Starting phenix.real_space_refine on Wed Feb 21 02:49:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vau_31864/02_2024/7vau_31864_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vau_31864/02_2024/7vau_31864.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vau_31864/02_2024/7vau_31864.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vau_31864/02_2024/7vau_31864.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vau_31864/02_2024/7vau_31864_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vau_31864/02_2024/7vau_31864_updated.pdb" } resolution = 3.3 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 5 5.49 5 Mg 2 5.21 5 S 103 5.16 5 C 18720 2.51 5 N 5125 2.21 5 O 5558 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 363": "OE1" <-> "OE2" Residue "A TYR 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 447": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 522": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 67": "OD1" <-> "OD2" Residue "D TYR 383": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 450": "OE1" <-> "OE2" Residue "E TYR 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 200": "OE1" <-> "OE2" Residue "E PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 283": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 414": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 463": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 145": "OE1" <-> "OE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 29513 Number of models: 1 Model: "" Number of chains: 14 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: 4466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 577, 4466 Classifications: {'peptide': 577} Link IDs: {'PTRANS': 35, 'TRANS': 541} Chain breaks: 1 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 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: 19.27, per 1000 atoms: 0.65 Number of scatterers: 29513 At special positions: 0 Unit cell: (137.28, 178.64, 153.12, 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 5 15.00 Mg 2 11.99 O 5558 8.00 N 5125 7.00 C 18720 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 12.20 Conformation dependent library (CDL) restraints added in 5.6 seconds 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6916 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 135 helices and 34 sheets defined 41.8% alpha, 13.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.16 Creating SS restraints... Processing helix chain 'A' and resid 91 through 97 Processing helix chain 'A' and resid 210 through 214 Processing helix chain 'A' and resid 234 through 244 Processing helix chain 'A' and resid 259 through 271 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: 3.511A pdb=" N ARG A 299 " --> pdb=" O VAL A 296 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N GLU A 300 " --> pdb=" O ALA A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 341 Processing helix chain 'A' and resid 352 through 364 removed outlier: 4.275A pdb=" N ALA A 355 " --> pdb=" O PRO A 352 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLU A 363 " --> pdb=" O ALA A 360 " (cutoff:3.500A) 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 433 through 442 Proline residue: A 437 - end of helix Processing helix chain 'A' and resid 447 through 471 removed outlier: 4.124A pdb=" N GLU A 466 " --> pdb=" O ALA A 462 " (cutoff:3.500A) removed outlier: 4.565A 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 Processing helix chain 'A' and resid 536 through 541 Processing helix chain 'A' and resid 543 through 553 removed outlier: 4.391A pdb=" N ARG A 552 " --> pdb=" O GLY A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 556 through 577 Proline residue: A 560 - end of helix removed outlier: 3.604A pdb=" N GLU A 564 " --> pdb=" O PRO A 560 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N PHE A 574 " --> pdb=" O ILE A 570 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU A 577 " --> pdb=" O ALA A 573 " (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: 4.826A pdb=" N ILE B 303 " --> pdb=" O ARG B 299 " (cutoff:3.500A) removed outlier: 5.028A 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 347 through 349 No H-bonds generated for 'chain 'B' and resid 347 through 349' Processing helix chain 'B' and resid 354 through 364 Processing helix chain 'B' and resid 394 through 401 Processing helix chain 'B' and resid 411 through 416 Processing helix chain 'B' and resid 432 through 442 Proline residue: B 437 - end of helix Processing helix chain 'B' and resid 447 through 471 removed outlier: 3.641A pdb=" N LEU B 464 " --> pdb=" O ARG B 460 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLN B 465 " --> pdb=" O GLU B 461 " (cutoff:3.500A) removed outlier: 5.235A pdb=" N GLU B 466 " --> pdb=" O ALA B 462 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N ILE B 467 " --> pdb=" O GLY B 463 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLN B 469 " --> pdb=" O GLN B 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 473 through 475 No H-bonds generated for 'chain 'B' and resid 473 through 475' 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 Processing helix chain 'B' and resid 543 through 549 Processing helix chain 'B' and resid 551 through 553 No H-bonds generated for 'chain 'B' and resid 551 through 553' Processing helix chain 'B' and resid 559 through 572 Processing helix chain 'B' and resid 574 through 576 No H-bonds generated for 'chain 'B' and resid 574 through 576' 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 244 Processing helix chain 'C' and resid 260 through 268 Processing helix chain 'C' and resid 281 through 284 Processing helix chain 'C' and resid 296 through 315 removed outlier: 3.960A pdb=" N GLU C 300 " --> pdb=" O ALA C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 327 through 340 Processing helix chain 'C' and resid 354 through 364 removed outlier: 4.024A 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 399 Processing helix chain 'C' and resid 411 through 415 Processing helix chain 'C' and resid 436 through 442 Processing helix chain 'C' and resid 447 through 471 removed outlier: 4.336A pdb=" N GLU C 466 " --> pdb=" O ALA C 462 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N ILE C 467 " --> pdb=" O GLY C 463 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LEU C 470 " --> pdb=" O GLU C 466 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL C 471 " --> pdb=" O ILE C 467 " (cutoff:3.500A) Processing helix chain 'C' and resid 473 through 475 No H-bonds generated for 'chain 'C' and resid 473 through 475' 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 543 through 549 Processing helix chain 'C' and resid 551 through 553 No H-bonds generated for 'chain 'C' and resid 551 through 553' Processing helix chain 'C' and resid 556 through 577 Proline residue: C 560 - end of helix removed outlier: 3.802A pdb=" N PHE C 574 " --> pdb=" O ILE C 570 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N LYS C 575 " --> pdb=" O GLN C 571 " (cutoff:3.500A) Processing helix chain 'D' and resid 136 through 141 Processing helix chain 'D' and resid 160 through 170 Processing helix chain 'D' and resid 175 through 178 No H-bonds generated for 'chain 'D' and resid 175 through 178' Processing helix chain 'D' and resid 198 through 210 Processing helix chain 'D' and resid 213 through 216 removed outlier: 3.595A pdb=" N ARG D 216 " --> pdb=" O ALA D 213 " (cutoff:3.500A) No H-bonds generated for '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 274 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 287 through 295 Processing helix chain 'D' and resid 324 through 332 Processing helix chain 'D' and resid 341 through 346 Processing helix chain 'D' and resid 362 through 364 No H-bonds generated for 'chain 'D' and resid 362 through 364' Processing helix chain 'D' and resid 375 through 399 removed outlier: 3.813A pdb=" N ALA D 397 " --> pdb=" O ARG D 393 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N ILE D 398 " --> pdb=" O LYS D 394 " (cutoff:3.500A) Processing helix chain 'D' and resid 406 through 421 Processing helix chain 'D' and resid 432 through 445 removed outlier: 3.819A 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 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: 3.871A pdb=" N THR E 234 " --> pdb=" O ARG E 231 " (cutoff:3.500A) Proline residue: E 235 - end of helix removed outlier: 3.526A pdb=" N LEU E 239 " --> pdb=" O ARG E 236 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N PHE E 247 " --> pdb=" O TYR E 244 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLU E 248 " --> pdb=" O LEU E 245 " (cutoff:3.500A) removed outlier: 4.210A 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: 3.641A pdb=" N ILE E 294 " --> pdb=" O ASP E 290 " (cutoff:3.500A) removed outlier: 4.719A 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 332 removed outlier: 3.694A pdb=" N ILE E 332 " --> pdb=" O LEU E 328 " (cutoff:3.500A) Processing helix chain 'E' and resid 341 through 345 Processing helix chain 'E' and resid 362 through 365 No H-bonds generated for 'chain 'E' and resid 362 through 365' Processing helix chain 'E' and resid 375 through 399 removed outlier: 3.892A pdb=" N ILE E 398 " --> pdb=" O LYS E 394 " (cutoff:3.500A) Processing helix chain 'E' and resid 401 through 403 No H-bonds generated for 'chain 'E' and resid 401 through 403' Processing helix chain 'E' and resid 406 through 421 Processing helix chain 'E' and resid 432 through 445 removed outlier: 3.912A pdb=" N MET E 445 " --> pdb=" O ALA E 441 " (cutoff:3.500A) Processing helix chain 'E' and resid 458 through 461 No H-bonds generated for 'chain 'E' and resid 458 through 461' 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 213 through 216 Processing helix chain 'F' and resid 228 through 249 removed outlier: 3.707A pdb=" N ARG F 231 " --> pdb=" O THR F 228 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N THR F 234 " --> pdb=" O ARG F 231 " (cutoff:3.500A) Proline residue: F 235 - end of helix removed outlier: 3.593A pdb=" N PHE F 247 " --> pdb=" O TYR F 244 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLU F 248 " --> pdb=" O LEU F 245 " (cutoff:3.500A) removed outlier: 3.799A 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 287 through 297 removed outlier: 3.661A pdb=" N ILE F 294 " --> pdb=" O ASP F 290 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N ARG F 297 " --> pdb=" O THR F 293 " (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 345 Processing helix chain 'F' and resid 362 through 364 No H-bonds generated for 'chain 'F' and resid 362 through 364' Processing helix chain 'F' and resid 373 through 398 removed outlier: 4.487A pdb=" N LYS F 376 " --> pdb=" O GLU F 373 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLN F 377 " --> pdb=" O ASP F 374 " (cutoff:3.500A) Processing helix chain 'F' and resid 401 through 403 No H-bonds generated for 'chain 'F' and resid 401 through 403' Processing helix chain 'F' and resid 406 through 421 Processing helix chain 'F' and resid 432 through 445 removed outlier: 4.086A 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 469 No H-bonds generated for 'chain 'F' and resid 467 through 469' Processing helix chain 'G' and resid 8 through 70 removed outlier: 3.696A pdb=" N ARG G 44 " --> pdb=" O PHE G 40 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA G 67 " --> pdb=" O ALA G 63 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA G 69 " --> pdb=" O LEU G 65 " (cutoff:3.500A) Processing helix chain 'G' and resid 73 through 82 Processing helix chain 'G' and resid 110 through 112 No H-bonds generated for 'chain 'G' and resid 110 through 112' Processing helix chain 'G' and resid 121 through 166 removed outlier: 3.813A pdb=" N GLU G 125 " --> pdb=" O ALA G 121 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ARG G 139 " --> pdb=" O GLU G 135 " (cutoff:3.500A) Processing helix chain 'G' and resid 168 through 208 Processing helix chain 'H' and resid 7 through 15 removed outlier: 4.223A pdb=" N GLY H 12 " --> pdb=" O GLU H 8 " (cutoff:3.500A) Processing helix chain 'H' and resid 26 through 38 Processing helix chain 'H' and resid 55 through 58 No H-bonds generated for 'chain 'H' and resid 55 through 58' Processing helix chain 'H' and resid 77 through 80 No H-bonds generated for 'chain 'H' and resid 77 through 80' Processing helix chain 'H' and resid 86 through 97 Processing helix chain 'I' and resid 82 through 105 removed outlier: 3.840A pdb=" N GLU I 90 " --> pdb=" O ALA I 86 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ALA I 105 " --> pdb=" O GLU I 101 " (cutoff:3.500A) Processing helix chain 'I' and resid 107 through 118 Processing helix chain 'J' and resid 62 through 93 Processing