Starting phenix.real_space_refine (version: 1.19rc7) on Wed Jan 6 01:37:29 2021 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jpo_22417/01_2021/7jpo_22417_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jpo_22417/01_2021/7jpo_22417.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jpo_22417/01_2021/7jpo_22417.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jpo_22417/01_2021/7jpo_22417.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jpo_22417/01_2021/7jpo_22417_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jpo_22417/01_2021/7jpo_22417_neut_updated.pdb" } resolution = 3.2 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= 0.001 sd= 0.003 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 "C PHE 276": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 581": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.19rc7-4070/modules/chem_data/mon_lib" Total number of atoms: 16087 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 2795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2795 Classifications: {'peptide': 352} Link IDs: {'PTRANS': 12, 'TRANS': 339} Chain breaks: 3 Chain: "B" Number of atoms: 1726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1726 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 4, 'TRANS': 204} Chain breaks: 1 Chain: "C" Number of atoms: 4863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 594, 4863 Classifications: {'peptide': 594} Link IDs: {'PTRANS': 24, 'TRANS': 569} Chain breaks: 7 Chain: "D" Number of atoms: 3305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 406, 3305 Classifications: {'peptide': 406} Link IDs: {'PTRANS': 13, 'TRANS': 392} Chain breaks: 1 Chain: "E" Number of atoms: 3301 Number of conformers: 1 Conformer: "" Number of residues, atoms: 405, 3301 Classifications: {'peptide': 405} Link IDs: {'PTRANS': 19, 'TRANS': 385} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 4 Chain: "A" 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: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} 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: 8.75, per 1000 atoms: 0.54 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Number of scatterers: 16087 At special positions: 0 Unit cell: (90.95, 133.75, 160.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) K 1 19.00 S 82 16.00 P 9 15.00 Mg 3 11.99 O 2962 8.00 N 2724 7.00 C 10306 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: 6.55 Conformation dependent library (CDL) restraints added in 2.6 seconds 3856 Ramachandran restraints generated. 1928 Oldfield and 0 Emsley and 1928 emsley8k. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3822 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 98 helices and 8 sheets defined 53.8% alpha, 6.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.80 Creating SS restraints... Processing helix chain 'A' and resid 488 through 495 Processing helix chain 'A' and resid 508 through 522 removed outlier: 3.860A pdb=" N LYS A 521 " --> pdb=" O PHE A 517 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 556 Processing helix chain 'A' and resid 576 through 587 removed outlier: 3.664A pdb=" N VAL A 579 " --> pdb=" O PRO A 576 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N VAL A 581 " --> pdb=" O GLN A 578 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ILE A 583 " --> pdb=" O TYR A 580 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N LEU A 584 " --> pdb=" O VAL A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 594 through 604 Processing helix chain 'A' and resid 622 through 625 Processing helix chain 'A' and resid 631 through 638 Processing helix chain 'A' and resid 658 through 660 No H-bonds generated for 'chain 'A' and resid 658 through 660' Processing helix chain 'A' and resid 683 through 693 Processing helix chain 'A' and resid 702 through 715 Processing helix chain 'A' and resid 719 through 735 Processing helix chain 'A' and resid 748 through 759 removed outlier: 3.565A pdb=" N ASP A 756 " --> pdb=" O MET A 752 " (cutoff:3.500A) Processing helix chain 'A' and resid 763 through 768 Processing helix chain 'A' and resid 772 through 788 Processing helix chain 'A' and resid 795 through 809 removed outlier: 3.952A pdb=" N ALA A 804 " --> pdb=" O SER A 800 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 828 removed outlier: 3.934A pdb=" N ALA A 821 " --> pdb=" O SER A 817 " (cutoff:3.500A) Processing helix chain 'A' and resid 851 through 858 Processing helix chain 'B' and resid 240 through 247 Processing helix chain 'B' and resid 271 through 275 removed outlier: 4.023A pdb=" N LEU B 275 " --> pdb=" O THR B 271 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 271 through 275' Processing helix chain 'B' and resid 284 through 288 Processing helix chain 'B' and resid 296 through 306 removed outlier: 4.010A pdb=" N HIS B 299 " --> pdb=" O LYS B 296 " (cutoff:3.500A) removed outlier: 3.881A 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 382 Processing helix chain 'B' and resid 403 through 413 Processing helix chain 'B' and resid 429 through 432 Processing helix