Starting phenix.real_space_refine on Wed Feb 21 03:44:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vao_31854/02_2024/7vao_31854_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vao_31854/02_2024/7vao_31854.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vao_31854/02_2024/7vao_31854.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vao_31854/02_2024/7vao_31854.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vao_31854/02_2024/7vao_31854_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vao_31854/02_2024/7vao_31854_updated.pdb" } resolution = 3.4 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= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 9 5.49 5 Mg 2 5.21 5 S 103 5.16 5 C 18735 2.51 5 N 5131 2.21 5 O 5578 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 33": "OE1" <-> "OE2" Residue "F TYR 463": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 29558 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 4475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 578, 4475 Classifications: {'peptide': 578} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 542} Chain: "B" Number of atoms: 4475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 578, 4475 Classifications: {'peptide': 578} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 542} Chain: "C" Number of atoms: 4475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 578, 4475 Classifications: {'peptide': 578} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 542} Chain: "D" Number of atoms: 3682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3682 Classifications: {'peptide': 470} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 442} Chain: "E" Number of atoms: 3668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 3668 Classifications: {'peptide': 468} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 441} Chain: "F" Number of atoms: 3694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3694 Classifications: {'peptide': 471} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 444} Chain: "G" Number of atoms: 1619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1619 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 9, 'TRANS': 196} Chain: "H" Number of atoms: 792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 792 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain: "I" Number of atoms: 313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 313 Classifications: {'peptide': 40} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "J" Number of atoms: 976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 976 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 7, 'TRANS': 119} Chain: "K" Number of atoms: 313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 313 Classifications: {'peptide': 40} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "L" Number of atoms: 980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 980 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 7, 'TRANS': 120} Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 15.13, per 1000 atoms: 0.51 Number of scatterers: 29558 At special positions: 0 Unit cell: (149.6, 139.92, 177.76, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 103 16.00 P 9 15.00 Mg 2 11.99 O 5578 8.00 N 5131 7.00 C 18735 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 11.20 Conformation dependent library (CDL) restraints added in 5.8 seconds 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6918 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 130 helices and 38 sheets defined 41.4% alpha, 13.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.58 Creating SS restraints... Processing helix chain 'A' and resid 91 through 98 Processing helix chain 'A' and resid 210 through 214 Processing helix chain 'A' and resid 234 through 243 Processing helix chain 'A' and resid 259 through 271 removed outlier: 3.867A pdb=" N VAL A 265 " --> pdb=" O GLU A 261 " (cutoff:3.500A) Proline residue: A 270 - end of helix Processing helix chain 'A' and resid 281 through 284 Processing helix chain 'A' and resid 296 through 316 removed outlier: 4.629A pdb=" N ILE A 303 " --> pdb=" O ARG A 299 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N TYR A 304 " --> pdb=" O GLU A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 340 removed outlier: 3.835A pdb=" N ALA A 333 " --> pdb=" O ARG A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 364 removed outlier: 4.166A pdb=" N ALA A 355 " --> pdb=" O PRO A 352 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLU A 363 " --> pdb=" O ALA A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 389 No H-bonds generated for 'chain 'A' and resid 387 through 389' Processing helix chain 'A' and resid 394 through 401 Processing helix chain 'A' and resid 411 through 415 Processing helix chain 'A' and resid 432 through 442 removed outlier: 3.525A pdb=" N ASP A 436 " --> pdb=" O THR A 432 " (cutoff:3.500A) Proline residue: A 437 - end of helix removed outlier: 3.534A pdb=" N GLU A 441 " --> pdb=" O PRO A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 471 removed outlier: 3.961A pdb=" N GLU A 466 " --> pdb=" O ALA A 462 " (cutoff:3.500A) removed outlier: 4.356A 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 543 through 551 removed outlier: 3.751A pdb=" N ARG A 550 " --> pdb=" O ARG A 547 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 577 removed outlier: 3.783A pdb=" N GLU A 564 " --> pdb=" O PRO A 560 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N PHE A 574 " --> pdb=" O ILE A 570 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LYS A 575 " --> pdb=" O GLN A 571 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 98 Processing helix chain 'B' and resid 210 through 214 Processing helix chain 'B' and resid 234 through 244 Processing helix chain 'B' and resid 259 through 271 removed outlier: 3.799A pdb=" N PHE B 269 " --> pdb=" O VAL B 265 " (cutoff:3.500A) 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: 4.945A pdb=" N ILE B 303 " --> pdb=" O ARG B 299 " (cutoff:3.500A) removed outlier: 4.893A 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 354 through 364 removed outlier: 3.781A pdb=" N ARG B 364 " --> pdb=" O ALA B 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 401 Processing helix chain 'B' and resid 411 through 415 Processing helix chain 'B' and resid 432 through 442 Proline residue: B 437 - end of helix Processing helix chain 'B' and resid 447 through 470 removed outlier: 3.719A pdb=" N LEU B 464 " --> pdb=" O ARG B 460 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N GLN B 465 " --> pdb=" O GLU B 461 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N GLU B 466 " --> pdb=" O ALA B 462 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N ILE B 467 " --> pdb=" O GLY B 463 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N VAL B 468 " --> pdb=" O LEU B 464 " (cutoff:3.500A) Processing helix chain 'B' and resid 478 through 493 Processing helix chain 'B' and resid 509 through 532 Processing helix chain 'B' and resid 536 through 541 removed outlier: 4.352A pdb=" N GLN B 541 " --> pdb=" O ASP B 537 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 551 Processing helix chain 'B' and resid 559 through 576 removed outlier: 4.018A pdb=" N LYS B 575 " --> pdb=" O GLN B 571 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 98 Processing helix chain 'C' and resid 210 through 214 Processing helix chain 'C' and resid 234 through 243 Processing helix chain 'C' and resid 259 through 271 Proline residue: C 270 - end of helix Processing helix chain 'C' and resid 281 through 284 Processing helix chain 'C' and resid 297 through 315 removed outlier: 3.932A pdb=" N ALA C 301 " --> pdb=" O ALA C 297 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE C 303 " --> pdb=" O ARG C 299 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N TYR C 304 " --> pdb=" O GLU C 300 " (cutoff:3.500A) Processing helix chain 'C' and resid 327 through 340 Processing helix chain 'C' and resid 354 through 364 removed outlier: 3.922A 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 401 removed outlier: 3.537A pdb=" N ARG C 401 " --> pdb=" O GLN C 397 " (cutoff:3.500A) Processing helix chain 'C' and resid 411 through 415 Processing helix chain 'C' and resid 433 through 442 Proline residue: C 437 - end of helix Processing helix chain 'C' and resid 447 through 471 removed outlier: 4.240A pdb=" N GLU C 466 " --> pdb=" O ALA C 462 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ILE C 467 " --> pdb=" O GLY C 463 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N LEU C 470 " --> pdb=" O GLU C 466 " (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 559 through 573 Processing helix chain 'C' and resid 575 through 577 No H-bonds generated for 'chain 'C' and resid 575 through 577' Processing helix chain 'D' and resid 86 through 88 No H-bonds generated for 'chain 'D' and resid 86 through 88' Processing helix chain 'D' and resid 121 through 123 No H-bonds generated for 'chain 'D' and resid 121 through 123' Processing helix chain 'D' and resid 136 through 139 No H-bonds generated for 'chain 'D' and resid 136 through 139' Processing helix chain 'D' and resid 160 through 170 Processing helix chain 'D' and resid 175 through 178 Processing helix chain 'D' and resid 198 through 210 Processing helix chain 'D' and resid 213 through 216 Processing helix chain 'D' and resid 228 through 248 Proline residue: D 235 - end of helix Processing helix chain 'D' and resid 260 through 273 Processing helix chain 'D' and resid 280 through 282 No H-bonds generated for 'chain 'D' and resid 280 through 282' Processing helix chain 'D' and resid 287 through 297 removed outlier: 3.577A pdb=" N ILE D 294 " --> pdb=" O ASP D 290 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N ARG D 297 " --> pdb=" O THR D 293 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 332 Processing helix chain 'D' and resid 341 through 345 Processing helix chain 'D' and resid 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: 3.862A pdb=" N ASP D 391 " --> pdb=" O ALA D 387 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILE D 392 " --> pdb=" O ASN D 388 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LYS D 394 " --> pdb=" O VAL D 390 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ALA D 397 " --> pdb=" O ARG D 393 " (cutoff:3.500A) removed outlier: 4.059A 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: 3.908A pdb=" N MET D 445 " --> pdb=" O ALA D 441 " (cutoff:3.500A) Processing helix chain 'D' and resid 456 through 462 Processing helix chain 'E' and resid 86 through 88 No H-bonds generated for 'chain 'E' and resid 86 through 88' Processing helix chain 'E' and resid 121 through 123 No H-bonds generated for 'chain 'E' and resid 121 through 123' Processing helix chain 'E' and resid 136 through 139 No H-bonds generated for 'chain 'E' and resid 136 through 139' Processing helix chain 'E' and resid 160 through 170 Processing helix chain 'E' and resid 175 through 178 No H-bonds generated for 'chain 'E' and resid 175 through 178' Processing helix chain 'E' and resid 198 through 211 Processing helix chain 'E' and resid 214 through 216 No H-bonds generated for 'chain 'E' and resid 214 through 216' Processing helix chain 'E' and resid 229 through 249 removed outlier: 3.747A pdb=" N THR E 234 " --> pdb=" O ARG E 231 " (cutoff:3.500A) Proline residue: E 235 - end of helix removed outlier: 3.535A pdb=" N PHE E 247 " --> pdb=" O TYR E 244 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLU E 248 " --> pdb=" O LEU E 245 " (cutoff:3.500A) removed outlier: 4.071A 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: 3.608A pdb=" N ILE E 294 " --> pdb=" O ASP E 290 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N ARG E 297 " --> pdb=" O THR E 293 " (cutoff:3.500A) Processing helix chain 'E' and resid 317 through 319 No H-bonds generated for 'chain 'E' and resid 317 through 319' Processing helix chain 'E' and resid 324 through 330 Processing helix chain 'E' and resid 341 through 345 Processing helix chain 'E' and resid 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: 4.073A pdb=" N ILE E 398 " --> pdb=" O LYS E 394 " (cutoff:3.500A) Processing helix chain 