Starting phenix.real_space_refine (version: 1.19rc7) on Mon Dec 7 02:11:17 2020 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jpq_22419/12_2020/7jpq_22419_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jpq_22419/12_2020/7jpq_22419.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jpq_22419/12_2020/7jpq_22419.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jpq_22419/12_2020/7jpq_22419.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jpq_22419/12_2020/7jpq_22419_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jpq_22419/12_2020/7jpq_22419_updated.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set model interpretation parameters Set stop_for_unknowns flag Set to: True Assert model is a single copy model Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "B PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 377": "OE1" <-> "OE2" Residue "E TYR 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.19rc7-4070/modules/chem_data/mon_lib" Total number of atoms: 13863 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 2436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 2436 Classifications: {'peptide': 297} Link IDs: {'PTRANS': 7, 'TRANS': 289} Chain breaks: 2 Chain: "C" Number of atoms: 4788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 587, 4788 Classifications: {'peptide': 587} Link IDs: {'PTRANS': 24, 'TRANS': 562} Chain breaks: 9 Chain: "D" Number of atoms: 3281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 403, 3281 Classifications: {'peptide': 403} Link IDs: {'PTRANS': 13, 'TRANS': 389} Chain breaks: 2 Chain: "E" Number of atoms: 3294 Number of conformers: 1 Conformer: "" Number of residues, atoms: 404, 3294 Classifications: {'peptide': 404} Link IDs: {'PTRANS': 19, 'TRANS': 384} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 7.52, per 1000 atoms: 0.54 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Number of scatterers: 13863 At special positions: 0 Unit cell: (92.02, 113.42, 162.64, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 65 16.00 P 6 15.00 Mg 2 11.99 O 2540 8.00 N 2339 7.00 C 8911 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 Amimo 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: 5.47 Conformation dependent library (CDL) restraints added in 1.9 seconds 3306 Ramachandran restraints generated. 1653 Oldfield and 0 Emsley and 1653 emsley8k. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3286 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 86 helices and 6 sheets defined 53.6% alpha, 5.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.56 Creating SS restraints... Processing helix chain 'B' and resid 270 through 276 Processing helix chain 'B' and resid 285 through 291 Processing helix chain 'B' and resid 296 through 306 removed outlier: 4.162A pdb=" N HIS B 299 " --> pdb=" O LYS B 296 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU B 303 " --> pdb=" O LYS B 300 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLN B 304 " --> pdb=" O TRP B 301 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LEU B 305 " --> pdb=" O MET B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 320 through 329 Processing helix chain 'B' and resid 348 through 358 Processing helix chain 'B' and resid 369 through 378 Processing helix chain 'B' and resid 403 through 413 Processing helix chain 'B' and resid 429 through 432 Processing helix chain 'B' and resid 435 through 441 Processing helix chain 'B' and resid 474 through 482 Processing helix chain 'B' and resid 486 through 501 removed outlier: 3.816A pdb=" N LEU B 495 " --> pdb=" O ILE B 491 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ASP B 501 " --> pdb=" O LYS B 497 " (cutoff:3.500A) Processing helix chain 'B' and resid 513 through 521 Processing helix chain 'B' and resid 529 through 542 removed outlier: 3.692A pdb=" N GLU B 538 " --> pdb=" O ALA B 534 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N PHE B 539 " --> pdb=" O GLN B 535 " (cutoff:3.500A) Processing helix chain 'B' and resid 563 through 569 Processing helix chain 'C' and resid 26 through 30 Processing helix chain 'C' and resid 40 through 65 removed outlier: 3.555A pdb=" N TYR C 47 " --> pdb=" O ARG C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 87 removed outlier: 3.776A pdb=" N ASN C 72 " --> pdb=" O ASN C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 128 removed outlier: 3.606A pdb=" N GLN C 126 " --> pdb=" O THR C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 144 through 157 removed outlier: 3.529A pdb=" N LEU C 148 " --> pdb=" O MET C 144 " (cutoff:3.500A) Processing helix chain 'C' and resid 181 through 191 Processing helix chain 'C' and resid 227 through 239 removed outlier: 3.812A pdb=" N GLN C 239 " --> pdb=" O ILE C 235 " (cutoff:3.500A) Processing helix chain 'C' and resid 256 through 262 Processing helix chain 'C' and resid 265 through 270 removed outlier: 3.587A pdb=" N SER C 269 " --> pdb=" O HIS