chain 'C' and resid 39 through 65 Processing helix chain 'C' and resid 67 through 86 removed outlier: 4.237A pdb=" N GLY C 83 " --> pdb=" O LYS C 79 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N PHE C 84 " --> pdb=" O SER C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 128 removed outlier: 4.479A pdb=" N ASP C 115 " --> pdb=" O VAL C 111 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N LEU C 116 " --> pdb=" O THR C 112 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ALA C 124 " --> pdb=" O SER C 120 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU C 125 " --> pdb=" O LEU C 121 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 140 No H-bonds generated for 'chain 'C' and resid 138 through 140' Processing helix chain 'C' and resid 144 through 157 removed outlier: 3.579A pdb=" N SER C 153 " --> pdb=" O GLN C 149 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLN C 154 " --> pdb=" O LYS C 150 " (cutoff:3.500A) Processing helix chain 'C' and resid 181 through 192 Processing helix chain 'C' and resid 227 through 239 removed outlier: 3.860A pdb=" N GLN C 239 " --> pdb=" O ILE C 235 " (cutoff:3.500A) Processing helix chain 'C' and resid 256 through 262 removed outlier: 3.640A pdb=" N LEU C 262 " --> pdb=" O ILE C 259 " (cutoff:3.500A) Processing helix chain 'C' and resid 265 through 270 removed outlier: 5.115A pdb=" N LEU C 270 " --> pdb=" O ALA C 266 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 292 Processing helix chain 'C' and resid 304 through 315 Processing helix chain 'C' and resid 321 through 338 Processing helix chain 'C' and resid 342 through 344 No H-bonds generated for 'chain 'C' and resid 342 through 344' Processing helix chain 'C' and resid 348 through 356 Processing helix chain 'C' and resid 360 through 367 removed outlier: 3.671A pdb=" N GLU C 364 " --> pdb=" O ASN C 360 " (cutoff:3.500A) Processing helix chain 'C' and resid 370 through 377 Processing helix chain 'C' and resid 381 through 389 removed outlier: 3.887A pdb=" N VAL C 385 " --> pdb=" O SER C 381 " (cutoff:3.500A) Processing helix chain 'C' and resid 391 through 425 removed outlier: 3.704A pdb=" N GLU C 403 " --> pdb=" O GLN C 399 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LYS C 421 " --> pdb=" O ARG C 417 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N PHE C 422 " --> pdb=" O CYS C 418 " (cutoff:3.500A) Processing helix chain 'C' and resid 435 through 443 Processing helix chain 'C' and resid 452 through 460 removed outlier: 3.518A pdb=" N VAL C 456 " --> pdb=" O GLU C 452 " (cutoff:3.500A) Processing helix chain 'C' and resid 465 through 481 Processing helix chain 'C' and resid 488 through 500 removed outlier: 3.814A pdb=" N LYS C 492 " --> pdb=" O GLY C 488 " (cutoff:3.500A) Processing helix chain 'C' and resid 548 through 565 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 595 through 604 Processing helix chain 'C' and resid 628 through 636 removed outlier: 3.711A pdb=" N LYS C 634 " --> pdb=" O CYS C 630 " (cutoff:3.500A) Processing helix chain 'C' and resid 645 through 659 Processing helix chain 'C' and resid 676 through 689 removed outlier: 3.854A pdb=" N LEU C 687 " --> pdb=" O ALA C 683 " (cutoff:3.500A) Processing helix chain 'D' and resid 18 through 28 Processing helix chain 'D' and resid 41 through 56 Processing helix chain 'D' and resid 73 through 86 Processing helix chain 'D' and resid 88 through 92 Processing helix chain 'D' and resid 107 through 117 Processing helix chain 'D' and resid 121 through 124 No H-bonds generated for 'chain 'D' and resid 121 through 124' Processing helix chain 'D' and resid 132 through 140 Processing helix chain 'D' and resid 161 through 164 No H-bonds generated for 'chain 'D' and resid 161 through 164' Processing helix chain 'D' and resid 171 through 182 removed outlier: 3.717A pdb=" N ILE D 179 " --> pdb=" O ASN D 175 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 201 No H-bonds generated for 'chain 'D' and resid 198 through 201' 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 258 removed outlier: 3.809A pdb=" N GLU D 258 " --> pdb=" O GLN D 254 " (cutoff:3.500A) Processing helix chain 'D' and resid 260 through 272 removed outlier: 3.784A pdb=" N VAL D 265 " --> pdb=" O SER D 261 " (cutoff:3.500A) Processing helix chain 'D' and resid 276 through 289 removed outlier: 4.322A 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 removed outlier: 3.684A pdb=" N GLY D 320 " --> pdb=" O ASN D 316 " (cutoff:3.500A) Processing helix chain 'D' and resid 323 through 338 Processing helix chain 'D' and resid 346 through 359 removed outlier: 3.831A pdb=" N ARG D 359 " --> pdb=" O LYS D 355 " (cutoff:3.500A) Processing helix chain 'D' and resid 369 through 381 Processing helix chain 'D' and resid 408 through 416 Processing helix chain 'D' and resid 423 through 430 Processing helix chain 'E' and resid 13 through 22 Processing helix chain 'E' and resid 43 through 53 removed outlier: 3.575A pdb=" N THR E 47 " --> pdb=" O LYS E 43 " (cutoff:3.500A) Processing helix chain 'E' and resid 69 through 84 Processing helix