Starting phenix.real_space_refine on Thu Mar 21 07:10:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gxu_34362/03_2024/8gxu_34362_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gxu_34362/03_2024/8gxu_34362.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gxu_34362/03_2024/8gxu_34362.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gxu_34362/03_2024/8gxu_34362.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gxu_34362/03_2024/8gxu_34362_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gxu_34362/03_2024/8gxu_34362_updated.pdb" } resolution = 2.5 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= 0.003 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: 5 Type Number sf(0) Gaussians P 3 5.49 5 S 105 5.16 5 C 18715 2.51 5 N 5121 2.21 5 O 5559 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B TYR 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 29503 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: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'SO4': 1} Classifications: {'undetermined': 1} 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: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'SO4': 1} Classifications: {'undetermined': 1} Time building chain proxies: 15.76, per 1000 atoms: 0.53 Number of scatterers: 29503 At special positions: 0 Unit cell: (147.74, 149.4, 177.62, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 105 16.00 P 3 15.00 O 5559 8.00 N 5121 7.00 C 18715 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: 11.89 Conformation dependent library (CDL) restraints added in 5.5 seconds 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6918 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 139 helices and 34 sheets defined 42.7% alpha, 14.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.63 Creating SS restraints... Processing helix chain 'A' and resid 91 through 97 Processing helix chain 'A' and resid 210 through 214 Processing helix chain 'A' and resid 234 through 244 Processing helix chain 'A' and resid 259 through 271 removed outlier: 3.540A 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 298 through 315 Processing helix chain 'A' and resid 327 through 341 Processing helix chain 'A' and resid 352 through 364 removed outlier: 4.123A pdb=" N ALA A 355 " --> pdb=" O PRO A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 389 No H-bonds generated for 'chain 'A' and resid 387 through 389' Processing helix chain 'A' and resid 394 through 401 removed outlier: 3.528A pdb=" N ARG A 401 " --> pdb=" O GLN A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 415 Processing helix chain 'A' and resid 432 through 442 Proline residue: A 437 - end of helix Processing helix chain 'A' and resid 447 through 471 removed outlier: 4.001A pdb=" N GLU A 466 " --> pdb=" O ALA A 462 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N ILE A 467 " --> pdb=" O GLY A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 475 No H-bonds generated for 'chain 'A' and resid 473 through 475' Processing helix chain 'A' and resid 478 through 493 Processing helix chain 'A' and resid 509 through 532 Processing helix chain 'A' and resid 536 through 540 Processing helix chain 'A' and resid 543 through 553 removed outlier: 4.567A pdb=" N ARG A 552 " --> pdb=" O GLY A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 576 removed outlier: 3.671A pdb=" N GLN A 571 " --> pdb=" O MET A 567 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 98 Processing helix chain 'B' and resid 210 through 214 Processing helix chain 'B' and resid 234 through 244 Processing helix chain 'B' and resid 259 through 271 Proline residue: B 270 - end of helix Processing helix chain 'B' and resid 281 through 284 Processing helix chain 'B' and resid 296 through 315 removed outlier: 4.977A pdb=" N ILE B 303 " --> pdb=" O ARG B 299 " (cutoff:3.500A) removed outlier: 4.948A 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: 3.544A 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 removed outlier: 3.516A pdb=" N GLU B 441 " --> pdb=" O PRO B 437 " (cutoff:3.500A) Processing helix chain 'B' and resid 447 through 468 removed outlier: 3.728A pdb=" N GLN B 465 " --> pdb=" O GLU B 461 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N GLU B 466 " --> pdb=" O ALA B 462 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N ILE B 467 " --> pdb=" O GLY B 463 " (cutoff:3.500A) Processing helix chain 'B' and resid 473 through 475 No H-bonds generated for 'chain 'B' and