Starting phenix.real_space_refine (version: 1.21rc1) on Sat Apr 29 06:38:54 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vaq_31858/04_2023/7vaq_31858_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vaq_31858/04_2023/7vaq_31858.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vaq_31858/04_2023/7vaq_31858.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vaq_31858/04_2023/7vaq_31858.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vaq_31858/04_2023/7vaq_31858_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vaq_31858/04_2023/7vaq_31858_updated.pdb" } resolution = 3.6 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= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 9 5.49 5 Mg 2 5.21 5 S 103 5.16 5 C 18735 2.51 5 N 5131 2.21 5 O 5578 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "E GLU 243": "OE1" <-> "OE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 29558 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 4475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 578, 4475 Classifications: {'peptide': 578} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 542} Chain: "B" Number of atoms: 4475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 578, 4475 Classifications: {'peptide': 578} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 542} Chain: "C" Number of atoms: 4475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 578, 4475 Classifications: {'peptide': 578} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 542} Chain: "D" Number of atoms: 3682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3682 Classifications: {'peptide': 470} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 442} Chain: "E" Number of atoms: 3668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 3668 Classifications: {'peptide': 468} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 441} Chain: "F" Number of atoms: 3694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3694 Classifications: {'peptide': 471} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 444} Chain: "G" Number of atoms: 1619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1619 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 9, 'TRANS': 196} Chain: "H" Number of atoms: 792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 792 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain: "I" Number of atoms: 313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 313 Classifications: {'peptide': 40} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "J" Number of atoms: 976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 976 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 7, 'TRANS': 119} Chain: "K" Number of atoms: 313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 313 Classifications: {'peptide': 40} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "L" Number of atoms: 980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 980 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 7, 'TRANS': 120} Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "C" 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: 15.50, per 1000 atoms: 0.52 Number of scatterers: 29558 At special positions: 0 Unit cell: (136.4, 147.84, 173.36, 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 103 16.00 P 9 15.00 Mg 2 11.99 O 5578 8.00 N 5131 7.00 C 18735 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 12.74 Conformation dependent library (CDL) restraints added in 4.9 seconds 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6918 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 124 helices and 35 sheets defined 40.8% alpha, 12.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.02 Creating SS restraints... Processing helix chain 'A' and resid 91 through 98 Processing helix chain 'A' and resid 210 through 214 Processing helix chain 'A' and resid 234 through 243 Processing helix chain 'A' and resid 259 through 271 removed outlier: 3.794A pdb=" N VAL A 265 " --> pdb=" O GLU A 261 " (cutoff:3.500A) Proline residue: A 270 - end of helix Processing helix chain 'A' and resid 281 through 284 Processing helix chain 'A' and resid 296 through 315 removed outlier: 4.479A pdb=" N ILE A 303 " --> pdb=" O ARG A 299 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N TYR A 304 " --> pdb=" O GLU A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 341 removed outlier: 3.603A pdb=" N ALA A 333 " --> pdb=" O ARG A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 364 removed outlier: 4.272A pdb=" N ALA A 355 " --> pdb=" O PRO A 352 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLU A 363 " --> pdb=" O ALA A 360 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ARG A 364 " --> pdb=" O PHE A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 389 No H-bonds generated for 'chain 'A' and resid 387 through 389' Processing helix chain 'A' and resid 394 through 401 removed outlier: 3.613A pdb=" N ARG A 401 " --> pdb=" O GLN A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 415 Processing helix chain 'A' and resid 436 through 442 Processing helix chain 'A' and resid 447 through 471 removed outlier: 4.012A pdb=" N GLU A 466 " --> pdb=" O ALA A 462 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N ILE A 467 " --> pdb=" O GLY A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 475 No H-bonds generated for 'chain 'A' and resid 473 through 475' Processing helix chain 'A' and resid 478 through 493 Processing helix chain 'A' and resid 509 through 532 removed outlier: 3.615A pdb=" N ARG A 532 " --> pdb=" O ALA A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 553 removed outlier: 3.553A pdb=" N GLU A 546 " --> pdb=" O PRO A 543 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ARG A 550 " --> pdb=" O ARG A 547 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N ARG A 552 " --> pdb=" O GLY A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 577 removed outlier: 3.809A pdb=" N GLU A 564 " --> pdb=" O PRO A 560 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N PHE A 574 " --> pdb=" O ILE A 570 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYS A 575 " --> pdb=" O GLN A 571 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 98 Processing helix chain 'B' and resid 210 through 214 Processing helix chain 'B' and resid 234 through 244 Processing helix chain 'B' and resid 259 through 271 Proline residue: B 270 - end of helix Processing helix chain 'B' and resid 281 through 284 Processing helix chain 'B' and resid 296 through 315 removed outlier: 4.663A pdb=" N ILE B 303 " --> pdb=" O ARG B 299 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N TYR B 304 " --> pdb=" O GLU B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 340 Processing helix chain 'B' and resid 352 through 364 