chain 'E' and resid 99 through 110 Processing helix chain 'E' and resid 127 through 129 No H-bonds generated for 'chain 'E' and resid 127 through 129' 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 164 No H-bonds generated for 'chain 'E' and resid 162 through 164' Processing helix chain 'E' and resid 184 through 191 Processing helix chain 'E' and resid 201 through 215 Processing helix chain 'E' and resid 222 through 236 removed outlier: 3.594A pdb=" N PHE E 233 " --> pdb=" O ALA E 229 " (cutoff:3.500A) Proline residue: E 234 - end of helix Processing helix chain 'E' and resid 238 through 242 Processing helix chain 'E' and resid 250 through 267 Proline residue: E 259 - end of helix removed outlier: 3.500A pdb=" N MET E 265 " --> pdb=" O LEU E 261 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N GLN E 266 " --> pdb=" O LYS E 262 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N THR E 267 " --> pdb=" O LYS E 263 " (cutoff:3.500A) Processing helix chain 'E' and resid 275 through 283 Processing helix chain 'E' and resid 304 through 317 Processing helix chain 'E' and resid 321 through 327 removed outlier: 4.517A pdb=" N LYS E 325 " --> pdb=" O ARG E 322 " (cutoff:3.500A) Processing helix chain 'E' and resid 359 through 369 Processing helix chain 'E' and resid 378 through 389 removed outlier: 3.791A pdb=" N VAL E 388 " --> pdb=" O ILE E 384 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N THR E 389 " --> pdb=" O THR E 385 " (cutoff:3.500A) Processing helix chain 'E' and resid 413 through 422 Processing helix chain 'E' and resid 428 through 431 No H-bonds generated for 'chain 'E' and resid 428 through 431' Processing sheet with id= A, first strand: chain 'A' and resid 674 through 678 Processing sheet with id= B, first strand: chain 'A' and resid 792 through 794 Processing sheet with id= C, first strand: chain 'B' and resid 443 through 447 removed outlier: 6.701A pdb=" N ASN B 310 " --> pdb=" O LEU B 444 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N TYR B 446 " --> pdb=" O ASN B 310 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N VAL B 312 " --> pdb=" O TYR B 446 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE B 311 " --> pdb=" O LEU B 420 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N LEU B 388 " --> pdb=" O TYR B 419 " (cutoff:3.500A) removed outlier: 8.374A pdb=" N ILE B 421 " --> pdb=" O LEU B 388 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N LEU B 390 " --> pdb=" O ILE B 421 " (cutoff:3.500A) removed outlier: 8.186A pdb=" N SER B 423 " --> pdb=" O LEU B 390 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N ILE B 392 " --> pdb=" O SER B 423 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N ILE B 335 " --> pdb=" O PHE B 389 " (cutoff:3.500A) removed outlier: 8.341A pdb=" N LEU B 391 " --> pdb=" O ILE B 335 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N VAL B 337 " --> pdb=" O LEU B 391 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 271 through 277 removed outlier: 6.507A pdb=" N ILE C 100 " --> pdb=" O CYS C 272 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N GLU C 274 " --> pdb=" O ILE C 100 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N THR C 102 " --> pdb=" O GLU C 274 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N PHE C 276 " --> pdb=" O THR C 102 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N ALA C 104 " --> pdb=" O PHE C 276 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N VAL C 215 " --> pdb=" O ILE C 247 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N ILE C 249 " --> pdb=" O VAL C 215 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N VAL C 217 " --> pdb=" O ILE C 249 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N GLY C 251 " --> pdb=" O VAL C 217 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N LEU C 219 " --> pdb=" O GLY C 251 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'D' and resid 214 through 216 removed outlier: 8.030A pdb=" N ILE D 215 " --> pdb=" O SER D 62 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N LEU D 64 " --> pdb=" O ILE D 215 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N VAL D 154 " --> pdb=" O ALA D 188 " (cutoff:3.500A) removed outlier: 8.246A pdb=" N ILE D 190 " --> pdb=" O VAL D 154 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N PHE D 156 " --> pdb=" O ILE D 190 " (cutoff:3.500A) removed outlier: 7.944A pdb=" N LEU D 192 " --> pdb=" O PHE D 156 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N LEU D 158 " --> pdb=" O LEU D 192 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'D' and resid 385 through 387 Processing sheet with id= G, first strand: chain 'E' and resid 175 through 178 removed outlier: 8.159A pdb=" N ILE E 33 " --> pdb=" O VAL E 152 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N VAL E 154 " --> pdb=" O ILE E 33 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N ILE E 35 " --> pdb=" O VAL E 154 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N PHE E 156 " --> pdb=" O ILE E 35 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N VAL E 120 " --> pdb=" O THR E 153 " (cutoff:3.500A) removed outlier: 7.702A pdb=" N LEU E 155 " --> pdb=" O VAL E 120 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ILE E 122 " --> pdb=" O LEU E 155 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N LEU E 157 " --> pdb=" O ILE E 122 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N LEU E 124 " --> pdb=" O LEU E 157 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'E' and resid 393 through 395 680 hydrogen bonds defined for protein. 