Starting phenix.real_space_refine on Wed Feb 21 03:40:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vaq_31858/02_2024/7vaq_31858_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vaq_31858/02_2024/7vaq_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_31858/02_2024/7vaq_31858.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vaq_31858/02_2024/7vaq_31858.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vaq_31858/02_2024/7vaq_31858_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vaq_31858/02_2024/7vaq_31858_updated.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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-dev-5238/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: 16.34, per 1000 atoms: 0.55 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: 11.43 Conformation dependent library (CDL) restraints added in 5.5 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: 6.56 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: 10.12 Time building geometry restraints manager: 12.39 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: 17198 21.65 - 43.30: 1016 43.30 - 64.95: 113 64.95 - 86.61: 51 86.61 - 108.26: 5 Dihedral angle restraints: 18383 sinusoidal: 7561 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 18380 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: 1.700 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: 7.680 Check model and map are aligned: 0.510 Set scattering table: 0.300 Process input model: 79.680 Find NCS groups from input model: 2.170 Set up NCS constraints: 0.220 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 95.120 ------------------------------------------------------------------------------- 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 : 13.776 108.257 11465 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 % Allowed : 0.06 % Favored : 99.94 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 330 HIS 0.003 0.001 HIS A 185 PHE 0.021 0.001 PHE C 269 TYR 0.013 0.001 TYR D 331 ARG 0.002 0.000 ARG C 154 *********************** 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 : 3.595 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 ASP cc_start: 0.7709 (m-30) cc_final: 0.7456 (m-30) REVERT: A 158 LYS cc_start: 0.7391 (ttmt) cc_final: 0.7095 (tmtt) REVERT: A 159 GLU cc_start: 0.6364 (pt0) cc_final: 0.6157 (pt0) REVERT: A 166 TYR cc_start: 0.7875 (m-80) cc_final: 0.7486 (m-80) REVERT: A 179 THR cc_start: 0.7312 (m) cc_final: 0.6877 (t) REVERT: A 282 MET cc_start: 0.8302 (mmm) cc_final: 0.8087 (tpp) REVERT: A 304 TYR cc_start: 0.7936 (m-80) cc_final: 0.7596 (m-80) REVERT: A 329 ARG cc_start: 0.6070 (mtm-85) cc_final: 0.5830 (mmp80) REVERT: A 363 GLU cc_start: 0.7533 (mm-30) cc_final: 0.7260 (mt-10) REVERT: A 481 ARG cc_start: 0.7415 (mmm-85) cc_final: 0.6826 (ttm-80) REVERT: A 483 VAL cc_start: 0.8286 (t) cc_final: 0.8077 (t) REVERT: A 498 ASN cc_start: 0.7084 (t0) cc_final: 0.6489 (m-40) REVERT: A 524 LYS cc_start: 0.6077 (ttmt) cc_final: 0.5759 (mtmm) REVERT: B 25 TYR cc_start: 0.7857 (m-80) cc_final: 0.7372 (m-10) REVERT: B 93 ARG cc_start: 0.7908 (mmp80) cc_final: 0.7242 (mmm160) REVERT: B 244 TRP cc_start: 0.7223 (m100) cc_final: 0.6954 (m100) REVERT: B 293 ASN cc_start: 0.7795 (p0) cc_final: 0.6928 (t0) REVERT: B 370 THR cc_start: 0.7036 (p) cc_final: 0.6737 (p) REVERT: B 374 GLU cc_start: 0.6044 (mt-10) cc_final: 0.5821 (pm20) REVERT: B 396 THR cc_start: 0.8467 (m) cc_final: 0.7946 (p) REVERT: B 496 GLN cc_start: 0.4401 (tt0) cc_final: 0.3895 (tp40) REVERT: B 504 ASP cc_start: 0.4258 (t0) cc_final: 0.3769 (t0) REVERT: C 1 MET cc_start: 0.7047 (ptt) cc_final: 0.6826 (mtm) REVERT: C 84 TYR cc_start: 0.8347 (m-80) cc_final: 0.7914 (m-80) REVERT: C 123 VAL cc_start: 0.8198 (m) cc_final: 0.7988 (p) REVERT: C 124 LYS cc_start: 0.7545 (ptpp) cc_final: 0.6787 (ttmm) REVERT: C 191 ARG cc_start: 0.7724 (mmm-85) cc_final: 0.7213 (mtm-85) REVERT: C 202 ASN cc_start: 0.7546 (p0) cc_final: 0.7000 (t0) REVERT: C 220 MET cc_start: 0.6782 (mmt) cc_final: 0.6369 (ttp) REVERT: C 264 ASP cc_start: 0.7821 (m-30) cc_final: 0.7612 (m-30) REVERT: C 343 GLU cc_start: 0.7242 (mt-10) cc_final: 0.7033 (mm-30) REVERT: C 524 LYS cc_start: 0.7872 (ttmt) cc_final: 0.7485 (tmtt) REVERT: D 176 ASP cc_start: 0.8062 (t0) cc_final: 0.7840 (t0) REVERT: D 325 ILE cc_start: 0.7945 (mt) cc_final: 0.7570 (mt) REVERT: D 349 TYR cc_start: 0.8253 (t80) cc_final: 0.7573 (t80) REVERT: D 368 LYS cc_start: 0.7590 (tptp) cc_final: 0.7329 (tptt) REVERT: D 376 LYS cc_start: 0.7022 (tttp) cc_final: 0.6800 (tptt) REVERT: D 410 ARG cc_start: 0.6410 (mmm-85) cc_final: 0.5849 (mmt180) REVERT: D 437 GLN cc_start: 0.7864 (mt0) cc_final: 0.7258 (mt0) REVERT: D 452 LYS cc_start: 0.5023 (mmtp) cc_final: 0.4818 (pttt) REVERT: E 126 LYS cc_start: 0.7805 (ttpt) cc_final: 0.7235 (mtpp) REVERT: E 194 MET cc_start: 0.7103 (mtm) cc_final: 0.6251 (mtm) REVERT: E 210 ARG cc_start: 0.7759 (ttp80) cc_final: 0.7526 (ttp-110) REVERT: E 216 ARG cc_start: 0.6516 (mtm-85) cc_final: 0.5956 (ptt180) REVERT: E 420 ARG cc_start: 0.5984 (tmm-80) cc_final: 0.5769 (mmm-85) REVERT: E 468 GLU cc_start: 0.5839 (pp20) cc_final: 0.5435 (tt0) REVERT: F 54 TYR cc_start: 0.7512 (p90) cc_final: 0.6550 (p90) REVERT: F 61 GLU cc_start: 0.5785 (mt-10) cc_final: 0.5567 (mt-10) REVERT: F 108 PRO cc_start: 0.8268 (Cg_endo) cc_final: 0.7995 (Cg_exo) REVERT: F 260 MET cc_start: 0.7661 (mmm) cc_final: 0.7317 (mmt) REVERT: F 315 SER cc_start: 0.8611 (m) cc_final: 0.8359 (p) REVERT: F 372 ARG cc_start: 0.7872 (ttp-170) cc_final: 0.7643 (mtp180) REVERT: G 23 LYS cc_start: 0.6751 (mttt) cc_final: 0.6320 (tppt) REVERT: G 198 LYS cc_start: 0.7977 (tmmt) cc_final: 0.7512 (tttt) REVERT: H 92 GLU cc_start: 0.6639 (tt0) cc_final: 0.5962 (mm-30) REVERT: H 97 THR cc_start: 0.6741 (p) cc_final: 0.6388 (t) REVERT: J 84 ARG cc_start: 0.4157 (ptm160) cc_final: 0.3611 (ttt-90) REVERT: J 170 ARG cc_start: 0.3290 (mtp85) cc_final: 0.2674 (tpt170) REVERT: L 72 ARG cc_start: 0.4482 (ptm160) cc_final: 0.4129 (ptp90) REVERT: L 89 GLU cc_start: 0.5506 (mm-30) cc_final: 0.5272 (pt0) REVERT: L 94 LEU cc_start: 0.3793 (tt) cc_final: 0.3186 (mm) outliers start: 0 outliers final: 0 residues processed: 649 average time/residue: 0.5065 time to fit residues: 486.8757 Evaluate side-chains 343 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 343 time to evaluate : 3.291 ------------------------------------------------------------------------------- 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: 9.9990 chunk 282 optimal weight: 0.7980 chunk 156 optimal weight: 9.9990 chunk 96 optimal weight: 10.0000 chunk 190 optimal weight: 9.9990 chunk 151 optimal weight: 9.9990 chunk 292 optimal weight: 7.9990 chunk 113 optimal weight: 10.0000 chunk 177 optimal weight: 3.9990 chunk 217 optimal weight: 4.9990 chunk 338 optimal weight: 0.0970 overall best weight: 3.5784 ------------------------------------------------------------------------------- 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 459 GLN ** 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: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.1809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 30114 Z= 0.239 Angle : 0.558 13.606 40813 Z= 0.284 Chirality : 0.044 0.214 4572 Planarity : 0.005 0.048 5333 Dihedral : 6.148 96.059 4259 Min Nonbonded Distance : 1.779 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.49 % Allowed : 7.65 % Favored : 90.85 % 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: 0.84 (0.14), residues: 3764 helix: 1.30 (0.14), residues: 1548 sheet: -0.02 (0.22), residues: 596 loop : 0.20 (0.16), residues: 1620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 119 HIS 0.007 0.001 HIS B 501 PHE 0.017 0.002 PHE F 204 TYR 0.019 0.001 TYR A 513 ARG 0.008 0.001 ARG F 280 *********************** 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 400 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 354 time to evaluate : 3.840 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 ASP cc_start: 0.7719 (m-30) cc_final: 0.7497 (m-30) REVERT: A 156 ARG cc_start: 0.5860 (mtp180) cc_final: 0.5388 (mtp180) REVERT: A 311 GLU cc_start: 0.7869 (mt-10) cc_final: 0.7617 (mt-10) REVERT: A 329 ARG cc_start: 0.6288 (mtm-85) cc_final: 0.5995 (mmp80) REVERT: A 481 ARG cc_start: 0.7382 (mmm-85) cc_final: 0.6836 (ttm-80) REVERT: A 483 VAL cc_start: 0.8278 (t) cc_final: 0.8053 (t) REVERT: A 498 ASN cc_start: 0.7157 (t0) cc_final: 