C 265 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N LEU C 270 " --> pdb=" O ALA C 266 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 265 through 270' Processing helix chain 'C' and resid 281 through 292 Processing helix chain 'C' and resid 304 through 316 Processing helix chain 'C' and resid 321 through 337 Processing helix chain 'C' and resid 340 through 344 removed outlier: 3.707A pdb=" N VAL C 343 " --> pdb=" O PRO C 340 " (cutoff:3.500A) Processing helix chain 'C' and resid 348 through 356 removed outlier: 3.619A pdb=" N ARG C 353 " --> pdb=" O PRO C 349 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ASN C 356 " --> pdb=" O LYS C 352 " (cutoff:3.500A) Processing helix chain 'C' and resid 360 through 367 Processing helix chain 'C' and resid 370 through 377 Processing helix chain 'C' and resid 383 through 389 Processing helix chain 'C' and resid 391 through 425 removed outlier: 3.707A pdb=" N CYS C 418 " --> pdb=" O LEU C 414 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N SER C 425 " --> pdb=" O LYS C 421 " (cutoff:3.500A) Processing helix chain 'C' and resid 435 through 443 Processing helix chain 'C' and resid 451 through 461 Processing helix chain 'C' and resid 465 through 481 removed outlier: 4.248A pdb=" N THR C 470 " --> pdb=" O ASP C 466 " (cutoff:3.500A) Processing helix chain 'C' and resid 488 through 497 removed outlier: 3.721A pdb=" N GLU C 495 " --> pdb=" O ALA C 491 " (cutoff:3.500A) Processing helix chain 'C' and resid 548 through 566 removed outlier: 3.796A pdb=" N ASN C 554 " --> pdb=" O VAL C 550 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N VAL C 555 " --> pdb=" O LEU C 551 " (cutoff:3.500A) Processing helix chain 'C' and resid 570 through 572 No H-bonds generated for 'chain 'C' and resid 570 through 572' Processing helix chain 'C' and resid 576 through 578 No H-bonds generated for 'chain 'C' and resid 576 through 578' Processing helix chain 'C' and resid 584 through 591 Processing helix chain 'C' and resid 600 through 603 No H-bonds generated for 'chain 'C' and resid 600 through 603' Processing helix chain 'C' and resid 606 through 608 No H-bonds generated for 'chain 'C' and resid 606 through 608' Processing helix chain 'C' and resid 630 through 638 removed outlier: 3.979A pdb=" N GLU C 638 " --> pdb=" O LYS C 634 " (cutoff:3.500A) Processing helix chain 'C' and resid 645 through 656 removed outlier: 4.048A pdb=" N VAL C 655 " --> pdb=" O ALA C 651 " (cutoff:3.500A) Processing helix chain 'C' and resid 673 through 689 Processing helix chain 'D' and resid 19 through 28 Processing helix chain 'D' and resid 41 through 56 Processing helix chain 'D' and resid 73 through 85 Processing helix chain 'D' and resid 88 through 91 No H-bonds generated for 'chain 'D' and resid 88 through 91' Processing helix chain 'D' and resid 107 through 117 Processing helix chain 'D' and resid 132 through 141 Processing helix chain 'D' and resid 161 through 166 removed outlier: 3.583A pdb=" N ALA D 165 " --> pdb=" O PHE D 161 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N HIS D 166 " --> pdb=" O ASP D 162 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 161 through 166' Processing helix chain 'D' and resid 171 through 180 Processing helix chain 'D' and resid 198 through 200 No H-bonds generated for 'chain 'D' and resid 198 through 200' Processing helix chain 'D' and resid 204 through 209 Processing helix chain 'D' and resid 223 through 233 Processing helix chain 'D' and resid 243 through 257 Processing helix chain 'D' and resid 260 through 270 Processing helix chain 'D' and resid 276 through 289 removed outlier: 4.461A pdb=" N ARG D 289 " --> pdb=" O LEU D 285 " (cutoff:3.500A) Processing helix chain 'D' and resid 299 through 309 Processing helix chain 'D' and resid 313 through 320 Processing helix chain 'D' and resid 323 through 339 removed outlier: 3.713A pdb=" N ILE D 338 " --> pdb=" O HIS D 334 " (cutoff:3.500A) Processing helix chain 'D' and resid 346 through 357 Processing helix chain 'D' and resid 369 through 381 removed outlier: 3.769A pdb=" N HIS D 378 " --> pdb=" O LYS D 374 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU D 379 " --> pdb=" O ALA D 375 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLN D 380 " --> pdb=" O PHE D 376 " (cutoff:3.500A) Processing helix chain 'D' and resid 408 through 416 Processing helix chain 'D' and resid 423 through 430 Processing helix chain 'E' and resid 12 through 22 Processing helix chain 'E' and resid 43 through 54 removed outlier: 3.736A pdb=" N THR E 47 " --> pdb=" O LYS E 43 " (cutoff:3.500A) Processing helix chain 'E' and resid 69 through 83 removed outlier: 4.043A pdb=" N LEU E 83 " --> pdb=" O LYS E 79 " (cutoff:3.500A) Processing helix chain 'E' and resid 99 through 109 Processing helix chain 'E' and resid 127 through 132 Processing helix chain 'E' and resid 135 through 142 Proline residue: E 139 - end of helix Processing helix chain 'E' and resid 