helix chain 'J' and resid 100 through 114 removed outlier: 3.866A pdb=" N ARG J 105 " --> pdb=" O PRO J 101 " (cutoff:3.500A) Processing helix chain 'J' and resid 129 through 134 removed outlier: 4.349A pdb=" N LEU J 134 " --> pdb=" O HIS J 130 " (cutoff:3.500A) Processing helix chain 'J' and resid 171 through 186 removed outlier: 4.119A pdb=" N ASP J 176 " --> pdb=" O ASP J 172 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N ALA J 177 " --> pdb=" O ARG J 173 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N SER J 180 " --> pdb=" O ASP J 176 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N LYS J 181 " --> pdb=" O ALA J 177 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 118 removed outlier: 3.771A pdb=" N ALA K 105 " --> pdb=" O GLU K 101 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ARG K 106 " --> pdb=" O LYS K 102 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N ASP K 108 " --> pdb=" O MET K 104 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N GLU K 109 " --> pdb=" O ALA K 105 " (cutoff:3.500A) Processing helix chain 'L' and resid 62 through 92 Processing helix chain 'L' and resid 94 through 96 No H-bonds generated for 'chain 'L' and resid 94 through 96' Processing helix chain 'L' and resid 98 through 114 Proline residue: L 101 - end of helix Processing helix chain 'L' and resid 125 through 128 No H-bonds generated for 'chain 'L' and resid 125 through 128' Processing helix chain 'L' and resid 132 through 138 removed outlier: 3.617A pdb=" N ARG L 136 " --> pdb=" O GLU L 132 " (cutoff:3.500A) Processing helix chain 'L' and resid 167 through 186 removed outlier: 4.537A pdb=" N ASP L 176 " --> pdb=" O ASP L 172 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N ALA L 177 " --> pdb=" O ARG L 173 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N SER L 180 " --> pdb=" O ASP L 176 " (cutoff:3.500A) removed outlier: 4.586A 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: 6.471A pdb=" N PHE A 48 " --> pdb=" O ILE A 40 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N LEU A 42 " --> pdb=" O THR A 46 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N THR A 46 " --> pdb=" O LEU A 42 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N LYS A 17 " --> pdb=" O ILE A 6 " (cutoff:3.500A) removed outlier: 5.666A 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: 3.980A pdb=" N GLY A 82 " --> pdb=" O THR A 285 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N VAL A 250 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N ILE A 288 " --> pdb=" O VAL A 250 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N TYR A 252 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N ASN A 290 " --> pdb=" O TYR A 252 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N GLY A 254 " --> pdb=" O ASN A 290 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL A 249 " --> pdb=" O SER A 319 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N ALA A 377 " --> pdb=" O VAL A 320 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N LEU A 322 " --> pdb=" O ALA A 377 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N THR A 379 " --> pdb=" O LEU A 322 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N ALA A 324 " --> pdb=" O THR A 379 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N VAL A 381 " --> pdb=" O ALA A 324 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 164 through 166 removed outlier: 5.719A pdb=" N ALA A 118 " --> pdb=" O PRO A 139 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ILE A 147 " --> pdb=" O LEU A 135 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N THR A 137 " --> pdb=" O HIS A 145 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N HIS A 145 " --> pdb=" O THR A 137 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N PHE A 143 " --> pdb=" O PRO A 139 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 366 through 369 Processing sheet with id= F, first strand: chain 'A' and resid 157 through 160 removed outlier: 7.057A 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: 4.198A pdb=" N ILE B 2 " --> pdb=" O SER B 66 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N PHE B 48 " --> pdb=" O ILE B 40 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N LEU B 42 " --> pdb=" O THR B 46 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N THR B 46 " --> pdb=" O LEU B 42 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N LYS B 17 " --> pdb=" O ILE B 6 " (cutoff:3.500A) removed outlier: 5.736A 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: 3.938A pdb=" N GLY B 82 " --> pdb=" O THR B 285 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N VAL B 250 " --> pdb=" O VAL B 286 " (cutoff:3.500A) removed outlier: 8.093A pdb=" N ILE B 288 " --> pdb=" O VAL B 250 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N TYR B 252 " --> pdb=" O ILE B 288 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N ALA B 377 " --> pdb=" O VAL B 320 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N LEU B 322 " --> pdb=" O ALA B 377 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N THR B 379 " --> pdb=" O LEU B 322 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N ALA B 324 " --> pdb=" O THR B 379 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N VAL B 381 " --> pdb=" O ALA B 324 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 366 through 369 Processing sheet with id= K, first strand: chain 'B' and resid 134 through 140 removed outlier: 6.729A pdb=" N ILE B 147 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N THR B 137 " --> pdb=" O HIS B 145 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N HIS B 145 " --> pdb=" O THR B 137 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N PHE B 143 " --> pdb=" O PRO B 139 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 157 through 160 removed outlier: 6.814A pdb=" N VAL B 174 " --> pdb=" O LYS B 158 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 3 through 5 removed outlier: 6.602A pdb=" N PHE C 48 " --> pdb=" O ILE C 40 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N LEU C 42 " --> pdb=" O THR C 46 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N THR C 46 " --> pdb=" O LEU C 42 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N LYS C 17 " --> pdb=" O ILE C 6 " (cutoff:3.500A) removed outlier: 5.670A pdb=" N ILE C 6 " --> pdb=" O LYS C 17 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 72 through 75 Processing sheet with id= O, first strand: chain 'C' and resid 82 through 84 removed outlier: 4.056A pdb=" N GLY C 82 " --> pdb=" O THR C 285 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N VAL C 250 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N ILE C 288 " --> pdb=" O VAL C 250 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N TYR C 252 " --> pdb=" O ILE C 288 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N ASN C 290 " --> pdb=" O TYR C 252 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N GLY C 254 " --> pdb=" O ASN C 290 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL C 249 " --> pdb=" O SER C 319 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ALA C 377 " --> pdb=" O VAL C 320 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N LEU C 322 " --> pdb=" O ALA C 377 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N THR C 379 " --> pdb=" O LEU C 322 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N ALA C 324 " --> pdb=" O THR C 379 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N VAL C 381 " --> pdb=" O ALA C 324 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL C 384 " --> pdb=" O ILE C 226 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'C' and resid 164 through 166 removed outlier: 3.502A pdb=" N GLY C 164 " --> pdb=" O TRP C 119 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N ALA C 118 " --> pdb=" O PRO C 139 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ILE C 147 " --> pdb=" O LEU C 135 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N THR C 137 " --> pdb=" O HIS C 145 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N HIS C 145 " --> pdb=" O THR C 137 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N PHE C 143 " --> pdb=" O PRO C 139 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 366 through 369 Processing sheet with id= R, first strand: chain 'C' and resid 157 through 160 removed outlier: 6.788A pdb=" N VAL C 174 " --> pdb=" O LYS C 158 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'D' and resid 11 through 15 removed outlier: 6.560A pdb=" N PHE D 20 " --> pdb=" O THR D 12 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N ILE D 14 " --> pdb=" O LEU D 18 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N LEU D 18 " --> pdb=" O ILE D 14 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLU D 49 " --> pdb=" O VAL D 56 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N GLN D 58 " --> pdb=" O VAL D 47 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N VAL D 47 " --> pdb=" O GLN D 58 " (cutoff:3.500A) removed outlier: 5.769A pdb=" N ASP D 34 " --> pdb=" O LEU D 75 " (cutoff:3.500A) removed outlier: 5.657A pdb=" N LEU D 75 " --> pdb=" O ASP D 34 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N LYS D 36 " --> pdb=" O VAL D 73 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N VAL D 73 " --> pdb=" O LYS D 36 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'D' and resid 81 through 84 Processing sheet with id= U, first strand: chain 'D' and resid 336 through 338 Processing sheet with id= V, first strand: chain 'D' and resid 307 through 312 removed outlier: 8.101A pdb=" N LEU D 254 " --> pdb=" O PRO D 186 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ALA D 188 " --> pdb=" O LEU D 254 " (cutoff:3.500A) removed outlier: 8.229A pdb=" N ILE D 256 " --> pdb=" O ALA D 188 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N VAL D 190 " --> pdb=" O ILE D 256 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'E' and resid 11 through 15 removed outlier: 6.385A pdb=" N PHE E 20 " --> pdb=" O THR E 12 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N ILE E 14 " --> pdb=" O LEU E 18 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N LEU E 18 " --> pdb=" O ILE E 14 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLU E 49 " --> pdb=" O VAL E 56 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N GLN E 58 " --> pdb=" O VAL E 47 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N VAL E 47 " --> pdb=" O GLN E 58 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLY E 45 " --> pdb=" O VAL E 33 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLU E 77 " --> pdb=" O ILE E 32 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N ASP E 34 " --> pdb=" O LEU E 75 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N LEU E 75 " --> pdb=" O ASP E 34 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N LYS E 36 " --> pdb=" O VAL E 73 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N VAL E 73 " --> pdb=" O LYS E 36 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'E' and resid 92 through 94 removed outlier: 7.968A pdb=" N PHE E 93 " --> pdb=" O SER E 217 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N LEU E 219 " --> pdb=" O PHE E 93 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N VAL E 189 " --> pdb=" O VAL E 218 " (cutoff:3.500A) removed outlier: 8.113A pdb=" N PHE E 220 " --> pdb=" O VAL E 189 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N PHE E 191 " --> pdb=" O PHE E 220 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N SER E 307 " --> pdb=" O VAL E 253 " (cutoff:3.500A) removed outlier: 7.711A pdb=" N VAL E 255 " --> pdb=" O SER E 307 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N THR E 309 " --> pdb=" O VAL E 255 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N LEU E 257 " --> pdb=" O THR E 309 " (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 'F' and resid 11 through 15 removed outlier: 6.660A pdb=" N PHE F 20 " --> pdb=" O THR F 12 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N ILE F 14 " --> pdb=" O LEU F 18 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N LEU F 18 " --> pdb=" O ILE F 14 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLU F 49 " --> pdb=" O VAL F 56 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N GLN F 58 " --> pdb=" O VAL F 47 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N VAL F 47 " --> pdb=" O GLN F 58 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'F' and resid 81 through 84 removed outlier: 3.590A pdb=" N LYS F 110 " --> pdb=" O VAL F 84 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'F' and resid 91 through 94 removed outlier: 3.757A pdb=" N ARG F 91 " --> pdb=" O SER F 217 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N