removed outlier: 4.347A pdb=" N ALA B 355 " --> pdb=" O PRO B 352 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLU B 363 " --> pdb=" O ALA B 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 401 Processing helix chain 'B' and resid 411 through 415 Processing helix chain 'B' and resid 432 through 442 Proline residue: B 437 - end of helix Processing helix chain 'B' and resid 447 through 470 removed outlier: 3.875A pdb=" N LEU B 464 " --> pdb=" O ARG B 460 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLN B 465 " --> pdb=" O GLU B 461 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N GLU B 466 " --> pdb=" O ALA B 462 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ILE B 467 " --> pdb=" O GLY B 463 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N VAL B 468 " --> pdb=" O LEU B 464 " (cutoff:3.500A) Processing helix chain 'B' and resid 478 through 493 Processing helix chain 'B' and resid 509 through 532 Processing helix chain 'B' and resid 536 through 541 removed outlier: 4.052A pdb=" N GLN B 541 " --> pdb=" O ASP B 537 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 549 Processing helix chain 'B' and resid 559 through 576 removed outlier: 3.716A pdb=" N PHE B 574 " --> pdb=" O ILE B 570 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N LYS B 575 " --> pdb=" O GLN B 571 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 98 Processing helix chain 'C' and resid 210 through 214 Processing helix chain 'C' and resid 234 through 243 Processing helix chain 'C' and resid 259 through 271 Proline residue: C 270 - end of helix Processing helix chain 'C' and resid 281 through 284 Processing helix chain 'C' and resid 296 through 315 removed outlier: 3.809A pdb=" N GLU C 300 " --> pdb=" O ALA C 297 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE C 303 " --> pdb=" O GLU C 300 " (cutoff:3.500A) Processing helix chain 'C' and resid 327 through 340 Processing helix chain 'C' and resid 354 through 364 removed outlier: 3.753A pdb=" N ARG C 364 " --> pdb=" O ALA C 360 " (cutoff:3.500A) Processing helix chain 'C' and resid 387 through 389 No H-bonds generated for 'chain 'C' and resid 387 through 389' Processing helix chain 'C' and resid 394 through 400 Processing helix chain 'C' and resid 411 through 415 Processing helix chain 'C' and resid 433 through 442 removed outlier: 3.707A pdb=" N ASP C 436 " --> pdb=" O SER C 433 " (cutoff:3.500A) Proline residue: C 437 - end of helix Processing helix chain 'C' and resid 447 through 468 removed outlier: 3.764A pdb=" N GLU C 466 " --> pdb=" O ALA C 462 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ILE C 467 " --> pdb=" O GLY C 463 " (cutoff:3.500A) Processing helix chain 'C' and resid 478 through 493 Processing helix chain 'C' and resid 509 through 532 Processing helix chain 'C' and resid 536 through 540 Processing helix chain 'C' and resid 544 through 549 Processing helix chain 'C' and resid 559 through 573 Processing helix chain 'C' and resid 575 through 577 No H-bonds generated for 'chain 'C' and resid 575 through 577' Processing helix chain 'D' and resid 121 through 123 No H-bonds generated for 'chain 'D' and resid 121 through 123' Processing helix chain 'D' and resid 136 through 140 Processing helix chain 'D' and resid 160 through 170 Processing helix chain 'D' and resid 175 through 178 Processing helix chain 'D' and resid 198 through 211 removed outlier: 3.959A pdb=" N THR D 211 " --> pdb=" O GLU D 207 " (cutoff:3.500A) Processing helix chain 'D' and resid 213 through 216 Processing helix chain 'D' and resid 228 through 249 Proline residue: D 235 - end of helix Processing helix chain 'D' and resid 260 through 273 Processing helix chain 'D' and resid 280 through 282 No H-bonds generated for 'chain 'D' and resid 280 through 282' Processing helix chain 'D' and resid 285 through 297 removed outlier: 4.492A pdb=" N TYR D 288 " --> pdb=" O GLY D 285 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N TYR D 295 " --> pdb=" O ALA D 292 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N GLU D 296 " --> pdb=" O THR D 293 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ARG D 297 " --> pdb=" O ILE D 294 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 332 Processing helix chain 'D' and resid 341 through 345 Processing helix chain 'D' and resid 375 through 399 removed outlier: 3.867A pdb=" N ASP D 391 " --> pdb=" O ALA D 387 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ILE D 392 " --> pdb=" O ASN D 388 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N ALA D 397 " --> pdb=" O ARG D 393 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ILE D 398 " --> pdb=" O LYS D 394 " (cutoff:3.500A) Processing helix chain 'D' and resid 406 through 421 removed outlier: 3.561A pdb=" N ARG D 410 " --> pdb=" O GLU D 406 " (cutoff:3.500A) Processing helix chain 'D' and resid 432 through 445 removed outlier: 3.853A pdb=" N MET D 445 " --> pdb=" O ALA D 441 " (cutoff:3.500A) Processing helix chain 'D' and resid 456 through 462 Processing helix chain 'E' and resid 86 through 88 No H-bonds generated for 'chain 'E' and resid 86 through 88' Processing helix chain 'E' and resid 121 through 123 No H-bonds generated for 'chain 'E' and resid 121 through 123' Processing helix chain 'E' and resid 136 through 139 No H-bonds generated for 'chain 'E' and resid 136 through 139' Processing helix chain 'E' and resid 160 through 170 Processing helix chain 'E' and resid 175 through 178 No H-bonds generated for 'chain 'E' and resid 175 through 178' Processing helix chain 'E' and resid 198 through 211 Processing helix chain 'E' and resid 214 through 216 No H-bonds generated for 'chain 'E' and resid 214 through 216' Processing helix chain 'E' and resid 229 through 249 removed outlier: 3.716A pdb=" N THR E 234 " --> pdb=" O ARG E 231 " (cutoff:3.500A) Proline residue: E 235 - end of helix removed outlier: 3.524A pdb=" N PHE E 247 " --> pdb=" O TYR E 244 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLU E 248 " --> pdb=" O LEU E 245 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N HIS E 249 " --> pdb=" O ALA E 246 " (cutoff:3.500A) Processing helix chain 'E' and resid 260 through 274 Processing helix chain 'E' and resid 287 through 297 removed outlier: 3.564A pdb=" N ILE E 294 " --> pdb=" O ASP E 290 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N ARG E 297 " --> pdb=" O THR E 293 " (cutoff:3.500A) Processing helix chain 'E' and resid 317 through 319 No H-bonds generated for 'chain 'E' and resid 317 through 319' Processing helix chain 'E' and resid 324 through 330 Processing helix chain 'E' and resid 341 through 345 Processing helix chain 'E' and resid 375 through 399 removed outlier: 4.348A pdb=" N ILE E 398 " --> pdb=" O LYS E 394 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ILE