144 through 148 Processing helix chain 'E' and resid 162 through 165 No H-bonds generated for 'chain 'E' and resid 162 through 165' Processing helix chain 'E' and resid 184 through 191 Processing helix chain 'E' and resid 201 through 215 removed outlier: 3.777A pdb=" N VAL E 214 " --> pdb=" O ILE E 210 " (cutoff:3.500A) Processing helix chain 'E' and resid 222 through 231 Processing helix chain 'E' and resid 233 through 241 Proline residue: E 239 - end of helix Processing helix chain 'E' and resid 250 through 266 Proline residue: E 259 - end of helix removed outlier: 3.786A pdb=" N GLN E 266 " --> pdb=" O LYS E 262 " (cutoff:3.500A) Processing helix chain 'E' and resid 275 through 284 removed outlier: 4.031A pdb=" N ASP E 284 " --> pdb=" O LYS E 280 " (cutoff:3.500A) Processing helix chain 'E' and resid 304 through 317 Processing helix chain 'E' and resid 321 through 327 removed outlier: 3.753A pdb=" N ASP E 324 " --> pdb=" O ALA E 321 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N LYS E 325 " --> pdb=" O ARG E 322 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N PHE E 327 " --> pdb=" O ASP E 324 " (cutoff:3.500A) Processing helix chain 'E' and resid 359 through 369 Processing helix chain 'E' and resid 378 through 389 removed outlier: 3.605A pdb=" N VAL E 388 " --> pdb=" O ILE E 384 " (cutoff:3.500A) Processing helix chain 'E' and resid 413 through 422 Processing helix chain 'E' and resid 427 through 430 No H-bonds generated for 'chain 'E' and resid 427 through 430' Processing sheet with id= A, first strand: chain 'B' and resid 443 through 447 removed outlier: 6.215A pdb=" N ASN B 310 " --> pdb=" O LEU B 444 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N TYR B 446 " --> pdb=" O ASN B 310 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N VAL B 312 " --> pdb=" O TYR B 446 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ILE B 311 " --> pdb=" O LEU B 420 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N LEU B 388 " --> pdb=" O TYR B 419 " (cutoff:3.500A) removed outlier: 8.428A pdb=" N ILE B 421 " --> pdb=" O LEU B 388 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N LEU B 390 " --> pdb=" O ILE B 421 " (cutoff:3.500A) removed outlier: 8.561A pdb=" N SER B 423 " --> pdb=" O LEU B 390 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N ILE B 392 " --> pdb=" O SER B 423 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'C' and resid 272 through 277 removed outlier: 7.125A pdb=" N LEU C 246 " --> pdb=" O PRO C 101 " (cutoff:3.500A) removed outlier: 8.886A pdb=" N ALA C 103 " --> pdb=" O LEU C 246 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N LEU C 248 " --> pdb=" O ALA C 103 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N LEU C 105 " --> pdb=" O LEU C 248 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N PHE C 250 " --> pdb=" O LEU C 105 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N VAL C 215 " --> pdb=" O ILE C 247 " (cutoff:3.500A) removed outlier: 8.080A pdb=" N ILE C 249 " --> pdb=" O VAL C 215 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N VAL C 217 " --> pdb=" O ILE C 249 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N GLY C 251 " --> pdb=" O VAL C 217 " (cutoff:3.500A) removed outlier: 7.696A pdb=" N LEU C 219 " --> pdb=" O GLY C 251 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'D' and resid 214 through 216 removed outlier: 7.743A pdb=" N ILE D 215 " --> pdb=" O SER D 62 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N LEU D 64 " --> pdb=" O ILE D 215 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N VAL D 154 " --> pdb=" O ALA D 188 " (cutoff:3.500A) removed outlier: 8.170A pdb=" N ILE D 190 " --> pdb=" O VAL D 154 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N PHE D 156 " --> pdb=" O ILE D 190 " (cutoff:3.500A) removed outlier: 8.152A pdb=" N LEU D 192 " --> pdb=" O PHE D 156 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N LEU D 158 " --> pdb=" O LEU D 192 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N LEU D 95 " --> pdb=" O ILE D 155 " (cutoff:3.500A) removed outlier: 7.969A pdb=" N ILE D 157 " --> pdb=" O LEU D 95 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N VAL D 97 " --> pdb=" O ILE D 157 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N ASP D 159 " --> pdb=" O VAL D 97 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N LEU D 99 " --> pdb=" O ASP D 159 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'D' and resid 385 through 387 Processing sheet with id= E, first strand: chain 'E' and resid 175 through 178 removed outlier: 3.501A pdb=" N PHE E 175 " --> pdb=" O SER E 32 " (cutoff:3.500A) removed outlier: 8.370A pdb=" N ILE E 33 " --> pdb=" O VAL E 152 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N VAL E 154 " --> pdb=" O ILE E 33 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N ILE E 35 " --> pdb=" O VAL E 154 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N PHE E 156 " --> pdb=" O ILE E 35 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N VAL E 120 " --> pdb=" O THR E 153 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N LEU E 155 " --> pdb=" O VAL E 120 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N ILE E 122 " --> pdb=" O LEU E 155 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N LEU E 157 " --> pdb=" O ILE E 122 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N LEU E 124 " --> pdb=" O LEU E 157 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'E' and resid 393 through 395 553 hydrogen bonds defined for protein. 