'E' and resid 406 through 421 Processing helix chain 'E' and resid 432 through 445 removed outlier: 4.102A pdb=" N MET E 445 " --> pdb=" O ALA E 441 " (cutoff:3.500A) Processing helix chain 'E' and resid 448 through 450 No H-bonds generated for 'chain 'E' and resid 448 through 450' Processing helix chain 'E' and resid 456 through 462 Processing helix chain 'E' and resid 467 through 469 No H-bonds generated for 'chain 'E' and resid 467 through 469' Processing helix chain 'F' and resid 86 through 88 No H-bonds generated for 'chain 'F' and resid 86 through 88' Processing helix chain 'F' and resid 121 through 123 No H-bonds generated for 'chain 'F' and resid 121 through 123' Processing helix chain 'F' and resid 136 through 139 No H-bonds generated for 'chain 'F' and resid 136 through 139' Processing helix chain 'F' and resid 160 through 170 Processing helix chain 'F' and resid 175 through 178 No H-bonds generated for 'chain 'F' and resid 175 through 178' Processing helix chain 'F' and resid 198 through 211 Processing helix chain 'F' and resid 214 through 216 No H-bonds generated for 'chain 'F' and resid 214 through 216' Processing helix chain 'F' and resid 230 through 249 removed outlier: 3.845A pdb=" N THR F 234 " --> pdb=" O ARG F 231 " (cutoff:3.500A) Proline residue: F 235 - end of helix removed outlier: 3.524A pdb=" N PHE F 247 " --> pdb=" O TYR F 244 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLU F 248 " --> pdb=" O LEU F 245 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N HIS F 249 " --> pdb=" O ALA F 246 " (cutoff:3.500A) Processing helix chain 'F' and resid 260 through 274 Processing helix chain 'F' and resid 285 through 295 removed outlier: 4.396A pdb=" N TYR F 288 " --> pdb=" O GLY F 285 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N TYR F 295 " --> pdb=" O ALA F 292 " (cutoff:3.500A) Processing helix chain 'F' and resid 317 through 319 No H-bonds generated for 'chain 'F' and resid 317 through 319' Processing helix chain 'F' and resid 324 through 332 Processing helix chain 'F' and resid 341 through 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 399 removed outlier: 4.556A pdb=" N LYS F 376 " --> pdb=" O GLU F 373 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLN F 377 " --> pdb=" O ASP F 374 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ILE F 399 " --> pdb=" O VAL F 396 " (cutoff:3.500A) Processing helix chain 'F' and resid 406 through 421 Processing helix chain 'F' and resid 432 through 445 removed outlier: 4.003A pdb=" N MET F 445 " --> pdb=" O ALA F 441 " (cutoff:3.500A) Processing helix chain 'F' and resid 448 through 450 No H-bonds generated for 'chain 'F' and resid 448 through 450' Processing helix chain 'F' and resid 456 through 462 Processing helix chain 'G' and resid 8 through 68 removed outlier: 3.677A pdb=" N GLU G 48 " --> pdb=" O ARG G 44 " (cutoff:3.500A) Processing helix chain 'G' and resid 121 through 206 removed outlier: 3.744A pdb=" N LEU G 124 " --> pdb=" O ALA G 121 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLU G 125 " --> pdb=" O TYR G 122 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ALA G 126 " --> pdb=" O THR G 123 " (cutoff:3.500A) removed outlier: 5.289A pdb=" N SER G 127 " --> pdb=" O LEU G 124 " (cutoff:3.500A) removed outlier: 5.768A pdb=" N VAL G 168 " --> pdb=" O GLU G 165 " (cutoff:3.500A) removed outlier: 5.767A pdb=" N ILE G 169 " --> pdb=" O GLN G 166 " (cutoff:3.500A) Proline residue: G 170 - end of helix Processing helix chain 'H' and resid 7 through 16 removed outlier: 4.397A pdb=" N GLN H 11 " --> pdb=" O GLU H 8 " (cutoff:3.500A) Processing helix chain 'H' and resid 26 through 37 Processing helix chain 'H' and resid 55 through 59 removed outlier: 3.804A pdb=" N VAL H 59 " --> pdb=" O PRO H 55 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 55 through 59' Processing helix chain 'H' and resid 86 through 98 Processing helix chain 'I' and resid 82 through 118 removed outlier: 3.628A pdb=" N LYS I 97 " --> pdb=" O GLU I 93 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N ARG I 100 " --> pdb=" O ALA I 96 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N ALA I 105 " --> pdb=" O GLU I 101 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N ARG I 106 " --> pdb=" O LYS I 102 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU I 107 " --> pdb=" O ALA I 103 " (cutoff:3.500A) removed outlier: 5.630A pdb=" N ASP I 108 " --> pdb=" O MET I 104 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N GLU I 109 " --> pdb=" O ALA I 105 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLU I 117 " --> pdb=" O LEU I 113 " (cutoff:3.500A) Processing helix chain 'J' and resid 62 through 93 removed outlier: 3.846A pdb=" N ALA J 93 " --> pdb=" O GLU J 89 " (cutoff:3.500A) Processing helix chain 'J' and resid 100 through 114 removed outlier: 4.030A pdb=" N ARG J 105 " --> pdb=" O PRO J 101 " (cutoff:3.500A) Processing helix chain 'J' and resid 126 through 138 Proline residue: J 129 - end of helix removed outlier: 4.483A pdb=" N GLU J 132 " --> pdb=" O PRO J 129 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N ALA J 135 " --> pdb=" O GLU J 132 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ARG J 136 " --> pdb=" O ALA J 133 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ARG J 138 " --> pdb=" O ALA J 135 " (cutoff:3.500A) Processing helix chain 'J' and resid 167 through 186 removed outlier: 5.406A pdb=" N ASP J 176 " --> pdb=" O ASP J 172 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N ALA J 177 " --> pdb=" O ARG J 173 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ALA J 183 " --> pdb=" O SER J 179 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N GLN J 184 " --> pdb=" O SER J 180 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ALA J 185 " --> pdb=" O LYS J 181 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 105 removed outlier: 3.632A pdb=" N ALA K 105 " --> pdb=" O GLU K 101 " (cutoff:3.500A) Processing helix chain 'K' and resid 107 through 118 Processing helix chain 'L' and resid 62 through 92 removed outlier: 3.739A pdb=" N LEU L 67 " --> pdb=" O ALA L 63 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N VAL L 68 " --> pdb=" O GLY L 64 " (cutoff:3.500A) Processing helix chain 'L' and resid 100 through 114 removed outlier: 3.710A pdb=" N ARG L 105 " --> pdb=" O PRO L 101 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N LYS L 106 " --> pdb=" O GLU L 102 " (cutoff:3.500A) Processing helix chain 'L' and resid 125 through 138 Proline residue: L 129 - end of helix removed outlier: 4.311A pdb=" N ALA L 133 " --> pdb=" O PRO L 129 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N LEU L 134 " --> pdb=" O HIS L 130 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLU L 137 " --> pdb=" O ALA L 133 " (cutoff:3.500A) Processing helix chain 'L' and resid 167 through 186 removed outlier: 3.926A pdb=" N ASP L 172 " --> pdb=" O LEU L 168 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N ASP L 176 " --> pdb=" O ASP L 172 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N ALA L 177 " --> pdb=" O ARG L 173 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N SER L 180 " --> pdb=" O ASP L 176 " (cutoff:3.500A) removed outlier: 4.336A 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: 6.560A pdb=" N PHE A 48 " --> pdb=" O ILE A 40 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N LEU A 42 " --> pdb=" O THR A 46 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N THR A 46 " --> pdb=" O LEU A 42 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N LYS A 17 " --> pdb=" O ILE A 6 " (cutoff:3.500A) removed outlier: 5.595A 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 75 Processing sheet with id= C, first strand: chain 'A' and resid 82 through 84 removed outlier: 4.078A pdb=" N GLY A 82 " --> pdb=" O THR A 285 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N VAL A 250 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N ILE A 288 " --> pdb=" O VAL A 250 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N TYR A 252 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N ASN A 290 " --> pdb=" O TYR A 252 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N GLY A 254 " --> pdb=" O ASN A 290 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N ALA A 377 " --> pdb=" O VAL A 320 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N LEU A 322 " --> pdb=" O ALA A 377 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N THR A 379 " --> pdb=" O LEU A 322 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N ALA A 324 " --> pdb=" O THR A 379 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N VAL A 381 " --> pdb=" O ALA A 324 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 117 through 119 Processing sheet with id= E, first strand: chain 'A' and resid 137 through 140 Processing sheet with id= F, first strand: chain 'A' and resid 366 through 369 removed outlier: 3.655A pdb=" N VAL A 378 " --> pdb=" O GLY A 366 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 157 through 160 removed outlier: 6.734A pdb=" N VAL A 174 " --> pdb=" O LYS A 158 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 3 through 5 removed outlier: 6.641A pdb=" N PHE B 48 " --> pdb=" O ILE B 40 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N LEU B 42 " --> pdb=" O THR B 46 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N THR B 46 " --> pdb=" O LEU B 42 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N LYS B 17 " --> pdb=" O ILE B 6 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N ILE B 6 " --> pdb=" O LYS B 17 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 72 through 76 Processing sheet with id= J, first strand: chain 'B' and resid 82 through 84 removed outlier: 4.028A pdb=" N GLY B 82 " --> pdb=" O THR B 285 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N VAL B 250 " --> pdb=" O VAL B 286 " (cutoff:3.500A) removed outlier: 8.119A pdb=" N ILE B 288 " --> pdb=" O VAL B 250 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N TYR B 252 " --> pdb=" O ILE B 288 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ALA B 377 " --> pdb=" O VAL B 320 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N LEU B 322 " --> pdb=" O ALA B 377 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N THR B 379 " --> pdb=" O LEU B 322 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N ALA B 324 " --> pdb=" O THR B 379 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N VAL B 381 " --> pdb=" O ALA B 324 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N ALA B 405 " --> pdb=" O ALA B 225 " (cutoff:3.500A) removed outlier: 8.286A pdb=" N TRP B 407 " --> pdb=" O PRO B 227 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 117 through 119 Processing sheet with id= L, first strand: chain 'B' and resid 128 through 130 Processing sheet with id= M, first strand: chain 'B' and resid 197 through 199 removed outlier: 3.684A pdb=" N ARG B 197 " --> pdb=" O ILE B 369 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N LYS B 367 " --> pdb=" O LEU B 199 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'B' and resid 134 through 140 removed outlier: 6.753A pdb=" N ILE B 147 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N THR B 137 " --> pdb=" O HIS B 145 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N HIS B 145 " --> pdb=" O THR B 137 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N PHE B 143 " --> pdb=" O PRO B 139 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'B' and resid 157 through 160 removed outlier: 6.938A pdb=" N VAL B 174 " --> pdb=" O LYS B 158 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'C' and resid 2 through 5 removed outlier: 4.018A pdb=" N ILE C 2 " --> pdb=" O SER C 66 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N PHE C 48 " --> pdb=" O ILE C 40 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N LEU C 42 " --> pdb=" O THR C 46 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N THR C 46 " --> pdb=" O LEU C 42 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N LYS C 17 " --> pdb=" O ILE C 6 " (cutoff:3.500A) removed outlier: 5.647A pdb=" N ILE C 6 " --> pdb=" O LYS C 17 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 72 through 75 Processing sheet