E 399 " --> pdb=" O LEU E 395 " (cutoff:3.500A) Processing helix chain 'E' and resid 406 through 421 Processing helix chain 'E' and resid 432 through 445 removed outlier: 4.090A pdb=" N MET E 445 " --> pdb=" O ALA E 441 " (cutoff:3.500A) Processing helix chain 'E' and resid 456 through 462 Processing helix chain 'E' and resid 467 through 469 No H-bonds generated for 'chain 'E' and resid 467 through 469' Processing helix chain 'F' and resid 86 through 88 No H-bonds generated for 'chain 'F' and resid 86 through 88' Processing helix chain 'F' and resid 136 through 139 No H-bonds generated for 'chain 'F' and resid 136 through 139' Processing helix chain 'F' and resid 160 through 170 Processing helix chain 'F' and resid 175 through 178 No H-bonds generated for 'chain 'F' and resid 175 through 178' Processing helix chain 'F' and resid 198 through 211 Processing helix chain 'F' and resid 214 through 216 No H-bonds generated for 'chain 'F' and resid 214 through 216' Processing helix chain 'F' and resid 230 through 249 removed outlier: 3.951A pdb=" N THR F 234 " --> pdb=" O ARG F 231 " (cutoff:3.500A) Proline residue: F 235 - end of helix removed outlier: 3.652A pdb=" N GLU F 248 " --> pdb=" O LEU F 245 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N HIS F 249 " --> pdb=" O ALA F 246 " (cutoff:3.500A) Processing helix chain 'F' and resid 260 through 273 Processing helix chain 'F' and resid 285 through 295 removed outlier: 4.285A pdb=" N TYR F 288 " --> pdb=" O GLY F 285 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N TYR F 295 " --> pdb=" O ALA F 292 " (cutoff:3.500A) Processing helix chain 'F' and resid 317 through 319 No H-bonds generated for 'chain 'F' and resid 317 through 319' Processing helix chain 'F' and resid 324 through 332 Processing helix chain 'F' and resid 341 through 346 removed outlier: 3.596A pdb=" N LYS F 346 " --> pdb=" O GLU F 342 " (cutoff:3.500A) Processing helix chain 'F' and resid 362 through 365 No H-bonds generated for 'chain 'F' and resid 362 through 365' Processing helix chain 'F' and resid 375 through 399 removed outlier: 3.737A pdb=" N ILE F 398 " --> pdb=" O LYS F 394 " (cutoff:3.500A) Processing helix chain 'F' and resid 406 through 421 Processing helix chain 'F' and resid 432 through 445 removed outlier: 3.974A pdb=" N MET F 445 " --> pdb=" O ALA F 441 " (cutoff:3.500A) Processing helix chain 'F' and resid 456 through 462 Processing helix chain 'F' and resid 467 through 470 No H-bonds generated for 'chain 'F' and resid 467 through 470' Processing helix chain 'G' and resid 8 through 70 removed outlier: 3.699A pdb=" N GLU G 48 " --> pdb=" O ARG G 44 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA G 67 " --> pdb=" O ALA G 63 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLN G 68 " --> pdb=" O LEU G 64 " (cutoff:3.500A) Processing helix chain 'G' and resid 123 through 206 removed outlier: 3.901A pdb=" N SER G 127 " --> pdb=" O THR G 123 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N ARG G 128 " --> pdb=" O LEU G 124 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N ILE G 169 " --> pdb=" O GLU G 165 " (cutoff:3.500A) Proline residue: G 170 - end of helix Processing helix chain 'H' and resid 7 through 14 removed outlier: 4.169A pdb=" N GLN H 11 " --> pdb=" O GLU H 8 " (cutoff:3.500A) Processing helix chain 'H' and resid 26 through 39 removed outlier: 3.962A pdb=" N ARG H 39 " --> pdb=" O THR H 35 " (cutoff:3.500A) Processing helix chain 'H' and resid 86 through 98 Processing helix chain 'I' and resid 82 through 105 removed outlier: 3.886A pdb=" N ARG I 100 " --> pdb=" O ALA I 96 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ALA I 105 " --> pdb=" O GLU I 101 " (cutoff:3.500A) Processing helix chain 'I' and resid 107 through 118 removed outlier: 3.562A pdb=" N GLU I 117 " --> pdb=" O LEU I 113 " (cutoff:3.500A) Processing helix chain 'J' and resid 63 through 93 Processing helix chain 'J' and resid 100 through 114 removed outlier: 4.203A pdb=" N ARG J 105 " --> pdb=" O PRO J 101 " (cutoff:3.500A) Processing helix chain 'J' and resid 125 through 138 removed outlier: 3.819A pdb=" N LEU J 128 " --> pdb=" O PRO J 125 " (cutoff:3.500A) Proline residue: J 129 - end of helix removed outlier: 4.514A pdb=" N GLU J 132 " --> pdb=" O PRO J 129 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N ALA J 135 " --> pdb=" O GLU J 132 " (cutoff:3.500A) Processing helix chain 'J' and resid 146 through 148 No H-bonds generated for 'chain 'J' and resid 146 through 148' Processing helix chain 'J' and resid 167 through 186 removed outlier: 5.397A pdb=" N ASP J 176 " --> pdb=" O ASP J 172 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N ALA J 177 " --> pdb=" O ARG J 173 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N GLN J 184 " --> pdb=" O SER J 180 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ALA J 185 " --> pdb=" O LYS J 181 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 105 removed outlier: 3.819A pdb=" N ALA K 105 " --> pdb=" O GLU K 101 " (cutoff:3.500A) Processing helix chain 'K' and resid 107 through 118 Processing helix chain 'L' and resid 62 through 94 removed outlier: 3.624A pdb=" N VAL L 68 " --> pdb=" O GLY L 64 " (cutoff:3.500A) Processing helix chain 'L' and resid 98 through 114 Proline residue: L 101 - end of helix removed outlier: 3.994A pdb=" N VAL L 104 " --> pdb=" O PRO L 101 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N ARG L 105 " --> pdb=" O GLU L 102 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA L 114 " --> pdb=" O ALA L 111 " (cutoff:3.500A) Processing helix chain 'L' and resid 125 through 138 Proline residue: L 129 - end of helix removed outlier: 4.782A pdb=" N ALA L 133 " --> pdb=" O PRO L 129 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N LEU L 134 " --> pdb=" O HIS L 130 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLU L 137 " --> pdb=" O ALA L 133 " (cutoff:3.500A) Processing helix chain 'L' and resid 167 through 186 removed outlier: 4.280A pdb=" N ASP L 176 " --> pdb=" O ASP L 172 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N ALA L 177 " --> pdb=" O ARG L 173 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N SER L 180 " --> pdb=" O ASP L 176 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N LYS L 181 " --> pdb=" O ALA L 177 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 3 through 5 removed outlier: 6.581A pdb=" N PHE A 48 " --> pdb=" O ILE A 40 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N LEU A 42 " --> pdb=" O THR A 46 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N THR A 46 " --> pdb=" O LEU A 42 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N LYS A 17 " --> pdb=" O ILE A 6 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N ILE A 6 " --> pdb=" O LYS A 17 