1614 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: 4.44 Time building geometry restraints manager: 6.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3333 1.33 - 1.45: 2766 1.45 - 1.57: 7948 1.57 - 1.69: 11 1.69 - 1.81: 97 Bond restraints: 14155 Sorted by residual: bond pdb=" C4 ATP D 901 " pdb=" C5 ATP D 901 " ideal model delta sigma weight residual 1.388 1.460 -0.072 1.00e-02 1.00e+04 5.17e+01 bond pdb=" C4 ATP E 501 " pdb=" C5 ATP E 501 " ideal model delta sigma weight residual 1.388 1.458 -0.070 1.00e-02 1.00e+04 4.94e+01 bond pdb=" C5 ATP D 901 " pdb=" C6 ATP D 901 " ideal model delta sigma weight residual 1.409 1.473 -0.064 1.00e-02 1.00e+04 4.13e+01 bond pdb=" C5 ATP E 501 " pdb=" C6 ATP E 501 " ideal model delta sigma weight residual 1.409 1.471 -0.062 1.00e-02 1.00e+04 3.82e+01 bond pdb=" C4 ATP E 501 " pdb=" N9 ATP E 501 " ideal model delta sigma weight residual 1.374 1.325 0.049 1.00e-02 1.00e+04 2.44e+01 ... (remaining 14150 not shown) Histogram of bond angle deviations from ideal: 96.80 - 104.61: 208 104.61 - 112.42: 7060 112.42 - 120.23: 6257 120.23 - 128.05: 5499 128.05 - 135.86: 135 Bond angle restraints: 19159 Sorted by residual: angle pdb=" PB ATP E 501 " pdb=" O3B ATP E 501 " pdb=" PG ATP E 501 " ideal model delta sigma weight residual 139.87 121.27 18.60 1.00e+00 1.00e+00 3.46e+02 angle pdb=" PA ATP E 501 " pdb=" O3A ATP E 501 " pdb=" PB ATP E 501 " ideal model delta sigma weight residual 136.83 119.61 17.22 1.00e+00 1.00e+00 2.97e+02 angle pdb=" PB ATP D 901 " pdb=" O3B ATP D 901 " pdb=" PG ATP D 901 " ideal model delta sigma weight residual 139.87 123.07 16.80 1.00e+00 1.00e+00 2.82e+02 angle pdb=" PA ATP D 901 " pdb=" O3A ATP D 901 " pdb=" PB ATP D 901 " ideal model delta sigma weight residual 136.83 122.14 14.69 1.00e+00 1.00e+00 2.16e+02 angle pdb=" C5 ATP E 501 " pdb=" C4 ATP E 501 " pdb=" N3 ATP E 501 " ideal model delta sigma weight residual 126.80 119.11 7.69 1.00e+00 1.00e+00 5.92e+01 ... (remaining 19154 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.45: 7737 18.45 - 36.90: 663 36.90 - 55.35: 94 55.35 - 73.80: 24 73.80 - 92.24: 12 Dihedral angle restraints: 8530 sinusoidal: 3512 harmonic: 5018 Sorted by residual: dihedral pdb=" CA HIS D 34 " pdb=" C HIS D 34 " pdb=" N SER D 35 " pdb=" CA SER D 35 " ideal model delta harmonic sigma weight residual 180.00 -150.99 -29.01 0 5.00e+00 4.00e-02 3.37e+01 dihedral pdb=" CA ASN B 378 " pdb=" C ASN B 378 " pdb=" N LYS B 379 " pdb=" CA LYS B 379 " ideal model delta harmonic sigma weight residual 180.00 151.44 28.56 0 5.00e+00 4.00e-02 3.26e+01 dihedral pdb=" CA ARG D 397 " pdb=" C ARG D 397 " pdb=" N GLU D 398 " pdb=" CA GLU D 398 " ideal model delta harmonic sigma weight residual 180.00 154.84 25.16 0 5.00e+00 4.00e-02 2.53e+01 ... (remaining 8527 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 1787 0.078 - 0.156: 339 0.156 - 0.234: 54 0.234 - 0.312: 7 0.312 - 0.389: 1 Chirality restraints: 2188 Sorted by residual: chirality pdb=" CB ILE B 421 " pdb=" CA ILE B 421 " pdb=" CG1 ILE B 421 " pdb=" CG2 ILE B 421 " both_signs ideal model delta sigma weight residual False 2.64 2.26 0.39 2.00e-01 2.50e+01 3.79e+00 chirality pdb=" CB THR B 449 " pdb=" CA THR B 449 " pdb=" OG1 THR B 449 " pdb=" CG2 THR B 449 " both_signs ideal model delta sigma weight residual False 2.55 2.27 0.28 2.00e-01 2.50e+01 1.97e+00 chirality pdb=" CB ILE C 447 " pdb=" CA ILE C 447 " pdb=" CG1 ILE C 447 " pdb=" CG2 ILE C 447 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.26 2.00e-01 2.50e+01 1.75e+00 ... (remaining 2185 not shown) Planarity restraints: 2410 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR D 418 " -0.074 5.00e-02 4.00e+02 1.13e-01 2.03e+01 pdb=" N PRO D 419 " 0.195 5.00e-02 4.00e+02 pdb=" CA PRO D 419 " -0.060 5.00e-02 4.00e+02 pdb=" CD PRO D 419 " -0.061 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 443 " 0.019 2.00e-02 2.50e+03 2.48e-02 1.54e+01 pdb=" CG TRP B 443 " -0.061 2.00e-02 2.50e+03 pdb=" CD1 TRP B 443 " 0.042 2.00e-02 2.50e+03 pdb=" CD2 TRP B 443 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP B 443 " -0.013 2.00e-02 2.50e+03 pdb=" CE2 TRP B 443 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 443 " 0.008 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 443 " 0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 443 " 0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP B 443 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 240 " -0.010 2.00e-02 2.50e+03 2.40e-02 1.01e+01 pdb=" CG PHE D 240 " 0.050 2.00e-02 2.50e+03 pdb=" CD1 PHE D 240 " -0.021 2.00e-02 2.50e+03 pdb=" CD2 PHE D 240 " -0.029 2.00e-02 2.50e+03 pdb=" CE1 PHE D 240 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE D 240 " 0.010 2.00e-02 2.50e+03 pdb=" CZ PHE D 240 " -0.001 2.00e-02 2.50e+03 ... (remaining 2407 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 98 2.65 - 3.21: 12267 3.21 - 3.78: 20463 3.78 - 4.34: 27696 4.34 - 4.90: 45536 Nonbonded interactions: 106060 Sorted by model distance: nonbonded pdb=" OG1 THR D 74 " pdb="MG MG D 902 " model vdw 2.088 2.230 nonbonded pdb=" O3B ATP D 901 " pdb="MG MG D 902 " model vdw 2.097 2.230 nonbonded pdb=" OD1 ASN C 644 " pdb=" N THR C 700 " model vdw 2.319 2.520 nonbonded pdb=" O PHE B 380 " pdb=" ND2 ASN B 417 " model vdw 2.355 2.520 nonbonded pdb=" O THR B 448 " pdb=" OG1 THR B 448 " model vdw 2.356 2.440 ... (remaining 106055 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Set up NCS constraints 0 13863 True True No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 65 5.16 5 C 8911 2.51 5 N 2339 2.21 5 O 2540 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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 Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.690 Set model interpretation parameters: 0.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 8.740 Check model and map are aligned: 0.000 Convert atoms to be neutral: 0.060 Process input model: 40.390 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Set scattering table: 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:2.240 Internal consistency checks: 0.000 Total: 53.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.008 0.077 14155 Angle : 1.138 18.604 19159 Chirality : 0.063 0.389 2188 Planarity : 0.007 0.113 2410 Dihedral : 14.269 92.245 5244 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 2.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.05 (0.18), residues: 1653 helix: -1.00 (0.15), residues: 928 sheet: -1.07 (0.41), residues: 146 loop : -1.80 (0.22), residues: 579 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield and 0 Emsley and 1653 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield and 0 Emsley and 1653 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1566 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 221 time to evaluate : 1.639 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 221 average time/residue: 0.2890 time to fit residues: 66.6346 Evaluate side-chains 124 residues out of total 1566 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 124 time to evaluate : 1.765 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 141 optimal weight: 2.9990 chunk 126 optimal weight: 0.9980 chunk 70 optimal weight: 0.9990 chunk 43 optimal weight: 0.7980 chunk 85 optimal weight: 0.9990 chunk 67 optimal weight: 4.9990 chunk 130 optimal weight: 0.5980 chunk 50 optimal weight: 0.7980 chunk 79 optimal weight: 0.7980 chunk 97 optimal weight: 3.9990 chunk 151 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 393 HIS ** C 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 260 HIS C 500 GLN C 576 HIS C 677 HIS D 19 GLN D 36 ASN D 250 ASN D 420 ASN E 232 ASN E 256 ASN E 260 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.1647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.002 0.047 14155 Angle : 0.491 5.091 19159 Chirality : 0.039 0.137 2188 Planarity : 0.004 0.100 2410 Dihedral : 5.150 68.870 1813 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer Outliers : 0.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.19), residues: 1653 helix: 0.26 (0.16), residues: 946 sheet: -0.74 (0.42), residues: 136 loop : -1.68 (0.22), residues: 571 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield and 0 Emsley and 1653 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield and 0 Emsley and 1653 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1566 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 1 poor density : 168 time to evaluate : 1.974 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 169 average time/residue: 0.2701 time to fit residues: 48.5679 Evaluate side-chains 119 residues out of total 1566 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 119 time to evaluate : 1.744 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.3619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 84 optimal weight: 3.9990 chunk 47 optimal weight: 4.9990 chunk 126 optimal weight: 6.9990 chunk 103 optimal weight: 0.9980 chunk 41 optimal weight: 0.7980 chunk 151 optimal weight: 1.9990 chunk 164 optimal weight: 0.0870 chunk 135 optimal weight: 8.9990 chunk 150 optimal weight: 0.6980 chunk 51 optimal weight: 0.6980 chunk 121 optimal weight: 0.8980 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 269 GLN ** C 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 260 HIS D 36 ASN D 358 GLN D 420 ASN E 256 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.2073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.002 0.057 14155 Angle : 0.450 5.079 19159 Chirality : 0.038 0.134 2188 Planarity : 0.004 0.097 2410 Dihedral : 4.657 62.663 1813 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer Outliers : 0.