with id= R, first strand: chain 'C' and resid 82 through 84 removed outlier: 3.891A pdb=" N GLY C 82 " --> pdb=" O THR C 285 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N VAL C 250 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 7.977A pdb=" N ILE C 288 " --> pdb=" O VAL C 250 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N TYR C 252 " --> pdb=" O ILE C 288 " (cutoff:3.500A) removed outlier: 7.863A pdb=" N ASN C 290 " --> pdb=" O TYR C 252 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N GLY C 254 " --> pdb=" O ASN C 290 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N ALA C 377 " --> pdb=" O VAL C 320 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N LEU C 322 " --> pdb=" O ALA C 377 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N THR C 379 " --> pdb=" O LEU C 322 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N ALA C 324 " --> pdb=" O THR C 379 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N VAL C 381 " --> pdb=" O ALA C 324 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL C 384 " --> pdb=" O ILE C 226 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'C' and resid 164 through 166 removed outlier: 5.625A pdb=" N ALA C 118 " --> pdb=" O PRO C 139 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ILE C 147 " --> pdb=" O LEU C 135 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N THR C 137 " --> pdb=" O HIS C 145 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N HIS C 145 " --> pdb=" O THR C 137 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N PHE C 143 " --> pdb=" O PRO C 139 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'C' and resid 366 through 369 removed outlier: 3.606A pdb=" N VAL C 378 " --> pdb=" O GLY C 366 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'C' and resid 157 through 160 removed outlier: 6.977A pdb=" N VAL C 174 " --> pdb=" O LYS C 158 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'D' and resid 7 through 9 removed outlier: 6.804A pdb=" N ILE D 32 " --> pdb=" O VAL D 76 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N VAL D 56 " --> pdb=" O ILE D 48 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N VAL D 50 " --> pdb=" O TYR D 54 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N TYR D 54 " --> pdb=" O VAL D 50 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N TYR D 13 " --> pdb=" O PHE D 20 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N GLU D 22 " --> pdb=" O ILE D 11 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ILE D 11 " --> pdb=" O GLU D 22 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'D' and resid 81 through 84 removed outlier: 3.583A pdb=" N LYS D 110 " --> pdb=" O VAL D 84 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'D' and resid 336 through 338 Processing sheet with id= Y, first strand: chain 'D' and resid 217 through 221 removed outlier: 8.554A pdb=" N VAL D 218 " --> pdb=" O PHE D 187 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N VAL D 189 " --> pdb=" O VAL D 218 " (cutoff:3.500A) removed outlier: 7.904A pdb=" N PHE D 220 " --> pdb=" O VAL D 189 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N PHE D 191 " --> pdb=" O PHE D 220 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N HIS D 252 " --> pdb=" O ALA D 188 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N VAL D 190 " --> pdb=" O HIS D 252 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N LEU D 254 " --> pdb=" O VAL D 190 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N ALA D 192 " --> pdb=" O LEU D 254 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N ILE D 256 " --> pdb=" O ALA D 192 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N SER D 307 " --> pdb=" O VAL D 253 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N VAL D 255 " --> pdb=" O SER D 307 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N THR D 309 " --> pdb=" O VAL D 255 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N LEU D 257 " --> pdb=" O THR D 309 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N ILE D 311 " --> pdb=" O LEU D 257 " (cutoff:3.500A) No H-bonds generated for sheet with id= Y Processing sheet with id= Z, first strand: chain 'E' and resid 11 through 15 removed outlier: 6.671A pdb=" N PHE E 20 " --> pdb=" O THR E 12 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N ILE E 14 " --> pdb=" O LEU E 18 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N LEU E 18 " --> pdb=" O ILE E 14 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLU E 49 " --> pdb=" O VAL E 56 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N GLN E 58 " --> pdb=" O VAL E 47 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N VAL E 47 " --> pdb=" O GLN E 58 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N ASP E 34 " --> pdb=" O LEU E 75 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N LEU E 75 " --> pdb=" O ASP E 34 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N LYS E 36 " --> pdb=" O VAL E 73 " (cutoff:3.500A) removed outlier: 5.489A pdb=" N VAL E 73 " --> pdb=" O LYS E 36 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'E' and resid 81 through 84 Processing sheet with id= AB, first strand: chain 'E' and resid 336 through 338 Processing sheet with id= AC, first strand: chain 'E' and resid 307 through 312 removed outlier: 3.748A pdb=" N LEU E 257 " --> pdb=" O ILE E 311 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N ALA E 188 " --> pdb=" O LEU E 254 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N ILE E 256 " --> pdb=" O ALA E 188 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N VAL E 190 " --> pdb=" O ILE E 256 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'F' and resid 11 through 15 removed outlier: 6.501A pdb=" N PHE F 20 " --> pdb=" O THR F 12 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N ILE F 14 " --> pdb=" O LEU F 18 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N LEU F 18 " --> pdb=" O ILE F 14 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLU F 49 " --> pdb=" O VAL F 56 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N GLN F 58 " --> pdb=" O VAL F 47 " (cutoff:3.500A) removed outlier: 5.743A pdb=" N VAL F 47 " --> pdb=" O GLN F 58 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N ASP F 34 " --> pdb=" O LEU F 75 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N LEU F 75 " --> pdb=" O ASP F 34 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N LYS F 36 " --> pdb=" O VAL F 73 " (cutoff:3.500A) removed outlier: 5.578A pdb=" N VAL F 73 " --> pdb=" O LYS F 36 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'F' and resid 81 through 84 Processing sheet with id= AF, first strand: chain 'F' and resid 92 through 94 removed outlier: 7.969A pdb=" N PHE F 93 " --> pdb=" O SER F 217 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N LEU F 219 " --> pdb=" O PHE F 93 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N VAL F 189 " --> pdb=" O VAL F 218 " (cutoff:3.500A) removed outlier: 8.088A pdb=" N PHE F 220 " --> pdb=" O VAL F 189 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N PHE F 191 " --> pdb=" O PHE F 220 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N ASN F 222 " --> pdb=" O PHE F 191 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N ALA F 193 " --> pdb=" O ASN F 222 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N SER F 307 " --> pdb=" O VAL F 253 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N VAL F 255 " --> pdb=" O SER F 307 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N THR F 309 " --> pdb=" O VAL F 255 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N LEU F 257 " --> pdb=" O THR F 309 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N ILE F 311 " --> pdb=" O LEU F 257 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'F' and resid 336 through 338 Processing sheet with id= AH, first strand: chain 'G' and resid 90 through 96 removed outlier: 4.077A pdb=" N GLU G 90 " --> pdb=" O LYS G 105 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LYS G 105 " --> pdb=" O GLU G 90 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ARG G 103 " --> pdb=" O GLU G 92 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'H' and resid 19 through 22 Processing sheet with id= AJ, first strand: chain 'J' and resid 121 through 123 Processing sheet with id= AK, first strand: chain 'L' and resid 120 through 123 removed outlier: 6.191A pdb=" N GLU L 141 " --> pdb=" O LEU L 121 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N ALA L 123 " --> pdb=" O GLU L 141 " (cutoff:3.500A) removed outlier: 5.615A pdb=" N GLN L 143 " --> pdb=" O ALA L 123 " (cutoff:3.500A) No H-bonds generated for sheet with id= AK Processing sheet with id= AL, first strand: chain 'L' and resid 151 through 155 removed outlier: 3.682A pdb=" N VAL L 152 " --> pdb=" O ASN L 165 " (cutoff:3.500A) 1187 hydrogen bonds defined for protein. 2997 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: 10.31 Time building geometry restraints manager: 12.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9952 1.34 - 1.46: 3640 1.46 - 1.57: 16317 1.57 - 1.69: 11 1.69 - 1.80: 194 Bond restraints: 30114 Sorted by residual: bond pdb=" O4 PO4 A 603 " pdb=" P PO4 A 603 " ideal model delta sigma weight residual 1.568 1.467 0.101 2.00e-02 2.50e+03 2.56e+01 bond pdb=" O3 PO4 A 603 " pdb=" P PO4 A 603 " ideal model delta sigma weight residual 1.569 1.479 0.090 2.00e-02 2.50e+03 2.01e+01 bond pdb=" O1 PO4 A 603 " pdb=" P PO4 A 603 " ideal model delta sigma weight residual 1.565 1.480 0.085 2.00e-02 2.50e+03 1.80e+01 bond pdb=" O2 PO4 A 603 " pdb=" P PO4 A 603 " ideal model delta sigma weight residual 1.567 1.495 0.072 2.00e-02 2.50e+03 1.29e+01 bond pdb=" O3B ADP A 601 " pdb=" PB ADP A 601 " ideal model delta sigma weight residual 1.510 1.453 0.057 2.00e-02 2.50e+03 8.22e+00 ... (remaining 30109 not shown) Histogram of bond angle deviations from ideal: 99.16 - 107.29: 1167 107.29 - 115.42: 18218 115.42 - 123.54: 20644 123.54 - 131.67: 740 131.67 - 139.80: 44 Bond angle restraints: 40813 Sorted by residual: angle pdb=" O1B ADP A 601 " pdb=" PB ADP A 601 " pdb=" O3B ADP A 601 " ideal model delta sigma weight residual 119.90 106.78 13.12 3.00e+00 1.11e-01 1.91e+01 angle pdb=" N ILE H 98 " pdb=" CA ILE H 98 " pdb=" C ILE H 98 " ideal model delta sigma weight residual 113.71 110.56 3.15 9.50e-01 1.11e+00 1.10e+01 angle pdb=" N GLY J 151 " pdb=" CA GLY J 151 " pdb=" C GLY J 151 " ideal model delta sigma weight residual 111.03 117.03 -6.00 1.87e+00 2.86e-01 1.03e+01 angle pdb=" CA LEU L 150 " pdb=" CB LEU L 150 " pdb=" CG LEU L 150 " ideal model delta sigma weight residual 116.30 126.79 -10.49 3.50e+00 8.16e-02 8.99e+00 angle pdb=" N ILE F 100 " pdb=" CA ILE F 100 " pdb=" C ILE F 100 " ideal model delta sigma weight residual 113.20 110.34 2.86 9.60e-01 1.09e+00 8.86e+00 ... (remaining 40808 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.95: 17509 24.95 - 49.90: 763 49.90 - 74.86: 84 74.86 - 99.81: 26 99.81 - 124.76: 1 Dihedral angle restraints: 18383 sinusoidal: 7561 harmonic: 10822 Sorted by residual: dihedral pdb=" C5' ADP A 601 " pdb=" O5' ADP A 601 " pdb=" PA ADP A 601 " pdb=" O2A ADP A 601 " ideal model delta sinusoidal sigma weight residual -60.00 64.76 -124.76 1 2.00e+01 2.50e-03 3.77e+01 dihedral pdb=" CA ARG A 23 " pdb=" C ARG A 23 " pdb=" N MET A 24 " pdb=" CA MET A 24 " ideal model delta harmonic sigma weight residual -180.00 -160.69 -19.31 0 5.00e+00 4.00e-02 1.49e+01 dihedral pdb=" O1B ADP A 601 " pdb=" O3A ADP A 601 " pdb=" PB ADP A 601 " pdb=" PA ADP A 601 " ideal model delta sinusoidal sigma weight residual -60.00 -122.38 62.37 1 2.00e+01 2.50e-03 1.29e+01 ... (remaining 18380 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 3598 0.051 - 0.102: 802 0.102 - 0.153: 168 0.153 - 0.204: 3 0.204 - 0.254: 1 Chirality restraints: 4572 Sorted by residual: chirality pdb=" CB ILE B 211 " pdb=" CA ILE B 211 " pdb=" CG1 ILE B 211 " pdb=" CG2 ILE B 211 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.25 2.00e-01 2.50e+01 1.62e+00 chirality pdb=" CA PHE C 269 " pdb=" N PHE C 269 " pdb=" C PHE C 269 " pdb=" CB PHE C 269 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.77e-01 chirality pdb=" CB ILE C 226 " pdb=" CA ILE C 226 " pdb=" CG1 ILE C 226 " pdb=" CG2 ILE C 226 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.16 2.00e-01 2.50e+01 6.51e-01 ... (remaining 4569 not shown) Planarity restraints: 5333 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS E 323 " 0.031 5.00e-02 4.00e+02 4.73e-02 3.58e+00 pdb=" N PRO E 324 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO E 324 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO E 324 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 269 " 0.012 2.00e-02 2.50e+03 1.42e-02 3.51e+00 pdb=" CG PHE C 269 " -0.032 2.00e-02 2.50e+03 pdb=" CD1 PHE C 269 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 PHE C 269 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE C 269 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE C 269 " 0.005 2.00e-02 2.50e+03 pdb=" CZ PHE C 269 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE B 226 " 0.030 5.00e-02 4.00e+02 4.50e-02 3.24e+00 pdb=" N PRO B 227 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO B 227 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 227 " 0.025 5.00e-02 4.00e+02 ... (remaining 5330 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.70: 550 2.70 - 3.25: 29008 3.25 - 3.80: 45827 3.80 - 4.35: 60222 4.35 - 4.90: 102552 Nonbonded interactions: 238159 Sorted by model distance: nonbonded pdb=" O MET A 220 " pdb=" OG1 THR A 379 " model vdw 2.144 2.440 nonbonded pdb=" NH2 ARG G 50 " pdb=" OE2 GLU G 144 " model vdw 2.151 2.520 nonbonded pdb=" O LEU B 241 " pdb=" OG SER B 245 " model vdw 2.156 2.440 nonbonded pdb=" O2B ATP C 601 " pdb="MG MG C 602 " model vdw 2.158 2.170 nonbonded pdb=" O MET C 220 " pdb=" OG1 THR C 379 " model vdw 2.161 2.440 ... (remaining 238154 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 1 through 578) selection = (chain 'B' and resid 1 through 578) selection = (chain 'C' and resid 1 through 578) } ncs_group { reference = (chain 'D' and resid 5 through 470) selection = (chain 'E' and resid 5 through 470) selection = (chain 'F' and resid 5 through 470) } ncs_group { reference = chain 'I' selection = chain 'K' } ncs_group { reference = chain 'J' selection = (chain 'L' and resid 61 through 187) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 3.220 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: 0.010 Extract box with map and model: 7.430 Check model and map are aligned: 0.420 Set scattering table: 0.220 Process input model: 76.070 Find NCS groups from input model: 1.860 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:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 92.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 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 : 0.004 0.101 30114 Z= 0.279 Angle : 0.562 13.117 40813 Z= 0.300 Chirality : 0.043 0.254 4572 Planarity : 0.004 0.047 5333 Dihedral : 13.723 124.761 11465 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.14), residues: 3764 helix: 1.72 (0.14), residues: 1545 sheet: 0.02 (0.22), residues: 602 loop : 0.20 (0.16), residues: 1617 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 330 HIS 0.004 0.001 HIS C 185 PHE 0.032 0.001 PHE C 269 TYR 0.018 0.001 TYR B 184 ARG 0.003 0.000 ARG B 364 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 615 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 615 time to evaluate : 3.344 Fit side-chains revert: symmetry clash REVERT: A 197 ARG cc_start: 0.7252 (ttp-110) cc_final: 0.7015 (ptm-80) REVERT: A 300 GLU cc_start: 0.7658 (tm-30) cc_final: 0.7336 (tm-30) REVERT: A 340 ARG cc_start: 0.6472 (mpt-90) cc_final: 0.5826 (mmm160) REVERT: A 447 TYR cc_start: 0.7518 (t80) cc_final: 0.7207 (t80) REVERT: A 491 ARG cc_start: 0.7214 (mtt-85) cc_final: 0.6590 (mtp-110) REVERT: A 530 ILE cc_start: 0.6208 (mm) cc_final: 0.5967 (tt) REVERT: A 550 ARG cc_start: 0.5551 (mmt180) cc_final: 0.5073 (mmp80) REVERT: A 553 TYR cc_start: 0.8571 (m-80) cc_final: 0.8256 (m-80) REVERT: B 109 HIS cc_start: 0.7759 (m-70) cc_final: 0.7410 (m-70) REVERT: B 143 PHE cc_start: 0.5089 (m-80) cc_final: 0.4734 (m-80) REVERT: B 169 GLU cc_start: 0.6644 (mm-30) cc_final: 0.6417 (mm-30) REVERT: B 202 ASN cc_start: 0.7775 (m-40) cc_final: 0.7544 (m110) REVERT: B 243 LYS cc_start: 0.6707 (ttmt) cc_final: 0.6051 (ptpt) REVERT: B 244 TRP cc_start: 0.7697 (m100) cc_final: 0.7441 (m100) REVERT: B 284 ARG cc_start: 0.6844 (mtm180) cc_final: 0.6631 (ptp-170) REVERT: B 391 MET cc_start: 0.6330 (mtt) cc_final: 0.6063 (mmt) REVERT: B 441 GLU cc_start: 0.5832 (tp30) cc_final: 0.5046 (mt-10) REVERT: B 450 LEU cc_start: 0.5176 (tp) cc_final: 0.4875 (mm) REVERT: B 488 ARG cc_start: 0.5638 (ttp80) cc_final: 0.5247 (ttm110) REVERT: B 494 PHE cc_start: 0.6866 (t80) cc_final: 0.6607 (t80) REVERT: B 516 MET cc_start: 0.4666 (mtm) cc_final: 0.4207 (mtp) REVERT: B 518 MET cc_start: 0.6357 (mtp) cc_final: 0.5982 (mtt) REVERT: B 525 GLU cc_start: 0.6895 (mm-30) cc_final: 0.6253 (mt-10) REVERT: B 567 MET cc_start: 0.5347 (mmm) cc_final: 0.4839 (mmt) REVERT: C 220 MET cc_start: 0.7587 (tpp) cc_final: 0.7367 (tpt) REVERT: C 347 GLU cc_start: 0.7773 (mm-30) cc_final: 0.7333 (mt-10) REVERT: C 410 ASP cc_start: 0.7091 (t0) cc_final: 0.6810 (t70) REVERT: C 423 ASN cc_start: 0.8515 (t0) cc_final: 0.8278 (t0) REVERT: C 532 ARG cc_start: 0.5905 (ptt-90) cc_final: 0.5455 (ptm160) REVERT: D 50 VAL cc_start: 0.8682 (t) cc_final: 0.8312 (m) REVERT: D 62 GLU cc_start: 0.6608 (pm20) cc_final: 0.5793 (mp0) REVERT: D 67 ASP cc_start: 0.7480 (p0) cc_final: 0.7224 (p0) REVERT: D 237 MET cc_start: 0.7999 (mmt) cc_final: 0.7639 (mmt) REVERT: D 280 ARG cc_start: 0.6276 (ptm-80) cc_final: 0.5642 (ttp80) REVERT: D 380 ASP cc_start: 0.7003 (m-30) cc_final: 0.6454 (m-30) REVERT: D 456 LYS cc_start: 0.6889 (mmtt) cc_final: 0.6347 (mmmt) REVERT: E 78 ASP cc_start: 0.7442 (m-30) cc_final: 0.7164 (t0) REVERT: E 228 THR cc_start: 0.7801 (t) cc_final: 0.7577 (m) REVERT: E 373 GLU cc_start: 0.7407 (pm20) cc_final: 0.7065 (mp0) REVERT: E 390 VAL cc_start: 0.8018 (t) cc_final: 0.7763 (p) REVERT: E 399 ILE cc_start: 0.7047 (pt) cc_final: 0.6824 (mt) REVERT: E 405 THR cc_start: 0.7245 (p) cc_final: 0.6869 (p) REVERT: E 421 PHE cc_start: 0.6621 (m-80) cc_final: 0.6334 (m-80) REVERT: F 6 LYS cc_start: 0.7217 (tttt) cc_final: 0.6835 (mtmm) REVERT: F 53 GLU cc_start: 0.7489 (pt0) cc_final: 0.6893 (mm-30) REVERT: F 109 GLU cc_start: 0.7181 (tt0) cc_final: 0.6890 (tt0) REVERT: F 126 LYS cc_start: 0.8104 (ttpp) cc_final: 0.7756 (ttpp) REVERT: F 210 ARG cc_start: 0.7252 (ttp-110) cc_final: 0.6971 (ttt180) REVERT: F 280 ARG cc_start: 0.6659 (ttp-170) cc_final: 0.6309 (ttt90) REVERT: F 318 ASP cc_start: 0.7794 (p0) cc_final: 0.7233 (t0) REVERT: F 319 ASP cc_start: 0.8232 (m-30) cc_final: 0.7957 (m-30) REVERT: F 466 LYS cc_start: 0.7773 (mmmm) cc_final: 0.6977 (ptmt) REVERT: G 5 SER cc_start: 0.8061 (p) cc_final: 0.7684 (m) REVERT: G 155 LYS cc_start: 0.6388 (mttt) cc_final: 0.6035 (mttm) REVERT: G 156 LYS cc_start: 0.6595 (ttmm) cc_final: 0.5758 (tppt) REVERT: G 187 GLU cc_start: 0.7411 (mm-30) cc_final: 0.6836 (tt0) REVERT: G 209 GLU cc_start: 0.3650 (mt-10) cc_final: 0.2796 (tp30) REVERT: H 1 MET cc_start: 0.4489 (mpp) cc_final: 0.3677 (mpp) REVERT: H 18 LEU cc_start: 0.4357 (mt) cc_final: 0.3932 (pp) REVERT: H 90 MET cc_start: 0.6110 (mmm) cc_final: 0.4827 (tmm) REVERT: J 84 ARG cc_start: 0.1892 (ptm160) cc_final: 0.1519 (ttt-90) REVERT: J 89 GLU cc_start: 0.5049 (tp30) cc_final: 0.4612 (mm-30) REVERT: L 173 ARG cc_start: 0.4537 (ttt90) cc_final: 0.4198 (mtm-85) outliers start: 0 outliers final: 0 residues processed: 615 average time/residue: 0.4964 time to fit residues: 450.6886 Evaluate side-chains 348 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 348 time to evaluate : 3.355 ------------------------------------------------------------------------------- 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: 20.0000 chunk 282 optimal weight: 1.9990 chunk 156 optimal weight: 0.7980 chunk 96 optimal weight: 10.0000 chunk 190 optimal weight: 0.0050 chunk 151 optimal weight: 8.9990 chunk 292 optimal weight: 0.9990 chunk 113 optimal weight: 7.9990 chunk 177 optimal weight: 0.6980 chunk 217 optimal weight: 20.0000 chunk 338 optimal weight: 6.9990 overall best weight: 0.8998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 316 GLN ** A 541 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 336 GLN F 413 GLN G 17 GLN J 124 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.1542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 30114 Z= 0.140 Angle : 0.499 8.403 40813 Z= 0.257 Chirality : 0.042 0.148 4572 Planarity : 0.005 0.045 5333 Dihedral : 5.945 100.711 4259 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 1.01 % Allowed : 6.10 % Favored : 92.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.14), residues: 3764 helix: 1.36 (0.14), residues: 1554 sheet: 0.09 (0.21), residues: 616 loop : 0.33 (0.16), residues: 1594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 330 HIS 0.006 0.001 HIS A 145 PHE 0.016 0.001 PHE C 269 TYR 0.022 0.001 TYR D 13 ARG 0.007 0.000 ARG B 104 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 387 time to evaluate : 3.592 Fit side-chains revert: symmetry clash REVERT: A 85 ASP cc_start: 0.7781 (p0) cc_final: 0.7372 (t70) REVERT: A 287 LEU cc_start: 0.7897 (OUTLIER) cc_final: 0.7693 (mp) REVERT: A 340 ARG cc_start: 0.6542 (mpt-90) cc_final: 0.5910 (mmm160) REVERT: A 447 TYR cc_start: 0.7448 (t80) cc_final: 0.7123 (t80) REVERT: A 491 ARG cc_start: 0.7193 (mtt-85) cc_final: 0.6498 (mtp-110) REVERT: A 550 ARG cc_start: 0.5438 (mmt180) cc_final: 0.4888 (mmp80) REVERT: A 553 TYR cc_start: 0.8535 (m-80) cc_final: 0.8286 (m-80) REVERT: B 25 TYR cc_start: 0.8126 (m-80) cc_final: 0.7438 (m-80) REVERT: B 143 PHE cc_start: 0.5110 (m-80) cc_final: 0.4869 (m-80) REVERT: B 243 LYS cc_start: 0.6745 (ttmt) cc_final: 0.6131 (ptpt) REVERT: B 342 GLU cc_start: 0.7174 (tt0) cc_final: 0.6896 (mt-10) REVERT: B 441 GLU cc_start: 0.5978 (tp30) cc_final: 0.5156 (mt-10) REVERT: B 450 LEU cc_start: 0.5427 (tp) cc_final: 0.5078 (mm) REVERT: B 494 PHE cc_start: 0.6884 (t80) cc_final: 0.6543 (t80) REVERT: B 516 MET cc_start: 0.4818 (mtm) cc_final: 0.4408 (mtp) REVERT: B 525 GLU cc_start: 0.6898 (mm-30) cc_final: 0.6247 (mt-10) REVERT: B 567 MET cc_start: 0.5184 (mmm) cc_final: 0.4884 (mmt) REVERT: C 122 MET cc_start: 0.7866 (ttm) cc_final: 0.7583 (ttm) REVERT: C 323 MET cc_start: 0.8947 (mpp) cc_final: 0.8659 (mpp) REVERT: C 340 ARG cc_start: 0.7871 (mmt180) cc_final: 0.7625 (mmt-90) REVERT: C 347 GLU cc_start: 0.7706 (mm-30) cc_final: 0.7350 (mt-10) REVERT: C 410 ASP cc_start: 0.7052 (t0) cc_final: 0.6760 (t70) REVERT: C 532 ARG cc_start: 0.5807 (ptt-90) cc_final: 0.5504 (ptm160) REVERT: D 50 VAL cc_start: 0.8667 (t) cc_final: 0.8373 (m) REVERT: D 62 GLU cc_start: 0.6508 (pm20) cc_final: 0.5645 (mp0) REVERT: D 67 ASP cc_start: 0.7521 (p0) cc_final: 0.7319 (p0) REVERT: D 280 ARG cc_start: 0.6242 (ptm-80) cc_final: 0.5692 (ttp80) REVERT: D 456 LYS cc_start: 0.6803 (mmtt) cc_final: 0.6228 (mmmt) REVERT: E 110 LYS cc_start: 0.8213 (OUTLIER) cc_final: 0.7625 (tttt) REVERT: E 421 PHE cc_start: 0.6658 (m-80) cc_final: 0.6350 (m-80) REVERT: F 6 LYS cc_start: 0.7050 (tttt) cc_final: 0.6769 (mtmm) REVERT: F 53 GLU cc_start: 0.7450 (pt0) cc_final: 0.6800 (mm-30) REVERT: F 109 GLU cc_start: 0.7014 (tt0) cc_final: 0.6769 (tt0) REVERT: F 210 ARG cc_start: 0.7274 (ttp-110) cc_final: 0.6962 (ttt180) REVERT: F 280 ARG cc_start: 0.6663 (ttp-170) cc_final: 0.6287 (ttt90) REVERT: F 318 ASP cc_start: 0.7723 (p0) cc_final: 0.7196 (t70) REVERT: F 420 ARG cc_start: 0.8311 (mtp-110) cc_final: 0.7756 (ttp80) REVERT: G 156 LYS cc_start: 0.6309 (ttmm) cc_final: 0.5663 (tppt) REVERT: G 187 GLU cc_start: 0.7046 (mm-30) cc_final: 0.6541 (tt0) REVERT: G 209 GLU cc_start: 0.3614 (mt-10) cc_final: 0.2796 (tp30) REVERT: H 1 MET cc_start: 0.4946 (mpp) cc_final: 0.4347 (mpp) REVERT: H 18 LEU cc_start: 0.4572 (mt) cc_final: 0.4259 (pp) REVERT: I 104 MET cc_start: 0.3796 (mtp) cc_final: 0.3510 (mtp) REVERT: J 89 GLU cc_start: 0.5003 (tp30) cc_final: 0.4582 (mm-30) REVERT: L 138 ARG cc_start: 0.5072 (mtp85) cc_final: 0.4795 (mmm-85) REVERT: L 173 ARG cc_start: 0.4492 (ttt90) cc_final: 0.4210 (mtm-85) outliers start: 31 outliers final: 15 residues processed: 407 average time/residue: 0.5109 time to fit residues: 318.0504 Evaluate side-chains 339 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 322 time to evaluate : 3.