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 72 through 76 Processing sheet with id= C, first strand: chain 'A' and resid 82 through 84 removed outlier: 4.003A pdb=" N GLY A 82 " --> pdb=" O THR A 285 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N VAL A 250 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N ILE A 288 " --> pdb=" O VAL A 250 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N TYR A 252 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N ASN A 290 " --> pdb=" O TYR A 252 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N GLY A 254 " --> pdb=" O ASN A 290 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N ALA A 377 " --> pdb=" O VAL A 320 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N LEU A 322 " --> pdb=" O ALA A 377 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N THR A 379 " --> pdb=" O LEU A 322 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N ALA A 324 " --> pdb=" O THR A 379 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N VAL A 381 " --> pdb=" O ALA A 324 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 117 through 119 removed outlier: 3.660A pdb=" N GLY A 164 " --> pdb=" O TRP A 119 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 134 through 140 removed outlier: 6.601A pdb=" N ILE A 147 " --> pdb=" O LEU A 135 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N THR A 137 " --> pdb=" O HIS A 145 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N HIS A 145 " --> pdb=" O THR A 137 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N PHE A 143 " --> pdb=" O PRO A 139 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 157 through 160 removed outlier: 6.975A pdb=" N VAL A 174 " --> pdb=" O LYS A 158 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 2 through 5 removed outlier: 4.268A pdb=" N ILE B 2 " --> pdb=" O SER B 66 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N PHE B 48 " --> pdb=" O ILE B 40 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N LEU B 42 " --> pdb=" O THR B 46 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N THR B 46 " --> pdb=" O LEU B 42 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N LYS B 17 " --> pdb=" O ILE B 6 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N ILE B 6 " --> pdb=" O LYS B 17 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 72 through 76 Processing sheet with id= I, first strand: chain 'B' and resid 82 through 84 removed outlier: 4.018A pdb=" N GLY B 82 " --> pdb=" O THR B 285 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N VAL B 250 " --> pdb=" O VAL B 286 " (cutoff:3.500A) removed outlier: 8.250A pdb=" N ILE B 288 " --> pdb=" O VAL B 250 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N TYR B 252 " --> pdb=" O ILE B 288 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N ALA B 377 " --> pdb=" O VAL B 320 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N LEU B 322 " --> pdb=" O ALA B 377 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N THR B 379 " --> pdb=" O LEU B 322 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N ALA B 324 " --> pdb=" O THR B 379 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N VAL B 381 " --> pdb=" O ALA B 324 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ILE B 226 " --> pdb=" O GLY B 382 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 116 through 119 Processing sheet with id= K, first strand: chain 'B' and resid 197 through 199 removed outlier: 4.045A pdb=" N ARG B 197 " --> pdb=" O ILE B 369 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N LYS B 367 " --> pdb=" O LEU B 199 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 134 through 140 removed outlier: 6.584A pdb=" N ILE B 147 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N THR B 137 " --> pdb=" O HIS B 145 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N HIS B 145 " --> pdb=" O THR B 137 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N PHE B 143 " --> pdb=" O PRO B 139 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'B' and resid 171 through 174 removed outlier: 7.017A pdb=" N LEU B 181 " --> pdb=" O VAL B 172 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 2 through 5 removed outlier: 4.366A pdb=" N ILE C 2 " --> pdb=" O SER C 66 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N PHE C 48 " --> pdb=" O ILE C 40 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N LEU C 42 " --> pdb=" O THR C 46 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N THR C 46 " --> pdb=" O LEU C 42 " (cutoff:3.500A) removed outlier: 5.766A pdb=" N LYS C 17 " --> pdb=" O ILE C 6 " (cutoff:3.500A) removed outlier: 5.678A pdb=" N ILE C 6 " --> pdb=" O LYS C 17 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 72 through 75 Processing sheet with id= P, first strand: chain 'C' and resid 82 through 84 removed outlier: 4.047A pdb=" N GLY C 82 " --> pdb=" O THR C 285 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N VAL C 250 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N ILE C 288 " --> pdb=" O VAL C 250 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N TYR C 252 " --> pdb=" O ILE C 288 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N ASN C 290 " --> pdb=" O TYR C 252 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N GLY C 254 " --> pdb=" O ASN C 290 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL C 249 " --> pdb=" O SER C 319 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N ALA C 377 " --> pdb=" O VAL C 320 " (cutoff:3.500A) removed outlier: 7.646A pdb=" N LEU C 322 " --> pdb=" O ALA C 377 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N THR C 379 " --> pdb=" O LEU C 322 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N ALA C 324 " --> pdb=" O THR C 379 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N VAL C 381 " --> pdb=" O ALA C 324 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 117 through 119 Processing sheet with id= R, first strand: chain 'C' and resid 134 through 140 removed outlier: 6.755A pdb=" N ILE C 147 " --> pdb=" O LEU C 135 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N THR C 137 " --> pdb=" O HIS C 145 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N HIS C 145 " --> pdb=" O THR C 137 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N PHE C 143 " --> pdb=" O PRO C 139 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'C' and resid 157 through 160 removed outlier: 6.808A pdb=" N VAL C 174 " --> pdb=" O LYS C 158 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'D' and resid 11 through 15 removed outlier: 6.563A pdb=" N PHE D 20 " --> pdb=" O THR D 12 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N ILE D 14 " --> pdb=" O LEU D 18 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N LEU D 18 " --> pdb=" O ILE D 14 