VAL F 189 " --> pdb=" O VAL F 218 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N PHE F 220 " --> pdb=" O VAL F 189 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N PHE F 191 " --> pdb=" O PHE F 220 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N ASN F 222 " --> pdb=" O PHE F 191 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N ALA F 193 " --> pdb=" O ASN F 222 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N SER F 307 " --> pdb=" O VAL F 253 " (cutoff:3.500A) removed outlier: 7.589A pdb=" N VAL F 255 " --> pdb=" O SER F 307 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N THR F 309 " --> pdb=" O VAL F 255 " (cutoff:3.500A) removed outlier: 8.032A pdb=" N LEU F 257 " --> pdb=" O THR F 309 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N ILE F 311 " --> pdb=" O LEU F 257 " (cutoff:3.500A) 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 32 through 36 removed outlier: 3.509A pdb=" N GLU F 77 " --> pdb=" O ILE F 32 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N ASP F 34 " --> pdb=" O LEU F 75 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N LEU F 75 " --> pdb=" O ASP F 34 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N LYS F 36 " --> pdb=" O VAL F 73 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N VAL F 73 " --> pdb=" O LYS F 36 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'G' and resid 90 through 96 Processing sheet with id= AF, first strand: chain 'H' and resid 20 through 22 removed outlier: 6.000A pdb=" N VAL H 3 " --> pdb=" O TYR H 21 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU H 72 " --> pdb=" O VAL H 45 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'J' and resid 120 through 123 removed outlier: 6.699A pdb=" N VAL J 140 " --> pdb=" O LEU J 121 " (cutoff:3.500A) removed outlier: 8.289A pdb=" N ALA J 123 " --> pdb=" O VAL J 140 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N LEU J 142 " --> pdb=" O ALA J 123 " (cutoff:3.500A) No H-bonds generated for sheet with id= AG Processing sheet with id= AH, first strand: chain 'L' and resid 120 through 123 removed outlier: 3.686A pdb=" N ALA L 120 " --> pdb=" O VAL L 155 " (cutoff:3.500A) 1195 hydrogen bonds defined for protein. 3183 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: 10.02 Time building geometry restraints manager: 13.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 9328 1.33 - 1.45: 3589 1.45 - 1.57: 16948 1.57 - 1.69: 8 1.69 - 1.81: 194 Bond restraints: 30067 Sorted by residual: bond pdb=" C4 ADP A 601 " pdb=" C5 ADP A 601 " ideal model delta sigma weight residual 1.490 1.384 0.106 2.00e-02 2.50e+03 2.81e+01 bond pdb=" C5 ADP A 601 " pdb=" C6 ADP A 601 " ideal model delta sigma weight residual 1.490 1.408 0.082 2.00e-02 2.50e+03 1.69e+01 bond pdb=" O3B ADP A 601 " pdb=" PB ADP A 601 " ideal model delta sigma weight residual 1.510 1.584 -0.074 2.00e-02 2.50e+03 1.36e+01 bond pdb=" C VAL B 123 " pdb=" N LYS B 124 " ideal model delta sigma weight residual 1.327 1.371 -0.045 1.39e-02 5.18e+03 1.02e+01 bond pdb=" O2B ADP A 601 " pdb=" PB ADP A 601 " ideal model delta sigma weight residual 1.510 1.470 0.040 2.00e-02 2.50e+03 3.93e+00 ... (remaining 30062 not shown) Histogram of bond angle deviations from ideal: 99.03 - 107.13: 1078 107.13 - 115.23: 18081 115.23 - 123.32: 20542 123.32 - 131.42: 995 131.42 - 139.52: 44 Bond angle restraints: 40740 Sorted by residual: angle pdb=" PA ADP A 601 " pdb=" O3A ADP A 601 " pdb=" PB ADP A 601 " ideal model delta sigma weight residual 120.50 136.35 -15.85 3.00e+00 1.11e-01 2.79e+01 angle pdb=" O1B ADP A 601 " pdb=" PB ADP A 601 " pdb=" O3B ADP A 601 " ideal model delta sigma weight residual 119.90 107.17 12.73 3.00e+00 1.11e-01 1.80e+01 angle pdb=" C GLY B 256 " pdb=" N GLU B 257 " pdb=" CA GLU B 257 " ideal model delta sigma weight residual 121.91 113.61 8.30 2.03e+00 2.43e-01 1.67e+01 angle pdb=" N GLY B 256 " pdb=" CA GLY B 256 " pdb=" C GLY B 256 " ideal model delta sigma weight residual 113.18 104.76 8.42 2.37e+00 1.78e-01 1.26e+01 angle pdb=" CA GLU F 296 " pdb=" C GLU F 296 " pdb=" N ARG F 297 " ideal model delta sigma weight residual 118.27 123.19 -4.92 1.59e+00 3.96e-01 9.57e+00 ... (remaining 40735 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.47: 17205 22.47 - 44.94: 997 44.94 - 67.41: 108 67.41 - 89.88: 30 89.88 - 112.35: 2 Dihedral angle restraints: 18342 sinusoidal: 7524 harmonic: 10818 Sorted by residual: dihedral pdb=" CA ALA J 169 " pdb=" C ALA J 169 " pdb=" N ARG J 170 " pdb=" CA ARG J 170 " ideal model delta harmonic sigma weight residual 180.00 151.11 28.89 0 5.00e+00 4.00e-02 3.34e+01 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 -172.35 112.35 1 2.00e+01 2.50e-03 3.31e+01 dihedral pdb=" CA LEU J 168 " pdb=" C LEU J 168 " pdb=" N ALA J 169 " pdb=" CA ALA J 169 " ideal model delta harmonic sigma weight residual -180.00 -155.69 -24.31 0 5.00e+00 4.00e-02 2.36e+01 ... (remaining 18339 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 2921 0.041 - 0.082: 1206 0.082 - 0.123: 386 0.123 - 0.164: 52 0.164 - 0.205: 2 Chirality restraints: 4567 Sorted by residual: chirality pdb=" CA PHE B 419 " pdb=" N PHE B 419 " pdb=" C PHE B 419 " pdb=" CB PHE B 419 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.21 2.00e-01 2.50e+01 1.05e+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 -2.68 0.16 2.00e-01 2.50e+01 6.78e-01 chirality pdb=" CA GLU D 296 " pdb=" N GLU D 296 " pdb=" C GLU D 296 " pdb=" CB GLU D 296 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.32e-01 ... (remaining 4564 not shown) Planarity restraints: 5329 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU A 393 " -0.029 5.00e-02 4.00e+02 4.34e-02 3.02e+00 pdb=" N PRO A 394 " 0.075 5.00e-02 4.00e+02 pdb=" CA PRO A 394 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 394 " -0.024 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 4.24e-02 2.88e+00 pdb=" N PRO B 229 " 0.073 5.00e-02 4.00e+02 pdb=" CA PRO B 229 " -0.021 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 E 323 " 0.026 5.00e-02 4.00e+02 3.88e-02 2.41e+00 pdb=" N PRO E 324 " -0.067 5.00e-02 4.00e+02 pdb=" CA PRO E 324 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO E 324 " 0.022 5.00e-02 4.00e+02 ... (remaining 5326 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.55: 168 2.55 - 3.14: 23384 3.14 - 3.73: 44484 3.73 - 4.31: 62593 4.31 - 4.90: 107314 Nonbonded interactions: 237943 Sorted by model distance: nonbonded pdb=" OG SER C 235 " pdb="MG MG C 602 " model vdw 1.966 2.170 nonbonded pdb=" O2G ATP C 601 " pdb="MG MG C 602 " model vdw 1.967 2.170 nonbonded pdb=" OG SER E 431 " pdb=" OE1 GLU E 434 " model vdw 2.129 2.440 nonbonded pdb=" OE1 GLU F 109 " pdb=" OH TYR F 244 " model vdw 2.161 2.440 nonbonded pdb=" OH TYR D 263 " pdb=" OD2 ASP D 290 " model vdw 2.162 2.440 ... (remaining 237938 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 32 or resid 34 through 578)) selection = chain 'B' selection = (chain 'C' and (resid 1 through 32 or resid 34 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.060 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: 16.190 Check model and map are aligned: 0.440 Set scattering table: 0.280 Process input model: 82.490 Find NCS groups from input model: 1.920 Set up NCS constraints: 0.160 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:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 110.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 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 : 0.007 0.106 30067 Z= 0.487 Angle : 0.686 15.852 40740 Z= 0.362 Chirality : 0.048 0.205 4567 Planarity : 0.005 0.048 5329 Dihedral : 13.704 112.351 11426 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.34 % 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: 3761 helix: 1.62 (0.13), residues: 1542 sheet: -0.18 (0.23), residues: 561 loop : -0.10 (0.15), residues: 1658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 119 HIS 0.007 0.002 HIS D 249 PHE 0.017 0.002 PHE D 418 TYR 0.025 0.002 TYR D 331 ARG 0.012 0.001 ARG B 364 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 623 residues out of total 3082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 623 time to evaluate : 3.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.3710 (mtt) cc_final: 0.3285 (ptm) REVERT: A 20 LEU cc_start: 0.7378 (tp) cc_final: 0.7140 (tp) REVERT: A 29 LYS cc_start: 0.7892 (mmtp) cc_final: 0.7531 (mmmt) REVERT: A 54 ASP cc_start: 0.7649 (t0) cc_final: 0.7231 (t70) REVERT: A 158 LYS cc_start: 0.6661 (mtpt) cc_final: 0.6304 (mttt) REVERT: A 369 ILE cc_start: 0.8782 (mm) cc_final: 0.8438 (mm) REVERT: A 390 ASP cc_start: 0.7731 (t0) cc_final: 0.7519 (t70) REVERT: A 441 GLU cc_start: 0.7186 (mt-10) cc_final: 0.6933 (mm-30) REVERT: A 532 ARG cc_start: 0.6222 (mtm-85) cc_final: 0.5752 (ttp80) REVERT: A 550 ARG cc_start: 0.6793 (tpp-160) cc_final: 0.6279 (mmt90) REVERT: A 556 GLU cc_start: 0.7276 (mm-30) cc_final: 0.6834 (tp30) REVERT: A 568 LYS cc_start: 0.6730 (mtmt) cc_final: 0.6436 (tttt) REVERT: B 133 MET cc_start: 0.7343 (mtp) cc_final: 0.7067 (mtm) REVERT: B 143 PHE cc_start: 0.6081 (t80) cc_final: 0.5590 (m-80) REVERT: B 156 ARG cc_start: 0.6771 (ptm160) cc_final: 0.5999 (ptp90) REVERT: B 338 SER cc_start: 0.8193 (t) cc_final: 0.7735 (m) REVERT: B 342 GLU cc_start: 0.7864 (mt-10) cc_final: 0.7575 (mt-10) REVERT: B 408 ARG cc_start: 0.7545 (ttm-80) cc_final: 0.7220 (ttp80) REVERT: B 456 GLU cc_start: 0.7390 (tp30) cc_final: 0.7071 (tp30) REVERT: B 461 GLU cc_start: 0.7666 (tt0) cc_final: 0.7394 (tt0) REVERT: B 469 GLN cc_start: 0.7306 (mt0) cc_final: 0.6988 (tm-30) REVERT: B 481 ARG cc_start: 0.6854 (ttt90) cc_final: 0.6442 (ttp80) REVERT: B 485 GLU cc_start: 0.7125 (tp30) cc_final: 0.6678 (tp30) REVERT: B 498 ASN cc_start: 0.7199 (t0) cc_final: 0.6881 (t0) REVERT: B 517 LYS cc_start: 0.6995 (tppp) cc_final: 0.6698 (tttm) REVERT: B 547 ARG cc_start: 0.6816 (mmm-85) cc_final: 0.6591 (tpp-160) REVERT: C 2 ILE cc_start: 0.8429 (mm) cc_final: 0.8217 (mp) REVERT: C 271 GLU cc_start: 0.6768 (mm-30) cc_final: 0.6550 (tp30) REVERT: C 375 GLU cc_start: 0.7780 (tt0) cc_final: 0.7573 (mt-10) REVERT: C 408 ARG cc_start: 0.7751 (ttm170) cc_final: 0.7435 (ttt-90) REVERT: C 485 GLU cc_start: 0.6804 (mm-30) cc_final: 0.6285 (mm-30) REVERT: D 54 TYR cc_start: 0.8427 (p90) cc_final: 0.8018 (p90) REVERT: D 230 GLU cc_start: 0.6954 (mt-10) cc_final: 0.6734 (mp0) REVERT: D 280 ARG cc_start: 0.6935 (ttt180) cc_final: 0.6617 (ttp80) REVERT: D 394 LYS cc_start: 0.7392 (mttt) cc_final: 0.7029 (mmtt) REVERT: D 466 LYS cc_start: 0.6940 (tttp) cc_final: 0.6664 (tptt) REVERT: E 41 ARG cc_start: 0.6876 (mtp-110) cc_final: 0.6604 (mtp-110) REVERT: E 109 GLU cc_start: 0.7268 (tm-30) cc_final: 0.6941 (tm-30) REVERT: E 216 ARG cc_start: 0.7585 (mtm-85) cc_final: 0.7150 (ptp90) REVERT: E 319 ASP cc_start: 0.7875 (m-30) cc_final: 0.7674 (m-30) REVERT: E 448 GLN cc_start: 0.7115 (tt0) cc_final: 0.6902 (tt0) REVERT: E 453 ARG cc_start: 0.6041 (mmt90) cc_final: 0.5666 (mtt90) REVERT: F 6 LYS cc_start: 0.7177 (tttt) cc_final: 0.6695 (tttp) REVERT: F 72 SER cc_start: 0.8895 (p) cc_final: 0.8541 (p) REVERT: F 251 TYR cc_start: 0.8364 (m-80) cc_final: 0.7891 (m-80) REVERT: F 280 ARG cc_start: 0.6714 (mtm180) cc_final: 0.6488 (mtp180) REVERT: F 376 LYS cc_start: 0.7787 (tptp) cc_final: 0.7484 (tttm) REVERT: F 463 TYR cc_start: 0.8483 (t80) cc_final: 0.8280 (t80) REVERT: G 128 ARG cc_start: 0.4854 (mtp180) cc_final: 0.4513 (mtp85) REVERT: G 148 LYS cc_start: 0.6538 (mttp) cc_final: 0.6274 (mmtm) REVERT: G 184 GLU cc_start: 0.7096 (tt0) cc_final: 0.6862 (mm-30) REVERT: H 14 ARG cc_start: 0.5662 (mtm110) cc_final: 0.4866 (mmm-85) REVERT: H 34 GLU cc_start: 0.5420 (mt-10) cc_final: 0.4880 (mm-30) REVERT: H 49 GLU cc_start: 0.3405 (tm-30) cc_final: 0.2956 (tp30) REVERT: I 104 MET cc_start: 0.5917 (mmp) cc_final: 0.5517 (ttp) REVERT: J 81 GLU cc_start: 0.7292 (tm-30) cc_final: 0.6901 (mm-30) REVERT: J 84 ARG cc_start: 0.4668 (ttt180) cc_final: 0.4409 (ttt90) REVERT: J 86 ARG cc_start: 0.5330 (mtt-85) cc_final: 0.4944 (mmm160) REVERT: J 88 ARG cc_start: 0.6302 (ttm-80) cc_final: 0.5814 (ttp-170) REVERT: J 109 LEU cc_start: 0.5486 (mm) cc_final: 0.5229 (mt) REVERT: K 104 MET cc_start: 0.5283 (mmp) cc_final: 0.4623 (ttp) REVERT: K 106 ARG cc_start: 0.4880 (mmp80) cc_final: 0.3416 (ttm110) REVERT: L 81 GLU cc_start: 0.6090 (tp30) cc_final: 0.5790 (tm-30) REVERT: L 106 LYS cc_start: 0.6463 (ptpt) cc_final: 0.5984 (mmtp) REVERT: L 112 LEU cc_start: 0.5794 (mt) cc_final: 0.5581 (mt) outliers start: 0 outliers final: 0 residues processed: 623 average time/residue: 0.5151 time to fit residues: 470.0111 Evaluate side-chains 352 residues out of total 3082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 352 time to evaluate : 3.673 ------------------------------------------------------------------------------- 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: 5.9990 chunk 156 optimal weight: 3.9990 chunk 96 optimal weight: 6.9990 chunk 190 optimal weight: 8.9990 chunk 151 optimal weight: 5.9990 chunk 292 optimal weight: 0.2980 chunk 113 optimal weight: 9.9990 chunk 177 optimal weight: 4.9990 chunk 217 optimal weight: 8.9990 chunk 338 optimal weight: 7.9990 overall best weight: 4.