1974 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: 5.40 Time building geometry restraints manager: 7.22 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: 4137 1.33 - 1.46: 3174 1.46 - 1.58: 8968 1.58 - 1.70: 15 1.70 - 1.82: 125 Bond restraints: 16419 Sorted by residual: bond pdb=" C4 ATP E 501 " pdb=" C5 ATP E 501 " ideal model delta sigma weight residual 1.388 1.467 -0.079 1.00e-02 1.00e+04 6.23e+01 bond pdb=" C4 ATP A 901 " pdb=" C5 ATP A 901 " ideal model delta sigma weight residual 1.388 1.465 -0.077 1.00e-02 1.00e+04 5.97e+01 bond pdb=" C4 ATP D 901 " pdb=" C5 ATP D 901 " ideal model delta sigma weight residual 1.388 1.465 -0.077 1.00e-02 1.00e+04 5.89e+01 bond pdb=" C5 ATP A 901 " pdb=" C6 ATP A 901 " ideal model delta sigma weight residual 1.409 1.476 -0.067 1.00e-02 1.00e+04 4.52e+01 bond pdb=" C5 ATP E 501 " pdb=" C6 ATP E 501 " ideal model delta sigma weight residual 1.409 1.476 -0.067 1.00e-02 1.00e+04 4.48e+01 ... (remaining 16414 not shown) Histogram of bond angle deviations from ideal: 98.07 - 105.65: 298 105.65 - 113.23: 8930 113.23 - 120.81: 7969 120.81 - 128.40: 4896 128.40 - 135.98: 137 Bond angle restraints: 22230 Sorted by residual: angle pdb=" PB ATP D 901 " pdb=" O3B ATP D 901 " pdb=" PG ATP D 901 " ideal model delta sigma weight residual 139.87 119.33 20.54 1.00e+00 1.00e+00 4.22e+02 angle pdb=" PB ATP A 901 " pdb=" O3B ATP A 901 " pdb=" PG ATP A 901 " ideal model delta sigma weight residual 139.87 121.72 18.15 1.00e+00 1.00e+00 3.29e+02 angle pdb=" PB ATP E 501 " pdb=" O3B ATP E 501 " pdb=" PG ATP E 501 " ideal model delta sigma weight residual 139.87 123.09 16.78 1.00e+00 1.00e+00 2.81e+02 angle pdb=" PA ATP E 501 " pdb=" O3A ATP E 501 " pdb=" PB ATP E 501 " ideal model delta sigma weight residual 136.83 122.38 14.45 1.00e+00 1.00e+00 2.09e+02 angle pdb=" PA ATP D 901 " pdb=" O3A ATP D 901 " pdb=" PB ATP D 901 " ideal model delta sigma weight residual 136.83 123.11 13.72 1.00e+00 1.00e+00 1.88e+02 ... (remaining 22225 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 8794 17.94 - 35.89: 892 35.89 - 53.83: 159 53.83 - 71.77: 36 71.77 - 89.71: 27 Dihedral angle restraints: 9908 sinusoidal: 4070 harmonic: 5838 Sorted by residual: dihedral pdb=" CA GLN D 31 " pdb=" C GLN D 31 " pdb=" N SER D 32 " pdb=" CA SER D 32 " ideal model delta harmonic sigma weight residual -180.00 -156.71 -23.29 0 5.00e+00 4.00e-02 2.17e+01 dihedral pdb=" CA ARG D 359 " pdb=" C ARG D 359 " pdb=" N LYS D 360 " pdb=" CA LYS D 360 " ideal model delta harmonic sigma weight residual -180.00 -157.35 -22.65 0 5.00e+00 4.00e-02 2.05e+01 dihedral pdb=" CA VAL D 364 " pdb=" C VAL D 364 " pdb=" N TYR D 365 " pdb=" CA TYR D 365 " ideal model delta harmonic sigma weight residual -180.00 -158.28 -21.72 0 5.00e+00 4.00e-02 1.89e+01 ... (remaining 9905 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 2109 0.073 - 0.146: 369 0.146 - 0.219: 47 0.219 - 0.292: 9 0.292 - 0.365: 4 Chirality restraints: 2538 Sorted by residual: 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 2.19 0.36 2.00e-01 2.50e+01 3.32e+00 chirality pdb=" CB ILE C 435 " pdb=" CA ILE C 435 " pdb=" CG1 ILE C 435 " pdb=" CG2 ILE C 435 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.33 2.00e-01 2.50e+01 2.68e+00 chirality pdb=" CB ILE C 643 " pdb=" CA ILE C 643 " pdb=" CG1 ILE C 643 " pdb=" CG2 ILE C 643 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.31 2.00e-01 2.50e+01 2.48e+00 ... (remaining 2535 not shown) Planarity restraints: 2798 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 639 " -0.046 2.00e-02 2.50e+03 4.75e-02 5.65e+01 pdb=" CG TRP A 639 " 0.127 2.00e-02 2.50e+03 pdb=" CD1 TRP A 639 " -0.063 2.00e-02 2.50e+03 pdb=" CD2 TRP A 639 " 0.006 2.00e-02 2.50e+03 pdb=" NE1 TRP A 639 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP A 639 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 639 " -0.017 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 639 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 639 " -0.008 2.00e-02 2.50e+03 pdb=" CH2 TRP A 639 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU E 238 " 0.053 5.00e-02 4.00e+02 7.95e-02 1.01e+01 pdb=" N PRO E 239 " -0.137 5.00e-02 4.00e+02 pdb=" CA PRO E 239 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO E 239 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 448 " 0.015 2.00e-02 2.50e+03 1.82e-02 8.28e+00 pdb=" CG TRP C 448 " -0.045 2.00e-02 2.50e+03 pdb=" CD1 TRP C 448 " 0.031 2.00e-02 2.50e+03 pdb=" CD2 TRP C 448 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP C 448 " -0.009 2.00e-02 2.50e+03 pdb=" CE2 TRP C 448 