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 GLU Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 564 GLU Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 416 ARG Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 557 GLU Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 318 ASP Chi-restraints excluded: chain E residue 110 LYS Chi-restraints excluded: chain E residue 225 ASP Chi-restraints excluded: chain F residue 137 THR Chi-restraints excluded: chain F residue 290 ASP Chi-restraints excluded: chain F residue 396 VAL Chi-restraints excluded: chain F residue 407 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 188 optimal weight: 6.9990 chunk 105 optimal weight: 8.9990 chunk 281 optimal weight: 6.9990 chunk 230 optimal weight: 9.9990 chunk 93 optimal weight: 9.9990 chunk 339 optimal weight: 0.9990 chunk 366 optimal weight: 0.5980 chunk 302 optimal weight: 7.9990 chunk 336 optimal weight: 30.0000 chunk 115 optimal weight: 9.9990 chunk 272 optimal weight: 0.6980 overall best weight: 3.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 316 GLN A 541 GLN ** C 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 206 GLN D 310 GLN E 427 GLN F 161 ASN F 166 GLN F 170 GLN F 413 GLN F 437 GLN G 166 GLN G 180 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.1974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 30114 Z= 0.246 Angle : 0.534 8.032 40813 Z= 0.274 Chirality : 0.044 0.174 4572 Planarity : 0.005 0.049 5333 Dihedral : 5.936 99.009 4259 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 1.49 % Allowed : 9.08 % Favored : 89.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.14), residues: 3764 helix: 0.99 (0.14), residues: 1562 sheet: 0.21 (0.22), residues: 601 loop : 0.15 (0.16), residues: 1601 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 330 HIS 0.006 0.001 HIS C 185 PHE 0.021 0.002 PHE A 230 TYR 0.022 0.001 TYR D 13 ARG 0.005 0.000 ARG J 86 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 320 time to evaluate : 3.452 Fit side-chains REVERT: A 85 ASP cc_start: 0.7751 (p0) cc_final: 0.7399 (t70) REVERT: A 300 GLU cc_start: 0.7703 (tm-30) cc_final: 0.7490 (tm-30) REVERT: A 340 ARG cc_start: 0.6694 (mpt-90) cc_final: 0.6003 (mmm160) REVERT: A 491 ARG cc_start: 0.7261 (mtt-85) cc_final: 0.6561 (mtp-110) REVERT: A 530 ILE cc_start: 0.6385 (mm) cc_final: 0.6034 (tt) REVERT: A 550 ARG cc_start: 0.5550 (mmt180) cc_final: 0.4910 (mmp80) REVERT: B 243 LYS cc_start: 0.6907 (ttmt) cc_final: 0.6335 (ptpt) REVERT: B 441 GLU cc_start: 0.5955 (tp30) cc_final: 0.5152 (mt-10) REVERT: B 450 LEU cc_start: 0.5424 (tp) cc_final: 0.5139 (mm) REVERT: B 493 ASP cc_start: 0.6670 (OUTLIER) cc_final: 0.6448 (p0) REVERT: B 516 MET cc_start: 0.4634 (mtm) cc_final: 0.4416 (mtp) REVERT: B 525 GLU cc_start: 0.6741 (mm-30) cc_final: 0.6124 (mt-10) REVERT: B 567 MET cc_start: 0.5094 (mmm) cc_final: 0.4617 (mmt) REVERT: C 1 MET cc_start: 0.6014 (OUTLIER) cc_final: 0.5708 (mmm) REVERT: C 114 GLU cc_start: 0.7730 (mm-30) cc_final: 0.7467 (mm-30) REVERT: C 323 MET cc_start: 0.8864 (mpp) cc_final: 0.8647 (mpp) REVERT: C 340 ARG cc_start: 0.7856 (mmt180) cc_final: 0.7589 (mmt-90) REVERT: C 347 GLU cc_start: 0.7745 (mm-30) cc_final: 0.7408 (mt-10) REVERT: C 410 ASP cc_start: 0.7097 (t0) cc_final: 0.6777 (t70) REVERT: C 423 ASN cc_start: 0.8402 (t0) cc_final: 0.8169 (t0) REVERT: C 532 ARG cc_start: 0.5911 (ptt-90) cc_final: 0.5517 (ptm160) REVERT: D 50 VAL cc_start: 0.8774 (t) cc_final: 0.8492 (m) REVERT: D 62 GLU cc_start: 0.6496 (pm20) cc_final: 0.6200 (pt0) REVERT: D 67 ASP cc_start: 0.7614 (p0) cc_final: 0.7300 (p0) REVERT: D 276 GLU cc_start: 0.7286 (mt-10) cc_final: 0.6318 (tp30) REVERT: D 280 ARG cc_start: 0.6323 (ptm-80) cc_final: 0.5708 (ttp80) REVERT: D 406 GLU cc_start: 0.5099 (pm20) cc_final: 0.4755 (tm-30) REVERT: D 456 LYS cc_start: 0.6900 (mmtt) cc_final: 0.6323 (mmmt) REVERT: E 110 LYS cc_start: 0.8307 (OUTLIER) cc_final: 0.7950 (ttmm) REVERT: E 421 PHE cc_start: 0.6737 (m-80) cc_final: 0.6532 (m-80) REVERT: F 6 LYS cc_start: 0.7264 (tttt) cc_final: 0.6867 (mtmm) REVERT: F 53 GLU cc_start: 0.7462 (pt0) cc_final: 0.6725 (mm-30) REVERT: F 109 GLU cc_start: 0.7038 (tt0) cc_final: 0.6801 (tt0) REVERT: F 210 ARG cc_start: 0.7389 (ttp-110) cc_final: 0.7029 (ttt180) REVERT: F 280 ARG cc_start: 0.6859 (ttp-170) cc_final: 0.6352 (ttt90) REVERT: F 318 ASP cc_start: 0.7624 (p0) cc_final: 0.7329 (t0) REVERT: F 420 ARG cc_start: 0.8407 (mtp-110) cc_final: 0.7944 (ttp80) REVERT: G 5 SER cc_start: 0.7840 (p) cc_final: 0.7463 (m) REVERT: G 156 LYS cc_start: 0.6424 (ttmm) cc_final: 0.5769 (tppt) REVERT: G 187 GLU cc_start: 0.7131 (mm-30) cc_final: 0.6575 (tt0) REVERT: G 209 GLU cc_start: 0.3652 (mt-10) cc_final: 0.2714 (tp30) REVERT: H 1 MET cc_start: 0.4616 (mpp) cc_final: 0.4044 (mpp) REVERT: H 18 LEU cc_start: 0.4825 (mt) cc_final: 0.4517 (pp) REVERT: I 104 MET cc_start: 0.3182 (mtp) cc_final: 0.2935 (mtp) REVERT: J 89 GLU cc_start: 0.4878 (tp30) cc_final: 0.4350 (mm-30) REVERT: L 61 GLU cc_start: 0.2004 (pm20) cc_final: 0.1680 (mt-10) REVERT: L 138 ARG cc_start: 0.5044 (mtp85) cc_final: 0.4797 (mmm-85) REVERT: L 173 ARG cc_start: 0.4607 (ttt90) cc_final: 0.4158 (mtm-85) outliers start: 46 outliers final: 28 residues processed: 351 average time/residue: 0.4910 time to fit residues: 265.3196 Evaluate side-chains 327 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 296 time to evaluate : 3.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 114 GLU Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 416 ARG Chi-restraints excluded: chain B residue 466 GLU Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 493 ASP Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 443 VAL Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 318 ASP Chi-restraints excluded: chain E residue 74 SER Chi-restraints excluded: chain E residue 110 LYS Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 225 ASP Chi-restraints excluded: chain E residue 390 VAL Chi-restraints excluded: chain F residue 137 THR Chi-restraints excluded: chain F residue 290 ASP Chi-restraints excluded: chain F residue 396 VAL Chi-restraints excluded: chain F residue 407 ASN Chi-restraints excluded: chain F residue 412 LEU Chi-restraints excluded: chain G residue 142 ASN Chi-restraints excluded: chain G residue 158 THR Chi-restraints excluded: chain G residue 201 ILE Chi-restraints excluded: chain J residue 121 LEU Chi-restraints excluded: chain L residue 161 THR 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: 20.0000 chunk 176 optimal weight: 9.9990 chunk 37 optimal weight: 5.9990 chunk 161 optimal weight: 20.0000 chunk 227 optimal weight: 10.0000 chunk 340 optimal weight: 10.0000 chunk 360 optimal weight: 0.5980 chunk 177 optimal weight: 8.9990 chunk 322 optimal weight: 6.9990 chunk 97 optimal weight: 8.9990 overall best weight: 6.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 397 GLN ** C 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 249 HIS E 336 GLN G 17 GLN G 142 ASN G 166 GLN G 180 GLN H 82 GLN L 96 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.2679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 30114 Z= 0.415 Angle : 0.667 8.116 40813 Z= 0.343 Chirality : 0.049 0.182 4572 Planarity : 0.006 0.065 5333 Dihedral : 6.458 105.941 4259 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.50 % Allowed : 11.71 % Favored : 85.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.14), residues: 3764 helix: 0.35 (0.13), residues: 1556 sheet: -0.07 (0.22), residues: 591 loop : -0.38 (0.15), residues: 1617 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 471 HIS 0.009 0.002 HIS C 185 PHE 0.030 0.002 PHE A 230 TYR 0.025 0.002 TYR D 13 ARG 0.010 0.001 ARG J 86 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 306 time to evaluate : 3.444 Fit side-chains REVERT: A 340 ARG cc_start: 0.6781 (mpt-90) cc_final: 0.6130 (mmm160) REVERT: A 491 ARG cc_start: 0.7384 (mtt-85) cc_final: 0.6691 (mtp-110) REVERT: A 517 LYS cc_start: 0.7215 (tttt) cc_final: 0.6790 (tptp) REVERT: A 530 ILE cc_start: 0.6383 (mm) cc_final: 0.6101 (tt) REVERT: A 550 ARG cc_start: 0.5446 (mmt180) cc_final: 0.4718 (mmp80) REVERT: B 244 TRP cc_start: 0.7893 (m100) cc_final: 0.7293 (m100) REVERT: B 441 GLU cc_start: 0.5844 (tp30) cc_final: 0.5030 (mt-10) REVERT: B 450 LEU cc_start: 0.5632 (tp) cc_final: 0.5288 (mm) REVERT: B 509 MET cc_start: 0.3801 (mmm) cc_final: 0.3597 (mmm) REVERT: B 516 MET cc_start: 0.4994 (mtm) cc_final: 0.4729 (mtp) REVERT: B 525 GLU cc_start: 0.6663 (mm-30) cc_final: 0.5835 (mt-10) REVERT: B 567 MET cc_start: 0.5134 (mmm) cc_final: 0.4659 (mmt) REVERT: C 209 MET cc_start: 0.7816 (mtp) cc_final: 0.7252 (mtp) REVERT: C 347 GLU cc_start: 0.7705 (mm-30) cc_final: 0.7375 (mt-10) REVERT: C 410 ASP cc_start: 0.7115 (t0) cc_final: 0.6811 (t0) REVERT: C 564 GLU cc_start: 0.6504 (OUTLIER) cc_final: 0.6302 (pt0) REVERT: D 62 GLU cc_start: 0.6623 (pm20) cc_final: 0.6296 (pt0) REVERT: D 67 ASP cc_start: 0.8146 (p0) cc_final: 0.7824 (p0) REVERT: D 280 ARG cc_start: 0.6556 (ptm-80) cc_final: 0.5918 (ttp80) REVERT: D 456 LYS cc_start: 0.7369 (mmtt) cc_final: 0.6527 (mmmt) REVERT: E 110 LYS cc_start: 0.8362 (OUTLIER) cc_final: 0.8067 (ttmm) REVERT: E 320 ASP cc_start: 0.6731 (t0) cc_final: 0.6145 (p0) REVERT: E 406 GLU cc_start: 0.6859 (tp30) cc_final: 0.6615 (tp30) REVERT: E 421 PHE cc_start: 0.7054 (m-80) cc_final: 0.6792 (m-80) REVERT: F 6 LYS cc_start: 0.7269 (tttt) cc_final: 0.6837 (mtmm) REVERT: F 53 GLU cc_start: 0.7478 (pt0) cc_final: 0.7038 (mm-30) REVERT: F 109 GLU cc_start: 0.7149 (tt0) cc_final: 0.6940 (tt0) REVERT: F 210 ARG cc_start: 0.7509 (ttp-110) cc_final: 0.7139 (ttt180) REVERT: G 5 SER cc_start: 0.7795 (p) cc_final: 0.7499 (m) REVERT: G 156 LYS cc_start: 0.6300 (ttmm) cc_final: 0.5790 (tppt) REVERT: G 187 GLU cc_start: 0.7051 (mm-30) cc_final: 0.6622 (tt0) REVERT: J 121 LEU cc_start: 0.3199 (OUTLIER) cc_final: 0.2985 (tt) REVERT: J 149 ARG cc_start: 0.4375 (mtm180) cc_final: 0.3706 (mmm160) REVERT: L 61 GLU cc_start: 0.2794 (pm20) cc_final: 0.1996 (mm-30) REVERT: L 86 ARG cc_start: 0.4403 (mtp180) cc_final: 0.4201 (mtm180) REVERT: L 173 ARG cc_start: 0.4561 (ttt90) cc_final: 0.4039 (ttt180) outliers start: 77 outliers final: 45 residues processed: 363 average time/residue: 0.4522 time to fit residues: 253.2106 Evaluate side-chains 322 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 274 time to evaluate : 3.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 114 GLU Chi-restraints excluded: chain A residue 268 GLU Chi-restraints excluded: chain A residue 344 MET Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 527 GLU Chi-restraints excluded: chain B residue 7 GLN Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 284 ARG Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 416 ARG Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 466 GLU Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 152 ASP Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 369 ILE Chi-restraints excluded: chain C residue 443 VAL Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 540 LEU Chi-restraints excluded: chain C residue 564 GLU Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain E residue 74 SER Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 110 LYS Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 143 THR Chi-restraints excluded: chain E residue 211 THR Chi-restraints excluded: chain E residue 216 ARG Chi-restraints excluded: chain E residue 225 ASP Chi-restraints excluded: chain E residue 373 GLU Chi-restraints excluded: chain E residue 390 VAL Chi-restraints excluded: chain F residue 96 ILE Chi-restraints excluded: chain F residue 137 THR Chi-restraints excluded: chain F residue 290 ASP Chi-restraints excluded: chain F residue 396 VAL Chi-restraints excluded: chain F residue 407 ASN Chi-restraints excluded: chain F residue 412 LEU Chi-restraints excluded: chain G residue 96 VAL Chi-restraints excluded: chain G residue 142 ASN Chi-restraints excluded: chain G residue 158 THR Chi-restraints excluded: chain G residue 201 ILE Chi-restraints excluded: chain J residue 121 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 300 optimal weight: 2.9990 chunk 204 optimal weight: 10.0000 chunk 5 optimal weight: 0.9980 chunk 268 optimal weight: 7.9990 chunk 148 optimal weight: 4.9990 chunk 307 optimal weight: 3.9990 chunk 249 optimal weight: 6.9990 chunk 0 optimal weight: 6.9990 chunk 184 optimal weight: 10.0000 chunk 323 optimal weight: 6.9990 chunk 90 optimal weight: 7.