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.20), residues: 1653 helix: 0.82 (0.17), residues: 953 sheet: -0.35 (0.43), residues: 130 loop : -1.57 (0.23), residues: 570 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield and 0 Emsley and 1653 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield and 0 Emsley and 1653 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1566 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 1 poor density : 168 time to evaluate : 1.783 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 169 average time/residue: 0.2784 time to fit residues: 49.9749 Evaluate side-chains 123 residues out of total 1566 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 123 time to evaluate : 1.700 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.2297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 150 optimal weight: 2.9990 chunk 114 optimal weight: 1.9990 chunk 78 optimal weight: 0.0030 chunk 16 optimal weight: 0.6980 chunk 72 optimal weight: 4.9990 chunk 102 optimal weight: 3.9990 chunk 152 optimal weight: 3.9990 chunk 161 optimal weight: 0.2980 chunk 79 optimal weight: 0.8980 chunk 144 optimal weight: 0.7980 chunk 43 optimal weight: 4.9990 overall best weight: 0.5390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 52 GLN ** C 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 406 HIS ** C 486 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 254 GLN D 420 ASN E 256 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.2400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.002 0.070 14155 Angle : 0.428 5.636 19159 Chirality : 0.037 0.131 2188 Planarity : 0.003 0.095 2410 Dihedral : 4.418 59.149 1813 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.21), residues: 1653 helix: 1.14 (0.17), residues: 964 sheet: 0.04 (0.45), residues: 123 loop : -1.45 (0.24), residues: 566 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield and 0 Emsley and 1653 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield and 0 Emsley and 1653 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1566 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 166 time to evaluate : 1.746 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 166 average time/residue: 0.2741 time to fit residues: 48.2526 Evaluate side-chains 124 residues out of total 1566 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 124 time to evaluate : 1.803 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.4444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 134 optimal weight: 3.9990 chunk 91 optimal weight: 0.9980 chunk 2 optimal weight: 0.0870 chunk 120 optimal weight: 0.4980 chunk 66 optimal weight: 0.8980 chunk 137 optimal weight: 0.6980 chunk 111 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 82 optimal weight: 0.0870 chunk 144 optimal weight: 0.9980 chunk 40 optimal weight: 3.9990 overall best weight: 0.4536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 486 HIS D 96 GLN D 175 ASN E 256 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.2637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.002 0.079 14155 Angle : 0.416 5.471 19159 Chirality : 0.037 0.143 2188 Planarity : 0.003 0.105 2410 Dihedral : 4.241 54.746 1813 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.21), residues: 1653 helix: 1.35 (0.17), residues: 962 sheet: 0.20 (0.45), residues: 123 loop : -1.33 (0.24), residues: 568 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield and 0 Emsley and 1653 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield and 0 Emsley and 1653 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1566 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 170 time to evaluate : 1.759 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 170 average time/residue: 0.2752 time to fit residues: 49.6004 Evaluate side-chains 127 residues out of total 1566 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 127 time to evaluate : 1.721 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.2089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 54 optimal weight: 2.9990 chunk 145 optimal weight: 5.9990 chunk 31 optimal weight: 0.7980 chunk 94 optimal weight: 4.9990 chunk 39 optimal weight: 3.9990 chunk 161 optimal weight: 1.9990 chunk 134 optimal weight: 2.9990 chunk 74 optimal weight: 8.9990 chunk 13 optimal weight: 0.0870 chunk 53 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 overall best weight: 1.7764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 269 GLN ** B 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 