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N GLN D 58 " --> pdb=" O VAL D 47 " (cutoff:3.500A) removed outlier: 5.703A pdb=" N VAL D 47 " --> pdb=" O GLN D 58 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N ASP D 34 " --> pdb=" O LEU D 75 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N LEU D 75 " --> pdb=" O ASP D 34 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N LYS D 36 " --> pdb=" O VAL D 73 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N VAL D 73 " --> pdb=" O LYS D 36 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'D' and resid 81 through 84 removed outlier: 3.589A pdb=" N LYS D 110 " --> pdb=" O VAL D 84 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'D' and resid 336 through 338 removed outlier: 3.573A pdb=" N LEU D 257 " --> pdb=" O ILE D 311 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'E' and resid 11 through 15 removed outlier: 6.629A pdb=" N PHE E 20 " --> pdb=" O THR E 12 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N ILE E 14 " --> pdb=" O LEU E 18 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N LEU E 18 " --> pdb=" O ILE E 14 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N GLN E 58 " --> pdb=" O VAL E 47 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N VAL E 47 " --> pdb=" O GLN E 58 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL E 33 " --> pdb=" O GLY E 45 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N ASP E 34 " --> pdb=" O LEU E 75 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N LEU E 75 " --> pdb=" O ASP E 34 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N LYS E 36 " --> pdb=" O VAL E 73 " (cutoff:3.500A) removed outlier: 5.379A pdb=" N VAL E 73 " --> pdb=" O LYS E 36 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'E' and resid 81 through 84 removed outlier: 3.689A pdb=" N LYS E 110 " --> pdb=" O VAL E 84 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'E' and resid 336 through 338 Processing sheet with id= Z, first strand: chain 'E' and resid 217 through 220 removed outlier: 6.857A pdb=" N VAL E 189 " --> pdb=" O VAL E 218 " (cutoff:3.500A) removed outlier: 8.125A pdb=" N PHE E 220 " --> pdb=" O VAL E 189 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N PHE E 191 " --> pdb=" O PHE E 220 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N SER E 307 " --> pdb=" O VAL E 253 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N VAL E 255 " --> pdb=" O SER E 307 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N THR E 309 " --> pdb=" O VAL E 255 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N LEU E 257 " --> pdb=" O THR E 309 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N ILE E 311 " --> pdb=" O LEU E 257 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'F' and resid 7 through 9 removed outlier: 6.888A pdb=" N ILE F 32 " --> pdb=" O VAL F 76 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N VAL F 56 " --> pdb=" O ILE F 48 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N SER F 15 " --> pdb=" O LEU F 18 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N TYR F 13 " --> pdb=" O PHE F 20 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'F' and resid 81 through 84 Processing sheet with id= AC, first strand: chain 'F' and resid 336 through 338 Processing sheet with id= AD, first strand: chain 'F' and resid 217 through 220 removed outlier: 6.360A pdb=" N VAL F 189 " --> pdb=" O VAL F 218 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N PHE F 220 " --> pdb=" O VAL F 189 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N PHE F 191 " --> pdb=" O PHE F 220 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N SER F 307 " --> pdb=" O VAL F 253 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N VAL F 255 " --> pdb=" O SER F 307 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N THR F 309 " --> pdb=" O VAL F 255 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N LEU F 257 " --> pdb=" O THR F 309 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'G' and resid 90 through 95 removed outlier: 4.061A pdb=" N GLU G 90 " --> pdb=" O LYS G 105 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ARG G 103 " --> pdb=" O GLU G 92 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'H' and resid 2 through 5 removed outlier: 5.904A pdb=" N GLU H 19 " --> pdb=" O VAL H 3 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N ALA H 5 " --> pdb=" O GLU H 19 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N TYR H 21 " --> pdb=" O ALA H 5 " (cutoff:3.500A) No H-bonds generated for sheet with id= AF Processing sheet with id= AG, first strand: chain 'H' and resid 44 through 48 removed outlier: 5.823A pdb=" N VAL H 70 " --> pdb=" O VAL H 45 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N VAL H 47 " --> pdb=" O VAL H 70 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N LEU H 72 " --> pdb=" O VAL H 47 " (cutoff:3.500A) No H-bonds generated for sheet with id= AG Processing sheet with id= AH, first strand: chain 'J' and resid 153 through 155 Processing sheet with id= AI, first strand: chain 'L' and resid 120 through 123 removed outlier: 4.185A pdb=" N ALA L 120 " --> pdb=" O VAL L 155 " (cutoff:3.500A) 1181 hydrogen bonds defined for protein. 3192 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: 10.59 Time building geometry restraints manager: 13.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9938 1.34 - 1.46: 3563 1.46 - 1.57: 16406 1.57 - 1.69: 13 1.69 - 1.81: 194 Bond restraints: 30114 Sorted by residual: bond pdb=" O3 PO4 A 603 " pdb=" P PO4 A 603 " ideal model delta sigma weight residual 1.569 1.500 0.069 2.00e-02 2.50e+03 1.19e+01 bond pdb=" O4 PO4 A 603 " pdb=" P PO4 A 603 " ideal model delta sigma weight residual 1.568 1.500 0.068 2.00e-02 2.50e+03 1.17e+01 bond pdb=" O1 PO4 A 603 " pdb=" P PO4 A 603 " ideal model delta sigma weight residual 1.565 1.498 0.067 2.00e-02 2.50e+03 1.12e+01 bond pdb=" O2 PO4 A 603 " pdb=" P PO4 A 603 " ideal model delta sigma weight residual 1.567 1.508 0.059 2.00e-02 2.50e+03 8.64e+00 bond pdb=" C TRP J 100 " pdb=" N PRO J 101 " ideal model delta sigma weight residual 1.334 1.367 -0.033 2.34e-02 1.83e+03 2.00e+00 ... (remaining 30109 not shown) Histogram of bond angle deviations from ideal: 99.33 - 107.41: 1181 107.41 - 115.49: 18278 115.49 - 123.58: 20596 123.58 - 131.66: 714 131.66 - 139.75: 44 Bond angle restraints: 40813 Sorted by residual: angle pdb=" C VAL B 214 " pdb=" N LEU B 215 " pdb=" CA LEU B 215 " ideal model delta sigma weight residual 122.53 116.24 6.29 1.92e+00 2.71e-01 1.07e+01 angle pdb=" CA LEU L 150 " pdb=" CB LEU L 150 " pdb=" CG LEU L 150 " ideal model delta sigma weight residual 116.30 126.90 -10.60 3.50e+00 8.16e-02 9.17e+00 angle pdb=" C GLN G 166 " pdb=" N VAL G 167 " pdb=" CA VAL