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 7 GLN A 283 HIS B 423 ASN ** C 418 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 477 GLN ** C 496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 364 ASN ** F 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 181 GLN J 130 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.1876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 30067 Z= 0.322 Angle : 0.615 8.350 40740 Z= 0.315 Chirality : 0.046 0.178 4567 Planarity : 0.006 0.059 5329 Dihedral : 5.642 110.400 4223 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.20 % Allowed : 8.83 % Favored : 89.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.34 % 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: 0.43 (0.14), residues: 3761 helix: 1.17 (0.13), residues: 1531 sheet: -0.24 (0.23), residues: 521 loop : -0.26 (0.15), residues: 1709 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 471 HIS 0.006 0.001 HIS A 283 PHE 0.021 0.002 PHE B 143 TYR 0.016 0.002 TYR C 428 ARG 0.008 0.001 ARG C 416 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 3082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 370 time to evaluate : 3.437 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.3571 (mtt) cc_final: 0.3171 (ptm) REVERT: A 20 LEU cc_start: 0.7428 (tp) cc_final: 0.7184 (tp) REVERT: A 29 LYS cc_start: 0.7854 (mmtp) cc_final: 0.7228 (mmtt) REVERT: A 54 ASP cc_start: 0.7702 (t0) cc_final: 0.7321 (t70) REVERT: A 98 THR cc_start: 0.8029 (m) cc_final: 0.7549 (p) REVERT: A 158 LYS cc_start: 0.6637 (mtpt) cc_final: 0.6401 (mttt) REVERT: A 241 LEU cc_start: 0.7950 (OUTLIER) cc_final: 0.7658 (mp) REVERT: A 390 ASP cc_start: 0.7903 (t0) cc_final: 0.7645 (t70) REVERT: A 532 ARG cc_start: 0.6550 (mtm-85) cc_final: 0.6086 (ttp80) REVERT: A 556 GLU cc_start: 0.7408 (mm-30) cc_final: 0.6861 (tp30) REVERT: A 568 LYS cc_start: 0.6836 (mtmt) cc_final: 0.6465 (tttt) REVERT: B 85 ASP cc_start: 0.7489 (p0) cc_final: 0.7092 (p0) REVERT: B 143 PHE cc_start: 0.6287 (t80) cc_final: 0.5828 (m-80) REVERT: B 156 ARG cc_start: 0.6833 (ptm160) cc_final: 0.6014 (ptp90) REVERT: B 209 MET cc_start: 0.7465 (mtm) cc_final: 0.7079 (mtm) REVERT: B 234 LYS cc_start: 0.8648 (ttpp) cc_final: 0.8322 (tttp) REVERT: B 338 SER cc_start: 0.8354 (t) cc_final: 0.7828 (m) REVERT: B 342 GLU cc_start: 0.7876 (mt-10) cc_final: 0.7567 (mt-10) REVERT: B 408 ARG cc_start: 0.7569 (ttm-80) cc_final: 0.7201 (ttp80) REVERT: B 410 ASP cc_start: 0.6818 (t0) cc_final: 0.6571 (t0) REVERT: B 456 GLU cc_start: 0.7287 (tp30) cc_final: 0.7034 (tp30) REVERT: B 461 GLU cc_start: 0.7617 (tt0) cc_final: 0.7272 (tt0) REVERT: B 469 GLN cc_start: 0.7344 (mt0) cc_final: 0.6898 (pp30) REVERT: B 485 GLU cc_start: 0.7017 (tp30) cc_final: 0.6808 (tp30) REVERT: B 498 ASN cc_start: 0.7293 (t0) cc_final: 0.6891 (t0) REVERT: C 2 ILE cc_start: 0.8231 (mm) cc_final: 0.8005 (mp) REVERT: C 130 ARG cc_start: 0.6739 (mtt90) cc_final: 0.6382 (ttm-80) REVERT: C 271 GLU cc_start: 0.6916 (mm-30) cc_final: 0.6575 (tp30) REVERT: C 375 GLU cc_start: 0.7846 (tt0) cc_final: 0.7602 (mt-10) REVERT: C 408 ARG cc_start: 0.7624 (ttm170) cc_final: 0.7249 (ttt-90) REVERT: C 488 ARG cc_start: 0.7420 (ttp-110) cc_final: 0.7088 (ttp80) REVERT: D 281 ARG cc_start: 0.7959 (mmm-85) cc_final: 0.7480 (tpp80) REVERT: D 394 LYS cc_start: 0.7291 (mttt) cc_final: 0.7002 (mmtt) REVERT: E 41 ARG cc_start: 0.7070 (mtp-110) cc_final: 0.6735 (mtp-110) REVERT: E 61 GLU cc_start: 0.6813 (mt-10) cc_final: 0.6496 (mt-10) REVERT: E 109 GLU cc_start: 0.7125 (tm-30) cc_final: 0.6896 (tm-30) REVERT: E 216 ARG cc_start: 0.7710 (mtm-85) cc_final: 0.7336 (ptp90) REVERT: E 311 ILE cc_start: 0.8550 (pt) cc_final: 0.8309 (mt) REVERT: F 6 LYS cc_start: 0.7174 (tttt) cc_final: 0.6839 (tttp) REVERT: F 280 ARG cc_start: 0.6758 (mtm180) cc_final: 0.6493 (mtp85) REVERT: F 368 LYS cc_start: 0.7068 (tptt) cc_final: 0.6863 (tptt) REVERT: G 128 ARG cc_start: 0.4726 (mtp180) cc_final: 0.4255 (mtp85) REVERT: G 184 GLU cc_start: 0.7090 (tt0) cc_final: 0.6831 (mm-30) REVERT: H 14 ARG cc_start: 0.5647 (mtm110) cc_final: 0.4978 (mmm-85) REVERT: H 34 GLU cc_start: 0.5503 (mt-10) cc_final: 0.5190 (mm-30) REVERT: H 49 GLU cc_start: 0.3481 (tm-30) cc_final: 0.3011 (tp30) REVERT: I 104 MET cc_start: 0.5736 (mmp) cc_final: 0.5346 (ttp) REVERT: J 74 GLN cc_start: 0.7062 (tp40) cc_final: 0.6678 (tt0) REVERT: J 81 GLU cc_start: 0.7291 (tm-30) cc_final: 0.6921 (mm-30) REVERT: J 84 ARG cc_start: 0.4607 (ttt180) cc_final: 0.3905 (ttt-90) REVERT: J 88 ARG cc_start: 0.6035 (ttm-80) cc_final: 0.5792 (ttp-170) REVERT: J 109 LEU cc_start: 0.5558 (mm) cc_final: 0.5284 (mt) REVERT: J 119 LYS cc_start: 0.6326 (tptp) cc_final: 0.5682 (ptmt) REVERT: K 104 MET cc_start: 0.5507 (mmp) cc_final: 0.4716 (ttp) REVERT: K 106 ARG cc_start: 0.4878 (mmp80) cc_final: 0.3468 (ttm110) REVERT: L 106 LYS cc_start: 0.6188 (ptpt) cc_final: 0.5646 (mmtp) REVERT: L 119 LYS cc_start: 0.6261 (pttt) cc_final: 0.5558 (mmmt) outliers start: 37 outliers final: 24 residues processed: 395 average time/residue: 0.4801 time to fit residues: 285.8917 Evaluate side-chains 338 residues out of total 3082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 313 time to evaluate : 3.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 CYS Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 502 GLU Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 433 SER Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 467 ILE Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 156 SER Chi-restraints excluded: chain D residue 265 GLU Chi-restraints excluded: chain D residue 380 ASP Chi-restraints excluded: chain D residue 459 ILE Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 402 ASP Chi-restraints excluded: chain F residue 39 THR Chi-restraints excluded: chain G residue 143 THR Chi-restraints excluded: chain I residue 115 LEU Chi-restraints excluded: chain L residue 102 GLU Chi-restraints excluded: chain L residue 161 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 188 optimal weight: 8.9990 chunk 105 optimal weight: 6.9990 chunk 281 optimal weight: 9.9990 chunk 230 optimal weight: 8.9990 chunk 93 optimal weight: 10.0000 chunk 339 optimal weight: 10.0000 chunk 366 optimal weight: 10.0000 chunk 302 optimal weight: 3.9990 chunk 336 optimal weight: 0.9990 chunk 115 optimal weight: 10.0000 chunk 272 optimal weight: 3.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 418 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 23 ASN E 363 ASN E 364 ASN E 448 GLN F 310 GLN ** F 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 130 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.2331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 30067 Z= 0.366 Angle : 0.620 7.830 40740 Z= 0.318 Chirality : 0.047 0.182 4567 Planarity : 0.006 0.055 5329 Dihedral : 5.700 96.869 4223 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.24 % Allowed : 12.04 % Favored : 85.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.34 % 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 (0.13), residues: 3761 helix: 0.89 (0.13), residues: 1531 sheet: -0.41 (0.22), residues: 554 loop : -0.38 (0.15), residues: 1676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 119 HIS 0.005 0.001 HIS B 145 PHE 0.023 0.002 PHE B 143 TYR 0.017 0.002 TYR C 428 ARG 0.006 0.001 ARG G 50 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 3082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 323 time to evaluate : 3.613 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.3595 (mtt) cc_final: 0.3169 (ptm) REVERT: A 20 LEU cc_start: 0.7336 (tp) cc_final: 0.7119 (tp) REVERT: A 29 LYS cc_start: 0.7894 (mmtp) cc_final: 0.7256 (mmtt) REVERT: A 54 ASP cc_start: 0.7807 (t0) cc_final: 0.7239 (t0) REVERT: A 98 THR cc_start: 0.7966 (m) cc_final: 0.7523 (p) REVERT: A 241 LEU cc_start: 0.7940 (OUTLIER) cc_final: 0.7540 (mp) REVERT: A 532 ARG cc_start: 0.6369 (mtm-85) cc_final: 0.5950 (ttp80) REVERT: A 556 GLU cc_start: 0.7530 (mm-30) cc_final: 0.6973 (tp30) REVERT: A 568 LYS cc_start: 0.6848 (mtmt) cc_final: 0.6466 (tttt) REVERT: B 85 ASP cc_start: 0.7394 (p0) cc_final: 0.7152 (p0) REVERT: B 143 PHE cc_start: 0.6467 (t80) cc_final: 0.5966 (m-80) REVERT: B 156 ARG cc_start: 0.6881 (ptm160) cc_final: 0.6014 (ptp90) REVERT: B 209 MET cc_start: 0.7426 (OUTLIER) cc_final: 0.7045 (mtm) REVERT: B 234 LYS cc_start: 0.8688 (ttpp) cc_final: 0.8344 (tttp) REVERT: B 338 SER cc_start: 0.8395 (t) cc_final: 0.7844 (m) REVERT: B 342 GLU cc_start: 0.7856 (mt-10) cc_final: 0.7457 (mt-10) REVERT: B 408 ARG cc_start: 0.7620 (ttm-80) cc_final: 0.7231 (ttp80) REVERT: B 410 ASP cc_start: 0.7057 (t0) cc_final: 0.6804 (t0) REVERT: B 469 GLN cc_start: 0.7401 (mt0) cc_final: 0.6925 (pp30) REVERT: B 481 ARG cc_start: 0.7093 (ttt90) cc_final: 0.6862 (ttp80) REVERT: B 485 GLU cc_start: 0.7056 (tp30) cc_final: 0.6840 (tp30) REVERT: B 498 ASN cc_start: 0.7338 (t0) cc_final: 0.6854 (t0) REVERT: B 547 ARG cc_start: 0.7746 (tpp-160) cc_final: 0.7382 (tpp-160) REVERT: C 2 ILE cc_start: 0.8257 (mm) cc_final: 0.8031 (mp) REVERT: C 130 ARG cc_start: 0.6670 (mtt90) cc_final: 0.6342 (ttm-80) REVERT: C 271 GLU cc_start: 0.7096 (mm-30) cc_final: 0.6698 (tp30) REVERT: C 375 GLU cc_start: 0.7812 (tt0) cc_final: 0.7558 (mt-10) REVERT: C 488 ARG cc_start: 0.7482 (ttp-110) cc_final: 0.7085 (ttp80) REVERT: D 394 LYS cc_start: 0.7186 (mttt) cc_final: 0.6830 (mmtt) REVERT: D 413 GLN cc_start: 0.7135 (mp10) cc_final: 0.6918 (mp10) REVERT: E 41 ARG cc_start: 0.6915 (mtp-110) cc_final: 0.6631 (mtp-110) REVERT: E 61 GLU cc_start: 0.6866 (mt-10) cc_final: 0.6456 (mt-10) REVERT: E 216 ARG cc_start: 0.7785 (mtm-85) cc_final: 0.7431 (ptp90) REVERT: E 311 ILE cc_start: 0.8567 (pt) cc_final: 0.8315 (mt) REVERT: F 6 LYS cc_start: 0.7250 (tttt) cc_final: 0.6856 (tttp) REVERT: F 280 ARG cc_start: 0.6840 (mtm180) cc_final: 0.6536 (mtp85) REVERT: G 184 GLU cc_start: 0.6987 (tt0) cc_final: 0.6692 (mm-30) REVERT: H 14 ARG cc_start: 0.5788 (mtm110) cc_final: 0.5046 (mmm-85) REVERT: H 34 GLU cc_start: 0.5573 (mt-10) cc_final: 0.5262 (mm-30) REVERT: H 49 GLU cc_start: 0.3358 (tm-30) cc_final: 0.2935 (tp30) REVERT: H 87 GLU cc_start: 0.6811 (OUTLIER) cc_final: 0.6121 (mm-30) REVERT: I 104 MET cc_start: 0.5652 (mmp) cc_final: 0.5284 (ttp) REVERT: J 74 GLN cc_start: 0.7155 (tp40) cc_final: 0.6741 (tt0) REVERT: J 81 GLU cc_start: 0.7276 (tm-30) cc_final: 0.6889 (mm-30) REVERT: J 109 LEU cc_start: 0.5559 (mm) cc_final: 0.5281 (mt) REVERT: J 119 LYS cc_start: 0.6339 (tptp) cc_final: 0.5724 (ptmt) REVERT: K 104 MET cc_start: 0.5325 (mmp) cc_final: 0.4684 (ttp) REVERT: K 106 ARG cc_start: 0.4893 (mmp80) cc_final: 0.3332 (ttm-80) REVERT: L 106 LYS cc_start: 0.6265 (ptpt) cc_final: 0.5733 (mttt) outliers start: 69 outliers final: 47 residues processed: 373 average time/residue: 0.5314 time to fit residues: 301.7197 Evaluate side-chains 352 residues out of total 3082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 302 time to evaluate : 3.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 CYS Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 369 ILE Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 502 GLU Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain B residue 3 GLN Chi-restraints excluded: chain B residue 158 LYS Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 209 MET Chi-restraints excluded: chain B residue 326 SER Chi-restraints excluded: chain B residue 433 SER Chi-restraints excluded: chain B residue 484 ILE Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 432 THR Chi-restraints excluded: chain C residue 461 GLU Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 265 GLU Chi-restraints excluded: chain D residue 459 ILE Chi-restraints excluded: chain E residue 36 LYS Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain E residue 366 VAL Chi-restraints excluded: chain E residue 371 THR Chi-restraints excluded: chain E residue 405 THR Chi-restraints excluded: chain F residue 39 THR Chi-restraints excluded: chain F residue 459 ILE Chi-restraints excluded: chain G residue 143 THR Chi-restraints excluded: chain H residue 87 GLU Chi-restraints excluded: chain J residue 94 LEU Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain L residue 102 GLU Chi-restraints excluded: chain L residue 161 THR Chi-restraints excluded: chain L residue 186 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 335 optimal weight: 20.0000 chunk 255 optimal weight: 0.1980 chunk 176 optimal weight: 8.9990 chunk 37 optimal weight: 9.9990 chunk 161 optimal weight: 6.9990 chunk 227 optimal weight: 4.9990 chunk 340 optimal weight: 20.0000 chunk 360 optimal weight: 5.9990 chunk 177 optimal weight: 6.9990 chunk 322 optimal weight: 0.0980 chunk 97 optimal weight: 7.9990 overall best weight: 3.