resid 473 through 475' Processing helix chain 'B' and resid 478 through 494 Processing helix chain 'B' and resid 509 through 531 Processing helix chain 'B' and resid 536 through 541 Processing helix chain 'B' and resid 543 through 553 removed outlier: 3.592A pdb=" N ALA B 551 " --> pdb=" O ARG B 547 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N ARG B 552 " --> pdb=" O ILE B 548 " (cutoff:3.500A) removed outlier: 5.474A pdb=" N TYR B 553 " --> pdb=" O GLY B 549 " (cutoff:3.500A) Processing helix chain 'B' and resid 556 through 574 Proline residue: B 560 - end of helix removed outlier: 3.813A pdb=" N PHE B 574 " --> pdb=" O ILE B 570 " (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 244 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: 3.523A pdb=" N GLU C 300 " --> pdb=" O ALA C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 327 through 341 Processing helix chain 'C' and resid 347 through 349 No H-bonds generated for 'chain 'C' and resid 347 through 349' Processing helix chain 'C' and resid 354 through 364 removed outlier: 3.677A pdb=" N ARG C 364 " --> pdb=" O ALA C 360 " (cutoff:3.500A) Processing helix chain 'C' and resid 387 through 389 No H-bonds generated for 'chain 'C' and resid 387 through 389' Processing helix chain 'C' and resid 394 through 400 Processing helix chain 'C' and resid 411 through 415 Processing helix chain 'C' and resid 436 through 442 removed outlier: 3.606A pdb=" N GLU C 441 " --> pdb=" O PRO C 437 " (cutoff:3.500A) Processing helix chain 'C' and resid 447 through 471 removed outlier: 3.908A pdb=" N GLU C 466 " --> pdb=" O ALA C 462 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ILE C 467 " --> pdb=" O GLY C 463 " (cutoff:3.500A) removed outlier: 3.938A 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 531 Processing helix chain 'C' and resid 536 through 540 Processing helix chain 'C' and resid 544 through 549 Processing helix chain 'C' and resid 556 through 577 Proline residue: C 560 - end of helix removed outlier: 3.685A pdb=" N GLN C 571 " --> pdb=" O MET C 567 " (cutoff:3.500A) 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 177 No H-bonds generated for 'chain 'D' and resid 175 through 177' 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 249 Proline residue: D 235 - end of helix Processing helix chain 'D' and resid 260 through 273 Processing helix chain 'D' and resid 280 through 282 No H-bonds generated for 'chain 'D' and resid 280 through 282' Processing helix chain 'D' and resid 287 through 297 removed outlier: 4.371A 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: 3.809A pdb=" N ALA D 397 " --> pdb=" O ARG D 393 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ILE D 398 " --> pdb=" O LYS D 394 " (cutoff:3.500A) Processing helix chain 'D' and resid 406 through 421 removed outlier: 3.559A pdb=" N ASP D 416 " --> pdb=" O LEU D 412 " (cutoff:3.500A) Processing helix chain 'D' and resid 432 through 445 removed outlier: 3.891A 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 'D' and resid 467 through 471 removed outlier: 3.533A pdb=" N TRP D 471 " --> pdb=" O GLU D 468 " (cutoff:3.500A) 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 213 through 215 No H-bonds generated for 'chain 'E' and resid 213 through 215' Processing helix chain 'E' and resid 229 through 249 removed outlier: 3.775A pdb=" N THR E 234 " --> pdb=" O ARG E 231 " (cutoff:3.500A) Proline residue: E 235 - end of helix removed outlier: 3.572A pdb=" N PHE E 247 " --> pdb=" O TYR E 244 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLU E 248 " --> pdb=" O LEU E 245 " (cutoff:3.500A) removed outlier: 4.163A 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: 3.566A pdb=" N ILE E 294 " --> pdb=" O ASP E 290 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N ARG E 297 " --> pdb=" O THR E 293 " (cutoff:3.500A) Processing helix chain 'E' and resid 317 through 319 No H-bonds generated for 'chain 'E' and resid 317 through 319' Processing helix chain 'E' and resid 324 through 332 Processing helix chain 'E' and resid 341 through 345 Processing helix chain 'E' and resid 363 through 365 No H-bonds generated for 'chain 'E' and resid 363 through 365' Processing helix chain 'E' and resid 375 through 399 removed outlier: 3.776A pdb=" N ILE E 398 " --> pdb=" O LYS E 394 " (cutoff:3.500A) Processing helix chain 'E' and resid 401 through 403 No H-bonds generated for 'chain 'E' and resid 401 through 403' Processing helix chain 'E' and resid 406 through 421 