G 167 " ideal model delta sigma weight residual 121.85 118.33 3.52 1.19e+00 7.06e-01 8.75e+00 angle pdb=" C ASP C 213 " pdb=" N VAL C 214 " pdb=" CA VAL C 214 " ideal model delta sigma weight residual 122.97 120.18 2.79 9.80e-01 1.04e+00 8.12e+00 angle pdb=" C ILE A 536 " pdb=" N ASP A 537 " pdb=" CA ASP A 537 " ideal model delta sigma weight residual 125.66 130.40 -4.74 1.85e+00 2.92e-01 6.57e+00 ... (remaining 40808 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.65: 17183 21.65 - 43.30: 991 43.30 - 64.95: 92 64.95 - 86.61: 50 86.61 - 108.26: 5 Dihedral angle restraints: 18321 sinusoidal: 7499 harmonic: 10822 Sorted by residual: dihedral pdb=" C5' ADP A 601 " pdb=" O5' ADP A 601 " pdb=" PA ADP A 601 " pdb=" O2A ADP A 601 " ideal model delta sinusoidal sigma weight residual -60.00 48.26 -108.26 1 2.00e+01 2.50e-03 3.15e+01 dihedral pdb=" O1B ADP A 601 " pdb=" O3A ADP A 601 " pdb=" PB ADP A 601 " pdb=" PA ADP A 601 " ideal model delta sinusoidal sigma weight residual -60.00 -143.31 83.31 1 2.00e+01 2.50e-03 2.12e+01 dihedral pdb=" CA ARG D 372 " pdb=" C ARG D 372 " pdb=" N GLU D 373 " pdb=" CA GLU D 373 " ideal model delta harmonic sigma weight residual -180.00 -160.46 -19.54 0 5.00e+00 4.00e-02 1.53e+01 ... (remaining 18318 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 3820 0.055 - 0.111: 672 0.111 - 0.166: 77 0.166 - 0.222: 1 0.222 - 0.277: 2 Chirality restraints: 4572 Sorted by residual: chirality pdb=" CB ILE A 226 " pdb=" CA ILE A 226 " pdb=" CG1 ILE A 226 " pdb=" CG2 ILE A 226 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.28 2.00e-01 2.50e+01 1.92e+00 chirality pdb=" CB ILE B 211 " pdb=" CA ILE B 211 " pdb=" CG1 ILE B 211 " pdb=" CG2 ILE B 211 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.26 2.00e-01 2.50e+01 1.71e+00 chirality pdb=" C2' ADP A 601 " pdb=" C1' ADP A 601 " pdb=" C3' ADP A 601 " pdb=" O2' ADP A 601 " both_signs ideal model delta sigma weight residual False -2.51 -2.69 0.18 2.00e-01 2.50e+01 8.12e-01 ... (remaining 4569 not shown) Planarity restraints: 5333 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS E 323 " 0.029 5.00e-02 4.00e+02 4.42e-02 3.13e+00 pdb=" N PRO E 324 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO E 324 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO E 324 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B 228 " -0.028 5.00e-02 4.00e+02 4.27e-02 2.91e+00 pdb=" N PRO B 229 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO B 229 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 229 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS F 323 " -0.026 5.00e-02 4.00e+02 4.01e-02 2.57e+00 pdb=" N PRO F 324 " 0.069 5.00e-02 4.00e+02 pdb=" CA PRO F 324 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO F 324 " -0.022 5.00e-02 4.00e+02 ... (remaining 5330 not shown) Histogram of nonbonded interaction distances: 1.07 - 1.83: 1 1.83 - 2.60: 276 2.60 - 3.37: 38004 3.37 - 4.13: 69184 4.13 - 4.90: 130805 Nonbonded interactions: 238270 Sorted by model distance: nonbonded pdb=" OG SER A 235 " pdb="MG MG A 602 " model vdw 1.066 2.170 nonbonded pdb=" OG SER C 235 " pdb="MG MG C 601 " model vdw 1.957 2.170 nonbonded pdb=" OE2 GLU C 261 " pdb="MG MG C 601 " model vdw 2.076 2.170 nonbonded pdb=" O MET A 220 " pdb=" OG1 THR A 379 " model vdw 2.130 2.440 nonbonded pdb=" O MET C 220 " pdb=" OG1 THR C 379 " model vdw 2.182 2.440 ... (remaining 238265 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 1 through 578) selection = (chain 'B' and resid 1 through 578) selection = (chain 'C' and resid 1 through 578) } ncs_group { reference = (chain 'D' and resid 5 through 470) selection = (chain 'E' and resid 5 through 470) selection = (chain 'F' and resid 5 through 470) } ncs_group { reference = chain 'I' selection = chain 'K' } ncs_group { reference = chain 'J' selection = (chain 'L' and resid 61 through 187) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 8.830 Check model and map are aligned: 0.440 Set scattering table: 0.280 Process input model: 74.710 Find NCS groups from input model: 2.020 Set up NCS constraints: 0.190 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 91.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7462 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.069 30114 Z= 0.187 Angle : 0.529 10.599 40813 Z= 0.287 Chirality : 0.042 0.277 4572 Planarity : 0.004 0.044 5333 Dihedral : 13.519 108.257 11403 Min Nonbonded Distance : 1.066 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % 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: 1.14 (0.14), residues: 3764 helix: 1.73 (0.14), residues: 1554 sheet: 0.01 (0.22), residues: 596 loop : 0.21 (0.16), residues: 1614 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 649 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 649 time to evaluate : 3.577 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 649 average time/residue: 0.5086 time to fit residues: 489.2894 Evaluate side-chains 321 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 321 time to evaluate : 3.315 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.5868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 314 optimal weight: 10.0000 chunk 282 optimal weight: 0.7980 chunk 156 optimal weight: 9.9990 chunk 96 optimal weight: 8.9990 chunk 190 optimal weight: 10.0000 chunk 151 optimal weight: 10.0000 chunk 292 optimal weight: 4.9990 chunk 113 optimal weight: 10.0000 chunk 177 optimal weight: 3.9990 chunk 217 optimal weight: 6.9990 chunk 338 optimal weight: 0.0970 overall best weight: 3.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 260 ASN B 316 GLN ** B 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 501 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 363 ASN F 206 GLN F 428 GLN G 166 GLN H 82 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.1974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.052 30114 Z= 0.236 Angle : 0.560 13.604 40813 Z= 0.285 Chirality : 0.044 0.211 4572 Planarity : 0.005 0.047 5333 Dihedral : 4.669 96.048 4197 Min Nonbonded Distance : 1.786 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer Outliers : 1.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % 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: 0.86 (0.14), residues: 3764 helix: 1.32 (0.14), residues: 1550 sheet: 0.00 (0.22), residues: 606 loop : 0.21 (0.16), residues: 1608 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 331 time to evaluate : 3.629 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 48 outliers final: 32 residues processed: 366 average time/residue: 0.4594 time to fit residues: 262.2694 Evaluate side-chains 300 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 268 time to evaluate : 3.431 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 0 residues processed: 32 average time/residue: 0.2769 time to fit residues: 21.2809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 188 optimal weight: 10.0000 chunk 105 optimal weight: 10.0000 chunk 281 optimal weight: 0.5980 chunk 230 optimal weight: 9.9990 chunk 93 optimal weight: 10.0000 chunk 339 optimal weight: 20.0000 chunk 366 optimal weight: 8.9990 chunk 302 optimal weight: 9.9990 chunk 336 optimal weight: 9.9990 chunk 115 optimal weight: 0.9990 chunk 272 optimal weight: 8.9990 overall best weight: 5.