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 418 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 363 ASN F 310 GLN ** F 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 96 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.2556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 30067 Z= 0.273 Angle : 0.553 6.788 40740 Z= 0.282 Chirality : 0.044 0.182 4567 Planarity : 0.005 0.048 5329 Dihedral : 5.500 91.428 4223 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.30 % Allowed : 13.47 % Favored : 84.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.14), residues: 3761 helix: 0.93 (0.13), residues: 1544 sheet: -0.44 (0.23), residues: 517 loop : -0.40 (0.15), residues: 1700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 119 HIS 0.003 0.001 HIS B 145 PHE 0.019 0.002 PHE B 143 TYR 0.015 0.001 TYR C 428 ARG 0.004 0.000 ARG G 50 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 3082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 306 time to evaluate : 3.322 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.3554 (mtt) cc_final: 0.3139 (ptm) REVERT: A 29 LYS cc_start: 0.7864 (mmtp) cc_final: 0.7242 (mmtt) REVERT: A 45 ASP cc_start: 0.8086 (OUTLIER) cc_final: 0.7645 (t0) REVERT: A 54 ASP cc_start: 0.7795 (t0) cc_final: 0.7363 (t70) REVERT: A 98 THR cc_start: 0.7955 (m) cc_final: 0.7554 (p) REVERT: A 241 LEU cc_start: 0.7942 (OUTLIER) cc_final: 0.7573 (mp) REVERT: A 375 GLU cc_start: 0.7415 (mm-30) cc_final: 0.7058 (mm-30) REVERT: A 532 ARG cc_start: 0.6469 (mtm-85) cc_final: 0.6005 (ttp80) REVERT: A 556 GLU cc_start: 0.7536 (mm-30) cc_final: 0.6978 (tp30) REVERT: A 568 LYS cc_start: 0.6839 (mtmt) cc_final: 0.6445 (tttt) REVERT: B 85 ASP cc_start: 0.7426 (p0) cc_final: 0.7116 (p0) REVERT: B 87 ILE cc_start: 0.7947 (pt) cc_final: 0.7686 (pt) REVERT: B 143 PHE cc_start: 0.6427 (t80) cc_final: 0.5937 (m-80) REVERT: B 156 ARG cc_start: 0.6908 (ptm160) cc_final: 0.6034 (ptp90) REVERT: B 234 LYS cc_start: 0.8659 (ttpp) cc_final: 0.8254 (ttpp) REVERT: B 338 SER cc_start: 0.8406 (t) cc_final: 0.7850 (m) REVERT: B 408 ARG cc_start: 0.7573 (ttm-80) cc_final: 0.7177 (ttp80) REVERT: B 410 ASP cc_start: 0.7037 (t0) cc_final: 0.6777 (t0) REVERT: B 469 GLN cc_start: 0.7340 (mt0) cc_final: 0.6875 (pp30) REVERT: B 485 GLU cc_start: 0.6953 (tp30) cc_final: 0.6746 (tp30) REVERT: B 498 ASN cc_start: 0.7281 (t0) cc_final: 0.6780 (t0) REVERT: B 547 ARG cc_start: 0.7744 (tpp-160) cc_final: 0.7392 (tpp-160) REVERT: C 2 ILE cc_start: 0.8253 (mm) cc_final: 0.8022 (mp) REVERT: C 130 ARG cc_start: 0.6756 (mtt90) cc_final: 0.6326 (ttm-80) REVERT: C 271 GLU cc_start: 0.7074 (mm-30) cc_final: 0.6649 (tp30) REVERT: C 375 GLU cc_start: 0.7819 (tt0) cc_final: 0.7577 (mt-10) REVERT: C 488 ARG cc_start: 0.7456 (ttp-110) cc_final: 0.7102 (ttp80) REVERT: D 394 LYS cc_start: 0.7253 (mttt) cc_final: 0.6832 (mmtt) REVERT: E 41 ARG cc_start: 0.6900 (mtp-110) cc_final: 0.6635 (mtp-110) REVERT: E 216 ARG cc_start: 0.7664 (mtm-85) cc_final: 0.7356 (ptp90) REVERT: F 6 LYS cc_start: 0.7257 (tttt) cc_final: 0.6822 (tttp) REVERT: F 280 ARG cc_start: 0.6764 (mtm180) cc_final: 0.6479 (mtp85) REVERT: F 409 ARG cc_start: 0.7289 (mtt-85) cc_final: 0.6909 (mtt-85) REVERT: G 184 GLU cc_start: 0.6967 (tt0) cc_final: 0.6686 (mm-30) REVERT: H 14 ARG cc_start: 0.5777 (mtm110) cc_final: 0.5083 (mmm-85) REVERT: H 34 GLU cc_start: 0.5553 (mt-10) cc_final: 0.5245 (mm-30) REVERT: H 49 GLU cc_start: 0.3355 (tm-30) cc_final: 0.2927 (tp30) REVERT: I 87 ARG cc_start: 0.5756 (ptm-80) cc_final: 0.5320 (ptm-80) REVERT: J 74 GLN cc_start: 0.7038 (tp40) cc_final: 0.6697 (tt0) REVERT: J 81 GLU cc_start: 0.7221 (tm-30) cc_final: 0.6879 (mm-30) REVERT: J 86 ARG cc_start: 0.5324 (mtt180) cc_final: 0.5050 (mmt90) REVERT: J 109 LEU cc_start: 0.5595 (mm) cc_final: 0.5267 (mt) REVERT: K 104 MET cc_start: 0.5320 (mmp) cc_final: 0.4658 (ttp) REVERT: K 106 ARG cc_start: 0.4839 (mmp80) cc_final: 0.3482 (ttp-110) REVERT: L 106 LYS cc_start: 0.6198 (ptpt) cc_final: 0.5645 (mttt) outliers start: 71 outliers final: 45 residues processed: 354 average time/residue: 0.4836 time to fit residues: 263.7416 Evaluate side-chains 342 residues out of total 3082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 295 time to evaluate : 3.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 CYS Chi-restraints excluded: chain A residue 45 ASP Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 369 ILE Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 502 GLU Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain B residue 3 GLN Chi-restraints excluded: chain B residue 158 LYS Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 326 SER Chi-restraints excluded: chain B residue 390 ASP Chi-restraints excluded: chain B residue 484 ILE Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 461 GLU Chi-restraints excluded: chain C residue 467 ILE Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 255 VAL Chi-restraints excluded: chain D residue 265 GLU Chi-restraints excluded: chain D residue 319 ASP Chi-restraints excluded: chain D residue 459 ILE Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain E residue 277 ILE Chi-restraints excluded: chain E residue 364 ASN Chi-restraints excluded: chain F residue 39 THR Chi-restraints excluded: chain F residue 290 ASP Chi-restraints excluded: chain F residue 459 ILE Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 143 THR Chi-restraints excluded: chain H residue 81 PHE Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain J residue 94 LEU Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain L residue 186 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 300 optimal weight: 9.9990 chunk 204 optimal weight: 8.9990 chunk 5 optimal weight: 3.9990 chunk 268 optimal weight: 2.9990 chunk 148 optimal weight: 2.9990 chunk 307 optimal weight: 4.9990 chunk 249 optimal weight: 10.0000 chunk 0 optimal weight: 4.9990 chunk 184 optimal weight: 9.9990 chunk 323 optimal weight: 3.9990 chunk 90 optimal weight: 9.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 418 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 206 GLN ** F 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.2710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 30067 Z= 0.286 Angle : 0.562 7.468 40740 Z= 0.286 Chirality : 0.044 0.214 4567 Planarity : 0.005 0.048 5329 Dihedral : 5.485 86.922 4223 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.82 % Allowed : 14.21 % Favored : 82.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.34 % 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: 0.08 (0.14), residues: 3761 helix: 0.91 (0.13), residues: 1534 sheet: -0.50 (0.23), residues: 520 loop : -0.45 (0.14), residues: 1707 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 119 HIS 0.004 0.001 HIS A 185 PHE 0.020 0.002 PHE B 143 TYR 0.015 0.002 TYR C 428 ARG 0.004 0.000 ARG E 216 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 3082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 311 time to evaluate : 3.643 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.3469 (mtt) cc_final: 0.3072 (ptm) REVERT: A 29 LYS cc_start: 0.7861 (mmtp) cc_final: 0.7246 (mmtt) REVERT: A 45 ASP cc_start: 0.8060 (OUTLIER) cc_final: 0.7669 (t0) REVERT: A 54 ASP cc_start: 0.7780 (t0) cc_final: 0.7416 (t70) REVERT: A 98 THR cc_start: 0.7911 (m) cc_final: 0.7541 (p) REVERT: A 532 ARG cc_start: 0.6496 (mtm-85) cc_final: 0.6286 (ttp80) REVERT: A 556 GLU cc_start: 0.7590 (mm-30) cc_final: 0.7050 (tp30) REVERT: A 568 LYS cc_start: 0.6806 (mtmt) cc_final: 0.6410 (tttt) REVERT: B 143 PHE cc_start: 0.6469 (t80) cc_final: 0.6026 (m-80) REVERT: B 156 ARG cc_start: 0.6908 (ptm160) cc_final: 0.6020 (ptp90) REVERT: B 209 MET cc_start: 0.7400 (OUTLIER) cc_final: 0.7030 (mtm) REVERT: B 234 LYS cc_start: 0.8664 (ttpp) cc_final: 0.8270 (ttpp) REVERT: B 338 SER cc_start: 0.8428 (t) cc_final: 0.7862 (m) REVERT: B 408 ARG cc_start: 0.7517 (ttm-80) cc_final: 0.7179 (ttp80) REVERT: B 410 ASP cc_start: 0.7102 (t0) cc_final: 0.6833 (t0) REVERT: B 469 GLN cc_start: 0.7360 (mt0) cc_final: 0.6878 (pp30) REVERT: B 481 ARG cc_start: 0.7106 (ttt90) cc_final: 0.6891 (ttp80) REVERT: B 485 GLU cc_start: 0.7003 (tp30) cc_final: 0.6786 (tp30) REVERT: B 498 ASN cc_start: 0.7389 (t0) cc_final: 0.6863 (t0) REVERT: B 558 GLU cc_start: 0.5580 (OUTLIER) cc_final: 0.5290 (tp30) REVERT: C 2 ILE cc_start: 0.8114 (mm) cc_final: 0.7903 (mp) REVERT: C 130 ARG cc_start: 0.6751 (mtt90) cc_final: 0.6353 (ttm-80) REVERT: C 375 GLU cc_start: 0.7817 (tt0) cc_final: 0.7580 (mt-10) REVERT: C 488 ARG cc_start: 0.7453 (ttp-110) cc_final: 0.7056 (ttp80) REVERT: D 206 GLN cc_start: 0.6923 (mt0) cc_final: 0.6554 (tm-30) REVERT: D 394 LYS cc_start: 0.7314 (mttt) cc_final: 0.6859 (mmtt) REVERT: D 412 LEU cc_start: 0.8096 (OUTLIER) cc_final: 0.7806 (mp) REVERT: D 413 GLN cc_start: 0.7142 (mp10) cc_final: 0.6849 (mp10) REVERT: E 41 ARG cc_start: 0.6875 (mtp-110) cc_final: 0.6628 (mtp-110) REVERT: E 206 GLN cc_start: 0.7068 (OUTLIER) cc_final: 0.6709 (mt0) REVERT: E 216 ARG cc_start: 0.7679 (mtm-85) cc_final: 0.7303 (ptp-170) REVERT: E 318 ASP cc_start: 0.6927 (OUTLIER) cc_final: 0.6540 (m-30) REVERT: F 6 LYS cc_start: 0.7233 (tttt) cc_final: 0.6779 (tttp) REVERT: F 251 TYR cc_start: 0.8200 (m-80) cc_final: 0.7840 (m-80) REVERT: F 280 ARG cc_start: 0.6742 (mtm180) cc_final: 0.6411 (mtp-110) REVERT: G 148 LYS cc_start: 0.6569 (mttp) cc_final: 0.6287 (mmtm) REVERT: G 184 GLU cc_start: 0.6946 (tt0) cc_final: 0.6660 (mm-30) REVERT: H 14 ARG cc_start: 0.5823 (mtm110) cc_final: 0.5120 (mmm-85) REVERT: H 34 GLU cc_start: 0.5572 (mt-10) cc_final: 0.5253 (mm-30) REVERT: H 87 GLU cc_start: 0.6765 (OUTLIER) cc_final: 0.6083 (mm-30) REVERT: J 74 GLN cc_start: 0.7056 (tp40) cc_final: 0.6706 (tt0) REVERT: J 81 GLU cc_start: 0.7180 (tm-30) cc_final: 0.6950 (tt0) REVERT: J 86 ARG cc_start: 0.5285 (mtt180) cc_final: 0.5004 (mmt90) REVERT: J 109 LEU cc_start: 0.5729 (mm) cc_final: 0.5385 (mt) REVERT: K 104 MET cc_start: 0.5273 (mmp) cc_final: 0.4605 (ttp) REVERT: K 106 ARG cc_start: 0.4860 (mmp80) cc_final: 0.3338 (ttm-80) REVERT: L 106 LYS cc_start: 0.6227 (ptpt) cc_final: 0.5594 (mmtp) REVERT: L 113 GLU cc_start: 0.6833 (tm-30) cc_final: 0.6616 (mt-10) outliers start: 87 outliers final: 62 residues processed: 376 average time/residue: 0.4840 time to fit residues: 279.1907 Evaluate side-chains 366 residues out of total 3082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 297 time to evaluate : 3.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 CYS Chi-restraints excluded: chain A residue 45 ASP Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 369 ILE Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 502 GLU Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain B residue 3 GLN Chi-restraints excluded: chain B residue 43 ASP Chi-restraints excluded: chain B residue 158 LYS Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 209 MET Chi-restraints excluded: chain B residue 291 THR Chi-restraints excluded: chain B residue 326 SER Chi-restraints excluded: chain B residue 390 ASP Chi-restraints excluded: chain B residue 433 SER Chi-restraints excluded: chain B residue 484 ILE Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 558 GLU Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 152 ASP Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 432 THR Chi-restraints excluded: chain C residue 461 GLU Chi-restraints excluded: chain C residue 467 ILE Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain D residue 26 ASP Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 265 GLU Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 319 ASP Chi-restraints excluded: chain D residue 380 ASP Chi-restraints excluded: chain D residue 412 LEU Chi-restraints excluded: chain D residue 459 ILE Chi-restraints excluded: chain E residue 36 LYS Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 206 GLN Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain E residue 277 ILE Chi-restraints excluded: chain E residue 318 ASP Chi-restraints excluded: chain E residue 364 ASN Chi-restraints excluded: chain E residue 366 VAL Chi-restraints excluded: chain E residue 371 THR Chi-restraints excluded: chain E residue 405 THR Chi-restraints excluded: chain F residue 39 THR Chi-restraints excluded: chain F residue 290 ASP Chi-restraints excluded: chain F residue 459 ILE Chi-restraints excluded: chain G residue 143 THR Chi-restraints excluded: chain H residue 47 VAL Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain H residue 87 GLU Chi-restraints excluded: chain J residue 94 LEU Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain L residue 186 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 121 optimal weight: 6.9990 chunk 324 optimal weight: 5.9990 chunk 71 optimal weight: 6.9990 chunk 211 optimal weight: 9.9990 chunk 89 optimal weight: 9.9990 chunk 360 optimal weight: 5.9990 chunk 299 optimal weight: 0.9990 chunk 167 optimal weight: 0.3980 chunk 30 optimal weight: 0.8980 chunk 119 optimal weight: 4.9990 chunk 189 optimal weight: 5.9990 overall best weight: 2.