0.6560 (m110) REVERT: A 524 LYS cc_start: 0.6091 (ttmt) cc_final: 0.5818 (mttt) REVERT: A 550 ARG cc_start: 0.6371 (mmt180) cc_final: 0.5411 (ttp-170) REVERT: A 565 GLU cc_start: 0.7220 (mp0) cc_final: 0.6693 (tp30) REVERT: B 25 TYR cc_start: 0.7775 (m-80) cc_final: 0.7426 (m-80) REVERT: B 93 ARG cc_start: 0.7916 (mmp80) cc_final: 0.7255 (mmm160) REVERT: B 293 ASN cc_start: 0.7862 (p0) cc_final: 0.7025 (t0) REVERT: B 323 MET cc_start: 0.7890 (mpp) cc_final: 0.7536 (mmm) REVERT: B 374 GLU cc_start: 0.6050 (mt-10) cc_final: 0.5655 (pm20) REVERT: B 375 GLU cc_start: 0.5214 (mt-10) cc_final: 0.4778 (mt-10) REVERT: B 396 THR cc_start: 0.8413 (m) cc_final: 0.7926 (p) REVERT: B 400 LEU cc_start: 0.7665 (mt) cc_final: 0.7365 (mp) REVERT: C 84 TYR cc_start: 0.8433 (m-80) cc_final: 0.8038 (m-80) REVERT: C 123 VAL cc_start: 0.8152 (m) cc_final: 0.7920 (p) REVERT: C 124 LYS cc_start: 0.7649 (ptpp) cc_final: 0.6875 (ttmm) REVERT: C 197 ARG cc_start: 0.7527 (ptm-80) cc_final: 0.7276 (ptm-80) REVERT: C 220 MET cc_start: 0.6844 (mmt) cc_final: 0.6382 (ttp) REVERT: C 363 GLU cc_start: 0.6933 (tp30) cc_final: 0.6714 (tp30) REVERT: C 489 ILE cc_start: 0.7943 (OUTLIER) cc_final: 0.7675 (mp) REVERT: C 524 LYS cc_start: 0.7895 (ttmt) cc_final: 0.7608 (tmtt) REVERT: D 176 ASP cc_start: 0.8043 (t0) cc_final: 0.7831 (t70) REVERT: D 353 ASP cc_start: 0.7845 (t0) cc_final: 0.7628 (m-30) REVERT: D 401 GLU cc_start: 0.7746 (OUTLIER) cc_final: 0.7544 (tm-30) REVERT: D 406 GLU cc_start: 0.7323 (tm-30) cc_final: 0.6618 (tm-30) REVERT: D 410 ARG cc_start: 0.6346 (mmm-85) cc_final: 0.5741 (mmm160) REVERT: D 437 GLN cc_start: 0.7817 (mt0) cc_final: 0.7500 (mt0) REVERT: D 452 LYS cc_start: 0.5118 (mmtp) cc_final: 0.4905 (pttt) REVERT: E 6 LYS cc_start: 0.5775 (ttmt) cc_final: 0.4889 (tptm) REVERT: E 216 ARG cc_start: 0.6605 (mtm-85) cc_final: 0.6210 (ptt180) REVERT: F 54 TYR cc_start: 0.7570 (p90) cc_final: 0.6503 (p90) REVERT: F 61 GLU cc_start: 0.5821 (mt-10) cc_final: 0.5521 (mt-10) REVERT: F 108 PRO cc_start: 0.8278 (Cg_endo) cc_final: 0.7950 (Cg_exo) REVERT: F 260 MET cc_start: 0.7675 (mmm) cc_final: 0.7403 (mmm) REVERT: F 305 LYS cc_start: 0.7738 (mtmt) cc_final: 0.7243 (mptt) REVERT: G 17 GLN cc_start: 0.7512 (mm-40) cc_final: 0.6998 (mt0) REVERT: G 23 LYS cc_start: 0.6887 (mttt) cc_final: 0.6456 (tppt) REVERT: G 198 LYS cc_start: 0.7999 (tmmt) cc_final: 0.7514 (tttt) REVERT: H 1 MET cc_start: 0.3602 (ttm) cc_final: 0.3340 (ttm) REVERT: H 86 VAL cc_start: 0.3586 (t) cc_final: 0.3043 (t) REVERT: H 92 GLU cc_start: 0.6515 (tt0) cc_final: 0.5798 (mm-30) REVERT: J 170 ARG cc_start: 0.3319 (mtp85) cc_final: 0.2676 (tpt170) REVERT: L 72 ARG cc_start: 0.4382 (ptm160) cc_final: 0.3905 (ptp90) REVERT: L 89 GLU cc_start: 0.5529 (mm-30) cc_final: 0.5295 (pt0) outliers start: 46 outliers final: 32 residues processed: 387 average time/residue: 0.4746 time to fit residues: 283.7954 Evaluate side-chains 327 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 293 time to evaluate : 3.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 424 TRP Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain C residue 489 ILE Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain C residue 545 LEU Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 72 SER Chi-restraints excluded: chain D residue 130 PHE Chi-restraints excluded: chain D residue 232 ILE Chi-restraints excluded: chain D residue 239 LEU Chi-restraints excluded: chain D residue 401 GLU Chi-restraints excluded: chain D residue 456 LYS Chi-restraints excluded: chain E residue 26 ASP Chi-restraints excluded: chain E residue 72 SER Chi-restraints excluded: chain E residue 205 ILE Chi-restraints excluded: chain E residue 308 VAL Chi-restraints excluded: chain E residue 363 ASN Chi-restraints excluded: chain E residue 457 ASP Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 223 LYS Chi-restraints excluded: chain F residue 428 GLN Chi-restraints excluded: chain F residue 444 SER Chi-restraints excluded: chain G residue 35 LEU Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 201 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 188 optimal weight: 9.9990 chunk 105 optimal weight: 10.0000 chunk 281 optimal weight: 0.0870 chunk 230 optimal weight: 8.9990 chunk 93 optimal weight: 9.9990 chunk 339 optimal weight: 8.9990 chunk 366 optimal weight: 10.0000 chunk 302 optimal weight: 10.0000 chunk 336 optimal weight: 6.9990 chunk 115 optimal weight: 1.9990 chunk 272 optimal weight: 4.9990 overall best weight: 4.6166 ------------------------------------------------------------------------------- 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 442 ASN E 166 GLN E 170 GLN L 96 GLN ** L 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.2406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 30114 Z= 0.287 Angle : 0.573 13.793 40813 Z= 0.292 Chirality : 0.045 0.195 4572 Planarity : 0.005 0.054 5333 Dihedral : 6.146 87.746 4259 Min Nonbonded Distance : 1.841 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.88 % Allowed : 11.09 % Favored : 87.03 % 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: 0.51 (0.14), residues: 3764 helix: 1.00 (0.14), residues: 1556 sheet: -0.02 (0.22), residues: 606 loop : -0.02 (0.16), residues: 1602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 119 HIS 0.006 0.001 HIS F 375 PHE 0.018 0.002 PHE E 414 TYR 0.015 0.002 TYR A 513 ARG 0.007 0.001 ARG B 210 *********************** 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 368 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 310 time to evaluate : 3.355 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 ASP cc_start: 0.7701 (m-30) cc_final: 0.7493 (m-30) REVERT: A 311 GLU cc_start: 0.7856 (mt-10) cc_final: 0.7603 (mt-10) REVERT: A 329 ARG cc_start: 0.6631 (mtm-85) cc_final: 0.6137 (mmp80) REVERT: A 481 ARG cc_start: 0.7336 (mmm-85) cc_final: 0.6800 (ttm-80) REVERT: A 483 VAL cc_start: 0.8248 (t) cc_final: 0.7984 (t) REVERT: A 498 ASN cc_start: 0.7228 (t0) cc_final: 0.6674 (m110) REVERT: A 503 VAL cc_start: 0.8355 (OUTLIER) cc_final: 0.8099 (p) REVERT: A 524 LYS cc_start: 0.6035 (ttmt) cc_final: 0.5786 (mttt) REVERT: A 550 ARG cc_start: 0.6372 (mmt180) cc_final: 0.5860 (mmt90) REVERT: A 565 GLU cc_start: 0.7280 (OUTLIER) cc_final: 0.6842 (tp30) REVERT: B 25 TYR cc_start: 0.7739 (m-80) cc_final: 0.7368 (m-80) REVERT: B 93 ARG cc_start: 0.7935 (mmp80) cc_final: 0.7275 (mmm160) REVERT: B 220 MET cc_start: 0.6730 (mtt) cc_final: 0.6501 (mtt) REVERT: B 293 ASN cc_start: 0.7974 (p0) cc_final: 0.7075 (t0) REVERT: B 374 GLU cc_start: 0.6047 (mt-10) cc_final: 0.5710 (pm20) REVERT: B 375 GLU cc_start: 0.5407 (mt-10) cc_final: 0.4922 (mt-10) REVERT: B 396 THR cc_start: 0.8394 (m) cc_final: 0.7959 (p) REVERT: B 400 LEU cc_start: 0.7642 (mt) cc_final: 0.7331 (mp) REVERT: B 564 GLU cc_start: 0.7336 (mm-30) cc_final: 0.6928 (pt0) REVERT: C 123 VAL cc_start: 0.8096 (m) cc_final: 0.7799 (p) REVERT: C 124 LYS cc_start: 0.7681 (ptpp) cc_final: 0.7012 (tptt) REVERT: C 165 GLU cc_start: 0.7891 (mt-10) cc_final: 0.7656 (mt-10) REVERT: C 220 MET cc_start: 0.6893 (mmt) cc_final: 0.6448 (ttp) REVERT: C 363 GLU cc_start: 0.6919 (tp30) cc_final: 0.6663 (tp30) REVERT: C 489 ILE cc_start: 0.7880 (OUTLIER) cc_final: 0.7589 (mp) REVERT: C 524 LYS cc_start: 0.7976 (ttmt) cc_final: 0.7620 (tmtt) REVERT: D 176 ASP cc_start: 0.8101 (t0) cc_final: 0.7804 (t0) REVERT: D 353 ASP cc_start: 0.7857 (t0) cc_final: 0.7620 (m-30) REVERT: D 406 GLU cc_start: 0.7354 (tm-30) cc_final: 0.6942 (tm-30) REVERT: D 410 ARG cc_start: 0.6322 (mmm-85) cc_final: 0.5952 (mmm160) REVERT: D 420 ARG cc_start: 0.6549 (mmm-85) cc_final: 0.6299 (ptt180) REVERT: D 437 GLN cc_start: 0.7805 (mt0) cc_final: 0.7228 (mt0) REVERT: D 452 LYS cc_start: 0.5210 (mmtp) cc_final: 0.4894 (pttt) REVERT: E 6 LYS cc_start: 0.5915 (ttmt) cc_final: 0.5114 (tptm) REVERT: F 54 TYR cc_start: 0.7691 (p90) cc_final: 0.6577 (p90) REVERT: F 61 GLU cc_start: 0.5800 (mt-10) cc_final: 0.5490 (mt-10) REVERT: F 260 MET cc_start: 0.7639 (mmm) cc_final: 0.7338 (mmm) REVERT: F 305 LYS cc_start: 0.7692 (mtmt) cc_final: 0.7218 (mptt) REVERT: G 17 GLN cc_start: 0.7504 (mm-40) cc_final: 0.7125 (mt0) REVERT: G 23 LYS cc_start: 0.6927 (mttt) cc_final: 0.6461 (tppt) REVERT: H 1 MET cc_start: 0.3856 (ttm) cc_final: 0.3570 (ttm) REVERT: H 86 VAL cc_start: 0.3700 (OUTLIER) cc_final: 0.3481 (t) REVERT: H 92 GLU cc_start: 0.6530 (tt0) cc_final: 0.5790 (mm-30) REVERT: J 170 ARG cc_start: 0.3211 (mtp85) cc_final: 0.2640 (tpt170) REVERT: L 89 GLU cc_start: 0.5476 (mm-30) cc_final: 0.5263 (pt0) REVERT: L 150 LEU cc_start: 0.5822 (pt) cc_final: 0.4920 (mt) outliers start: 58 outliers final: 41 residues processed: 352 average time/residue: 0.4418 time to fit residues: 242.9625 Evaluate side-chains 334 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 289 time to evaluate : 3.