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP C 448 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 448 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 448 " 0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP C 448 " -0.000 2.00e-02 2.50e+03 ... (remaining 2795 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.96: 6341 2.96 - 3.84: 37235 3.84 - 4.73: 63823 4.73 - 5.61: 102339 5.61 - 6.50: 124223 Nonbonded interactions: 333961 Sorted by model distance: nonbonded pdb=" OG1 THR E 44 " pdb="MG MG E 502 " model vdw 2.073 2.230 nonbonded pdb=" O3G ATP E 501 " pdb="MG MG E 502 " model vdw 2.090 2.230 nonbonded pdb=" O1B ATP A 901 " pdb="MG MG A 902 " model vdw 2.091 2.230 nonbonded pdb=" OG1 THR A 541 " pdb="MG MG A 902 " model vdw 2.123 2.230 nonbonded pdb=" O3B ATP D 901 " pdb="MG MG D 902 " model vdw 2.124 2.230 ... (remaining 333956 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Set up NCS constraints 0 16087 True True No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians K 1 8.98 5 P 9 5.49 5 Mg 3 5.21 5 S 82 5.16 5 C 10306 2.51 5 N 2724 2.21 5 O 2962 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: 11.980 Set model interpretation parameters: 0.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 4.140 Check model and map are aligned: 0.000 Convert atoms to be neutral: 0.070 Process input model: 55.970 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Set scattering table: 0.020 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:2.320 Internal consistency checks: 0.000 Total: 74.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.007 0.081 16419 Angle : 1.085 20.536 22230 Chirality : 0.059 0.365 2538 Planarity : 0.007 0.079 2798 Dihedral : 15.527 89.714 6086 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 2.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % 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: -1.99 (0.16), residues: 1928 helix: -1.10 (0.13), residues: 1105 sheet: -0.33 (0.35), residues: 187 loop : -1.74 (0.21), residues: 636 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3856 Ramachandran restraints generated. 1928 Oldfield and 0 Emsley and 1928 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3856 Ramachandran restraints generated. 1928 Oldfield and 0 Emsley and 1928 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1804 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 249 time to evaluate : 2.146 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 249 average time/residue: 0.3366 time to fit residues: 87.1491 Evaluate side-chains 184 residues out of total 1804 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 184 time to evaluate : 2.091 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.8694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 163 optimal weight: 0.8980 chunk 147 optimal weight: 0.0040 chunk 81 optimal weight: 0.9990 chunk 50 optimal weight: 0.7980 chunk 99 optimal weight: 0.9990 chunk 78 optimal weight: 0.7980 chunk 152 optimal weight: 2.9990 chunk 58 optimal weight: 0.0470 chunk 92 optimal weight: 2.9990 chunk 113 optimal weight: 7.9990 chunk 176 optimal weight: 1.9990 overall best weight: 0.5090 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 496 HIS C 458 GLN C 624 ASN D 46 HIS D 117 GLN D 254 GLN D 362 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.1151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.002 0.050 16419 Angle : 0.481 6.185 22230 Chirality : 0.038 0.170 2538 Planarity : 0.004 0.081 2798 Dihedral : 5.338 70.674 2115 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % 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: -0.56 (0.18), residues: 1928 helix: 0.21 (0.15), residues: 1123 sheet: -0.07 (0.36), residues: 189 loop : -1.37 (0.23), residues: 616 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3856 Ramachandran restraints generated. 1928 Oldfield and 0 Emsley and 1928 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3856 Ramachandran restraints generated. 1928 Oldfield and 0 Emsley and 1928 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1804 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 1 poor density : 235 time to evaluate : 2.155 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 235 average time/residue: 0.3200 time to fit residues: 78.6597 Evaluate side-chains 176 residues out of total 1804 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 176 time to evaluate : 2.107 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.7075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 97 optimal weight: 3.9990 chunk 54 optimal weight: 4.9990 chunk 146 optimal weight: 3.9990 chunk 119 optimal weight: 0.7980 chunk 48 optimal weight: 3.9990 chunk 176 optimal weight: 2.9990 chunk 190 optimal weight: 4.9990 chunk 157 optimal weight: 2.9990 chunk 175 optimal weight: 0.9980 chunk 60 optimal weight: 5.9990 chunk 141 optimal weight: 5.