260 HIS C 702 HIS D 34 HIS D 175 ASN E 256 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.2587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.004 0.093 14155 Angle : 0.512 5.505 19159 Chirality : 0.041 0.141 2188 Planarity : 0.004 0.114 2410 Dihedral : 4.716 59.054 1813 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.21), residues: 1653 helix: 1.11 (0.17), residues: 958 sheet: 0.31 (0.45), residues: 123 loop : -1.37 (0.24), residues: 572 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield and 0 Emsley and 1653 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield and 0 Emsley and 1653 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1566 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 146 time to evaluate : 1.674 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 146 average time/residue: 0.2553 time to fit residues: 40.0829 Evaluate side-chains 112 residues out of total 1566 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 112 time to evaluate : 1.692 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.3107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 155 optimal weight: 5.9990 chunk 18 optimal weight: 4.9990 chunk 92 optimal weight: 2.9990 chunk 117 optimal weight: 0.7980 chunk 91 optimal weight: 0.9980 chunk 136 optimal weight: 0.9990 chunk 90 optimal weight: 0.7980 chunk 160 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 98 optimal weight: 0.0980 chunk 74 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 269 GLN ** C 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 260 HIS D 34 HIS D 212 HIS D 358 GLN E 256 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.2734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.002 0.107 14155 Angle : 0.437 7.105 19159 Chirality : 0.037 0.131 2188 Planarity : 0.004 0.117 2410 Dihedral : 4.420 55.053 1813 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.21), residues: 1653 helix: 1.28 (0.18), residues: 960 sheet: 0.50 (0.46), residues: 123 loop : -1.31 (0.24), residues: 570 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield and 0 Emsley and 1653 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield and 0 Emsley and 1653 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1566 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 142 time to evaluate : 1.708 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 142 average time/residue: 0.2454 time to fit residues: 37.5782 Evaluate side-chains 111 residues out of total 1566 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 111 time to evaluate : 1.668 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.2486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 99 optimal weight: 0.6980 chunk 64 optimal weight: 5.9990 chunk 96 optimal weight: 0.5980 chunk 48 optimal weight: 3.9990 chunk 31 optimal weight: 4.9990 chunk 102 optimal weight: 0.0980 chunk 109 optimal weight: 6.9990 chunk 79 optimal weight: 4.9990 chunk 15 optimal weight: 4.9990 chunk 126 optimal weight: 0.9990 chunk 146 optimal weight: 0.8980 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 269 GLN B 417 ASN ** C 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 260 HIS E 256 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.2880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.002 0.127 14155 Angle : 0.432 7.946 19159 Chirality : 0.037 0.176 2188 Planarity : 0.004 0.125 2410 Dihedral : 4.229 46.149 1813 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.21), residues: 1653 helix: 1.39 (0.18), residues: 962 sheet: 0.63 (0.47), residues: 123 loop : -1.27 (0.25), residues: 568 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield and 0 Emsley and 1653 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield and 0 Emsley and 1653 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1566 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 145 time to evaluate : 1.791 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 145 average time/residue: 0.2469 time to fit residues: 38.4729 Evaluate side-chains 115 residues out of total 1566 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 115 time to evaluate : 1.892 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 154 optimal weight: 1.9990 chunk 140 optimal weight: 3.9990 chunk 149 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 117 optimal weight: 0.8980 chunk 46 optimal weight: 1.9990 chunk 135 optimal weight: 1.9990 chunk 141 optimal weight: 3.9990 chunk 98 optimal weight: 1.9990 chunk 158 optimal weight: 6.