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 501 HIS ** C 418 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.2783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 30067 Z= 0.215 Angle : 0.519 7.196 40740 Z= 0.264 Chirality : 0.043 0.227 4567 Planarity : 0.005 0.047 5329 Dihedral : 5.322 86.730 4223 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.92 % Allowed : 14.63 % Favored : 82.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.34 % 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: 0.24 (0.14), residues: 3761 helix: 1.07 (0.14), residues: 1526 sheet: -0.47 (0.23), residues: 526 loop : -0.37 (0.15), residues: 1709 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 119 HIS 0.003 0.001 HIS A 185 PHE 0.017 0.001 PHE B 143 TYR 0.013 0.001 TYR C 428 ARG 0.003 0.000 ARG J 153 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 3082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 304 time to evaluate : 3.741 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.3686 (mtt) cc_final: 0.3223 (ptm) REVERT: A 29 LYS cc_start: 0.7828 (mmtp) cc_final: 0.7200 (mmtt) REVERT: A 45 ASP cc_start: 0.8029 (OUTLIER) cc_final: 0.7641 (t0) REVERT: A 54 ASP cc_start: 0.7729 (t0) cc_final: 0.7356 (t70) REVERT: A 98 THR cc_start: 0.7909 (m) cc_final: 0.7563 (p) REVERT: A 375 GLU cc_start: 0.7391 (mm-30) cc_final: 0.7100 (mm-30) REVERT: A 532 ARG cc_start: 0.6454 (mtm-85) cc_final: 0.6234 (ttp80) REVERT: A 556 GLU cc_start: 0.7528 (mm-30) cc_final: 0.6999 (tp30) REVERT: A 568 LYS cc_start: 0.6777 (mtmt) cc_final: 0.6357 (tttt) REVERT: B 143 PHE cc_start: 0.6468 (t80) cc_final: 0.5994 (m-80) REVERT: B 156 ARG cc_start: 0.6911 (ptm160) cc_final: 0.6018 (ptp90) REVERT: B 209 MET cc_start: 0.7451 (OUTLIER) cc_final: 0.7020 (mtm) REVERT: B 234 LYS cc_start: 0.8657 (ttpp) cc_final: 0.8268 (ttpp) REVERT: B 338 SER cc_start: 0.8402 (t) cc_final: 0.7822 (m) REVERT: B 408 ARG cc_start: 0.7505 (ttm-80) cc_final: 0.7167 (ttp80) REVERT: B 410 ASP cc_start: 0.7100 (t0) cc_final: 0.6806 (t0) REVERT: B 469 GLN cc_start: 0.7355 (mt0) cc_final: 0.6876 (pp30) REVERT: B 485 GLU cc_start: 0.6718 (tp30) cc_final: 0.6501 (tp30) REVERT: B 498 ASN cc_start: 0.7248 (t0) cc_final: 0.6702 (t0) REVERT: B 558 GLU cc_start: 0.5557 (OUTLIER) cc_final: 0.5260 (tp30) REVERT: C 2 ILE cc_start: 0.8004 (mm) cc_final: 0.7796 (mp) REVERT: C 130 ARG cc_start: 0.6808 (mtt90) cc_final: 0.6349 (ttm-80) REVERT: C 375 GLU cc_start: 0.7809 (tt0) cc_final: 0.7595 (mt-10) REVERT: C 488 ARG cc_start: 0.7441 (ttp-110) cc_final: 0.7046 (ttp80) REVERT: D 206 GLN cc_start: 0.6952 (mt0) cc_final: 0.6617 (tm-30) REVERT: D 394 LYS cc_start: 0.7343 (mttt) cc_final: 0.6889 (mmtt) REVERT: D 412 LEU cc_start: 0.8115 (OUTLIER) cc_final: 0.7872 (mp) REVERT: E 41 ARG cc_start: 0.6861 (mtp-110) cc_final: 0.6634 (mtp-110) REVERT: E 216 ARG cc_start: 0.7646 (mtm-85) cc_final: 0.7327 (ptp90) REVERT: F 6 LYS cc_start: 0.7275 (tttt) cc_final: 0.6835 (tttp) REVERT: F 251 TYR cc_start: 0.8150 (m-80) cc_final: 0.7814 (m-80) REVERT: F 280 ARG cc_start: 0.6687 (mtm180) cc_final: 0.6379 (mtp85) REVERT: G 148 LYS cc_start: 0.6549 (mttp) cc_final: 0.6337 (mmtm) REVERT: G 184 GLU cc_start: 0.6959 (tt0) cc_final: 0.6678 (mm-30) REVERT: H 14 ARG cc_start: 0.5799 (mtm110) cc_final: 0.5039 (mmm-85) REVERT: H 34 GLU cc_start: 0.5602 (mt-10) cc_final: 0.5278 (mm-30) REVERT: H 47 VAL cc_start: 0.6533 (OUTLIER) cc_final: 0.6087 (p) REVERT: H 87 GLU cc_start: 0.6709 (OUTLIER) cc_final: 0.6034 (mm-30) REVERT: I 87 ARG cc_start: 0.5843 (ptm-80) cc_final: 0.5388 (ptm-80) REVERT: J 74 GLN cc_start: 0.6992 (tp40) cc_final: 0.6677 (tt0) REVERT: J 81 GLU cc_start: 0.7107 (tm-30) cc_final: 0.6871 (tt0) REVERT: J 109 LEU cc_start: 0.5735 (mm) cc_final: 0.5407 (mt) REVERT: K 104 MET cc_start: 0.5321 (mmp) cc_final: 0.4688 (ttp) REVERT: K 106 ARG cc_start: 0.4804 (mmp80) cc_final: 0.3337 (ttm-80) REVERT: L 106 LYS cc_start: 0.6183 (ptpt) cc_final: 0.5593 (mmtp) outliers start: 90 outliers final: 63 residues processed: 372 average time/residue: 0.4764 time to fit residues: 270.9309 Evaluate side-chains 361 residues out of total 3082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 292 time to evaluate : 3.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 CYS Chi-restraints excluded: chain A residue 45 ASP Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 369 ILE Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 502 GLU Chi-restraints excluded: chain B residue 3 GLN Chi-restraints excluded: chain B residue 43 ASP Chi-restraints excluded: chain B residue 122 MET Chi-restraints excluded: chain B residue 158 LYS Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 209 MET Chi-restraints excluded: chain B residue 326 SER Chi-restraints excluded: chain B residue 390 ASP Chi-restraints excluded: chain B residue 433 SER Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 558 GLU Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 152 ASP Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 432 THR Chi-restraints excluded: chain C residue 461 GLU Chi-restraints excluded: chain C residue 467 ILE Chi-restraints excluded: chain D residue 26 ASP Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 255 VAL Chi-restraints excluded: chain D residue 265 GLU Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 319 ASP Chi-restraints excluded: chain D residue 362 MET Chi-restraints excluded: chain D residue 380 ASP Chi-restraints excluded: chain D residue 412 LEU Chi-restraints excluded: chain D residue 459 ILE Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 100 ILE Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain E residue 277 ILE Chi-restraints excluded: chain E residue 364 ASN Chi-restraints excluded: chain E residue 366 VAL Chi-restraints excluded: chain E residue 371 THR Chi-restraints excluded: chain E residue 405 THR Chi-restraints excluded: chain F residue 39 THR Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain F residue 290 ASP Chi-restraints excluded: chain F residue 442 LEU Chi-restraints excluded: chain F residue 459 ILE Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 58 LYS Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 143 THR Chi-restraints excluded: chain H residue 47 VAL Chi-restraints excluded: chain H residue 74 ILE Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain H residue 87 GLU Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain J residue 161 THR Chi-restraints excluded: chain J residue 176 ASP Chi-restraints excluded: chain L residue 186 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 347 optimal weight: 7.9990 chunk 40 optimal weight: 10.0000 chunk 205 optimal weight: 6.9990 chunk 263 optimal weight: 6.9990 chunk 204 optimal weight: 0.8980 chunk 303 optimal weight: 0.9980 chunk 201 optimal weight: 9.9990 chunk 359 optimal weight: 9.9990 chunk 224 optimal weight: 7.9990 chunk 219 optimal weight: 1.9990 chunk 165 optimal weight: 8.9990 overall best weight: 3.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 418 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 310 GLN ** F 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.2883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 30067 Z= 0.271 Angle : 0.550 7.520 40740 Z= 0.279 Chirality : 0.044 0.232 4567 Planarity : 0.005 0.047 5329 Dihedral : 5.381 86.916 4223 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 3.15 % Allowed : 15.09 % Favored : 81.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.34 % 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: 0.14 (0.14), residues: 3761 helix: 0.98 (0.14), residues: 1530 sheet: -0.59 (0.23), residues: 541 loop : -0.39 (0.15), residues: 1690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 119 HIS 0.004 0.001 HIS A 185 PHE 0.018 0.002 PHE B 143 TYR 0.015 0.001 TYR C 428 ARG 0.010 0.000 ARG J 86 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 3082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 298 time to evaluate : 3.813 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.3783 (mtt) cc_final: 0.3436 (ptm) REVERT: A 29 LYS cc_start: 0.7836 (mmtp) cc_final: 0.7211 (mmtt) REVERT: A 45 ASP cc_start: 0.8036 (OUTLIER) cc_final: 0.7647 (t0) REVERT: A 54 ASP cc_start: 0.7774 (t0) cc_final: 0.7391 (t70) REVERT: A 98 THR cc_start: 0.7909 (m) cc_final: 0.7566 (p) REVERT: A 241 LEU cc_start: 0.7892 (OUTLIER) cc_final: 0.7533 (mp) REVERT: A 532 ARG cc_start: 0.6517 (mtm-85) cc_final: 0.6246 (ttp80) REVERT: A 556 GLU cc_start: 0.7538 (mm-30) cc_final: 0.7020 (tp30) REVERT: A 568 LYS cc_start: 0.6792 (mtmt) cc_final: 0.6371 (tttt) REVERT: B 143 PHE cc_start: 0.6531 (t80) cc_final: 0.6085 (m-80) REVERT: B 156 ARG cc_start: 0.6880 (ptm160) cc_final: 0.5999 (ptp90) REVERT: B 209 MET cc_start: 0.7434 (OUTLIER) cc_final: 0.7067 (mtm) REVERT: B 234 LYS cc_start: 0.8676 (ttpp) cc_final: 0.8293 (ttpp) REVERT: B 338 SER cc_start: 0.8427 (t) cc_final: 0.7852 (m) REVERT: B 408 ARG cc_start: 0.7483 (ttm-80) cc_final: 0.7171 (ttp80) REVERT: B 410 ASP cc_start: 0.7151 (t0) cc_final: 0.6843 (t0) REVERT: B 469 GLN cc_start: 0.7377 (mt0) cc_final: 0.6890 (pp30) REVERT: B 485 GLU cc_start: 0.6779 (tp30) cc_final: 0.6570 (tp30) REVERT: B 498 ASN cc_start: 0.7342 (t0) cc_final: 0.6793 (t0) REVERT: B 558 GLU cc_start: 0.5613 (OUTLIER) cc_final: 0.5279 (tp30) REVERT: C 2 ILE cc_start: 0.7960 (mm) cc_final: 0.7753 (mp) REVERT: C 130 ARG cc_start: 0.6805 (mtt90) cc_final: 0.6319 (ttm-80) REVERT: C 375 GLU cc_start: 0.7759 (tt0) cc_final: 0.7556 (mt-10) REVERT: C 488 ARG cc_start: 0.7474 (ttp-110) cc_final: 0.7066 (ttp80) REVERT: D 206 GLN cc_start: 0.6947 (mt0) cc_final: 0.6604 (tm-30) REVERT: D 394 LYS cc_start: 0.7193 (mttt) cc_final: 0.6784 (mmtt) REVERT: D 412 LEU cc_start: 0.8033 (OUTLIER) cc_final: 0.7762 (mp) REVERT: E 41 ARG cc_start: 0.6869 (mtp-110) cc_final: 0.6652 (mtp-110) REVERT: E 216 ARG cc_start: 0.7730 (mtm-85) cc_final: 0.7341 (ptp-170) REVERT: E 318 ASP cc_start: 0.6926 (OUTLIER) cc_final: 0.6380 (m-30) REVERT: F 6 LYS cc_start: 0.7295 (tttt) cc_final: 0.6819 (tttp) REVERT: F 251 TYR cc_start: 0.8233 (m-80) cc_final: 0.7917 (m-80) REVERT: F 280 ARG cc_start: 0.6685 (mtm180) cc_final: 0.6387 (mtp-110) REVERT: G 148 LYS cc_start: 0.6615 (mttp) cc_final: 0.6344 (mmtm) REVERT: G 184 GLU cc_start: 0.6973 (tt0) cc_final: 0.6671 (mm-30) REVERT: H 1 MET cc_start: 0.5474 (tpp) cc_final: 0.5259 (tpp) REVERT: H 14 ARG cc_start: 0.5784 (mtm110) cc_final: 0.5012 (mmm-85) REVERT: H 34 GLU cc_start: 0.5657 (mt-10) cc_final: 0.5302 (mm-30) REVERT: H 87 GLU cc_start: 0.6727 (OUTLIER) cc_final: 0.6038 (mm-30) REVERT: J 74 GLN cc_start: 0.7001 (tp40) cc_final: 0.6678 (tt0) REVERT: J 81 GLU cc_start: 0.7136 (tm-30) cc_final: 0.6847 (tt0) REVERT: J 109 LEU cc_start: 0.5695 (mm) cc_final: 0.5348 (mt) REVERT: K 104 MET cc_start: 0.5362 (mmp) cc_final: 0.4695 (ttp) REVERT: K 106 ARG cc_start: 0.4782 (mmp80) cc_final: 0.3307 (ttm-80) REVERT: L 106 LYS cc_start: 0.5979 (ptpt) cc_final: 0.5556 (mmtp) outliers start: 97 outliers final: 74 residues processed: 374 average time/residue: 0.4870 time to fit residues: 280.0768 Evaluate side-chains 368 residues out of total 3082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 287 time to evaluate : 3.