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 496 HIS A 654 ASN B 270 GLN B 462 ASN C 624 ASN ** D 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 6 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.1847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.006 0.043 16419 Angle : 0.640 9.179 22230 Chirality : 0.045 0.195 2538 Planarity : 0.005 0.046 2798 Dihedral : 5.598 67.926 2115 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % 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: -0.57 (0.18), residues: 1928 helix: 0.23 (0.15), residues: 1136 sheet: -0.17 (0.36), residues: 187 loop : -1.46 (0.24), residues: 605 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3856 Ramachandran restraints generated. 1928 Oldfield and 0 Emsley and 1928 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3856 Ramachandran restraints generated. 1928 Oldfield and 0 Emsley and 1928 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1804 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 222 time to evaluate : 2.261 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 222 average time/residue: 0.3796 time to fit residues: 87.7975 Evaluate side-chains 166 residues out of total 1804 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 166 time to evaluate : 2.173 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.8871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 174 optimal weight: 2.9990 chunk 132 optimal weight: 0.8980 chunk 91 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 84 optimal weight: 0.3980 chunk 118 optimal weight: 2.9990 chunk 177 optimal weight: 2.9990 chunk 187 optimal weight: 0.9990 chunk 92 optimal weight: 0.9990 chunk 167 optimal weight: 0.7980 chunk 50 optimal weight: 3.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 525 HIS A 654 ASN C 486 HIS D 46 HIS D 57 HIS D 117 GLN ** E 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.1979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.003 0.053 16419 Angle : 0.487 6.350 22230 Chirality : 0.039 0.152 2538 Planarity : 0.003 0.038 2798 Dihedral : 5.035 64.319 2115 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % 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: 0.03 (0.19), residues: 1928 helix: 0.75 (0.16), residues: 1131 sheet: -0.08 (0.36), residues: 187 loop : -1.22 (0.24), residues: 610 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3856 Ramachandran restraints generated. 1928 Oldfield and 0 Emsley and 1928 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3856 Ramachandran restraints generated. 1928 Oldfield and 0 Emsley and 1928 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1804 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 224 time to evaluate : 2.095 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 224 average time/residue: 0.3509 time to fit residues: 81.9851 Evaluate side-chains 162 residues out of total 1804 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 162 time to evaluate : 2.175 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.7500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 156 optimal weight: 4.9990 chunk 106 optimal weight: 0.4980 chunk 2 optimal weight: 2.9990 chunk 139 optimal weight: 0.9980 chunk 77 optimal weight: 0.8980 chunk 160 optimal weight: 2.9990 chunk 129 optimal weight: 4.9990 chunk 0 optimal weight: 7.9990 chunk 95 optimal weight: 4.9990 chunk 168 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 525 HIS D 96 GLN ** D 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 381 GLN ** E 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.2157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.004 0.037 16419 Angle : 0.541 7.781 22230 Chirality : 0.041 0.155 2538 Planarity : 0.004 0.041 2798 Dihedral : 5.125 59.702 2115 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % 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: 0.04 (0.19), residues: 1928 helix: 0.80 (0.16), residues: 1123 sheet: -0.10 (0.37), residues: 187 loop : -1.27 (0.24), residues: 618 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3856 Ramachandran restraints generated. 1928 Oldfield and 0 Emsley and 1928 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3856 Ramachandran restraints generated. 1928 Oldfield and 0 Emsley and 1928 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1804 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 233 time to evaluate : 2.184 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 233 average time/residue: 0.3318 time to fit residues: 80.6946 Evaluate side-chains 170 residues out of total 1804 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 170 time to evaluate : 2.035 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.7126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 63 optimal weight: 3.9990 chunk 168 optimal weight: 3.9990 chunk 37 optimal weight: 8.9990 chunk 110 optimal weight: 5.9990 chunk 46 optimal weight: 2.9990 chunk 187 optimal weight: 0.8980 chunk 155 optimal weight: 2.9990 chunk 86 optimal weight: 5.9990 chunk 15 optimal weight: 3.9990 chunk 62 optimal weight: 0.7980 chunk 98 optimal weight: 4.