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 490 ILE Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 565 GLU Chi-restraints excluded: chain B residue 183 MET Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 424 TRP Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 519 ILE Chi-restraints excluded: chain B residue 525 GLU Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 177 ASP Chi-restraints excluded: chain C residue 203 THR Chi-restraints excluded: chain C residue 489 ILE Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain C residue 545 LEU Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 72 SER Chi-restraints excluded: chain D residue 130 PHE Chi-restraints excluded: chain D residue 156 SER Chi-restraints excluded: chain D residue 232 ILE Chi-restraints excluded: chain D residue 239 LEU Chi-restraints excluded: chain D residue 331 TYR Chi-restraints excluded: chain D residue 456 LYS Chi-restraints excluded: chain E residue 26 ASP Chi-restraints excluded: chain E residue 72 SER Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 308 VAL Chi-restraints excluded: chain E residue 431 SER Chi-restraints excluded: chain E residue 457 ASP Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 396 VAL Chi-restraints excluded: chain F residue 444 SER Chi-restraints excluded: chain G residue 35 LEU Chi-restraints excluded: chain G residue 96 VAL Chi-restraints excluded: chain G residue 201 ILE Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain I residue 104 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 335 optimal weight: 30.0000 chunk 255 optimal weight: 8.9990 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: 6.9990 chunk 360 optimal weight: 4.9990 chunk 177 optimal weight: 6.9990 chunk 322 optimal weight: 0.8980 chunk 97 optimal weight: 9.9990 overall best weight: 5.1788 ------------------------------------------------------------------------------- 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 166 GLN E 310 GLN F 206 GLN L 124 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.2922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 30114 Z= 0.314 Angle : 0.589 13.296 40813 Z= 0.302 Chirality : 0.045 0.182 4572 Planarity : 0.005 0.057 5333 Dihedral : 6.138 85.549 4259 Min Nonbonded Distance : 1.827 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.59 % Allowed : 13.36 % Favored : 84.04 % 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: 0.19 (0.14), residues: 3764 helix: 0.77 (0.14), residues: 1527 sheet: -0.18 (0.22), residues: 604 loop : -0.23 (0.15), residues: 1633 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 244 HIS 0.007 0.002 HIS F 375 PHE 0.018 0.002 PHE E 414 TYR 0.019 0.002 TYR D 349 ARG 0.008 0.001 ARG B 210 *********************** 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 381 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 301 time to evaluate : 3.443 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 481 ARG cc_start: 0.7274 (mmm-85) cc_final: 0.6739 (ttm-80) REVERT: A 483 VAL cc_start: 0.8205 (t) cc_final: 0.7956 (t) REVERT: A 498 ASN cc_start: 0.7127 (t0) cc_final: 0.6686 (m-40) REVERT: A 524 LYS cc_start: 0.6239 (ttmt) cc_final: 0.5937 (mttt) REVERT: A 550 ARG cc_start: 0.6415 (mmt180) cc_final: 0.5906 (mmt90) REVERT: A 565 GLU cc_start: 0.7145 (OUTLIER) cc_final: 0.6778 (mm-30) REVERT: B 93 ARG cc_start: 0.7883 (mmp80) cc_final: 0.7256 (mmm160) REVERT: B 212 LEU cc_start: 0.6748 (OUTLIER) cc_final: 0.6297 (mm) REVERT: B 293 ASN cc_start: 0.8010 (p0) cc_final: 0.7095 (t0) REVERT: B 374 GLU cc_start: 0.6114 (mt-10) cc_final: 0.5903 (pm20) REVERT: B 396 THR cc_start: 0.8480 (m) cc_final: 0.8067 (p) REVERT: B 400 LEU cc_start: 0.7539 (mt) cc_final: 0.7238 (mp) REVERT: B 506 TYR cc_start: 0.7512 (t80) cc_final: 0.7258 (t80) REVERT: C 124 LYS cc_start: 0.7585 (ptpp) cc_final: 0.7171 (tptt) REVERT: C 130 ARG cc_start: 0.7040 (mtm180) cc_final: 0.6316 (mmt-90) REVERT: C 220 MET cc_start: 0.6873 (mmt) cc_final: 0.6455 (ttp) REVERT: C 363 GLU cc_start: 0.6951 (tp30) cc_final: 0.6670 (tp30) REVERT: C 489 ILE cc_start: 0.7918 (OUTLIER) cc_final: 0.7650 (mp) REVERT: C 524 LYS cc_start: 0.7986 (ttmt) cc_final: 0.7559 (tmtt) REVERT: D 88 MET cc_start: 0.8750 (mmm) cc_final: 0.8371 (mmm) REVERT: D 176 ASP cc_start: 0.8135 (t0) cc_final: 0.7851 (t0) REVERT: D 353 ASP cc_start: 0.7767 (t0) cc_final: 0.7502 (m-30) REVERT: D 406 GLU cc_start: 0.7260 (tm-30) cc_final: 0.6979 (tm-30) REVERT: D 410 ARG cc_start: 0.6283 (mmm-85) cc_final: 0.5661 (mmt180) REVERT: D 420 ARG cc_start: 0.6623 (mmm-85) cc_final: 0.6359 (ptt180) REVERT: D 437 GLN cc_start: 0.7767 (mt0) cc_final: 0.7427 (tt0) REVERT: D 452 LYS cc_start: 0.5284 (mmtp) cc_final: 0.4954 (pttt) REVERT: E 210 ARG cc_start: 0.7569 (ttp-110) cc_final: 0.7279 (mtm110) REVERT: F 61 GLU cc_start: 0.5916 (mt-10) cc_final: 0.5658 (mt-10) REVERT: F 305 LYS cc_start: 0.7772 (mtmt) cc_final: 0.7260 (mptt) REVERT: G 17 GLN cc_start: 0.7476 (mm-40) cc_final: 0.7196 (mt0) REVERT: G 23 LYS cc_start: 0.6888 (mttt) cc_final: 0.6418 (tppt) REVERT: H 86 VAL cc_start: 0.3603 (t) cc_final: 0.3315 (t) REVERT: H 87 GLU cc_start: 0.6442 (mm-30) cc_final: 0.6217 (mm-30) REVERT: H 92 GLU cc_start: 0.6549 (tt0) cc_final: 0.5760 (mm-30) REVERT: J 170 ARG cc_start: 0.3319 (mtp85) cc_final: 0.2674 (tpt170) REVERT: L 89 GLU cc_start: 0.5515 (mm-30) cc_final: 0.5262 (pt0) REVERT: L 150 LEU cc_start: 0.5756 (pt) cc_final: 0.4673 (mt) outliers start: 80 outliers final: 53 residues processed: 363 average time/residue: 0.4326 time to fit residues: 246.9135 Evaluate side-chains 332 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 276 time to evaluate : 3.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 490 ILE Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 507 CYS Chi-restraints excluded: chain A residue 565 GLU Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 183 MET Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 424 TRP Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 470 LEU Chi-restraints excluded: chain B residue 519 ILE Chi-restraints excluded: chain B residue 525 GLU Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 177 ASP Chi-restraints excluded: chain C residue 489 ILE Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 72 SER Chi-restraints excluded: chain D residue 78 ASP Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 130 PHE Chi-restraints excluded: chain D residue 156 SER Chi-restraints excluded: chain D residue 232 ILE Chi-restraints excluded: chain D residue 239 LEU Chi-restraints excluded: chain D residue 456 LYS Chi-restraints excluded: chain E residue 26 ASP Chi-restraints excluded: chain E residue 72 SER Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 189 VAL Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain E residue 308 VAL Chi-restraints excluded: chain E residue 405 THR Chi-restraints excluded: chain E residue 431 SER Chi-restraints excluded: chain E residue 457 ASP Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 396 VAL Chi-restraints excluded: chain F residue 428 GLN Chi-restraints excluded: chain F residue 444 SER Chi-restraints excluded: chain G residue 25 VAL Chi-restraints excluded: chain G residue 35 LEU Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 96 VAL Chi-restraints excluded: chain G residue 201 ILE Chi-restraints excluded: chain I residue 104 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 300 optimal weight: 20.0000 chunk 204 optimal weight: 10.0000 chunk 5 optimal weight: 9.9990 chunk 268 optimal weight: 5.9990 chunk 148 optimal weight: 7.9990 chunk 307 optimal weight: 8.9990 chunk 249 optimal weight: 7.9990 chunk 0 optimal weight: 7.9990 chunk 184 optimal weight: 5.9990 chunk 323 optimal weight: 30.0000 chunk 90 optimal weight: 6.