9990 chunk 116 optimal weight: 0.0020 overall best weight: 1.0170 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: o 135 GLN ** o 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 63 GLN ** p 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 566 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7199 moved from start: 0.2642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 15405 Z= 0.200 Angle : 0.741 15.500 20934 Z= 0.377 Chirality : 0.050 0.204 2352 Planarity : 0.004 0.047 2745 Dihedral : 5.613 34.258 2139 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 20.93 Ramachandran Plot: Outliers : 0.30 % Allowed : 7.87 % Favored : 91.83 % Rotamer: Outliers : 0.67 % Allowed : 34.87 % Favored : 64.46 % 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: -2.32 (0.18), residues: 1983 helix: -1.27 (0.53), residues: 88 sheet: -1.23 (0.25), residues: 401 loop : -1.77 (0.15), residues: 1494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP p 208 HIS 0.005 0.001 HIS o 469 PHE 0.022 0.002 PHE q 153 TYR 0.031 0.002 TYR o 356 ARG 0.007 0.001 ARG p 14 *********************** 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 349 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 338 time to evaluate : 1.694 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 7 residues processed: 343 average time/residue: 0.3269 time to fit residues: 157.7641 Evaluate side-chains 339 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 332 time to evaluate : 1.629 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.2383 time to fit residues: 4.8713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 188 optimal weight: 10.0000 chunk 114 optimal weight: 9.9990 chunk 89 optimal weight: 7.9990 chunk 130 optimal weight: 3.9990 chunk 197 optimal weight: 5.9990 chunk 181 optimal weight: 10.0000 chunk 157 optimal weight: 4.9990 chunk 16 optimal weight: 7.9990 chunk 121 optimal weight: 7.9990 chunk 96 optimal weight: 9.9990 chunk 124 optimal weight: 20.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: o 213 GLN ** o 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 258 ASN o 298 ASN ** o 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 63 GLN p 113 GLN ** p 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 566 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 582 ASN ** q 611 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7348 moved from start: 0.3305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.150 15405 Z= 0.628 Angle : 0.948 15.150 20934 Z= 0.498 Chirality : 0.058 0.248 2352 Planarity : 0.006 0.057 2745 Dihedral : 6.777 31.989 2139 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 31.33 Ramachandran Plot: Outliers : 0.30 % Allowed : 12.86 % Favored : 86.84 % Rotamer: Outliers : 1.16 % Allowed : 34.80 % Favored : 64.03 % 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: -2.97 (0.18), residues: 1983 helix: -2.53 (0.45), residues: 90 sheet: -1.85 (0.21), residues: 541 loop : -2.09 (0.16), residues: 1352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.004 TRP o 203 HIS 0.012 0.002 HIS o 469 PHE 0.028 0.003 PHE p 382 TYR 0.036 0.003 TYR q 233 ARG 0.016 0.002 ARG p 383 ********************** 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 380 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 361 time to evaluate : 1.686 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 12 residues processed: 367 average time/residue: 0.3277 time to fit residues: 172.1451 Evaluate side-chains 369 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 357 time to evaluate : 1.611 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1572 time to fit residues: 5.6945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 167 optimal weight: 0.9990 chunk 48 optimal weight: 3.9990 chunk 144 optimal weight: 0.9990 chunk 23 optimal weight: 3.9990 chunk 43 optimal weight: 0.9990 chunk 157 optimal weight: 0.9980 chunk 65 optimal weight: 9.9990 chunk 161 optimal weight: 3.9990 chunk 19 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 138 optimal weight: 1.9990 overall best weight: 0.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: o 213 GLN ** o 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 53 ASN ** p 566 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4357 r_free = 0.4357 target = 0.176778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.136623 restraints weight = 26519.312| |-----------------------------------------------------------------------------| r_work (start): 0.3823 rms_B_bonded: 3.54 r_work: 0.3678 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7263 moved from start: 0.3132 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= 0.216 Angle : 0.799 15.447 20934 Z= 0.406 Chirality : 0.052 0.275 2352 Planarity : 0.005 0.063 2745 Dihedral : 5.994 33.168 2139 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 23.81 Ramachandran Plot: Outliers : 0.30 % Allowed : 7.92 % Favored : 91.78 % Rotamer: Outliers : 0.61 % Allowed : 36.21 % Favored : 63.17 % 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: -2.50 (0.18), residues: 1983 helix: -1.83 (0.51), residues: 88 sheet: -1.49 (0.24), residues: 438 loop : -1.82 (0.16), residues: 1457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.003 TRP o 203 HIS 0.006 0.001 HIS o 469 PHE 0.028 0.002 PHE p 442 TYR 0.031 0.002 TYR o 356 ARG 0.013 0.001 ARG q 266 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4220.61 seconds wall clock time: 77 minutes 29.75 seconds (4649.75 seconds total)