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 685 GLN C 35 ASN D 46 HIS D 381 GLN D 394 ASN D 396 GLN ** E 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.2446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.006 0.046 16419 Angle : 0.626 8.668 22230 Chirality : 0.044 0.156 2538 Planarity : 0.004 0.046 2798 Dihedral : 5.424 57.624 2115 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % 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: -0.37 (0.19), residues: 1928 helix: 0.45 (0.15), residues: 1119 sheet: -0.18 (0.37), residues: 187 loop : -1.41 (0.24), residues: 622 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3856 Ramachandran restraints generated. 1928 Oldfield and 0 Emsley and 1928 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3856 Ramachandran restraints generated. 1928 Oldfield and 0 Emsley and 1928 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1804 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 221 time to evaluate : 2.249 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 221 average time/residue: 0.3291 time to fit residues: 76.1402 Evaluate side-chains 159 residues out of total 1804 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 159 time to evaluate : 2.038 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.7665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 180 optimal weight: 3.9990 chunk 21 optimal weight: 7.9990 chunk 106 optimal weight: 0.9990 chunk 137 optimal weight: 0.8980 chunk 158 optimal weight: 2.9990 chunk 104 optimal weight: 3.9990 chunk 186 optimal weight: 0.0040 chunk 117 optimal weight: 0.8980 chunk 113 optimal weight: 0.1980 chunk 86 optimal weight: 5.9990 chunk 115 optimal weight: 0.8980 overall best weight: 0.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 525 HIS A 628 HIS C 308 GLN D 46 HIS D 96 GLN D 381 GLN ** E 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.2459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.002 0.038 16419 Angle : 0.478 6.740 22230 Chirality : 0.038 0.178 2538 Planarity : 0.003 0.038 2798 Dihedral : 4.850 55.774 2115 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % 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: 0.23 (0.19), residues: 1928 helix: 0.98 (0.16), residues: 1118 sheet: -0.09 (0.36), residues: 192 loop : -1.21 (0.24), residues: 618 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3856 Ramachandran restraints generated. 1928 Oldfield and 0 Emsley and 1928 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3856 Ramachandran restraints generated. 1928 Oldfield and 0 Emsley and 1928 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1804 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 239 time to evaluate : 2.277 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 239 average time/residue: 0.3249 time to fit residues: 81.2029 Evaluate side-chains 171 residues out of total 1804 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 171 time to evaluate : 2.046 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.7972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 74 optimal weight: 0.0980 chunk 111 optimal weight: 3.9990 chunk 56 optimal weight: 0.9980 chunk 36 optimal weight: 0.0030 chunk 118 optimal weight: 4.9990 chunk 127 optimal weight: 0.9980 chunk 92 optimal weight: 0.7980 chunk 17 optimal weight: 8.9990 chunk 146 optimal weight: 0.8980 chunk 170 optimal weight: 0.0020 chunk 179 optimal weight: 3.9990 overall best weight: 0.3598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 635 ASN B 394 ASN C 409 HIS D 46 HIS E 6 ASN ** E 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 188 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.2588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.002 0.039 16419 Angle : 0.458 6.278 22230 Chirality : 0.038 0.171 2538 Planarity : 0.003 0.033 2798 Dihedral : 4.568 56.169 2115 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % 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: 0.59 (0.20), residues: 1928 helix: 1.30 (0.16), residues: 1117 sheet: -0.00 (0.37), residues: 191 loop : -1.10 (0.25), residues: 620 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3856 Ramachandran restraints generated. 1928 Oldfield and 0 Emsley and 1928 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3856 Ramachandran restraints generated. 1928 Oldfield and 0 Emsley and 1928 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1804 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 235 time to evaluate : 2.107 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 235 average time/residue: 0.3135 time to fit residues: 76.9066 Evaluate side-chains 171 residues out of total 1804 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 171 time to evaluate : 1.913 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.5638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 163 optimal weight: 0.6980 chunk 174 optimal weight: 0.1980 chunk 179 optimal weight: 0.9990 chunk 104 optimal weight: 0.8980 chunk 75 optimal weight: 1.9990 chunk 136 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 157 optimal weight: 2.9990 chunk 164 optimal weight: 0.7980 chunk 173 optimal weight: 0.7980 chunk 114 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 585 GLN A 630 GLN B 394 ASN D 46 HIS D 381 GLN ** E 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.2641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.002 0.039 16419 Angle : 0.483 9.384 22230 Chirality : 0.038 0.168 2538 Planarity : 0.003 0.032 2798 Dihedral : 4.594 56.364 2115 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % 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: 0.61 (0.20), residues: 1928 helix: 1.30 (0.16), residues: 1121 sheet: 0.01 (0.37), residues: 191 loop : -1.09 (0.25), residues: 616 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3856 Ramachandran restraints generated. 