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- 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** F 206 GLN F 427 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.3377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 30114 Z= 0.409 Angle : 0.666 13.572 40813 Z= 0.342 Chirality : 0.048 0.290 4572 Planarity : 0.006 0.065 5333 Dihedral : 6.499 81.911 4259 Min Nonbonded Distance : 1.804 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 3.50 % Allowed : 15.05 % Favored : 81.45 % 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: 0.41 (0.13), residues: 1521 sheet: -0.35 (0.22), residues: 591 loop : -0.54 (0.15), residues: 1652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP J 100 HIS 0.008 0.002 HIS F 375 PHE 0.032 0.002 PHE B 415 TYR 0.021 0.002 TYR D 349 ARG 0.005 0.001 ARG I 87 *********************** 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 399 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 291 time to evaluate : 3.716 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 ASP cc_start: 0.4645 (m-30) cc_final: 0.4247 (t0) REVERT: A 311 GLU cc_start: 0.7889 (mt-10) cc_final: 0.7622 (mt-10) REVERT: A 329 ARG cc_start: 0.6913 (mtt90) cc_final: 0.6095 (mmp80) REVERT: A 481 ARG cc_start: 0.7262 (mmm-85) cc_final: 0.6687 (ttm-80) REVERT: A 483 VAL cc_start: 0.8187 (t) cc_final: 0.7927 (t) REVERT: A 498 ASN cc_start: 0.7217 (t0) cc_final: 0.6748 (m-40) REVERT: A 524 LYS cc_start: 0.6278 (ttmt) cc_final: 0.5997 (mttt) REVERT: A 565 GLU cc_start: 0.7095 (OUTLIER) cc_final: 0.6818 (mm-30) REVERT: B 93 ARG cc_start: 0.7856 (mmp80) cc_final: 0.7295 (mmm160) REVERT: B 212 LEU cc_start: 0.6799 (OUTLIER) cc_final: 0.6327 (mm) REVERT: B 400 LEU cc_start: 0.7541 (mt) cc_final: 0.7210 (mp) REVERT: B 464 LEU cc_start: 0.3947 (OUTLIER) cc_final: 0.3729 (pp) REVERT: C 124 LYS cc_start: 0.7512 (ptpp) cc_final: 0.7100 (mmtt) REVERT: C 130 ARG cc_start: 0.7138 (mtm180) cc_final: 0.6268 (mmt-90) REVERT: C 220 MET cc_start: 0.6891 (mmt) cc_final: 0.6507 (ttp) REVERT: C 363 GLU cc_start: 0.6978 (tp30) cc_final: 0.6686 (tp30) REVERT: C 489 ILE cc_start: 0.7877 (OUTLIER) cc_final: 0.7606 (mp) REVERT: C 524 LYS cc_start: 0.8020 (ttmt) cc_final: 0.7536 (tmtt) REVERT: C 571 GLN cc_start: 0.7984 (pt0) cc_final: 0.7549 (pp30) REVERT: D 176 ASP cc_start: 0.8237 (t0) cc_final: 0.7958 (t0) REVERT: D 353 ASP cc_start: 0.7833 (t0) cc_final: 0.7578 (m-30) REVERT: D 401 GLU cc_start: 0.7678 (tt0) cc_final: 0.7420 (tt0) REVERT: D 410 ARG cc_start: 0.6217 (mmm-85) cc_final: 0.5973 (mmm160) REVERT: D 437 GLN cc_start: 0.7813 (mt0) cc_final: 0.7535 (tt0) REVERT: D 452 LYS cc_start: 0.5335 (mmtp) cc_final: 0.4950 (pttt) REVERT: F 2 ASP cc_start: -0.0339 (OUTLIER) cc_final: -0.1415 (m-30) REVERT: F 61 GLU cc_start: 0.5912 (mt-10) cc_final: 0.5644 (mt-10) REVERT: F 200 GLU cc_start: 0.6539 (OUTLIER) cc_final: 0.6207 (mp0) REVERT: F 305 LYS cc_start: 0.7740 (mtmt) cc_final: 0.7248 (mptt) REVERT: G 17 GLN cc_start: 0.7493 (mm-40) cc_final: 0.7203 (mt0) REVERT: G 23 LYS cc_start: 0.6856 (mttt) cc_final: 0.6376 (tppt) REVERT: H 1 MET cc_start: 0.4177 (ttm) cc_final: 0.2919 (ttp) REVERT: H 86 VAL cc_start: 0.3683 (t) cc_final: 0.3414 (t) REVERT: H 92 GLU cc_start: 0.6672 (tt0) cc_final: 0.5760 (mm-30) REVERT: J 92 GLU cc_start: 0.2886 (tt0) cc_final: 0.2673 (tt0) REVERT: J 164 GLU cc_start: 0.3529 (tm-30) cc_final: 0.2947 (tm-30) REVERT: J 170 ARG cc_start: 0.3290 (mtp85) cc_final: 0.2560 (tpt170) REVERT: L 150 LEU cc_start: 0.5823 (pt) cc_final: 0.4688 (mt) outliers start: 108 outliers final: 74 residues processed: 383 average time/residue: 0.4161 time to fit residues: 254.1752 Evaluate side-chains 351 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 271 time to evaluate : 3.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 490 ILE Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 507 CYS Chi-restraints excluded: chain A residue 539 ILE Chi-restraints excluded: chain A residue 565 GLU Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 183 MET Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 424 TRP Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 490 ILE Chi-restraints excluded: chain B residue 519 ILE Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 83 ILE Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 177 ASP Chi-restraints excluded: chain C residue 203 THR Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 489 ILE Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 72 SER Chi-restraints excluded: chain D residue 78 ASP Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 130 PHE Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 156 SER Chi-restraints excluded: chain D residue 232 ILE Chi-restraints excluded: chain D residue 239 LEU Chi-restraints excluded: chain D residue 269 GLU Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain D residue 456 LYS Chi-restraints excluded: chain E residue 26 ASP Chi-restraints excluded: chain E residue 72 SER Chi-restraints excluded: chain E residue 101 ASP Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 189 VAL Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 234 THR Chi-restraints excluded: chain E residue 308 VAL Chi-restraints excluded: chain E residue 405 THR Chi-restraints excluded: chain E residue 431 SER Chi-restraints excluded: chain E residue 457 ASP Chi-restraints excluded: chain F residue 2 ASP Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 176 ASP Chi-restraints excluded: chain F residue 200 GLU Chi-restraints excluded: chain F residue 336 GLN Chi-restraints excluded: chain F residue 396 VAL Chi-restraints excluded: chain F residue 427 GLN Chi-restraints excluded: chain F residue 428 GLN Chi-restraints excluded: chain F residue 444 SER Chi-restraints excluded: chain G residue 25 VAL Chi-restraints excluded: chain G residue 35 LEU Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 96 VAL Chi-restraints excluded: chain G residue 119 THR Chi-restraints excluded: chain G residue 158 THR Chi-restraints excluded: chain G residue 164 LEU Chi-restraints excluded: chain G residue 201 ILE Chi-restraints excluded: chain H residue 42 TYR Chi-restraints excluded: chain H residue 63 MET Chi-restraints excluded: chain I residue 104 MET Chi-restraints excluded: chain K residue 99 VAL Chi-restraints excluded: chain L residue 83 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 121 optimal weight: 10.0000 chunk 324 optimal weight: 9.9990 chunk 71 optimal weight: 9.9990 chunk 211 optimal weight: 8.9990 chunk 89 optimal weight: 9.9990 chunk 360 optimal weight: 8.9990 chunk 299 optimal weight: 7.9990 chunk 167 optimal weight: 20.0000 chunk 30 optimal weight: 0.9990 chunk 119 optimal weight: 9.9990 chunk 189 optimal weight: 6.9990 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** F 427 GLN F 428 GLN H 30 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.3585 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= 0.389 Angle : 0.649 14.143 40813 Z= 0.332 Chirality : 0.047 0.194 4572 Planarity : 0.006 0.064 5333 Dihedral : 6.415 85.874 4259 Min Nonbonded Distance : 1.808 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 3.60 % Allowed : 16.02 % Favored : 80.38 % 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: -0.42 (0.14), residues: 3764 helix: 0.34 (0.13), residues: 1511 sheet: -0.38 (0.22), residues: 596 loop : -0.70 (0.15), residues: 1657 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP J 100 HIS 0.008 0.002 HIS A 185 PHE 0.019 0.002 PHE A 230 TYR 0.020 0.002 TYR D 349 ARG 0.004 0.001 ARG C 190 *********************** 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 392 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 281 time to evaluate : 3.771 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 ASP cc_start: 0.4639 (m-30) cc_final: 0.4291 (t0) REVERT: A 450 LEU cc_start: 0.7407 (OUTLIER) cc_final: 0.7183 (mp) REVERT: A 481 ARG cc_start: 0.7216 (mmm-85) cc_final: 0.6457 (ttt180) REVERT: A 483 VAL cc_start: 0.8183 (t) cc_final: 0.7934 (t) REVERT: A 498 ASN cc_start: 0.7125 (t0) cc_final: 0.6757 (m110) REVERT: A 524 LYS cc_start: 0.6316 (ttmt) cc_final: 0.6033 (mttt) REVERT: A 565 GLU cc_start: 0.7109 (OUTLIER) cc_final: 0.6806 (mm-30) REVERT: B 212 LEU cc_start: 0.6844 (OUTLIER) cc_final: 0.6393 (mm) REVERT: B 391 MET cc_start: 0.7654 (mmp) cc_final: 0.7237 (mmp) REVERT: B 400 LEU cc_start: 0.7566 (mt) cc_final: 0.7248 (mp) REVERT: B 435 LEU cc_start: 0.5923 (OUTLIER) cc_final: 0.5296 (mm) REVERT: B 464 LEU cc_start: 0.4047 (OUTLIER) cc_final: 0.3795 (pp) REVERT: C 124 LYS cc_start: 0.7498 (ptpp) cc_final: 0.7195 (tptt) REVERT: C 130 ARG cc_start: 0.7120 (mtm180) cc_final: 0.6262 (mmt-90) REVERT: C 220 MET cc_start: 