Processing helix chain 'E' and resid 432 through 445 removed outlier: 3.778A pdb=" N MET E 445 " --> pdb=" O ALA E 441 " (cutoff:3.500A) Processing helix chain 'E' and resid 456 through 462 Processing helix chain 'F' and resid 86 through 88 No H-bonds generated for 'chain 'F' and resid 86 through 88' Processing helix chain 'F' and resid 136 through 139 No H-bonds generated for 'chain 'F' and resid 136 through 139' Processing helix chain 'F' and resid 160 through 170 Processing helix chain 'F' and resid 175 through 178 No H-bonds generated for 'chain 'F' and resid 175 through 178' Processing helix chain 'F' and resid 198 through 211 Processing helix chain 'F' and resid 214 through 216 No H-bonds generated for 'chain 'F' and resid 214 through 216' Processing helix chain 'F' and resid 229 through 249 removed outlier: 3.649A pdb=" N THR F 234 " --> pdb=" O ARG F 231 " (cutoff:3.500A) Proline residue: F 235 - end of helix removed outlier: 3.559A pdb=" N PHE F 247 " --> pdb=" O TYR F 244 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLU F 248 " --> pdb=" O LEU F 245 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N HIS F 249 " --> pdb=" O ALA F 246 " (cutoff:3.500A) Processing helix chain 'F' and resid 260 through 273 Processing helix chain 'F' and resid 280 through 282 No H-bonds generated for 'chain 'F' and resid 280 through 282' Processing helix chain 'F' and resid 287 through 297 removed outlier: 4.649A pdb=" N ARG F 297 " --> pdb=" O THR F 293 " (cutoff:3.500A) Processing helix chain 'F' and resid 324 through 332 Processing helix chain 'F' and resid 341 through 346 Processing helix chain 'F' and resid 362 through 365 Processing helix chain 'F' and resid 375 through 399 removed outlier: 3.870A pdb=" N ALA F 397 " --> pdb=" O ARG F 393 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ILE F 398 " --> pdb=" O LYS F 394 " (cutoff:3.500A) Processing helix chain 'F' and resid 401 through 403 No H-bonds generated for 'chain 'F' and resid 401 through 403' Processing helix chain 'F' and resid 406 through 421 Processing helix chain 'F' and resid 432 through 445 removed outlier: 3.790A 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 'F' and resid 467 through 469 No H-bonds generated for 'chain 'F' and resid 467 through 469' Processing helix chain 'G' and resid 8 through 70 Processing helix chain 'G' and resid 73 through 82 Processing helix chain 'G' and resid 110 through 112 No H-bonds generated for 'chain 'G' and resid 110 through 112' Processing helix chain 'G' and resid 123 through 166 removed outlier: 3.531A pdb=" N ARG G 146 " --> pdb=" O ASN G 142 " (cutoff:3.500A) Processing helix chain 'G' and resid 168 through 208 Processing helix chain 'H' and resid 7 through 15 removed outlier: 4.479A pdb=" N GLY H 12 " --> pdb=" O GLU H 8 " (cutoff:3.500A) Processing helix chain 'H' and resid 26 through 38 Processing helix chain 'H' and resid 55 through 58 No H-bonds generated for 'chain 'H' and resid 55 through 58' Processing helix chain 'H' and resid 60 through 63 No H-bonds generated for 'chain 'H' and resid 60 through 63' Processing helix chain 'H' and resid 77 through 82 Processing helix chain 'H' and resid 86 through 98 Processing helix chain 'I' and resid 82 through 105 removed outlier: 3.922A pdb=" N ALA I 105 " --> pdb=" O GLU I 101 " (cutoff:3.500A) Processing helix chain 'I' and resid 107 through 118 Processing helix chain 'J' and resid 63 through 92 Processing helix chain 'J' and resid 94 through 96 No H-bonds generated for 'chain 'J' and resid 94 through 96' Processing helix chain 'J' and resid 98 through 114 Proline residue: J 101 - end of helix Processing helix chain 'J' and resid 125 through 137 Proline residue: J 129 - end of helix removed outlier: 5.345A pdb=" N ALA J 133 " --> pdb=" O PRO J 129 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N LEU J 134 " --> pdb=" O HIS J 130 " (cutoff:3.500A) Processing helix chain 'J' and resid 167 through 186 removed outlier: 4.854A pdb=" N ASP J 176 " --> pdb=" O ASP J 172 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N ALA J 177 " --> pdb=" O ARG J 173 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N SER J 180 " --> pdb=" O ASP J 176 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N LYS J 181 " --> pdb=" O ALA J 177 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 118 removed outlier: 3.835A pdb=" N ALA K 105 " --> pdb=" O GLU K 101 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N ARG K 106 " --> pdb=" O LYS K 102 " (cutoff:3.500A) removed outlier: 5.379A pdb=" N ASP K 108 " --> pdb=" O MET K 104 " (cutoff:3.500A) removed outlier: 5.704A pdb=" N GLU K 109 " --> pdb=" O ALA K 105 " (cutoff:3.500A) Processing helix chain 'L' and resid 62 through 92 Processing helix chain 'L' and resid 94 through 96 No H-bonds generated for 'chain 'L' and resid 94 through 96' Processing helix chain 'L' and resid 98 through 114 Proline residue: L 101 - end of helix Processing helix chain 'L' and resid 125 through 138 Proline residue: L 129 - end of helix removed outlier: 4.658A pdb=" N ALA L 133 " --> pdb=" O PRO L 129 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N LEU L 134 " --> pdb=" O HIS L 130 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ARG L 136 " --> pdb=" O GLU L 132 " (cutoff:3.500A) Processing helix chain 'L' and resid 167 through 187 removed outlier: 4.922A pdb=" N ASP L 176 " --> pdb=" O ASP L 172 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N ALA L 177 " --> pdb=" O ARG L 173 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N SER L 180 " --> pdb=" O ASP L 176 " (cutoff:3.500A) removed outlier: 4.323A 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: 6.468A pdb=" N PHE A 48 " --> pdb=" O ILE A 40 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N LEU A 42 " --> pdb=" O THR A 46 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N THR A 46 " --> pdb=" O LEU A 42 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N LYS A 17 " --> pdb=" O ILE A 6 " (cutoff:3.500A) removed outlier: 5.582A 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: 3.941A pdb=" N GLY A 82 " --> pdb=" O THR A 285 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N VAL A 250 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N ILE A 288 " --> pdb=" O VAL A 250 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N TYR A 252 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N ASN A 290 " --> pdb=" O TYR A 252 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N GLY A 254 " --> pdb=" O ASN A 290 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N ALA A 377 " --> pdb=" O VAL A 320 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N LEU A 322 " --> pdb=" O ALA A 377 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N THR A 379 " --> pdb=" O LEU A 322 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N ALA A 324 " --> pdb=" O THR A 379 " (cutoff:3.500A) removed outlier: 6.797A 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 138 through 140 Processing sheet with id= F, first strand: chain 'A' and resid 197 through 199 removed outlier: 3.585A pdb=" N ARG A 197 " --> pdb=" O ILE A 369 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N LYS A 367 " --> pdb=" O LEU A 199 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 157 through 160 removed outlier: 6.868A pdb=" N VAL A 174 " --> pdb=" O LYS A 158 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 2 through 5 removed outlier: 4.006A pdb=" N ILE B 2 " --> pdb=" O SER B 66 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N PHE B 48 " --> pdb=" O ILE B 40 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N LEU B 42 " --> pdb=" O THR B 46 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N THR B 46 " --> pdb=" O LEU B 42 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N LYS B 17 " --> pdb=" O ILE B 6 " (cutoff:3.500A) removed outlier: 5.605A 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 75 Processing sheet with id= J, first strand: chain 'B' and resid 82 through 84 removed outlier: 4.010A pdb=" N GLY B 82 " --> pdb=" O THR B 285 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N VAL B 250 " --> pdb=" O VAL B 286 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N ILE B 288 " --> pdb=" O VAL B 250 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N TYR B 252 " --> pdb=" O ILE B 288 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N ALA B 377 " --> pdb=" O VAL B 320 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N LEU B 322 " --> pdb=" O ALA B 377 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N THR B 379 " --> pdb=" O LEU B 322 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N ALA B 324 " --> pdb=" O THR B 379 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N VAL B 381 " --> pdb=" O ALA B 324 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N ALA B 405 " --> pdb=" O ALA B 225 " (cutoff:3.500A) removed outlier: 8.019A pdb=" N TRP B 407 " --> pdb=" O PRO B 227 