1928 Oldfield and 0 Emsley and 1928 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3856 Ramachandran restraints generated. 1928 Oldfield and 0 Emsley and 1928 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1804 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 218 time to evaluate : 2.201 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 218 average time/residue: 0.3320 time to fit residues: 75.8442 Evaluate side-chains 167 residues out of total 1804 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 167 time to evaluate : 2.226 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.9713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 184 optimal weight: 1.9990 chunk 112 optimal weight: 3.9990 chunk 87 optimal weight: 0.4980 chunk 128 optimal weight: 4.9990 chunk 193 optimal weight: 0.8980 chunk 177 optimal weight: 0.7980 chunk 153 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 118 optimal weight: 2.9990 chunk 94 optimal weight: 0.5980 chunk 122 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 46 HIS D 381 GLN D 396 GLN ** E 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.2725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.002 0.039 16419 Angle : 0.485 6.824 22230 Chirality : 0.038 0.163 2538 Planarity : 0.003 0.032 2798 Dihedral : 4.605 56.295 2115 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % 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: 0.62 (0.20), residues: 1928 helix: 1.29 (0.16), residues: 1121 sheet: 0.06 (0.37), residues: 191 loop : -1.06 (0.25), residues: 616 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3856 Ramachandran restraints generated. 1928 Oldfield and 0 Emsley and 1928 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3856 Ramachandran restraints generated. 1928 Oldfield and 0 Emsley and 1928 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1804 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 218 time to evaluate : 2.086 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 218 average time/residue: 0.3214 time to fit residues: 73.4854 Evaluate side-chains 171 residues out of total 1804 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 171 time to evaluate : 2.078 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.6608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 163 optimal weight: 0.6980 chunk 47 optimal weight: 0.9980 chunk 141 optimal weight: 0.7980 chunk 22 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 154 optimal weight: 1.9990 chunk 64 optimal weight: 0.9980 chunk 158 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 chunk 135 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 394 ASN D 46 HIS D 381 GLN ** E 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Group ADP refinement ******************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.124147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.103608 restraints weight = 26684.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.105336 restraints weight = 16678.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.106728 restraints weight = 13267.127| |-----------------------------------------------------------------------------| GEOMETRY RESTRAINTS LIBRARY: GEOSTD + MONOMER LIBRARY + CDL V1.2 DEVIATIONS FROM IDEAL VALUES. BOND : 0.003 0.039 16419 ANGLE : 0.502 9.450 22230 CHIRALITY : 0.039 0.161 2538 PLANARITY : 0.003 0.033 2798 DIHEDRAL : 4.661 56.396 2115 MIN NONBONDED DISTANCE : 2.014 MOLPROBITY STATISTICS. ALL-ATOM CLASHSCORE : 5.77 RAMACHANDRAN PLOT: OUTLIERS : 0.00 % ALLOWED : 2.85 % FAVORED : 97.15 % 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 (0.20), RESIDUES: 1928 HELIX: 1.31 (0.16), RESIDUES: 1114 SHEET: 0.07 (0.37), RESIDUES: 191 LOOP : -1.12 (0.24), RESIDUES: 623 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.2710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.003 0.039 16419 Angle : 0.502 9.450 22230 Chirality : 0.039 0.161 2538 Planarity : 0.003 0.033 2798 Dihedral : 4.661 56.396 2115 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % 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 (0.20), residues: 1928 helix: 1.31 (0.16), residues: 1114 sheet: 0.07 (0.37), residues: 191 loop : -1.12 (0.24), residues: 623 =============================================================================== Job complete usr+sys time: 2875.98 seconds wall clock time: 54 minutes 7.35 seconds (3247.35 seconds total)