0.6876 (mmt) cc_final: 0.6580 (ttp) REVERT: C 363 GLU cc_start: 0.7078 (tp30) cc_final: 0.6758 (tp30) REVERT: C 489 ILE cc_start: 0.7889 (OUTLIER) cc_final: 0.7619 (mp) REVERT: C 524 LYS cc_start: 0.8042 (ttmt) cc_final: 0.7530 (tmtt) REVERT: C 571 GLN cc_start: 0.7999 (pt0) cc_final: 0.7549 (pp30) REVERT: D 176 ASP cc_start: 0.8267 (t0) cc_final: 0.8010 (t0) REVERT: D 353 ASP cc_start: 0.7851 (t0) cc_final: 0.7571 (m-30) REVERT: D 401 GLU cc_start: 0.7926 (tt0) cc_final: 0.7603 (tt0) REVERT: D 410 ARG cc_start: 0.6305 (mmm-85) cc_final: 0.6007 (mmm160) REVERT: D 437 GLN cc_start: 0.7756 (mt0) cc_final: 0.7451 (tt0) REVERT: D 452 LYS cc_start: 0.5453 (mmtp) cc_final: 0.5033 (pttt) REVERT: F 2 ASP cc_start: -0.0793 (OUTLIER) cc_final: -0.1710 (m-30) REVERT: F 61 GLU cc_start: 0.5898 (mt-10) cc_final: 0.5637 (mt-10) REVERT: F 200 GLU cc_start: 0.6546 (OUTLIER) cc_final: 0.6334 (mp0) REVERT: F 305 LYS cc_start: 0.7679 (mtmt) cc_final: 0.7284 (mptt) REVERT: G 17 GLN cc_start: 0.7416 (mm-40) cc_final: 0.7156 (mt0) REVERT: G 23 LYS cc_start: 0.6864 (mttt) cc_final: 0.6375 (tppt) REVERT: H 92 GLU cc_start: 0.6683 (tt0) cc_final: 0.5732 (mm-30) REVERT: J 65 GLU cc_start: 0.2252 (OUTLIER) cc_final: 0.1842 (mp0) REVERT: J 164 GLU cc_start: 0.3251 (tm-30) cc_final: 0.2731 (tm-30) REVERT: J 170 ARG cc_start: 0.3496 (mtp85) cc_final: 0.2674 (tpt170) REVERT: L 150 LEU cc_start: 0.5745 (pt) cc_final: 0.4595 (mt) outliers start: 111 outliers final: 75 residues processed: 377 average time/residue: 0.4030 time to fit residues: 244.1260 Evaluate side-chains 352 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 268 time to evaluate : 3.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 490 ILE Chi-restraints excluded: chain A residue 507 CYS Chi-restraints excluded: chain A residue 539 ILE Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 565 GLU Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 183 MET Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 424 TRP Chi-restraints excluded: chain B residue 435 LEU Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 470 LEU Chi-restraints excluded: chain B residue 490 ILE Chi-restraints excluded: chain B residue 519 ILE Chi-restraints excluded: chain B residue 525 GLU Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 177 ASP Chi-restraints excluded: chain C residue 203 THR Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 489 ILE Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain D residue 72 SER Chi-restraints excluded: chain D residue 78 ASP Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 130 PHE Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 217 SER Chi-restraints excluded: chain D residue 232 ILE Chi-restraints excluded: chain D residue 239 LEU Chi-restraints excluded: chain D residue 269 GLU Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain D residue 456 LYS Chi-restraints excluded: chain E residue 26 ASP Chi-restraints excluded: chain E residue 72 SER Chi-restraints excluded: chain E residue 101 ASP Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 189 VAL Chi-restraints excluded: chain E residue 205 ILE Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 234 THR Chi-restraints excluded: chain E residue 308 VAL Chi-restraints excluded: chain E residue 405 THR Chi-restraints excluded: chain E residue 457 ASP Chi-restraints excluded: chain F residue 2 ASP Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 176 ASP Chi-restraints excluded: chain F residue 200 GLU Chi-restraints excluded: chain F residue 228 THR Chi-restraints excluded: chain F residue 396 VAL Chi-restraints excluded: chain F residue 427 GLN Chi-restraints excluded: chain F residue 428 GLN Chi-restraints excluded: chain F residue 444 SER Chi-restraints excluded: chain G residue 25 VAL Chi-restraints excluded: chain G residue 35 LEU Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 96 VAL Chi-restraints excluded: chain G residue 114 LEU Chi-restraints excluded: chain G residue 158 THR Chi-restraints excluded: chain G residue 164 LEU Chi-restraints excluded: chain G residue 201 ILE Chi-restraints excluded: chain H residue 42 TYR Chi-restraints excluded: chain H residue 63 MET Chi-restraints excluded: chain I residue 104 MET Chi-restraints excluded: chain J residue 65 GLU Chi-restraints excluded: chain K residue 99 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 347 optimal weight: 5.9990 chunk 40 optimal weight: 9.9990 chunk 205 optimal weight: 0.9990 chunk 263 optimal weight: 10.0000 chunk 204 optimal weight: 1.9990 chunk 303 optimal weight: 8.9990 chunk 201 optimal weight: 6.9990 chunk 359 optimal weight: 6.9990 chunk 224 optimal weight: 9.9990 chunk 219 optimal weight: 2.9990 chunk 165 optimal weight: 8.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- 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** B 290 ASN D 377 GLN F 427 GLN ** H 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.3606 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= 0.244 Angle : 0.562 13.143 40813 Z= 0.286 Chirality : 0.044 0.176 4572 Planarity : 0.005 0.058 5333 Dihedral : 6.035 81.903 4259 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.79 % Allowed : 17.35 % Favored : 79.86 % 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: -0.19 (0.14), residues: 3764 helix: 0.60 (0.14), residues: 1509 sheet: -0.38 (0.21), residues: 613 loop : -0.60 (0.15), residues: 1642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP J 100 HIS 0.006 0.001 HIS B 145 PHE 0.025 0.002 PHE A 563 TYR 0.017 0.001 TYR D 349 ARG 0.003 0.000 ARG B 41 *********************** 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 372 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 286 time to evaluate : 3.446 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 ASP cc_start: 0.4646 (m-30) cc_final: 0.4332 (t0) REVERT: A 329 ARG cc_start: 0.6928 (mtt90) cc_final: 0.6047 (mmp80) REVERT: A 481 ARG cc_start: 0.7190 (mmm-85) cc_final: 0.6433 (ttt180) REVERT: A 483 VAL cc_start: 0.8178 (t) cc_final: 0.7931 (t) REVERT: A 490 ILE cc_start: 0.7910 (OUTLIER) cc_final: 0.7534 (tp) REVERT: A 498 ASN cc_start: 0.6931 (t0) cc_final: 0.6681 (m110) REVERT: A 524 LYS cc_start: 0.6277 (ttmt) cc_final: 0.6005 (mttt) REVERT: A 565 GLU cc_start: 0.7072 (OUTLIER) cc_final: 0.6718 (mm-30) REVERT: B 212 LEU cc_start: 0.6805 (OUTLIER) cc_final: 0.6363 (mm) REVERT: B 400 LEU cc_start: 0.7532 (mt) cc_final: 0.7207 (mp) REVERT: B 415 PHE cc_start: 0.6173 (t80) cc_final: 0.5911 (m-10) REVERT: B 464 LEU cc_start: 0.4077 (OUTLIER) cc_final: 0.3839 (pp) REVERT: C 124 LYS cc_start: 0.7463 (ptpp) cc_final: 0.7151 (mmtt) REVERT: C 130 ARG cc_start: 0.7143 (mtm180) cc_final: 0.6305 (mmt-90) REVERT: C 220 MET cc_start: 0.6838 (mmt) cc_final: 0.6588 (ttp) REVERT: C 363 GLU cc_start: 0.7039 (tp30) cc_final: 0.6716 (tp30) REVERT: C 489 ILE cc_start: 0.7903 (OUTLIER) cc_final: 0.7615 (mp) REVERT: C 524 LYS cc_start: 0.8013 (ttmt) cc_final: 0.7507 (tmtt) REVERT: C 571 GLN cc_start: 0.7991 (pt0) cc_final: 0.7565 (pp30) REVERT: D 176 ASP cc_start: 0.8162 (t0) cc_final: 0.7867 (t0) REVERT: D 353 ASP cc_start: 0.7808 (t0) cc_final: 0.7553 (m-30) REVERT: D 401 GLU cc_start: 0.7937 (tt0) cc_final: 0.7640 (tt0) REVERT: D 410 ARG cc_start: 0.6258 (mmm-85) cc_final: 0.5717 (mmt180) REVERT: D 437 GLN cc_start: 0.7719 (mt0) cc_final: 0.7296 (mt0) REVERT: D 452 LYS cc_start: 0.5402 (mmtp) cc_final: 0.5013 (pttt) REVERT: F 2 ASP cc_start: -0.0758 (OUTLIER) cc_final: -0.1698 (m-30) REVERT: F 61 GLU cc_start: 0.5889 (mt-10) cc_final: 0.5628 (mt-10) REVERT: F 200 GLU cc_start: 0.6563 (OUTLIER) cc_final: 0.6228 (mp0) REVERT: F 305 LYS cc_start: 0.7675 (mtmt) cc_final: 0.7282 (mptt) REVERT: G 17 GLN cc_start: 0.7431 (mm-40) cc_final: 0.7217 (mt0) REVERT: G 47 MET cc_start: 0.5565 (tpt) cc_final: 0.5021 (mpp) REVERT: H 27 GLU cc_start: 0.2662 (OUTLIER) cc_final: 0.2202 (mm-30) REVERT: H 92 GLU cc_start: 0.6724 (tt0) cc_final: 0.5762 (mm-30) REVERT: J 65 GLU cc_start: 0.2278 (OUTLIER) cc_final: 0.1885 (mp0) REVERT: J 164 GLU cc_start: 0.3158 (OUTLIER) cc_final: 0.2952 (tm-30) REVERT: J 170 ARG cc_start: 0.3564 (mtp85) cc_final: 0.2727 (tpt170) REVERT: L 150 LEU cc_start: 0.5725 (pt) cc_final: 0.4648 (mt) outliers start: 86 outliers final: 60 residues processed: 357 average time/residue: 0.3876 time to fit residues: 222.1536 Evaluate side-chains 344 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 274 time to evaluate : 3.