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 CYS Chi-restraints excluded: chain A residue 45 ASP Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 369 ILE Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 502 GLU Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain B residue 3 GLN Chi-restraints excluded: chain B residue 43 ASP Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 122 MET Chi-restraints excluded: chain B residue 158 LYS Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 209 MET Chi-restraints excluded: chain B residue 291 THR Chi-restraints excluded: chain B residue 326 SER Chi-restraints excluded: chain B residue 390 ASP Chi-restraints excluded: chain B residue 433 SER Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 558 GLU Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 152 ASP Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 432 THR Chi-restraints excluded: chain C residue 461 GLU Chi-restraints excluded: chain C residue 467 ILE Chi-restraints excluded: chain C residue 539 ILE Chi-restraints excluded: chain D residue 26 ASP Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 156 SER Chi-restraints excluded: chain D residue 255 VAL Chi-restraints excluded: chain D residue 265 GLU Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 319 ASP Chi-restraints excluded: chain D residue 380 ASP Chi-restraints excluded: chain D residue 412 LEU Chi-restraints excluded: chain D residue 459 ILE Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 100 ILE Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain E residue 277 ILE Chi-restraints excluded: chain E residue 318 ASP Chi-restraints excluded: chain E residue 364 ASN Chi-restraints excluded: chain E residue 366 VAL Chi-restraints excluded: chain E residue 371 THR Chi-restraints excluded: chain E residue 402 ASP Chi-restraints excluded: chain E residue 405 THR Chi-restraints excluded: chain F residue 39 THR Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain F residue 290 ASP Chi-restraints excluded: chain F residue 442 LEU Chi-restraints excluded: chain F residue 459 ILE Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 58 LYS Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 143 THR Chi-restraints excluded: chain H residue 47 VAL Chi-restraints excluded: chain H residue 74 ILE Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain H residue 87 GLU Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain J residue 161 THR Chi-restraints excluded: chain J residue 176 ASP Chi-restraints excluded: chain L residue 186 LEU 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: 0.3980 chunk 214 optimal weight: 8.9990 chunk 108 optimal weight: 9.9990 chunk 70 optimal weight: 10.0000 chunk 69 optimal weight: 5.9990 chunk 228 optimal weight: 3.9990 chunk 244 optimal weight: 7.9990 chunk 177 optimal weight: 0.1980 chunk 33 optimal weight: 9.9990 chunk 282 optimal weight: 6.9990 overall best weight: 3.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 418 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 310 GLN ** F 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.2960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 30067 Z= 0.264 Angle : 0.546 7.835 40740 Z= 0.277 Chirality : 0.044 0.232 4567 Planarity : 0.005 0.047 5329 Dihedral : 5.365 86.901 4223 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 3.34 % Allowed : 15.31 % Favored : 81.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.14), residues: 3761 helix: 1.00 (0.14), residues: 1528 sheet: -0.51 (0.23), residues: 523 loop : -0.42 (0.15), residues: 1710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 119 HIS 0.004 0.001 HIS A 185 PHE 0.017 0.002 PHE B 143 TYR 0.014 0.001 TYR C 428 ARG 0.004 0.000 ARG C 460 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 3082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 297 time to evaluate : 3.454 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.3918 (mtt) cc_final: 0.3568 (ptm) REVERT: A 29 LYS cc_start: 0.7837 (mmtp) cc_final: 0.7200 (mmtt) REVERT: A 45 ASP cc_start: 0.8031 (OUTLIER) cc_final: 0.7650 (t0) REVERT: A 54 ASP cc_start: 0.7771 (t0) cc_final: 0.7388 (t70) REVERT: A 98 THR cc_start: 0.7950 (m) cc_final: 0.7616 (p) REVERT: A 241 LEU cc_start: 0.7889 (OUTLIER) cc_final: 0.7515 (mp) REVERT: A 375 GLU cc_start: 0.7432 (mm-30) cc_final: 0.7183 (mm-30) REVERT: A 556 GLU cc_start: 0.7502 (mm-30) cc_final: 0.7036 (tp30) REVERT: A 568 LYS cc_start: 0.6788 (mtmt) cc_final: 0.6369 (tttt) REVERT: B 143 PHE cc_start: 0.6509 (t80) cc_final: 0.6066 (m-80) REVERT: B 156 ARG cc_start: 0.6883 (ptm160) cc_final: 0.5990 (ptp90) REVERT: B 209 MET cc_start: 0.7456 (OUTLIER) cc_final: 0.7043 (mtm) REVERT: B 234 LYS cc_start: 0.8681 (ttpp) cc_final: 0.8299 (ttpp) REVERT: B 338 SER cc_start: 0.8435 (t) cc_final: 0.7860 (m) REVERT: B 408 ARG cc_start: 0.7466 (ttm-80) cc_final: 0.7156 (ttp80) REVERT: B 410 ASP cc_start: 0.7202 (t0) cc_final: 0.6879 (t0) REVERT: B 469 GLN cc_start: 0.7384 (mt0) cc_final: 0.6885 (pp30) REVERT: B 485 GLU cc_start: 0.6775 (tp30) cc_final: 0.6567 (tp30) REVERT: B 498 ASN cc_start: 0.7337 (t0) cc_final: 0.6794 (t0) REVERT: B 558 GLU cc_start: 0.5692 (OUTLIER) cc_final: 0.5339 (tp30) REVERT: C 130 ARG cc_start: 0.6799 (mtt90) cc_final: 0.6319 (ttm-80) REVERT: C 271 GLU cc_start: 0.6949 (mm-30) cc_final: 0.6448 (tp30) REVERT: C 375 GLU cc_start: 0.7747 (tt0) cc_final: 0.7545 (mt-10) REVERT: C 488 ARG cc_start: 0.7470 (ttp-110) cc_final: 0.7065 (ttp80) REVERT: C 524 LYS cc_start: 0.7605 (tttm) cc_final: 0.7388 (ttmt) REVERT: D 206 GLN cc_start: 0.6952 (mt0) cc_final: 0.6610 (tm-30) REVERT: E 41 ARG cc_start: 0.6874 (mtp-110) cc_final: 0.6664 (mtp-110) REVERT: E 216 ARG cc_start: 0.7769 (mtm-85) cc_final: 0.7365 (ptp-170) REVERT: E 318 ASP cc_start: 0.6832 (OUTLIER) cc_final: 0.6396 (m-30) REVERT: F 6 LYS cc_start: 0.7287 (tttt) cc_final: 0.6825 (tttp) REVERT: F 251 TYR cc_start: 0.8231 (m-80) cc_final: 0.7918 (m-80) REVERT: F 280 ARG cc_start: 0.6699 (mtm180) cc_final: 0.6403 (mtp-110) REVERT: G 148 LYS cc_start: 0.6617 (mttp) cc_final: 0.6349 (mmtm) REVERT: G 184 GLU cc_start: 0.6981 (tt0) cc_final: 0.6668 (mm-30) REVERT: H 1 MET cc_start: 0.5524 (tpp) cc_final: 0.5282 (tpp) REVERT: H 14 ARG cc_start: 0.5888 (mtm110) cc_final: 0.5121 (mmm-85) REVERT: H 34 GLU cc_start: 0.5661 (mt-10) cc_final: 0.5334 (mm-30) REVERT: H 47 VAL cc_start: 0.6538 (OUTLIER) cc_final: 0.6086 (p) REVERT: H 87 GLU cc_start: 0.6670 (OUTLIER) cc_final: 0.6073 (mm-30) REVERT: J 74 GLN cc_start: 0.6991 (tp40) cc_final: 0.6677 (tt0) REVERT: J 81 GLU cc_start: 0.7114 (tm-30) cc_final: 0.6853 (tt0) REVERT: J 109 LEU cc_start: 0.5781 (mm) cc_final: 0.5445 (mt) REVERT: K 104 MET cc_start: 0.5315 (mmp) cc_final: 0.4845 (mtp) REVERT: K 106 ARG cc_start: 0.4769 (mmp80) cc_final: 0.3259 (ttm-80) REVERT: L 106 LYS cc_start: 0.6037 (ptpt) cc_final: 0.5630 (mmtp) outliers start: 103 outliers final: 80 residues processed: 380 average time/residue: 0.4589 time to fit residues: 268.3879 Evaluate side-chains 370 residues out of total 3082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 283 time to evaluate : 3.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 CYS Chi-restraints excluded: chain A residue 45 ASP Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 369 ILE Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 502 GLU Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain B residue 3 GLN Chi-restraints excluded: chain B residue 43 ASP Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 122 MET Chi-restraints excluded: chain B residue 158 LYS Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 209 MET Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 291 THR Chi-restraints excluded: chain B residue 326 SER Chi-restraints excluded: chain B residue 390 ASP Chi-restraints excluded: chain B residue 433 SER Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 558 GLU Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 152 ASP Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 432 THR Chi-restraints excluded: chain C residue 461 GLU Chi-restraints excluded: chain C residue 467 ILE Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain D residue 26 ASP Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 156 SER Chi-restraints excluded: chain D residue 255 VAL Chi-restraints excluded: chain D residue 265 GLU Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 319 ASP Chi-restraints excluded: chain D residue 380 ASP Chi-restraints excluded: chain D residue 432 ILE Chi-restraints excluded: chain D residue 459 ILE Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 100 ILE Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain E residue 277 ILE Chi-restraints excluded: chain E residue 309 THR Chi-restraints excluded: chain E residue 318 ASP Chi-restraints excluded: chain E residue 364 ASN Chi-restraints excluded: chain E residue 366 VAL Chi-restraints excluded: chain E residue 371 THR Chi-restraints excluded: chain E residue 402 ASP Chi-restraints excluded: chain E residue 405 THR Chi-restraints excluded: chain F residue 39 THR Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain F residue 290 ASP Chi-restraints excluded: chain F residue 442 LEU Chi-restraints excluded: chain F residue 459 ILE Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 58 LYS Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 143 THR Chi-restraints excluded: chain H residue 47 VAL Chi-restraints excluded: chain H residue 74 ILE Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain H residue 87 GLU Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain J residue 161 THR Chi-restraints excluded: chain J residue 176 ASP Chi-restraints excluded: chain J residue 180 SER Chi-restraints excluded: chain L residue 186 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 327 optimal weight: 0.9980 chunk 344 optimal weight: 10.0000 chunk 314 optimal weight: 5.9990 chunk 335 optimal weight: 30.0000 chunk 201 optimal weight: 8.9990 chunk 145 optimal weight: 8.9990 chunk 263 optimal weight: 5.9990 chunk 102 optimal weight: 7.9990 chunk 302 optimal weight: 0.9990 chunk 316 optimal weight: 20.0000 chunk 333 optimal weight: 20.0000 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 418 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 310 GLN ** F 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.3048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 30067 Z= 0.318 Angle : 0.587 8.346 40740 Z= 0.298 Chirality : 0.045 0.239 4567 Planarity : 0.005 0.048 5329 Dihedral : 5.518 87.239 4223 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 3.28 % Allowed : 15.44 % Favored : 81.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.34 % 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: -0.00 (0.14), residues: 3761 helix: 0.85 (0.13), residues: 1529 sheet: -0.59 (0.23), residues: 524 loop : -0.49 (0.14), residues: 1708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 119 HIS 0.005 0.001 HIS A 185 PHE 0.019 0.002 PHE B 143 TYR 0.019 0.002 TYR E 463 ARG 0.005 0.000 ARG C 460 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 3082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 290 time to evaluate : 3.468 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 LYS cc_start: 0.7835 (mmtp) cc_final: 0.7208 (mmtt) REVERT: A 45 ASP cc_start: 0.8041 (OUTLIER) cc_final: 0.7669 (t0) REVERT: A 54 ASP cc_start: 0.7789 (t0) cc_final: 0.7405 (t70) REVERT: A 97 LYS cc_start: 0.7115 (mtpt) cc_final: 0.6102 (mmtm) REVERT: A 98 THR cc_start: 0.7934 (m) cc_final: 0.7607 (p) REVERT: A 241 LEU cc_start: 0.7910 (OUTLIER) cc_final: 0.7549 (mp) REVERT: A 375 GLU cc_start: 0.7432 (mm-30) cc_final: 0.7146 (mm-30) REVERT: A 556 GLU cc_start: 0.7502 (mm-30) cc_final: 0.7075 (tp30) REVERT: A 568 LYS cc_start: 0.6798 (mtmt) cc_final: 0.6399 (tttt) REVERT: B 143 PHE cc_start: 0.6554 (t80) cc_final: 0.6130 (m-80) REVERT: B 156 ARG cc_start: 0.6871 (ptm160) cc_final: 0.5981 (ptp90) REVERT: B 209 MET cc_start: 0.7411 (OUTLIER) cc_final: 0.7075 (mtm) REVERT: B 234 LYS cc_start: 0.8685 (ttpp) cc_final: 0.8322 (ttpp) REVERT: B 338 SER cc_start: 0.8422 (t) cc_final: 0.7854 (m) REVERT: B 408 ARG cc_start: 0.7466 (ttm-80) cc_final: 0.7154 (ttp80) REVERT: B 410 ASP cc_start: 0.7291 (t0) cc_final: 0.6982 (t0) REVERT: B 449 GLU cc_start: 0.7720 (mm-30) cc_final: 0.7299 (mt-10) REVERT: B 469 GLN cc_start: 0.7396 (mt0) cc_final: 0.6887 (pp30) REVERT: B 481 ARG cc_start: 0.7122 (ttt90) cc_final: 0.6918 (ttp80) REVERT: B 485 GLU cc_start: 0.6884 (tp30) cc_final: 0.6681 (tp30) REVERT: B 498 ASN cc_start: 0.7412 (t0) cc_final: 0.6831 (t0) REVERT: B 558 GLU cc_start: 0.5752 (OUTLIER) cc_final: 0.5410 (tp30) REVERT: C 130 ARG cc_start: 0.6782 (mtt90) cc_final: 0.6313 (ttm-80) REVERT: C 271 GLU cc_start: 0.6999 (mm-30) cc_final: 0.6496 (tp30) REVERT: C 375 GLU cc_start: 0.7783 (tt0) cc_final: 0.7572 (mt-10) REVERT: C 488 ARG cc_start: 0.7475 (ttp-110) cc_final: 0.7057 (ttp80) REVERT: C 524 LYS cc_start: 0.7615 (tttm) cc_final: 0.7398 (ttmt) REVERT: D 206 GLN cc_start: 0.6947 (mt0) cc_final: 0.6591 (tm-30) REVERT: D 413 GLN cc_start: 0.7067 (mp10) cc_final: 0.6780 (mp10) REVERT: E 41 ARG cc_start: 0.6883 (mtp-110) cc_final: 0.6661 (mtp-110) REVERT: E 200 GLU cc_start: 0.6832 (mt-10) cc_final: 0.6586 (mt-10) REVERT: E 216 ARG cc_start: 0.7842 (mtm-85) cc_final: 0.7438 (ptp-170) REVERT: E 318 ASP cc_start: 0.6844 (OUTLIER) cc_final: 0.6408 (m-30) REVERT: F 6 LYS cc_start: 0.7298 (tttt) cc_final: 0.6825 (tttp) REVERT: F 251 TYR cc_start: 0.8220 (m-80) cc_final: 0.7920 (m-80) REVERT: F 280 ARG cc_start: 0.6756 (mtm180) cc_final: 0.6518 (mtp-110) REVERT: G 148 LYS cc_start: 0.6646 (mttp) cc_final: 0.6365 (mmtm) REVERT: G 184 GLU cc_start: 0.6975 (tt0) cc_final: 0.6655 (mm-30) REVERT: H 1 MET cc_start: 0.5458 (tpp) cc_final: 0.5144 (tpp) REVERT: H 14 ARG cc_start: 0.5902 (mtm110) cc_final: 0.5172 (mmm-85) REVERT: H 34 GLU cc_start: 0.5609 (mt-10) cc_final: 0.5289 (mm-30) REVERT: H 87 GLU cc_start: 0.6649 (OUTLIER) cc_final: 0.6093 (mm-30) REVERT: J 74 GLN cc_start: 0.7011 (tp40) cc_final: 0.6683 (tt0) REVERT: J 81 GLU cc_start: 0.7132 (tm-30) cc_final: 0.6851 (tt0) REVERT: J 109 LEU cc_start: 0.5628 (OUTLIER) cc_final: 0.5284 (mt) REVERT: K 104 MET cc_start: 0.5379 (mmp) cc_final: 0.4897 (mtp) REVERT: K 106 ARG cc_start: 0.4783 (mmp80) cc_final: 0.3276 (ttm-80) REVERT: L 106 LYS cc_start: 0.6090 (ptpt) cc_final: 0.5733 (mmtp) outliers start: 101 outliers final: 84 residues processed: 370 average time/residue: 0.4518 time to fit residues: 258.2006 Evaluate side-chains 377 residues out of total 3082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 286 time to evaluate : 3.