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 417 ASN ** C 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 260 HIS D 34 HIS D 175 ASN D 420 ASN E 256 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.2831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.004 0.144 14155 Angle : 0.523 10.658 19159 Chirality : 0.041 0.175 2188 Planarity : 0.004 0.135 2410 Dihedral : 4.590 46.555 1813 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.21), residues: 1653 helix: 1.13 (0.17), residues: 955 sheet: 0.57 (0.47), residues: 123 loop : -1.39 (0.25), residues: 575 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield and 0 Emsley and 1653 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield and 0 Emsley and 1653 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1566 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 132 time to evaluate : 1.825 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 132 average time/residue: 0.2366 time to fit residues: 34.1515 Evaluate side-chains 107 residues out of total 1566 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 107 time to evaluate : 1.754 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.3386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 96 optimal weight: 0.7980 chunk 75 optimal weight: 0.0570 chunk 110 optimal weight: 0.9990 chunk 166 optimal weight: 0.3980 chunk 153 optimal weight: 3.9990 chunk 132 optimal weight: 0.5980 chunk 13 optimal weight: 5.9990 chunk 102 optimal weight: 0.7980 chunk 81 optimal weight: 0.7980 chunk 105 optimal weight: 0.9980 chunk 141 optimal weight: 3.9990 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 417 ASN ** C 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 175 ASN D 358 GLN D 420 ASN E 256 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.3012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.003 0.165 14155 Angle : 0.451 14.441 19159 Chirality : 0.037 0.162 2188 Planarity : 0.005 0.147 2410 Dihedral : 4.233 47.421 1813 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.21), residues: 1653 helix: 1.37 (0.18), residues: 959 sheet: 0.72 (0.48), residues: 123 loop : -1.38 (0.25), residues: 571 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield and 0 Emsley and 1653 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield and 0 Emsley and 1653 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1566 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 142 time to evaluate : 1.695 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 142 average time/residue: 0.2464 time to fit residues: 37.7723 Evaluate side-chains 113 residues out of total 1566 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 113 time to evaluate : 1.816 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.3006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 40 optimal weight: 3.9990 chunk 122 optimal weight: 0.6980 chunk 19 optimal weight: 6.9990 chunk 36 optimal weight: 3.9990 chunk 132 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 chunk 136 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 24 optimal weight: 0.0040 chunk 116 optimal weight: 1.9990 chunk 7 optimal weight: 0.0170 overall best weight: 0.7032 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 417 ASN ** C 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 420 ASN E 256 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Group ADP refinement ******************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.149322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.126873 restraints weight = 20860.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.127260 restraints weight = 17392.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.127852 restraints weight = 14434.525| |-----------------------------------------------------------------------------| GEOMETRY RESTRAINTS LIBRARY: GEOSTD + MONOMER LIBRARY + CDL V1.2 DEVIATIONS FROM IDEAL VALUES. BOND : 0.003 0.170 14155 ANGLE : 0.455 15.094 19159 CHIRALITY : 0.037 0.159 2188 PLANARITY : 0.004 0.146 2410 DIHEDRAL : 4.169 46.948 1813 MIN NONBONDED DISTANCE : 2.045 MOLPROBITY STATISTICS. ALL-ATOM CLASHSCORE : 4.07 RAMACHANDRAN PLOT: OUTLIERS : 0.00 % ALLOWED : 2.90 % FAVORED : 97.10 % ROTAMER OUTLIERS : 0.00 % CBETA DEVIATIONS : 0.00 % PEPTIDE PLANE: CIS-PROLINE : 0.00 % CIS-GENERAL : 0.00 % TWISTED PROLINE : 0.00 % TWISTED GENERAL : 0.00 % RAMA-Z (RAMACHANDRAN PLOT Z-SCORE): INTERPRETATION: BAD |RAMA-Z| > 3; SUSPICIOUS 2 < |RAMA-Z| < 3; GOOD |RAMA-Z| < 2. SCORES FOR WHOLE/HELIX/SHEET/LOOP ARE SCALED INDEPENDENTLY; THEREFORE, THE VALUES ARE NOT RELATED IN A SIMPLE MANNER. WHOLE: 0.66 (0.21), RESIDUES: 1653 HELIX: 1.44 (0.18), RESIDUES: 958 SHEET: 0.72 (0.48), RESIDUES: 123 LOOP : -1.37 (0.25), RESIDUES: 572 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.3053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.003 0.170 14155 Angle : 0.455 15.094 19159 Chirality : 0.037 0.159 2188 Planarity : 0.004 0.146 2410 Dihedral : 4.169 46.948 1813 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.21), residues: 1653 helix: 1.44 (0.18), residues: 958 sheet: 0.72 (0.48), residues: 123 loop : -1.37 (0.25), residues: 572 =============================================================================== Job complete usr+sys time: 2323.44 seconds wall clock time: 43 minutes 23.55 seconds (2603.55 seconds total)