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 ASP Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 490 ILE Chi-restraints excluded: chain A residue 507 CYS Chi-restraints excluded: chain A residue 565 GLU Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 209 MET Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 424 TRP Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 519 ILE Chi-restraints excluded: chain B residue 525 GLU Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 83 ILE Chi-restraints excluded: chain C residue 122 MET Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 177 ASP Chi-restraints excluded: chain C residue 203 THR Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 489 ILE Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain D residue 72 SER Chi-restraints excluded: chain D residue 78 ASP Chi-restraints excluded: chain D residue 130 PHE Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 217 SER Chi-restraints excluded: chain D residue 232 ILE Chi-restraints excluded: chain D residue 239 LEU Chi-restraints excluded: chain D residue 269 GLU Chi-restraints excluded: chain D residue 331 TYR Chi-restraints excluded: chain D residue 456 LYS Chi-restraints excluded: chain E residue 26 ASP Chi-restraints excluded: chain E residue 72 SER Chi-restraints excluded: chain E residue 234 THR Chi-restraints excluded: chain E residue 308 VAL Chi-restraints excluded: chain E residue 457 ASP Chi-restraints excluded: chain F residue 2 ASP Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 176 ASP Chi-restraints excluded: chain F residue 200 GLU Chi-restraints excluded: chain F residue 228 THR Chi-restraints excluded: chain F residue 336 GLN Chi-restraints excluded: chain F residue 427 GLN Chi-restraints excluded: chain F residue 428 GLN Chi-restraints excluded: chain F residue 444 SER Chi-restraints excluded: chain G residue 25 VAL Chi-restraints excluded: chain G residue 35 LEU Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 96 VAL Chi-restraints excluded: chain G residue 114 LEU Chi-restraints excluded: chain G residue 158 THR Chi-restraints excluded: chain G residue 201 ILE Chi-restraints excluded: chain H residue 27 GLU Chi-restraints excluded: chain H residue 63 MET Chi-restraints excluded: chain H residue 104 LEU Chi-restraints excluded: chain I residue 104 MET Chi-restraints excluded: chain J residue 65 GLU Chi-restraints excluded: chain J residue 164 GLU Chi-restraints excluded: chain K residue 99 VAL Chi-restraints excluded: chain L residue 83 VAL 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: 7.9990 chunk 108 optimal weight: 0.9980 chunk 70 optimal weight: 7.9990 chunk 69 optimal weight: 5.9990 chunk 228 optimal weight: 0.9990 chunk 244 optimal weight: 10.0000 chunk 177 optimal weight: 10.0000 chunk 33 optimal weight: 5.9990 chunk 282 optimal weight: 4.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- 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 377 GLN F 427 GLN F 428 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.3661 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= 0.245 Angle : 0.556 13.009 40813 Z= 0.282 Chirality : 0.044 0.175 4572 Planarity : 0.005 0.058 5333 Dihedral : 5.835 81.514 4259 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.98 % Allowed : 17.42 % Favored : 79.60 % 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: 0.72 (0.14), residues: 1504 sheet: -0.39 (0.21), residues: 616 loop : -0.55 (0.15), residues: 1644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP J 100 HIS 0.005 0.001 HIS A 185 PHE 0.016 0.002 PHE E 414 TYR 0.018 0.001 TYR D 349 ARG 0.004 0.000 ARG D 420 *********************** 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 384 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 292 time to evaluate : 3.473 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 ASP cc_start: 0.4685 (m-30) cc_final: 0.4367 (t0) REVERT: A 257 GLU cc_start: 0.8142 (tp30) cc_final: 0.7902 (tp30) REVERT: A 329 ARG cc_start: 0.6933 (mtt90) cc_final: 0.6063 (mmp80) REVERT: A 481 ARG cc_start: 0.7182 (mmm-85) cc_final: 0.6429 (ttt180) REVERT: A 483 VAL cc_start: 0.8183 (t) cc_final: 0.7943 (t) REVERT: A 490 ILE cc_start: 0.7888 (OUTLIER) cc_final: 0.7496 (tp) REVERT: A 498 ASN cc_start: 0.6915 (t0) cc_final: 0.6658 (m110) REVERT: A 524 LYS cc_start: 0.6257 (ttmt) cc_final: 0.5984 (mttt) REVERT: A 565 GLU cc_start: 0.6996 (OUTLIER) cc_final: 0.6700 (mm-30) REVERT: B 212 LEU cc_start: 0.6755 (OUTLIER) cc_final: 0.6283 (mm) REVERT: B 375 GLU cc_start: 0.6034 (mt-10) cc_final: 0.5224 (mt-10) REVERT: B 400 LEU cc_start: 0.7546 (mt) cc_final: 0.7197 (mp) REVERT: B 415 PHE cc_start: 0.6132 (t80) cc_final: 0.5905 (m-10) REVERT: B 464 LEU cc_start: 0.4076 (OUTLIER) cc_final: 0.3839 (pp) REVERT: B 509 MET cc_start: 0.5736 (mmt) cc_final: 0.5489 (mmt) REVERT: B 564 GLU cc_start: 0.7502 (mm-30) cc_final: 0.6945 (pt0) REVERT: C 124 LYS cc_start: 0.7477 (ptpp) cc_final: 0.7210 (mmtt) REVERT: C 130 ARG cc_start: 0.7218 (mtm180) cc_final: 0.6349 (mmt-90) REVERT: C 220 MET cc_start: 0.6829 (mmt) cc_final: 0.6567 (ttp) REVERT: C 264 ASP cc_start: 0.7349 (m-30) cc_final: 0.6953 (m-30) REVERT: C 363 GLU cc_start: 0.7042 (tp30) cc_final: 0.6713 (tp30) REVERT: C 489 ILE cc_start: 0.7923 (OUTLIER) cc_final: 0.7639 (mp) REVERT: C 524 LYS cc_start: 0.8012 (ttmt) cc_final: 0.7507 (tmtt) REVERT: C 571 GLN cc_start: 0.7992 (pt0) cc_final: 0.7565 (pp30) REVERT: D 49 GLU cc_start: 0.8104 (tm-30) cc_final: 0.7804 (tm-30) REVERT: D 176 ASP cc_start: 0.8136 (t0) cc_final: 0.7904 (t70) REVERT: D 353 ASP cc_start: 0.7809 (t0) cc_final: 0.7555 (m-30) REVERT: D 401 GLU cc_start: 0.8021 (tt0) cc_final: 0.7762 (tt0) REVERT: D 410 ARG cc_start: 0.6248 (mmm-85) cc_final: 0.5692 (mmt180) REVERT: D 437 GLN cc_start: 0.7715 (mt0) cc_final: 0.7287 (mt0) REVERT: D 452 LYS cc_start: 0.5334 (mmtp) cc_final: 0.5021 (pttt) REVERT: E 420 ARG cc_start: 0.7005 (mmm-85) cc_final: 0.6753 (mmm-85) REVERT: F 2 ASP cc_start: -0.0849 (OUTLIER) cc_final: -0.1768 (m-30) REVERT: F 61 GLU cc_start: 0.5785 (mt-10) cc_final: 0.5525 (mt-10) REVERT: F 200 GLU cc_start: 0.6523 (OUTLIER) cc_final: 0.6240 (mp0) REVERT: F 305 LYS cc_start: 0.7738 (mtmt) cc_final: 0.7358 (mptt) REVERT: G 47 MET cc_start: 0.5528 (tpt) cc_final: 0.4937 (mpp) REVERT: G 59 GLU cc_start: 0.3305 (mm-30) cc_final: 0.3058 (tt0) REVERT: H 92 GLU cc_start: 0.6761 (tt0) cc_final: 0.5790 (mm-30) REVERT: J 65 GLU cc_start: 0.2263 (OUTLIER) cc_final: 0.1869 (mp0) REVERT: J 164 GLU cc_start: 0.3176 (OUTLIER) cc_final: 0.2958 (tm-30) REVERT: J 170 ARG cc_start: 0.3389 (mtp85) cc_final: 0.2588 (tpt170) REVERT: L 150 LEU cc_start: 0.5827 (pt) cc_final: 0.4745 (mt) outliers start: 92 outliers final: 73 residues processed: 367 average time/residue: 0.4163 time to fit residues: 245.4635 Evaluate side-chains 358 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 276 time to evaluate : 3.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 GLU Chi-restraints excluded: chain A residue 177 ASP Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 490 ILE Chi-restraints excluded: chain A residue 507 CYS Chi-restraints excluded: chain A residue 565 GLU Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 209 MET Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 424 TRP Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 470 LEU Chi-restraints excluded: chain B residue 525 GLU Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 83 ILE Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 122 MET Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 177 ASP Chi-restraints excluded: chain C residue 203 THR Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 489 ILE Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain D residue 72 SER Chi-restraints excluded: chain D residue 78 ASP Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 130 PHE Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 217 SER Chi-restraints excluded: chain D residue 232 ILE Chi-restraints excluded: chain D residue 239 LEU Chi-restraints excluded: chain D residue 269 GLU Chi-restraints excluded: chain D residue 456 LYS Chi-restraints excluded: chain E residue 26 ASP Chi-restraints excluded: chain E residue 72 SER Chi-restraints excluded: chain E residue 101 ASP Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 234 THR Chi-restraints excluded: chain E residue 250 ASP Chi-restraints excluded: chain E residue 308 