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 316 GLN A 397 GLN ** C 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 222 ASN E 336 GLN F 166 GLN G 10 ASN G 17 GLN G 166 GLN G 180 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.2786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 30114 Z= 0.274 Angle : 0.561 7.934 40813 Z= 0.289 Chirality : 0.044 0.174 4572 Planarity : 0.005 0.051 5333 Dihedral : 6.173 101.049 4259 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.40 % Allowed : 13.85 % Favored : 83.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.14), residues: 3764 helix: 0.52 (0.13), residues: 1541 sheet: -0.13 (0.22), residues: 604 loop : -0.32 (0.15), residues: 1619 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 471 HIS 0.006 0.001 HIS C 185 PHE 0.025 0.002 PHE A 230 TYR 0.024 0.002 TYR B 428 ARG 0.010 0.000 ARG J 86 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 281 time to evaluate : 3.558 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 340 ARG cc_start: 0.6778 (mpt-90) cc_final: 0.6111 (mmm160) REVERT: A 491 ARG cc_start: 0.7369 (mtt-85) cc_final: 0.6733 (mtp-110) REVERT: A 517 LYS cc_start: 0.7250 (tttt) cc_final: 0.6784 (tptp) REVERT: A 530 ILE cc_start: 0.6388 (mm) cc_final: 0.6093 (tt) REVERT: A 550 ARG cc_start: 0.5543 (mmt180) cc_final: 0.4799 (mmp80) REVERT: B 191 ARG cc_start: 0.7630 (OUTLIER) cc_final: 0.6621 (ttm170) REVERT: B 244 TRP cc_start: 0.7928 (m100) cc_final: 0.7319 (m100) REVERT: B 393 GLU cc_start: 0.5750 (tm-30) cc_final: 0.5549 (tm-30) REVERT: B 441 GLU cc_start: 0.5829 (tp30) cc_final: 0.5013 (mt-10) REVERT: B 450 LEU cc_start: 0.5733 (tp) cc_final: 0.5360 (mm) REVERT: B 516 MET cc_start: 0.4920 (mtm) cc_final: 0.4650 (mtp) REVERT: B 525 GLU cc_start: 0.6687 (mm-30) cc_final: 0.6027 (mt-10) REVERT: B 567 MET cc_start: 0.5107 (mmm) cc_final: 0.4787 (mmt) REVERT: C 79 MET cc_start: 0.8244 (mtm) cc_final: 0.7983 (mpp) REVERT: C 209 MET cc_start: 0.7785 (mtp) cc_final: 0.7236 (mtp) REVERT: C 347 GLU cc_start: 0.7621 (mm-30) cc_final: 0.7346 (mt-10) REVERT: C 410 ASP cc_start: 0.7064 (t0) cc_final: 0.6765 (t0) REVERT: C 423 ASN cc_start: 0.8496 (t0) cc_final: 0.8267 (t0) REVERT: D 62 GLU cc_start: 0.6567 (pm20) cc_final: 0.6247 (pt0) REVERT: D 67 ASP cc_start: 0.8070 (p0) cc_final: 0.7788 (p0) REVERT: D 137 THR cc_start: 0.8914 (OUTLIER) cc_final: 0.8618 (p) REVERT: D 280 ARG cc_start: 0.6600 (ptm-80) cc_final: 0.5692 (ttp80) REVERT: D 406 GLU cc_start: 0.5323 (pm20) cc_final: 0.4848 (tm-30) REVERT: D 456 LYS cc_start: 0.7357 (mmtt) cc_final: 0.6530 (mmmt) REVERT: E 110 LYS cc_start: 0.8359 (OUTLIER) cc_final: 0.8046 (ttmm) REVERT: E 320 ASP cc_start: 0.6594 (t0) cc_final: 0.6091 (p0) REVERT: E 421 PHE cc_start: 0.6996 (m-80) cc_final: 0.6751 (m-80) REVERT: F 6 LYS cc_start: 0.7287 (tttt) cc_final: 0.6900 (mtmm) REVERT: F 53 GLU cc_start: 0.7453 (pt0) cc_final: 0.7014 (mm-30) REVERT: F 210 ARG cc_start: 0.7467 (ttp-110) cc_final: 0.7099 (ttt180) REVERT: G 5 SER cc_start: 0.7852 (p) cc_final: 0.7357 (m) REVERT: G 10 ASN cc_start: 0.7810 (OUTLIER) cc_final: 0.7447 (m110) REVERT: G 156 LYS cc_start: 0.6350 (ttmm) cc_final: 0.5767 (tppt) REVERT: G 187 GLU cc_start: 0.7030 (mm-30) cc_final: 0.6609 (tt0) REVERT: I 104 MET cc_start: 0.2944 (mtp) cc_final: 0.2712 (mtp) REVERT: J 89 GLU cc_start: 0.5347 (tp30) cc_final: 0.3868 (pt0) REVERT: J 121 LEU cc_start: 0.3260 (OUTLIER) cc_final: 0.2979 (tt) REVERT: J 149 ARG cc_start: 0.4305 (mtm180) cc_final: 0.3597 (mmm160) REVERT: L 61 GLU cc_start: 0.2586 (pm20) cc_final: 0.1718 (mm-30) REVERT: L 85 ARG cc_start: 0.4326 (ppt170) cc_final: 0.3610 (ttp-110) REVERT: L 127 ASP cc_start: 0.2690 (OUTLIER) cc_final: 0.2087 (t0) REVERT: L 168 LEU cc_start: 0.4791 (OUTLIER) cc_final: 0.4484 (mm) REVERT: L 173 ARG cc_start: 0.4608 (ttt90) cc_final: 0.3945 (ttt180) outliers start: 74 outliers final: 48 residues processed: 340 average time/residue: 0.4528 time to fit residues: 237.8485 Evaluate side-chains 326 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 271 time to evaluate : 3.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 114 GLU Chi-restraints excluded: chain A residue 268 GLU Chi-restraints excluded: chain A residue 344 MET Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain B residue 7 GLN Chi-restraints excluded: chain B residue 191 ARG Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 416 ARG Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 466 GLU Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 152 ASP Chi-restraints excluded: chain C residue 443 VAL Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 490 ILE Chi-restraints excluded: chain C residue 519 ILE Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 318 ASP Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain E residue 74 SER Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 110 LYS Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 143 THR Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 211 THR Chi-restraints excluded: chain E residue 216 ARG Chi-restraints excluded: chain E residue 225 ASP Chi-restraints excluded: chain E residue 336 GLN Chi-restraints excluded: chain E residue 373 GLU Chi-restraints excluded: chain E residue 390 VAL Chi-restraints excluded: chain F residue 137 THR Chi-restraints excluded: chain F residue 259 ASP Chi-restraints excluded: chain F residue 290 ASP Chi-restraints excluded: chain F residue 300 VAL Chi-restraints excluded: chain F residue 396 VAL Chi-restraints excluded: chain F residue 407 ASN Chi-restraints excluded: chain F residue 412 LEU Chi-restraints excluded: chain G residue 10 ASN Chi-restraints excluded: chain G residue 158 THR Chi-restraints excluded: chain G residue 180 GLN Chi-restraints excluded: chain G residue 197 ILE Chi-restraints excluded: chain G residue 201 ILE Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain J residue 68 VAL Chi-restraints excluded: chain J residue 121 LEU Chi-restraints excluded: chain L residue 102 GLU Chi-restraints excluded: chain L residue 127 ASP Chi-restraints excluded: chain L residue 168 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 121 optimal weight: 0.9980 chunk 324 optimal weight: 2.9990 chunk 71 optimal weight: 0.0370 chunk 211 optimal weight: 0.0370 chunk 89 optimal weight: 5.9990 chunk 360 optimal weight: 2.9990 chunk 299 optimal weight: 0.9990 chunk 167 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 119 optimal weight: 5.9990 chunk 189 optimal weight: 5.9990 overall best weight: 1.0140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 397 GLN ** C 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 413 GLN F 437 GLN G 10 ASN G 142 ASN G 180 GLN J 96 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.2803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 30114 Z= 0.138 Angle : 0.483 7.510 40813 Z= 0.249 Chirality : 0.042 0.165 4572 Planarity : 0.004 0.048 5333 Dihedral : 5.709 93.601 4259 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 1.85 % Allowed : 14.82 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.14), residues: 3764 helix: 0.81 (0.14), residues: 1538 sheet: 0.05 (0.23), residues: 579 loop : -0.12 (0.15), residues: 1647 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 330 HIS 0.003 0.000 HIS C 185 PHE 0.017 0.001 PHE A 230 TYR 0.022 0.001 TYR B 428 ARG 0.008 0.000 ARG B 488 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 290 time to evaluate : 3.311 Fit side-chains revert: symmetry clash REVERT: A 300 GLU cc_start: 0.7756 (tm-30) cc_final: 0.7514 (tm-30) REVERT: A 340 ARG cc_start: 0.6817 (mpt-90) cc_final: 0.6090 (mmm160) REVERT: A 491 ARG cc_start: 0.7356 (mtt-85) cc_final: 0.6709 (mtp-110) REVERT: A 530 ILE cc_start: 0.6394 (mm) cc_final: 0.6113 (tt) REVERT: A 550 ARG cc_start: 0.5564 (mmt180) cc_final: 0.4802 (mmp80) REVERT: B 244 TRP cc_start: 0.7849 (m100) cc_final: 0.7245 (m-90) REVERT: B 393 GLU cc_start: 0.5767 (tm-30) cc_final: 0.5374 (tm-30) REVERT: B 397 GLN cc_start: 0.6564 (OUTLIER) cc_final: 0.6006 (mp-120) REVERT: B 441 GLU cc_start: 0.5966 (tp30) cc_final: 0.5145 (mt-10) REVERT: B 450 LEU cc_start: 0.5956 (tp) cc_final: 0.5656 (mm) REVERT: B 516 MET cc_start: 0.4798 (mtm) cc_final: 0.4538 (mtp) REVERT: B 525 GLU cc_start: 0.6800 (mm-30) cc_final: 0.6051 (mt-10) REVERT: B 567 MET cc_start: 0.4998 (mmm) cc_final: 0.4682 (mmt) REVERT: C 19 MET cc_start: 0.8479 (mmm) cc_final: 0.8156 (mtp) REVERT: C 79 MET cc_start: 0.8097 (mtm) cc_final: 0.7863 (mtm) REVERT: C 347 GLU cc_start: 0.7532 (mm-30) cc_final: 0.7322 (mt-10) REVERT: C 410 ASP cc_start: 0.7072 (t0) cc_final: 0.6753 (t0) REVERT: D 62 GLU cc_start: 0.6568 (pm20) cc_final: 0.6194 (pt0) REVERT: D 67 ASP cc_start: 0.7855 (p0) cc_final: 0.7516 (p0) REVERT: D 137 THR cc_start: 0.8891 (OUTLIER) cc_final: 0.8585 (p) REVERT: D 280 ARG cc_start: 0.6597 (ptm-80) cc_final: 0.5674 (ttp80) REVERT: D 406 GLU cc_start: 0.5224 (pm20) cc_final: 0.4966 (tm-30) REVERT: D 456 LYS cc_start: 0.7301 (mmtt) cc_final: 0.6478 (mmmt) REVERT: E 320 ASP cc_start: 0.6484 (t0) cc_final: 0.5962 (p0) REVERT: E 421 PHE cc_start: 0.6853 (m-80) cc_final: 0.6620 (m-80) REVERT: F 6 LYS cc_start: 0.7224 (tttt) cc_final: 0.6893 (mtmm) REVERT: F 210 ARG cc_start: 0.7391 (ttp-110) cc_final: 0.7043 (ttt180) REVERT: F 280 ARG cc_start: 0.6775 (ttp-170) cc_final: 0.6291 (ttt90) REVERT: G 5 SER cc_start: 0.7935 (p) cc_final: 0.7643 (m) REVERT: G 156 LYS cc_start: 0.6390 (ttmm) cc_final: 0.5822 (tppt) REVERT: J 121 LEU cc_start: 0.3423 (OUTLIER) cc_final: 0.3132 (tt) REVERT: J 149 ARG cc_start: 0.4241 (mtm180) cc_final: 0.3644 (mmm160) REVERT: L 61 GLU cc_start: 0.2592 (pm20) cc_final: 0.1709 (tp30) REVERT: L 85 ARG cc_start: 0.4299 (ppt170) cc_final: 0.3580 (ttp-110) REVERT: L 173 ARG cc_start: 0.4566 (ttt90) cc_final: 0.3961 (ttt180) outliers start: 57 outliers final: 36 residues processed: 334 average time/residue: 0.4539 time to fit residues: 234.4857 Evaluate side-chains 317 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 278 time to evaluate : 3.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 344 MET Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 397 GLN Chi-restraints excluded: chain B residue 416 ARG Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 466 GLU Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 152 ASP Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 484 ILE Chi-restraints excluded: chain C residue 519 ILE Chi-restraints excluded: chain C residue 537 ASP Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 318 ASP Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain E residue 216 ARG Chi-restraints excluded: chain E residue 225 ASP Chi-restraints excluded: chain E residue 373 GLU Chi-restraints excluded: chain E residue 390 VAL Chi-restraints excluded: chain F residue 96 ILE Chi-restraints excluded: chain F residue 137 THR Chi-restraints excluded: chain F residue 259 ASP Chi-restraints excluded: chain F residue 290 ASP Chi-restraints excluded: chain F residue 300 VAL Chi-restraints excluded: chain F residue 396 VAL Chi-restraints excluded: chain F residue 407 ASN Chi-restraints excluded: chain F residue 412 LEU Chi-restraints excluded: chain G residue 96 VAL Chi-restraints excluded: chain G residue 158 THR Chi-restraints excluded: chain G residue 201 ILE Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain J residue 121 LEU Chi-restraints excluded: chain L residue 102 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 347 optimal weight: 8.9990 chunk 40 optimal weight: 2.9990 chunk 205 optimal weight: 0.0980 chunk 263 optimal weight: 9.9990 chunk 204 optimal weight: 1.9990 chunk 303 optimal weight: 5.9990 chunk 201 optimal weight: 8.9990 chunk 359 optimal weight: 7.9990 chunk 224 optimal weight: 9.9990 chunk 219 optimal weight: 0.7980 chunk 165 optimal weight: 2.