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 CYS Chi-restraints excluded: chain A residue 45 ASP Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 369 ILE Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 502 GLU Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain B residue 3 GLN Chi-restraints excluded: chain B residue 43 ASP Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 122 MET Chi-restraints excluded: chain B residue 158 LYS Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 209 MET Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 291 THR Chi-restraints excluded: chain B residue 326 SER Chi-restraints excluded: chain B residue 390 ASP Chi-restraints excluded: chain B residue 433 SER Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 558 GLU Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 152 ASP Chi-restraints excluded: chain C residue 344 MET Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 432 THR Chi-restraints excluded: chain C residue 461 GLU Chi-restraints excluded: chain C residue 467 ILE Chi-restraints excluded: chain C residue 539 ILE Chi-restraints excluded: chain D residue 26 ASP Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 156 SER Chi-restraints excluded: chain D residue 255 VAL Chi-restraints excluded: chain D residue 265 GLU Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 319 ASP Chi-restraints excluded: chain D residue 380 ASP Chi-restraints excluded: chain D residue 432 ILE Chi-restraints excluded: chain D residue 459 ILE Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 100 ILE Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain E residue 277 ILE Chi-restraints excluded: chain E residue 309 THR Chi-restraints excluded: chain E residue 318 ASP Chi-restraints excluded: chain E residue 364 ASN Chi-restraints excluded: chain E residue 366 VAL Chi-restraints excluded: chain E residue 371 THR Chi-restraints excluded: chain E residue 402 ASP Chi-restraints excluded: chain E residue 405 THR Chi-restraints excluded: chain F residue 39 THR Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain F residue 290 ASP Chi-restraints excluded: chain F residue 442 LEU Chi-restraints excluded: chain F residue 459 ILE Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 58 LYS Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 143 THR Chi-restraints excluded: chain H residue 28 GLU Chi-restraints excluded: chain H residue 47 VAL Chi-restraints excluded: chain H residue 74 ILE Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain H residue 87 GLU Chi-restraints excluded: chain I residue 95 GLU Chi-restraints excluded: chain J residue 109 LEU Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain J residue 161 THR Chi-restraints excluded: chain J residue 176 ASP Chi-restraints excluded: chain J residue 180 SER Chi-restraints excluded: chain L residue 186 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 219 optimal weight: 3.9990 chunk 354 optimal weight: 10.0000 chunk 216 optimal weight: 2.9990 chunk 168 optimal weight: 0.9990 chunk 246 optimal weight: 7.9990 chunk 371 optimal weight: 10.0000 chunk 342 optimal weight: 3.9990 chunk 295 optimal weight: 0.7980 chunk 30 optimal weight: 0.9980 chunk 228 optimal weight: 20.0000 chunk 181 optimal weight: 7.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 418 HIS F 310 GLN ** F 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.3101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 30067 Z= 0.179 Angle : 0.504 7.667 40740 Z= 0.255 Chirality : 0.042 0.226 4567 Planarity : 0.004 0.046 5329 Dihedral : 5.189 86.962 4223 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.53 % Allowed : 16.03 % Favored : 81.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.34 % 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: 0.33 (0.14), residues: 3761 helix: 1.19 (0.14), residues: 1521 sheet: -0.42 (0.23), residues: 512 loop : -0.37 (0.15), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 119 HIS 0.004 0.001 HIS C 418 PHE 0.015 0.001 PHE B 143 TYR 0.016 0.001 TYR E 463 ARG 0.006 0.000 ARG C 460 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 3082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 297 time to evaluate : 3.281 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 LYS cc_start: 0.7780 (mmtp) cc_final: 0.7139 (mmtt) REVERT: A 45 ASP cc_start: 0.8034 (OUTLIER) cc_final: 0.7655 (t0) REVERT: A 54 ASP cc_start: 0.7643 (t0) cc_final: 0.7359 (t70) REVERT: A 97 LYS cc_start: 0.7112 (mtpt) cc_final: 0.6139 (mmtm) REVERT: A 98 THR cc_start: 0.7915 (m) cc_final: 0.7622 (p) REVERT: A 241 LEU cc_start: 0.7871 (OUTLIER) cc_final: 0.7505 (mp) REVERT: A 375 GLU cc_start: 0.7447 (mm-30) cc_final: 0.7180 (mm-30) REVERT: A 556 GLU cc_start: 0.7500 (mm-30) cc_final: 0.7080 (tp30) REVERT: A 565 GLU cc_start: 0.6246 (mm-30) cc_final: 0.5666 (pt0) REVERT: A 568 LYS cc_start: 0.6755 (mtmt) cc_final: 0.6348 (tttt) REVERT: B 143 PHE cc_start: 0.6486 (t80) cc_final: 0.6024 (m-80) REVERT: B 156 ARG cc_start: 0.6899 (ptm160) cc_final: 0.5987 (ptp90) REVERT: B 209 MET cc_start: 0.7469 (OUTLIER) cc_final: 0.7019 (mtm) REVERT: B 234 LYS cc_start: 0.8596 (ttpp) cc_final: 0.8201 (ttpp) REVERT: B 338 SER cc_start: 0.8415 (t) cc_final: 0.7814 (m) REVERT: B 408 ARG cc_start: 0.7478 (ttm-80) cc_final: 0.7163 (ttp80) REVERT: B 410 ASP cc_start: 0.7291 (t0) cc_final: 0.6960 (t0) REVERT: B 449 GLU cc_start: 0.7655 (mm-30) cc_final: 0.7247 (mt-10) REVERT: B 469 GLN cc_start: 0.7326 (mt0) cc_final: 0.6873 (pp30) REVERT: B 498 ASN cc_start: 0.7245 (t0) cc_final: 0.6670 (t0) REVERT: B 558 GLU cc_start: 0.5715 (OUTLIER) cc_final: 0.5358 (tp30) REVERT: C 130 ARG cc_start: 0.6791 (mtt90) cc_final: 0.6330 (ttm-80) REVERT: C 271 GLU cc_start: 0.6999 (mm-30) cc_final: 0.6509 (tp30) REVERT: C 469 GLN cc_start: 0.7087 (tt0) cc_final: 0.6650 (tm-30) REVERT: C 524 LYS cc_start: 0.7456 (tttm) cc_final: 0.7245 (ttmt) REVERT: D 206 GLN cc_start: 0.6951 (mt0) cc_final: 0.6625 (tm-30) REVERT: D 413 GLN cc_start: 0.7049 (mp10) cc_final: 0.6792 (mp10) REVERT: E 200 GLU cc_start: 0.6830 (mt-10) cc_final: 0.6609 (mt-10) REVERT: E 216 ARG cc_start: 0.7749 (mtm-85) cc_final: 0.7382 (ptp-170) REVERT: E 318 ASP cc_start: 0.6813 (OUTLIER) cc_final: 0.6375 (m-30) REVERT: F 6 LYS cc_start: 0.7221 (tttt) cc_final: 0.6771 (tttp) REVERT: F 251 TYR cc_start: 0.8200 (m-80) cc_final: 0.7899 (m-80) REVERT: F 280 ARG cc_start: 0.6640 (mtm180) cc_final: 0.6360 (mtp-110) REVERT: G 148 LYS cc_start: 0.6615 (mttp) cc_final: 0.6339 (mmtm) REVERT: G 184 GLU cc_start: 0.6963 (tt0) cc_final: 0.6683 (mm-30) REVERT: H 1 MET cc_start: 0.5394 (tpp) cc_final: 0.5116 (tpp) REVERT: H 14 ARG cc_start: 0.5705 (mtm110) cc_final: 0.4960 (mmm-85) REVERT: H 34 GLU cc_start: 0.5647 (mt-10) cc_final: 0.5303 (mm-30) REVERT: H 47 VAL cc_start: 0.6551 (OUTLIER) cc_final: 0.6130 (p) REVERT: H 87 GLU cc_start: 0.6545 (OUTLIER) cc_final: 0.6013 (mm-30) REVERT: J 74 GLN cc_start: 0.6899 (tp40) cc_final: 0.6642 (tt0) REVERT: J 81 GLU cc_start: 0.7114 (tm-30) cc_final: 0.6864 (tt0) REVERT: J 109 LEU cc_start: 0.5672 (OUTLIER) cc_final: 0.5357 (mt) REVERT: K 104 MET cc_start: 0.5377 (mmp) cc_final: 0.4754 (ttp) REVERT: K 106 ARG cc_start: 0.4638 (mmp80) cc_final: 0.3214 (ttm-80) REVERT: L 106 LYS cc_start: 0.6118 (ptpt) cc_final: 0.5759 (mmtp) outliers start: 78 outliers final: 65 residues processed: 358 average time/residue: 0.4585 time to fit residues: 251.5189 Evaluate side-chains 358 residues out of total 3082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 285 time to evaluate : 3.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 CYS Chi-restraints excluded: chain A residue 45 ASP Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 369 ILE Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 502 GLU Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain B residue 43 ASP Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 122 MET Chi-restraints excluded: chain B residue 158 LYS Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 209 MET Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 326 SER Chi-restraints excluded: chain B residue 390 ASP Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 558 GLU Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 152 ASP Chi-restraints excluded: chain C residue 344 MET Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 432 THR Chi-restraints excluded: chain C residue 450 LEU Chi-restraints excluded: chain C residue 461 GLU Chi-restraints excluded: chain C residue 467 ILE Chi-restraints excluded: chain D residue 26 ASP Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 255 VAL Chi-restraints excluded: chain D residue 265 GLU Chi-restraints excluded: chain D residue 319 ASP Chi-restraints excluded: chain D residue 380 ASP Chi-restraints excluded: chain D residue 459 ILE Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 100 ILE Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain E residue 277 ILE Chi-restraints excluded: chain E residue 309 THR Chi-restraints excluded: chain E residue 318 ASP Chi-restraints excluded: chain E residue 364 ASN Chi-restraints excluded: chain E residue 371 THR Chi-restraints excluded: chain E residue 405 THR Chi-restraints excluded: chain F residue 39 THR Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain F residue 290 ASP Chi-restraints excluded: chain F residue 442 LEU Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 58 LYS Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 143 THR Chi-restraints excluded: chain H residue 47 VAL Chi-restraints excluded: chain H residue 74 ILE Chi-restraints excluded: chain H residue 87 GLU Chi-restraints excluded: chain J residue 109 LEU Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain J residue 161 THR Chi-restraints excluded: chain J residue 180 SER Chi-restraints excluded: chain L residue 186 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 235 optimal weight: 6.9990 chunk 315 optimal weight: 9.9990 chunk 90 optimal weight: 9.9990 chunk 272 optimal weight: 10.0000 chunk 43 optimal weight: 2.9990 chunk 82 optimal weight: 10.0000 chunk 296 optimal weight: 0.8980 chunk 124 optimal weight: 3.9990 chunk 304 optimal weight: 7.9990 chunk 37 optimal weight: 8.9990 chunk 54 optimal weight: 9.9990 overall best weight: 4.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 310 GLN ** F 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.125520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.102714 restraints weight = 47980.045| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 1.56 r_work: 0.3138 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3030 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.3144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 30067 Z= 0.327 Angle : 0.581 8.280 40740 Z= 0.295 Chirality : 0.045 0.235 4567 Planarity : 0.005 0.048 5329 Dihedral : 5.434 87.341 4223 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.79 % Allowed : 15.96 % Favored : 81.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.34 % 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: 3761 helix: 0.99 (0.14), residues: 1508 sheet: -0.66 (0.22), residues: 562 loop : -0.42 (0.15), residues: 1691 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 119 HIS 0.004 0.001 HIS A 185 PHE 0.018 0.002 PHE B 143 TYR 0.016 0.002 TYR E 463 ARG 0.009 0.001 ARG E 41 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6698.01 seconds wall clock time: 121 minutes 29.35 seconds (7289.35 seconds total)