VAL Chi-restraints excluded: chain E residue 457 ASP Chi-restraints excluded: chain F residue 2 ASP Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 176 ASP Chi-restraints excluded: chain F residue 200 GLU Chi-restraints excluded: chain F residue 228 THR Chi-restraints excluded: chain F residue 427 GLN Chi-restraints excluded: chain F residue 428 GLN Chi-restraints excluded: chain F residue 444 SER Chi-restraints excluded: chain G residue 9 MET Chi-restraints excluded: chain G residue 25 VAL Chi-restraints excluded: chain G residue 35 LEU Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 96 VAL Chi-restraints excluded: chain G residue 114 LEU Chi-restraints excluded: chain G residue 158 THR Chi-restraints excluded: chain G residue 164 LEU Chi-restraints excluded: chain G residue 201 ILE Chi-restraints excluded: chain H residue 42 TYR Chi-restraints excluded: chain H residue 63 MET Chi-restraints excluded: chain I residue 104 MET Chi-restraints excluded: chain J residue 65 GLU Chi-restraints excluded: chain J residue 164 GLU Chi-restraints excluded: chain J residue 178 LEU Chi-restraints excluded: chain K residue 99 VAL Chi-restraints excluded: chain L residue 83 VAL Chi-restraints excluded: chain L residue 109 LEU 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: 5.9990 chunk 314 optimal weight: 9.9990 chunk 335 optimal weight: 40.0000 chunk 201 optimal weight: 1.9990 chunk 145 optimal weight: 4.9990 chunk 263 optimal weight: 7.9990 chunk 102 optimal weight: 10.0000 chunk 302 optimal weight: 9.9990 chunk 316 optimal weight: 20.0000 chunk 333 optimal weight: 4.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- 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** D 377 GLN F 427 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.3755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 30114 Z= 0.310 Angle : 0.591 14.905 40813 Z= 0.300 Chirality : 0.045 0.182 4572 Planarity : 0.005 0.063 5333 Dihedral : 5.881 81.180 4259 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 3.34 % Allowed : 17.29 % Favored : 79.37 % 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: -0.21 (0.14), residues: 3764 helix: 0.62 (0.14), residues: 1505 sheet: -0.37 (0.21), residues: 614 loop : -0.65 (0.15), residues: 1645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP J 100 HIS 0.006 0.001 HIS B 185 PHE 0.017 0.002 PHE E 414 TYR 0.021 0.002 TYR D 349 ARG 0.004 0.000 ARG D 420 *********************** 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 389 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 286 time to evaluate : 3.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 ASP cc_start: 0.4705 (m-30) cc_final: 0.4366 (t0) REVERT: A 311 GLU cc_start: 0.7919 (mt-10) cc_final: 0.7665 (mt-10) REVERT: A 329 ARG cc_start: 0.6979 (mtt90) cc_final: 0.6123 (mmp80) REVERT: A 481 ARG cc_start: 0.7189 (mmm-85) cc_final: 0.6435 (ttt180) REVERT: A 483 VAL cc_start: 0.8191 (t) cc_final: 0.7955 (t) REVERT: A 498 ASN cc_start: 0.6939 (t0) cc_final: 0.6633 (m110) REVERT: A 524 LYS cc_start: 0.6276 (ttmt) cc_final: 0.5995 (mttt) REVERT: A 565 GLU cc_start: 0.7046 (OUTLIER) cc_final: 0.6722 (mm-30) REVERT: B 212 LEU cc_start: 0.6753 (OUTLIER) cc_final: 0.6283 (mm) REVERT: B 230 PHE cc_start: 0.6286 (t80) cc_final: 0.5979 (t80) REVERT: B 375 GLU cc_start: 0.6108 (mt-10) cc_final: 0.5308 (mt-10) REVERT: B 400 LEU cc_start: 0.7530 (mt) cc_final: 0.7185 (mp) REVERT: B 415 PHE cc_start: 0.6151 (t80) cc_final: 0.5922 (m-10) REVERT: B 435 LEU cc_start: 0.5846 (OUTLIER) cc_final: 0.5206 (mm) REVERT: B 464 LEU cc_start: 0.4032 (OUTLIER) cc_final: 0.3783 (pp) REVERT: B 564 GLU cc_start: 0.7553 (mm-30) cc_final: 0.6937 (pt0) REVERT: C 124 LYS cc_start: 0.7479 (ptpp) cc_final: 0.7227 (mmtt) REVERT: C 130 ARG cc_start: 0.7258 (mtm180) cc_final: 0.6374 (mmt-90) REVERT: C 220 MET cc_start: 0.6841 (mmt) cc_final: 0.6578 (ttp) REVERT: C 264 ASP cc_start: 0.7377 (m-30) cc_final: 0.6965 (m-30) REVERT: C 363 GLU cc_start: 0.7052 (tp30) cc_final: 0.6715 (tp30) REVERT: C 489 ILE cc_start: 0.7923 (OUTLIER) cc_final: 0.7637 (mp) REVERT: C 524 LYS cc_start: 0.8038 (ttmt) cc_final: 0.7527 (tmtt) REVERT: C 571 GLN cc_start: 0.8004 (pt0) cc_final: 0.7558 (pp30) REVERT: D 49 GLU cc_start: 0.8160 (tm-30) cc_final: 0.7858 (tm-30) REVERT: D 176 ASP cc_start: 0.8161 (t0) cc_final: 0.7930 (t70) REVERT: D 353 ASP cc_start: 0.7781 (t0) cc_final: 0.7510 (m-30) REVERT: D 410 ARG cc_start: 0.6239 (mmm-85) cc_final: 0.5831 (mmm160) REVERT: D 437 GLN cc_start: 0.7739 (mt0) cc_final: 0.7301 (mt0) REVERT: D 452 LYS cc_start: 0.5338 (mmtp) cc_final: 0.5021 (pttt) REVERT: F 2 ASP cc_start: -0.0832 (OUTLIER) cc_final: -0.1770 (m-30) REVERT: F 61 GLU cc_start: 0.5808 (mt-10) cc_final: 0.5547 (mt-10) REVERT: F 200 GLU cc_start: 0.6576 (OUTLIER) cc_final: 0.6364 (mp0) REVERT: F 305 LYS cc_start: 0.7774 (mtmt) cc_final: 0.7381 (mptt) REVERT: G 47 MET cc_start: 0.5525 (tpt) cc_final: 0.4943 (mpp) REVERT: G 59 GLU cc_start: 0.3341 (mm-30) cc_final: 0.3081 (tt0) REVERT: H 27 GLU cc_start: 0.2725 (OUTLIER) cc_final: 0.2280 (mm-30) REVERT: H 92 GLU cc_start: 0.6773 (tt0) cc_final: 0.5796 (mm-30) REVERT: J 65 GLU cc_start: 0.2340 (OUTLIER) cc_final: 0.1952 (mp0) REVERT: J 164 GLU cc_start: 0.3291 (OUTLIER) cc_final: 0.3040 (tm-30) REVERT: J 170 ARG cc_start: 0.3351 (mtp85) cc_final: 0.2557 (tpt170) REVERT: L 150 LEU cc_start: 0.5824 (pt) cc_final: 0.4732 (mt) outliers start: 103 outliers final: 83 residues processed: 373 average time/residue: 0.4034 time to fit residues: 243.1682 Evaluate side-chains 372 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 279 time to evaluate : 3.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 GLU Chi-restraints excluded: chain A residue 177 ASP Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 490 ILE Chi-restraints excluded: chain A residue 507 CYS Chi-restraints excluded: chain A residue 539 ILE Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 565 GLU Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 209 MET Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 424 TRP Chi-restraints excluded: chain B residue 435 LEU Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 470 LEU Chi-restraints excluded: chain B residue 525 GLU Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 83 ILE Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 122 MET Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 177 ASP Chi-restraints excluded: chain C residue 203 THR Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 489 ILE Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain D residue 72 SER Chi-restraints excluded: chain D residue 78 ASP Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 130 PHE Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 217 SER Chi-restraints excluded: chain D residue 232 ILE Chi-restraints excluded: chain D residue 239 LEU Chi-restraints excluded: chain D residue 269 GLU Chi-restraints excluded: chain D residue 331 TYR Chi-restraints excluded: chain D residue 456 LYS Chi-restraints excluded: chain E residue 26 ASP Chi-restraints excluded: chain E residue 72 SER Chi-restraints excluded: chain E residue 101 ASP Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 196 ILE Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 234 THR Chi-restraints excluded: chain E residue 250 ASP Chi-restraints excluded: chain E residue 308 VAL Chi-restraints excluded: chain E residue 396 VAL Chi-restraints excluded: chain E residue 416 ASP Chi-restraints excluded: chain E residue 457 ASP Chi-restraints excluded: chain F residue 2 ASP Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 176 ASP Chi-restraints excluded: chain F residue 200 GLU Chi-restraints excluded: chain F residue 228 THR Chi-restraints excluded: chain F residue 336 GLN Chi-restraints excluded: chain F residue 396 VAL Chi-restraints excluded: chain F residue 427 GLN Chi-restraints excluded: chain F residue 428 GLN Chi-restraints excluded: chain F residue 444 SER Chi-restraints excluded: chain G residue 9 MET Chi-restraints excluded: chain G residue 25 VAL Chi-restraints excluded: chain G residue 35 LEU Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 96 VAL Chi-restraints excluded: chain G residue 114 LEU Chi-restraints excluded: chain G residue 158 THR Chi-restraints excluded: chain G residue 164 LEU Chi-restraints excluded: chain G residue 201 ILE Chi-restraints excluded: chain H residue 27 GLU Chi-restraints excluded: chain H residue 42 TYR Chi-restraints excluded: chain H residue 63 MET Chi-restraints excluded: chain I residue 104 MET Chi-restraints excluded: chain J residue 65 GLU Chi-restraints excluded: chain J residue 164 GLU Chi-restraints excluded: chain K residue 99 VAL Chi-restraints excluded: chain L residue 83 VAL Chi-restraints excluded: chain L residue 109 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 219 optimal weight: 0.0020 chunk 354 optimal weight: 20.0000 chunk 216 optimal weight: 10.0000 chunk 168 optimal weight: 4.9990 chunk 246 optimal weight: 7.9990 chunk 371 optimal weight: 0.9990 chunk 342 optimal weight: 9.9990 chunk 295 optimal weight: 0.8980 chunk 30 optimal weight: 4.9990 chunk 228 optimal weight: 0.9990 chunk 181 optimal weight: 9.9990 overall best weight: 1.5794 ------------------------------------------------------------------------------- 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 397 GLN D 377 GLN F 427 GLN F 428 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.3728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 30114 Z= 0.156 Angle : 0.509 14.517 40813 Z= 0.256 Chirality : 0.042 0.164 4572 Planarity : 0.004 0.052 5333 Dihedral : 5.489 80.313 4259 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.85 % Allowed : 18.68 % Favored : 79.47 % 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: 0.13 (0.14), residues: 3764 helix: 0.89 (0.14), residues: 1527 sheet: -0.30 (0.22), residues: 601 loop : -0.41 (0.15), residues: 1636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F 471 HIS 0.005 0.001 HIS B 145 PHE 0.014 0.001 PHE B 494 TYR 0.013 0.001 TYR D 349 ARG 0.004 0.000 ARG D 420 ********************** 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 358 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 301 time to evaluate : 3.866 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 ASP cc_start: 0.4686 (m-30) cc_final: 0.4438 (t0) REVERT: A 257 GLU cc_start: 0.8101 (tp30) cc_final: 0.7871 (tp30) REVERT: A 329 ARG cc_start: 0.6801 (mtt90) cc_final: 0.5964 (mmp80) REVERT: A 481 ARG cc_start: 0.7179 (mmm-85) cc_final: 0.6414 (ttt180) REVERT: A 483 VAL cc_start: 0.8149 (t) cc_final: 0.7919 (t) REVERT: A 498 ASN cc_start: 0.6832 (t0) cc_final: 0.6569 (m110) REVERT: A 524 LYS cc_start: 0.6408 (ttmt) cc_final: 0.6057 (mttt) REVERT: A 565 GLU cc_start: 0.7028 (OUTLIER) cc_final: 0.6686 (mm-30) REVERT: B 212 LEU cc_start: 0.6685 (OUTLIER) cc_final: 0.6239 (mm) REVERT: B 230 PHE cc_start: 0.6283 (t80) cc_final: 0.5951 (t80) REVERT: B 375 GLU cc_start: 0.6011 (mt-10) cc_final: 0.5231 (mt-10) REVERT: B 396 THR cc_start: 0.8416 (m) cc_final: 0.7955 (p) REVERT: B 400 LEU cc_start: 0.7546 (mt) cc_final: 0.7175 (mp) REVERT: B 435 LEU cc_start: 0.5862 (OUTLIER) cc_final: 0.5210 (mm) REVERT: B 464 LEU cc_start: 0.4047 (OUTLIER) cc_final: 0.3806 (pp) REVERT: B 563 PHE cc_start: 0.6060 (t80) cc_final: 0.5823 (t80) REVERT: B 564 GLU cc_start: 0.7611 (mm-30) cc_final: 0.7049 (pt0) REVERT: C 123 VAL cc_start: 0.8232 (m) cc_final: 0.7947 (p) REVERT: C 124 LYS cc_start: 0.7496 (ptpp) cc_final: 0.7221 (tptt) REVERT: C 130 ARG cc_start: 0.7211 (mtm180) cc_final: 0.6293 (mmt-90) REVERT: C 191 ARG cc_start: 0.7837 (mmm-85) cc_final: 0.7125 (mtm-85) REVERT: C 220 MET cc_start: 0.6828 (mmt) cc_final: 0.6522 (ttp) REVERT: C 264 ASP cc_start: 0.7293 (m-30) cc_final: 0.6906 (m-30) REVERT: C 363 GLU cc_start: 0.7080 (tp30) cc_final: 0.6733 (tp30) REVERT: C 488 ARG cc_start: 0.7698 (tmm160) cc_final: 0.7414 (ttp80) REVERT: C 489 ILE cc_start: 0.7949 (OUTLIER) cc_final: 0.7670 (mp) REVERT: C 524 LYS cc_start: 0.8029 (ttmt) cc_final: 0.7493 (tmtt) REVERT: C 567 MET cc_start: 0.7968 (tpp) cc_final: 0.7393 (ttm) REVERT: C 571 GLN cc_start: 0.7991 (pt0) cc_final: 0.7549 (pp30) REVERT: D 5 LYS cc_start: 0.4830 (tptp) cc_final: 0.4366 (tppt) REVERT: D 176 ASP cc_start: 0.8024 (t0) cc_final: 0.7767 (t70) REVERT: D 353 ASP cc_start: 0.7764 (t0) cc_final: 0.7507 (m-30) REVERT: D 410 ARG cc_start: 0.6275 (mmm-85) cc_final: 0.5665 (mmt180) REVERT: D 437 GLN cc_start: 0.7658 (mt0) cc_final: 0.7104 (mt0) REVERT: D 452 LYS cc_start: 0.5196 (mmtp) cc_final: 0.4890 (pttt) REVERT: E 210 ARG cc_start: 0.7493 (ttp-110) cc_final: 0.7189 (mtm110) REVERT: E 420 ARG cc_start: 0.6960 (mmm-85) cc_final: 0.6719 (mmm-85) REVERT: F 2 ASP cc_start: -0.0757 (OUTLIER) cc_final: -0.1689 (m-30) REVERT: F 180 GLU cc_start: 0.5085 (OUTLIER) cc_final: 0.3564 (pp20) REVERT: F 200 GLU cc_start: 0.6547 (OUTLIER) cc_final: 0.6208 (mp0) REVERT: G 59 GLU cc_start: 0.3428 (mm-30) cc_final: 0.3202 (tt0) REVERT: H 92 GLU cc_start: 0.6745 (tt0) cc_final: 0.5775 (mm-30) REVERT: J 164 GLU cc_start: 0.3230 (OUTLIER) cc_final: 0.2954 (tm-30) REVERT: J 170 ARG cc_start: 0.3604 (mtp85) cc_final: 0.2750 (tpt170) REVERT: L 150 LEU cc_start: 0.5646 (pt) cc_final: 0.4616 (mt) outliers start: 57 outliers final: 40 residues processed: 350 average time/residue: 0.4436 time to fit residues: 247.6191 Evaluate side-chains 333 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 284 time to evaluate : 3.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 ASP Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 565 GLU Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 209 MET Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 435 LEU Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 525 GLU Chi-restraints excluded: chain C residue 122 MET Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 489 ILE Chi-restraints excluded: chain D residue 72 SER Chi-restraints excluded: chain D residue 78 ASP Chi-restraints excluded: chain D residue 130 PHE Chi-restraints excluded: chain D residue 232 ILE Chi-restraints excluded: chain D residue 456 LYS Chi-restraints excluded: chain E residue 26 ASP Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 250 ASP Chi-restraints excluded: chain E residue 308 VAL Chi-restraints excluded: chain E residue 457 ASP Chi-restraints excluded: chain F residue 2 ASP Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 176 ASP Chi-restraints excluded: chain F residue 180 GLU Chi-restraints excluded: chain F residue 200 GLU Chi-restraints excluded: chain F residue 228 THR Chi-restraints excluded: chain F residue 336 GLN Chi-restraints excluded: chain F residue 427 GLN Chi-restraints excluded: chain F residue 428 GLN Chi-restraints excluded: chain G residue 35 LEU Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 96 VAL Chi-restraints excluded: chain H residue 27 GLU Chi-restraints excluded: chain I residue 104 MET Chi-restraints excluded: chain J residue 164 GLU Chi-restraints excluded: chain J residue 186 LEU Chi-restraints excluded: chain L residue 83 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 235 optimal weight: 9.9990 chunk 315 optimal weight: 20.0000 chunk 90 optimal weight: 10.0000 chunk 272 optimal weight: 10.0000 chunk 43 optimal weight: 10.0000 chunk 82 optimal weight: 0.0770 chunk 296 optimal weight: 0.7980 chunk 124 optimal weight: 6.9990 chunk 304 optimal weight: 4.9990 chunk 37 optimal weight: 9.9990 chunk 54 optimal weight: 7.9990 overall best weight: 4.1744 ------------------------------------------------------------------------------- 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 377 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.141211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.121062 restraints weight = 49869.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.119809 restraints weight = 56137.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.121425 restraints weight = 44847.365| |-----------------------------------------------------------------------------| r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.3816 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= 0.260 Angle : 0.560 14.346 40813 Z= 0.282 Chirality : 0.044 0.407 4572 Planarity : 0.005 0.056 5333 Dihedral : 5.595 79.741 4259 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.04 % Allowed : 18.78 % Favored : 79.18 % 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: 0.86 (0.14), residues: 1510 sheet: -0.34 (0.22), residues: 609 loop : -0.51 (0.15), residues: 1645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP J 100 HIS 0.006 0.001 HIS A 185 PHE 0.022 0.002 PHE A 563 TYR 0.019 0.001 TYR D 349 ARG 0.003 0.000 ARG D 420 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6084.46 seconds wall clock time: 110 minutes 58.24 seconds (6658.24 seconds total)