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 316 GLN ** C 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 437 GLN E 336 GLN F 46 GLN F 58 GLN F 413 GLN F 437 GLN G 180 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.2882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 30114 Z= 0.160 Angle : 0.481 9.044 40813 Z= 0.245 Chirality : 0.042 0.167 4572 Planarity : 0.004 0.048 5333 Dihedral : 5.480 88.290 4259 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 1.98 % Allowed : 14.95 % Favored : 83.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.14), residues: 3764 helix: 0.83 (0.14), residues: 1564 sheet: 0.12 (0.22), residues: 591 loop : -0.06 (0.16), residues: 1609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 330 HIS 0.005 0.001 HIS C 185 PHE 0.017 0.001 PHE A 230 TYR 0.022 0.001 TYR B 428 ARG 0.008 0.000 ARG B 488 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 283 time to evaluate : 3.152 Fit side-chains REVERT: A 53 GLU cc_start: 0.7772 (OUTLIER) cc_final: 0.7177 (mm-30) REVERT: A 300 GLU cc_start: 0.7748 (tm-30) cc_final: 0.7500 (tm-30) REVERT: A 340 ARG cc_start: 0.6790 (mpt-90) cc_final: 0.6059 (mmm160) REVERT: A 491 ARG cc_start: 0.7410 (mtt-85) cc_final: 0.6744 (mtp-110) REVERT: A 550 ARG cc_start: 0.5558 (mmt180) cc_final: 0.4802 (mmp80) REVERT: B 244 TRP cc_start: 0.7872 (m100) cc_final: 0.7257 (m-90) REVERT: B 393 GLU cc_start: 0.5708 (tm-30) cc_final: 0.5336 (tm-30) REVERT: B 397 GLN cc_start: 0.6539 (OUTLIER) cc_final: 0.5696 (mp-120) REVERT: B 441 GLU cc_start: 0.6045 (tp30) cc_final: 0.5187 (mt-10) REVERT: B 459 GLN cc_start: 0.6477 (mm-40) cc_final: 0.6201 (tm-30) REVERT: B 525 GLU cc_start: 0.6711 (mm-30) cc_final: 0.5952 (mt-10) REVERT: B 567 MET cc_start: 0.5008 (mmm) cc_final: 0.4729 (mmt) REVERT: C 19 MET cc_start: 0.8467 (mmm) cc_final: 0.8132 (mtp) REVERT: C 347 GLU cc_start: 0.7566 (mm-30) cc_final: 0.7363 (mt-10) REVERT: C 410 ASP cc_start: 0.7069 (t0) cc_final: 0.6747 (t0) REVERT: D 62 GLU cc_start: 0.6579 (pm20) cc_final: 0.6179 (pt0) REVERT: D 67 ASP cc_start: 0.7813 (p0) cc_final: 0.7588 (p0) REVERT: D 137 THR cc_start: 0.8892 (OUTLIER) cc_final: 0.8593 (p) REVERT: D 280 ARG cc_start: 0.6611 (ptm-80) cc_final: 0.5670 (ttp80) REVERT: D 406 GLU cc_start: 0.5273 (pm20) cc_final: 0.4984 (tm-30) REVERT: D 456 LYS cc_start: 0.7366 (mmtt) cc_final: 0.6546 (mmmt) REVERT: E 110 LYS cc_start: 0.8308 (ttmm) cc_final: 0.7649 (tttt) REVERT: E 320 ASP cc_start: 0.6460 (t0) cc_final: 0.5935 (p0) REVERT: E 421 PHE cc_start: 0.6838 (m-80) cc_final: 0.6616 (m-80) REVERT: F 6 LYS cc_start: 0.7211 (tttt) cc_final: 0.6889 (mtmm) REVERT: F 210 ARG cc_start: 0.7382 (ttp-110) cc_final: 0.7040 (ttt180) REVERT: F 280 ARG cc_start: 0.6791 (ttp-170) cc_final: 0.6302 (ttt90) REVERT: F 420 ARG cc_start: 0.8289 (mtp-110) cc_final: 0.7728 (ttp80) REVERT: G 5 SER cc_start: 0.8043 (p) cc_final: 0.7770 (m) REVERT: G 156 LYS cc_start: 0.6359 (ttmm) cc_final: 0.5783 (tppt) REVERT: G 187 GLU cc_start: 0.6955 (mm-30) cc_final: 0.6552 (tt0) REVERT: H 18 LEU cc_start: 0.2848 (pp) cc_final: 0.2565 (mt) REVERT: J 89 GLU cc_start: 0.4603 (tp30) cc_final: 0.3421 (pt0) REVERT: J 121 LEU cc_start: 0.3443 (OUTLIER) cc_final: 0.3168 (tt) REVERT: J 149 ARG cc_start: 0.4288 (mtm110) cc_final: 0.3698 (mmm160) REVERT: L 61 GLU cc_start: 0.2592 (pm20) cc_final: 0.1700 (tp30) REVERT: L 85 ARG cc_start: 0.4316 (ppt170) cc_final: 0.3596 (ttp-110) REVERT: L 173 ARG cc_start: 0.4486 (ttt90) cc_final: 0.3843 (ttt180) outliers start: 61 outliers final: 44 residues processed: 329 average time/residue: 0.4638 time to fit residues: 235.5879 Evaluate side-chains 317 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 269 time to evaluate : 3.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 268 GLU Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 547 ARG Chi-restraints excluded: chain B residue 7 GLN Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 284 ARG Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 397 GLN Chi-restraints excluded: chain B residue 416 ARG Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 466 GLU Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 152 ASP Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 484 ILE Chi-restraints excluded: chain C residue 519 ILE Chi-restraints excluded: chain C residue 537 ASP Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 318 ASP Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain E residue 74 SER Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 140 VAL Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 216 ARG Chi-restraints excluded: chain E residue 225 ASP Chi-restraints excluded: chain E residue 314 LEU Chi-restraints excluded: chain E residue 370 LYS Chi-restraints excluded: chain E residue 373 GLU Chi-restraints excluded: chain E residue 390 VAL Chi-restraints excluded: chain F residue 96 ILE Chi-restraints excluded: chain F residue 137 THR Chi-restraints excluded: chain F residue 259 ASP Chi-restraints excluded: chain F residue 290 ASP Chi-restraints excluded: chain F residue 300 VAL Chi-restraints excluded: chain F residue 396 VAL Chi-restraints excluded: chain F residue 407 ASN Chi-restraints excluded: chain F residue 412 LEU Chi-restraints excluded: chain G residue 96 VAL Chi-restraints excluded: chain G residue 158 THR Chi-restraints excluded: chain G residue 201 ILE Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain J residue 121 LEU Chi-restraints excluded: chain L residue 102 GLU 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: 0.9990 chunk 214 optimal weight: 9.9990 chunk 108 optimal weight: 20.0000 chunk 70 optimal weight: 20.0000 chunk 69 optimal weight: 7.9990 chunk 228 optimal weight: 0.0370 chunk 244 optimal weight: 10.0000 chunk 177 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 282 optimal weight: 9.9990 overall best weight: 3.2066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 316 GLN A 571 GLN B 145 HIS ** C 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 437 GLN ** E 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 46 GLN F 58 GLN F 413 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.2983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 30114 Z= 0.227 Angle : 0.518 10.288 40813 Z= 0.265 Chirality : 0.043 0.169 4572 Planarity : 0.005 0.050 5333 Dihedral : 5.675 89.450 4259 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.04 % Allowed : 15.37 % Favored : 82.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.14), residues: 3764 helix: 0.79 (0.14), residues: 1556 sheet: 0.15 (0.23), residues: 566 loop : -0.16 (0.15), residues: 1642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 471 HIS 0.006 0.001 HIS C 185 PHE 0.021 0.001 PHE A 230 TYR 0.021 0.001 TYR B 428 ARG 0.008 0.000 ARG B 488 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 277 time to evaluate : 3.681 Fit side-chains REVERT: A 53 GLU cc_start: 0.7798 (OUTLIER) cc_final: 0.7143 (mm-30) REVERT: A 300 GLU cc_start: 0.7756 (tm-30) cc_final: 0.7511 (tm-30) REVERT: A 340 ARG cc_start: 0.6783 (mpt-90) cc_final: 0.6107 (mmm160) REVERT: A 491 ARG cc_start: 0.7381 (mtt-85) cc_final: 0.6745 (mtp-110) REVERT: A 530 ILE cc_start: 0.6408 (mm) cc_final: 0.6047 (tt) REVERT: A 550 ARG cc_start: 0.5524 (mmt180) cc_final: 0.4765 (mmp80) REVERT: B 191 ARG cc_start: 0.7649 (OUTLIER) cc_final: 0.6662 (ttm170) REVERT: B 244 TRP cc_start: 0.7877 (m100) cc_final: 0.7279 (m-90) REVERT: B 393 GLU cc_start: 0.5695 (tm-30) cc_final: 0.5297 (tm-30) REVERT: B 397 GLN cc_start: 0.6559 (OUTLIER) cc_final: 0.5703 (mp-120) REVERT: B 441 GLU cc_start: 0.6044 (tp30) cc_final: 0.5186 (mt-10) REVERT: B 525 GLU cc_start: 0.6732 (mm-30) cc_final: 0.5957 (mt-10) REVERT: B 567 MET cc_start: 0.5019 (mmm) cc_final: 0.4731 (mmt) REVERT: C 19 MET cc_start: 0.8494 (mmm) cc_final: 0.8135 (mtp) REVERT: C 347 GLU cc_start: 0.7497 (mm-30) cc_final: 0.7289 (mt-10) REVERT: C 410 ASP cc_start: 0.7063 (t0) cc_final: 0.6736 (t0) REVERT: D 62 GLU cc_start: 0.6605 (pm20) cc_final: 0.5736 (mp0) REVERT: D 67 ASP cc_start: 0.7855 (p0) cc_final: 0.7609 (p0) REVERT: D 137 THR cc_start: 0.8918 (OUTLIER) cc_final: 0.8617 (p) REVERT: D 280 ARG cc_start: 0.6633 (ptm-80) cc_final: 0.5646 (ttp80) REVERT: D 456 LYS cc_start: 0.7430 (mmtt) cc_final: 0.6597 (mmmt) REVERT: E 110 LYS cc_start: 0.8330 (OUTLIER) cc_final: 0.7759 (tttt) REVERT: E 320 ASP cc_start: 0.6529 (t0) cc_final: 0.6089 (p0) REVERT: E 421 PHE cc_start: 0.7027 (m-80) cc_final: 0.6790 (m-80) REVERT: F 6 LYS cc_start: 0.7238 (tttt) cc_final: 0.6909 (mtmm) REVERT: F 280 ARG cc_start: 0.6832 (ttp-170) cc_final: 0.6363 (ttt90) REVERT: G 5 SER cc_start: 0.7861 (p) cc_final: 0.7589 (m) REVERT: G 156 LYS cc_start: 0.6296 (ttmm) cc_final: 0.5772 (tppt) REVERT: G 187 GLU cc_start: 0.6987 (mm-30) cc_final: 0.6591 (tt0) REVERT: J 121 LEU cc_start: 0.3485 (OUTLIER) cc_final: 0.3237 (tt) REVERT: J 149 ARG cc_start: 0.4322 (mtm110) cc_final: 0.3671 (mmm160) REVERT: L 61 GLU cc_start: 0.2494 (pm20) cc_final: 0.1641 (tp30) REVERT: L 85 ARG cc_start: 0.4261 (ppt170) cc_final: 0.3560 (ttp-110) REVERT: L 173 ARG cc_start: 0.4398 (ttt90) cc_final: 0.3800 (ttt180) outliers start: 63 outliers final: 46 residues processed: 328 average time/residue: 0.4641 time to fit residues: 235.0333 Evaluate side-chains 325 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 273 time to evaluate : 3.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 268 GLU Chi-restraints excluded: chain A residue 316 GLN Chi-restraints excluded: chain A residue 344 MET Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 547 ARG Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 191 ARG Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 397 GLN Chi-restraints excluded: chain B residue 416 ARG Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 466 GLU Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 152 ASP Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 484 ILE Chi-restraints excluded: chain C residue 519 ILE Chi-restraints excluded: chain C residue 537 ASP Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain E residue 5 LYS Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain E residue 74 SER Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 110 LYS Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 140 VAL Chi-restraints excluded: chain E residue 143 THR Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 216 ARG Chi-restraints excluded: chain E residue 225 ASP Chi-restraints excluded: chain E residue 370 LYS Chi-restraints excluded: chain E residue 373 GLU Chi-restraints excluded: chain E residue 390 VAL Chi-restraints excluded: chain F residue 96 ILE Chi-restraints excluded: chain F residue 137 THR Chi-restraints excluded: chain F residue 259 ASP Chi-restraints excluded: chain F residue 290 ASP Chi-restraints excluded: chain F residue 300 VAL Chi-restraints excluded: chain F residue 396 VAL Chi-restraints excluded: chain F residue 407 ASN Chi-restraints excluded: chain F residue 412 LEU Chi-restraints excluded: chain G residue 96 VAL Chi-restraints excluded: chain G residue 158 THR Chi-restraints excluded: chain G residue 201 ILE Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain J residue 121 LEU Chi-restraints excluded: chain L residue 102 GLU Chi-restraints excluded: chain L residue 140 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 327 optimal weight: 0.0980 chunk 344 optimal weight: 7.9990 chunk 314 optimal weight: 5.9990 chunk 335 optimal weight: 6.9990 chunk 201 optimal weight: 1.9990 chunk 145 optimal weight: 0.9980 chunk 263 optimal weight: 5.9990 chunk 102 optimal weight: 20.0000 chunk 302 optimal weight: 0.9980 chunk 316 optimal weight: 3.9990 chunk 333 optimal weight: 30.0000 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 316 GLN ** C 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 46 GLN F 58 GLN F 413 GLN G 180 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.3025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 30114 Z= 0.154 Angle : 0.485 11.130 40813 Z= 0.247 Chirality : 0.042 0.165 4572 Planarity : 0.004 0.066 5333 Dihedral : 5.480 85.945 4259 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.78 % Allowed : 15.80 % Favored : 82.