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 GLN B 293 ASN B 442 ASN ** B 501 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 166 GLN E 170 GLN L 124 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.2694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.091 30114 Z= 0.358 Angle : 0.626 7.414 40813 Z= 0.322 Chirality : 0.046 0.204 4572 Planarity : 0.006 0.059 5333 Dihedral : 4.993 86.981 4197 Min Nonbonded Distance : 1.816 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer Outliers : 1.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % 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 (0.14), residues: 3764 helix: 0.83 (0.14), residues: 1527 sheet: -0.15 (0.22), residues: 596 loop : -0.17 (0.15), residues: 1641 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 297 time to evaluate : 3.552 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 38 outliers final: 20 residues processed: 325 average time/residue: 0.4303 time to fit residues: 221.8702 Evaluate side-chains 278 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 258 time to evaluate : 3.515 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.2629 time to fit residues: 14.8897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 335 optimal weight: 10.0000 chunk 255 optimal weight: 10.0000 chunk 176 optimal weight: 5.9990 chunk 37 optimal weight: 9.9990 chunk 161 optimal weight: 20.0000 chunk 227 optimal weight: 10.0000 chunk 340 optimal weight: 20.0000 chunk 360 optimal weight: 4.9990 chunk 177 optimal weight: 4.9990 chunk 322 optimal weight: 9.9990 chunk 97 optimal weight: 7.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 202 ASN E 166 GLN E 310 GLN F 427 GLN L 96 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.3277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.061 30114 Z= 0.392 Angle : 0.663 18.299 40813 Z= 0.339 Chirality : 0.048 0.197 4572 Planarity : 0.006 0.064 5333 Dihedral : 5.261 81.600 4197 Min Nonbonded Distance : 1.801 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer Outliers : 2.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.14), residues: 3764 helix: 0.42 (0.13), residues: 1524 sheet: -0.32 (0.22), residues: 593 loop : -0.44 (0.15), residues: 1647 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 279 time to evaluate : 3.727 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 68 outliers final: 34 residues processed: 335 average time/residue: 0.4359 time to fit residues: 233.8340 Evaluate side-chains 288 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 254 time to evaluate : 3.607 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 0 residues processed: 34 average time/residue: 0.2654 time to fit residues: 21.6106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 300 optimal weight: 9.9990 chunk 204 optimal weight: 5.9990 chunk 5 optimal weight: 8.9990 chunk 268 optimal weight: 10.0000 chunk 148 optimal weight: 5.9990 chunk 307 optimal weight: 0.7980 chunk 249 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 184 optimal weight: 6.9990 chunk 323 optimal weight: 20.0000 chunk 90 optimal weight: 10.0000 overall best weight: 5.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 381 GLN F 206 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.3462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.055 30114 Z= 0.328 Angle : 0.601 8.780 40813 Z= 0.309 Chirality : 0.046 0.204 4572 Planarity : 0.005 0.062 5333 Dihedral : 5.113 81.770 4197 Min Nonbonded Distance : 1.827 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer Outliers : 1.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.14), residues: 3764 helix: 0.48 (0.14), residues: 1540 sheet: -0.29 (0.22), residues: 601 loop : -0.54 (0.15), residues: 1623 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 278 time to evaluate : 3.553 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 53 outliers final: 29 residues processed: 321 average time/residue: 0.4527 time to fit residues: 231.6788 Evaluate side-chains 285 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 256 time to evaluate : 3.819 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 0 residues processed: 29 average time/residue: 0.2996 time to fit residues: 21.5237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 121 optimal weight: 6.9990 chunk 324 optimal weight: 20.0000 chunk 71 optimal weight: 0.0070 chunk 211 optimal weight: 5.9990 chunk 89 optimal weight: 9.9990 chunk 360 optimal weight: 8.9990 chunk 299 optimal weight: 2.9990 chunk 167 optimal weight: 8.9990 chunk 30 optimal weight: 2.9990 chunk 119 optimal weight: 9.9990 chunk 189 optimal weight: 6.9990 overall best weight: 3.8006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 290 ASN C 202 ASN F 206 GLN F 427 GLN H 30 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.3546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.043 30114 Z= 0.241 Angle : 0.552 13.849 40813 Z= 0.281 Chirality : 0.044 0.174 4572 Planarity : 0.005 0.057 5333 Dihedral : 4.911 82.061 4197 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer Outliers : 1.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % 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: -0.05 (0.14), residues: 3764 helix: 0.65 (0.14), residues: 1543 sheet: -0.29 (0.22), residues: 609 loop : -0.47 (0.15), residues: 1612 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 271 time to evaluate : 3.960 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 35 outliers final: 15 residues processed: 298 average time/residue: 0.4408 time to fit residues: 210.7638 Evaluate side-chains 276 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 261 time to evaluate : 3.628 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.2856 time to fit residues: 13.0122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 347 optimal weight: 9.9990 chunk 40 optimal weight: 7.9990 chunk 205 optimal weight: 9.9990 chunk 263 optimal weight: 0.0070 chunk 204 optimal weight: 4.9990 chunk 303 optimal weight: 9.9990 chunk 201 optimal weight: 9.9990 chunk 359 optimal weight: 0.0370 chunk 224 optimal weight: 7.9990 chunk 219 optimal weight: 1.9990 chunk 165 optimal weight: 5.9990 overall best weight: 2.6082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.3588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 30114 Z= 0.191 Angle : 0.525 14.406 40813 Z= 0.264 Chirality : 0.043 0.163 4572 Planarity : 0.004 0.052 5333 Dihedral : 4.671 81.343 4197 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer Outliers : 0.