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.14), residues: 3764 helix: 0.90 (0.14), residues: 1558 sheet: 0.14 (0.23), residues: 578 loop : -0.10 (0.16), residues: 1628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP J 100 HIS 0.005 0.001 HIS A 145 PHE 0.019 0.001 PHE A 318 TYR 0.019 0.001 TYR B 428 ARG 0.009 0.000 ARG B 488 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 272 time to evaluate : 3.588 Fit side-chains REVERT: A 300 GLU cc_start: 0.7710 (tm-30) cc_final: 0.7458 (tm-30) REVERT: A 340 ARG cc_start: 0.6770 (mpt-90) cc_final: 0.6062 (mmm160) REVERT: A 491 ARG cc_start: 0.7326 (mtt-85) cc_final: 0.6712 (mtp-110) REVERT: A 550 ARG cc_start: 0.5375 (mmt180) cc_final: 0.4779 (ttt-90) REVERT: B 211 ILE cc_start: 0.5746 (OUTLIER) cc_final: 0.5528 (tp) REVERT: B 393 GLU cc_start: 0.5699 (tm-30) cc_final: 0.5238 (tm-30) REVERT: B 397 GLN cc_start: 0.6505 (OUTLIER) cc_final: 0.5516 (mp-120) REVERT: B 441 GLU cc_start: 0.6024 (tp30) cc_final: 0.5161 (mt-10) REVERT: B 459 GLN cc_start: 0.6491 (mm-40) cc_final: 0.6202 (tm-30) REVERT: B 525 GLU cc_start: 0.6728 (mm-30) cc_final: 0.6034 (mt-10) REVERT: B 567 MET cc_start: 0.5025 (mmm) cc_final: 0.4733 (mmt) REVERT: C 19 MET cc_start: 0.8438 (mmm) cc_final: 0.8136 (mtp) REVERT: C 410 ASP cc_start: 0.7090 (t0) cc_final: 0.6747 (t0) REVERT: D 62 GLU cc_start: 0.6559 (pm20) cc_final: 0.5663 (mp0) REVERT: D 67 ASP cc_start: 0.7817 (p0) cc_final: 0.7590 (p0) REVERT: D 137 THR cc_start: 0.8905 (OUTLIER) cc_final: 0.8598 (p) REVERT: D 237 MET cc_start: 0.7917 (mmm) cc_final: 0.7561 (mmt) REVERT: D 280 ARG cc_start: 0.6602 (ptm-80) cc_final: 0.5849 (ttp-170) REVERT: D 406 GLU cc_start: 0.5116 (pm20) cc_final: 0.4651 (tm-30) REVERT: D 456 LYS cc_start: 0.7419 (mmtt) cc_final: 0.6585 (mmmt) REVERT: E 110 LYS cc_start: 0.8303 (ttmm) cc_final: 0.7773 (tttt) REVERT: E 320 ASP cc_start: 0.6514 (t0) cc_final: 0.6235 (p0) REVERT: E 421 PHE cc_start: 0.6904 (m-80) cc_final: 0.6676 (m-80) REVERT: F 3 LEU cc_start: 0.5319 (tp) cc_final: 0.5105 (tp) REVERT: F 6 LYS cc_start: 0.7207 (tttt) cc_final: 0.6887 (mtmm) REVERT: F 280 ARG cc_start: 0.6826 (ttp-170) cc_final: 0.6366 (ttt90) REVERT: F 420 ARG cc_start: 0.8322 (mtp-110) cc_final: 0.7778 (ttp80) REVERT: G 5 SER cc_start: 0.7944 (p) cc_final: 0.7680 (m) REVERT: G 156 LYS cc_start: 0.6373 (ttmm) cc_final: 0.5816 (tppt) REVERT: H 18 LEU cc_start: 0.3506 (tp) cc_final: 0.3018 (pp) REVERT: J 121 LEU cc_start: 0.3503 (OUTLIER) cc_final: 0.3252 (tt) REVERT: J 149 ARG cc_start: 0.4237 (mtm110) cc_final: 0.3617 (mmm160) REVERT: L 61 GLU cc_start: 0.2535 (pm20) cc_final: 0.1581 (tp30) REVERT: L 85 ARG cc_start: 0.4317 (ppt170) cc_final: 0.3611 (ttp-110) REVERT: L 173 ARG cc_start: 0.4435 (ttt90) cc_final: 0.3844 (ttt180) outliers start: 55 outliers final: 44 residues processed: 318 average time/residue: 0.4742 time to fit residues: 234.0939 Evaluate side-chains 316 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 268 time to evaluate : 3.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 GLU Chi-restraints excluded: chain A residue 268 GLU Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 547 ARG Chi-restraints excluded: chain B residue 7 GLN Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 397 GLN Chi-restraints excluded: chain B residue 416 ARG Chi-restraints excluded: chain B residue 466 GLU Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 152 ASP Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 484 ILE Chi-restraints excluded: chain C residue 519 ILE Chi-restraints excluded: chain C residue 537 ASP Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain E residue 5 LYS Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain E residue 74 SER Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 140 VAL Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 216 ARG Chi-restraints excluded: chain E residue 225 ASP Chi-restraints excluded: chain E residue 314 LEU Chi-restraints excluded: chain E residue 370 LYS Chi-restraints excluded: chain E residue 373 GLU Chi-restraints excluded: chain E residue 390 VAL Chi-restraints excluded: chain F residue 96 ILE Chi-restraints excluded: chain F residue 137 THR Chi-restraints excluded: chain F residue 259 ASP Chi-restraints excluded: chain F residue 290 ASP Chi-restraints excluded: chain F residue 300 VAL Chi-restraints excluded: chain F residue 396 VAL Chi-restraints excluded: chain F residue 407 ASN Chi-restraints excluded: chain F residue 412 LEU Chi-restraints excluded: chain G residue 96 VAL Chi-restraints excluded: chain G residue 158 THR Chi-restraints excluded: chain G residue 180 GLN Chi-restraints excluded: chain G residue 201 ILE Chi-restraints excluded: chain J residue 121 LEU Chi-restraints excluded: chain L residue 102 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 219 optimal weight: 1.9990 chunk 354 optimal weight: 30.0000 chunk 216 optimal weight: 3.9990 chunk 168 optimal weight: 9.9990 chunk 246 optimal weight: 8.9990 chunk 371 optimal weight: 20.0000 chunk 342 optimal weight: 20.0000 chunk 295 optimal weight: 0.9980 chunk 30 optimal weight: 10.0000 chunk 228 optimal weight: 2.9990 chunk 181 optimal weight: 8.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 316 GLN A 541 GLN ** C 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 46 GLN F 58 GLN F 413 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.3094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 30114 Z= 0.264 Angle : 0.542 9.712 40813 Z= 0.276 Chirality : 0.044 0.168 4572 Planarity : 0.005 0.049 5333 Dihedral : 5.833 89.176 4259 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.78 % Allowed : 15.80 % Favored : 82.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.14), residues: 3764 helix: 0.78 (0.14), residues: 1552 sheet: 0.09 (0.23), residues: 566 loop : -0.22 (0.15), residues: 1646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 471 HIS 0.006 0.001 HIS C 185 PHE 0.023 0.002 PHE A 230 TYR 0.021 0.001 TYR B 428 ARG 0.010 0.000 ARG B 488 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 275 time to evaluate : 3.356 Fit side-chains REVERT: A 53 GLU cc_start: 0.7850 (OUTLIER) cc_final: 0.7250 (mm-30) REVERT: A 300 GLU cc_start: 0.7758 (tm-30) cc_final: 0.7523 (tm-30) REVERT: A 340 ARG cc_start: 0.6877 (mpt-90) cc_final: 0.6123 (mmm160) REVERT: A 491 ARG cc_start: 0.7338 (mtt-85) cc_final: 0.6715 (mtp-110) REVERT: A 530 ILE cc_start: 0.6380 (mm) cc_final: 0.6018 (tt) REVERT: A 550 ARG cc_start: 0.5306 (mmt180) cc_final: 0.4571 (mmp80) REVERT: B 191 ARG cc_start: 0.7640 (OUTLIER) cc_final: 0.6654 (ttm170) REVERT: B 202 ASN cc_start: 0.7036 (m110) cc_final: 0.6770 (m110) REVERT: B 211 ILE cc_start: 0.5698 (OUTLIER) cc_final: 0.5493 (tp) REVERT: B 393 GLU cc_start: 0.5744 (tm-30) cc_final: 0.5323 (tm-30) REVERT: B 397 GLN cc_start: 0.6584 (OUTLIER) cc_final: 0.5664 (mp-120) REVERT: B 441 GLU cc_start: 0.5964 (tp30) cc_final: 0.5132 (mt-10) REVERT: B 525 GLU cc_start: 0.6757 (mm-30) cc_final: 0.6054 (mt-10) REVERT: B 567 MET cc_start: 0.5026 (mmm) cc_final: 0.4624 (mmt) REVERT: C 19 MET cc_start: 0.8519 (mmm) cc_final: 0.8197 (mtp) REVERT: C 410 ASP cc_start: 0.6996 (t0) cc_final: 0.6677 (t0) REVERT: C 423 ASN cc_start: 0.8445 (t0) cc_final: 0.8216 (t0) REVERT: C 569 GLU cc_start: 0.7319 (tm-30) cc_final: 0.6963 (tm-30) REVERT: D 62 GLU cc_start: 0.6613 (pm20) cc_final: 0.5742 (mp0) REVERT: D 67 ASP cc_start: 0.7966 (p0) cc_final: 0.7707 (p0) REVERT: D 137 THR cc_start: 0.8909 (OUTLIER) cc_final: 0.8617 (p) REVERT: D 280 ARG cc_start: 0.6646 (ptm-80) cc_final: 0.5876 (ttp-170) REVERT: D 406 GLU cc_start: 0.5133 (pm20) cc_final: 0.4648 (tm-30) REVERT: D 456 LYS cc_start: 0.7440 (mmtt) cc_final: 0.6626 (mmmt) REVERT: E 110 LYS cc_start: 0.8328 (ttmm) cc_final: 0.7750 (tttt) REVERT: E 320 ASP cc_start: 0.6501 (t0) cc_final: 0.6233 (p0) REVERT: E 421 PHE cc_start: 0.7121 (m-80) cc_final: 0.6871 (m-80) REVERT: F 6 LYS cc_start: 0.7211 (tttt) cc_final: 0.6884 (mtmm) REVERT: F 280 ARG cc_start: 0.6796 (ttp-170) cc_final: 0.6347 (ttt90) REVERT: F 420 ARG cc_start: 0.8388 (mtp-110) cc_final: 0.8148 (ttp-110) REVERT: G 5 SER cc_start: 0.7865 (p) cc_final: 0.7627 (m) REVERT: G 156 LYS cc_start: 0.6301 (ttmm) cc_final: 0.5766 (tppt) REVERT: G 187 GLU cc_start: 0.6969 (mm-30) cc_final: 0.6609 (tt0) REVERT: J 121 LEU cc_start: 0.3548 (OUTLIER) cc_final: 0.3309 (tt) REVERT: J 149 ARG cc_start: 0.4222 (mtm110) cc_final: 0.3588 (mmm160) REVERT: L 85 ARG cc_start: 0.4272 (ppt170) cc_final: 0.3581 (ttp-110) REVERT: L 173 ARG cc_start: 0.4378 (ttt90) cc_final: 0.3773 (ttt180) outliers start: 55 outliers final: 44 residues processed: 321 average time/residue: 0.4597 time to fit residues: 227.5306 Evaluate side-chains 321 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 271 time to evaluate : 3.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 114 GLU Chi-restraints excluded: chain A residue 268 GLU Chi-restraints excluded: chain A residue 316 GLN Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 547 ARG Chi-restraints excluded: chain B residue 7 GLN Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 191 ARG Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 397 GLN Chi-restraints excluded: chain B residue 416 ARG Chi-restraints excluded: chain B residue 466 GLU Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 152 ASP Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 484 ILE Chi-restraints excluded: chain C residue 519 ILE Chi-restraints excluded: chain C residue 537 ASP Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain E residue 5 LYS Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain E residue 74 SER Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 140 VAL Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 216 ARG Chi-restraints excluded: chain E residue 225 ASP Chi-restraints excluded: chain E residue 314 LEU Chi-restraints excluded: chain E residue 370 LYS Chi-restraints excluded: chain E residue 373 GLU Chi-restraints excluded: chain E residue 390 VAL Chi-restraints excluded: chain F residue 96 ILE Chi-restraints excluded: chain F residue 137 THR Chi-restraints excluded: chain F residue 259 ASP Chi-restraints excluded: chain F residue 290 ASP Chi-restraints excluded: chain F residue 300 VAL Chi-restraints excluded: chain F residue 396 VAL Chi-restraints excluded: chain F residue 407 ASN Chi-restraints excluded: chain F residue 412 LEU Chi-restraints excluded: chain G residue 96 VAL Chi-restraints excluded: chain G residue 158 THR Chi-restraints excluded: chain G residue 201 ILE Chi-restraints excluded: chain J residue 121 LEU Chi-restraints excluded: chain L residue 102 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 235 optimal weight: 5.9990 chunk 315 optimal weight: 3.9990 chunk 90 optimal weight: 9.9990 chunk 272 optimal weight: 9.9990 chunk 43 optimal weight: 0.9990 chunk 82 optimal weight: 3.9990 chunk 296 optimal weight: 0.0870 chunk 124 optimal weight: 2.9990 chunk 304 optimal weight: 9.9990 chunk 37 optimal weight: 5.9990 chunk 54 optimal weight: 8.9990 overall best weight: 2.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 413 GLN G 180 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.143991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.118577 restraints weight = 45462.437| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 1.42 r_work: 0.3201 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3091 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.3104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.150 30114 Z= 0.271 Angle : 0.655 59.193 40813 Z= 0.365 Chirality : 0.047 1.236 4572 Planarity : 0.005 0.050 5333 Dihedral : 5.850 89.076 4259 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.78 % Allowed : 15.96 % Favored : 82.26 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.14), residues: 3764 helix: 0.77 (0.14), residues: 1552 sheet: 0.08 (0.23), residues: 566 loop : -0.22 (0.15), residues: 1646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 471 HIS 0.006 0.001 HIS C 185 PHE 0.023 0.001 PHE A 230 TYR 0.020 0.001 TYR D 13 ARG 0.008 0.000 ARG B 488 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6362.56 seconds wall clock time: 115 minutes 44.12 seconds (6944.12 seconds total)