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % 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: 0.16 (0.14), residues: 3764 helix: 0.85 (0.14), residues: 1543 sheet: -0.26 (0.22), residues: 605 loop : -0.37 (0.15), residues: 1616 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 287 time to evaluate : 3.884 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 3 residues processed: 299 average time/residue: 0.4484 time to fit residues: 212.4847 Evaluate side-chains 261 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 258 time to evaluate : 3.524 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2628 time to fit residues: 6.4348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 222 optimal weight: 9.9990 chunk 143 optimal weight: 9.9990 chunk 214 optimal weight: 10.0000 chunk 108 optimal weight: 10.0000 chunk 70 optimal weight: 10.0000 chunk 69 optimal weight: 5.9990 chunk 228 optimal weight: 3.9990 chunk 244 optimal weight: 9.9990 chunk 177 optimal weight: 9.9990 chunk 33 optimal weight: 8.9990 chunk 282 optimal weight: 6.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 293 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.3859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.060 30114 Z= 0.414 Angle : 0.657 16.002 40813 Z= 0.334 Chirality : 0.047 0.212 4572 Planarity : 0.006 0.062 5333 Dihedral : 5.202 81.559 4197 Min Nonbonded Distance : 1.824 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer Outliers : 0.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % 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 (0.14), residues: 3764 helix: 0.50 (0.13), residues: 1527 sheet: -0.42 (0.21), residues: 618 loop : -0.61 (0.15), residues: 1619 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 256 time to evaluate : 3.691 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 16 residues processed: 271 average time/residue: 0.4709 time to fit residues: 203.4565 Evaluate side-chains 267 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 251 time to evaluate : 3.528 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.3333 time to fit residues: 14.4294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 327 optimal weight: 10.0000 chunk 344 optimal weight: 6.9990 chunk 314 optimal weight: 5.9990 chunk 335 optimal weight: 10.0000 chunk 201 optimal weight: 6.9990 chunk 145 optimal weight: 0.9990 chunk 263 optimal weight: 8.9990 chunk 102 optimal weight: 7.9990 chunk 302 optimal weight: 5.9990 chunk 316 optimal weight: 9.9990 chunk 333 optimal weight: 20.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.3935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.052 30114 Z= 0.316 Angle : 0.600 15.943 40813 Z= 0.304 Chirality : 0.045 0.185 4572 Planarity : 0.005 0.059 5333 Dihedral : 5.131 81.631 4197 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer Outliers : 0.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % 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: -0.31 (0.14), residues: 3764 helix: 0.50 (0.14), residues: 1527 sheet: -0.45 (0.21), residues: 612 loop : -0.67 (0.15), residues: 1625 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 274 time to evaluate : 3.608 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 4 residues processed: 282 average time/residue: 0.4507 time to fit residues: 202.8491 Evaluate side-chains 262 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 258 time to evaluate : 3.728 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.2639 time to fit residues: 7.0767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 219 optimal weight: 0.0000 chunk 354 optimal weight: 20.0000 chunk 216 optimal weight: 9.9990 chunk 168 optimal weight: 9.9990 chunk 246 optimal weight: 6.9990 chunk 371 optimal weight: 8.9990 chunk 342 optimal weight: 0.0980 chunk 295 optimal weight: 0.4980 chunk 30 optimal weight: 8.9990 chunk 228 optimal weight: 0.6980 chunk 181 optimal weight: 6.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.3917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.036 30114 Z= 0.161 Angle : 0.516 15.390 40813 Z= 0.259 Chirality : 0.042 0.192 4572 Planarity : 0.004 0.051 5333 Dihedral : 4.661 80.495 4197 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer Outliers : 0.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % 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: 0.10 (0.14), residues: 3764 helix: 0.87 (0.14), residues: 1532 sheet: -0.36 (0.22), residues: 609 loop : -0.42 (0.16), residues: 1623 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 272 time to evaluate : 3.701 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 5 residues processed: 279 average time/residue: 0.4747 time to fit residues: 212.4001 Evaluate side-chains 264 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 259 time to evaluate : 3.946 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.3722 time to fit residues: 10.0744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 235 optimal weight: 7.9990 chunk 315 optimal weight: 20.0000 chunk 90 optimal weight: 0.0870 chunk 272 optimal weight: 9.9990 chunk 43 optimal weight: 10.0000 chunk 82 optimal weight: 0.5980 chunk 296 optimal weight: 5.9990 chunk 124 optimal weight: 10.0000 chunk 304 optimal weight: 4.9990 chunk 37 optimal weight: 9.9990 chunk 54 optimal weight: 6.9990 overall best weight: 3.7364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.139562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.118723 restraints weight = 50453.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.117656 restraints weight = 50851.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.118623 restraints weight = 43398.743| |-----------------------------------------------------------------------------| r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.3976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.042 30114 Z= 0.242 Angle : 0.555 15.685 40813 Z= 0.279 Chirality : 0.044 0.176 4572 Planarity : 0.005 0.054 5333 Dihedral : 4.768 79.798 4197 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer Outliers : 0.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % 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 (0.14), residues: 3764 helix: 0.83 (0.14), residues: 1530 sheet: -0.33 (0.22), residues: 599 loop : -0.50 (0.15), residues: 1635 =============================================================================== Job complete usr+sys time: 5374.06 seconds wall clock time: 98 minutes 55.83 seconds (5935.83 seconds total)