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 164 through 166 removed outlier: 5.653A pdb=" N ALA B 118 " --> pdb=" O PRO B 139 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N ILE B 147 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N THR B 137 " --> pdb=" O HIS B 145 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N HIS B 145 " --> pdb=" O THR B 137 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N PHE B 143 " --> pdb=" O PRO B 139 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 366 through 369 Processing sheet with id= M, first strand: chain 'B' and resid 157 through 160 removed outlier: 6.580A pdb=" N VAL B 174 " --> pdb=" O LYS B 158 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 3 through 5 removed outlier: 6.496A pdb=" N PHE C 48 " --> pdb=" O ILE C 40 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N LEU C 42 " --> pdb=" O THR C 46 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N THR C 46 " --> pdb=" O LEU C 42 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N LYS C 17 " --> pdb=" O ILE C 6 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N ILE C 6 " --> pdb=" O LYS C 17 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 72 through 76 Processing sheet with id= P, first strand: chain 'C' and resid 82 through 84 removed outlier: 3.861A pdb=" N GLY C 82 " --> pdb=" O THR C 285 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N VAL C 250 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N ILE C 288 " --> pdb=" O VAL C 250 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N TYR C 252 " --> pdb=" O ILE C 288 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N ASN C 290 " --> pdb=" O TYR C 252 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N GLY C 254 " --> pdb=" O ASN C 290 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N ALA C 377 " --> pdb=" O VAL C 320 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N LEU C 322 " --> pdb=" O ALA C 377 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N THR C 379 " --> pdb=" O LEU C 322 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N ALA C 324 " --> pdb=" O THR C 379 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N VAL C 381 " --> pdb=" O ALA C 324 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL C 384 " --> pdb=" O ILE C 226 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 164 through 166 removed outlier: 5.616A pdb=" N ALA C 118 " --> pdb=" O PRO C 139 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ILE C 147 " --> pdb=" O LEU C 135 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N THR C 137 " --> pdb=" O HIS C 145 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N HIS C 145 " --> pdb=" O THR C 137 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'C' and resid 366 through 369 Processing sheet with id= S, first strand: chain 'C' and resid 157 through 160 removed outlier: 6.669A pdb=" N VAL C 174 " --> pdb=" O LYS C 158 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'D' and resid 11 through 15 removed outlier: 6.273A pdb=" N PHE D 20 " --> pdb=" O THR D 12 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N ILE D 14 " --> pdb=" O LEU D 18 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N LEU D 18 " --> pdb=" O ILE D 14 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLU D 49 " --> pdb=" O VAL D 56 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N GLN D 58 " --> pdb=" O VAL D 47 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N VAL D 47 " --> pdb=" O GLN D 58 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N PHE D 60 " --> pdb=" O GLY D 45 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N GLY D 45 " --> pdb=" O PHE D 60 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N ASP D 34 " --> pdb=" O LEU D 75 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N LEU D 75 " --> pdb=" O ASP D 34 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N LYS D 36 " --> pdb=" O VAL D 73 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N VAL D 73 " --> pdb=" O LYS D 36 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'D' and resid 81 through 84 removed outlier: 3.728A pdb=" N LYS D 110 " --> pdb=" O VAL D 84 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'D' and resid 91 through 93 removed outlier: 4.032A pdb=" N ARG D 91 " --> pdb=" O SER D 217 " (cutoff:3.500A) removed outlier: 8.631A pdb=" N VAL D 218 " --> pdb=" O PHE D 187 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N VAL D 189 " --> pdb=" O VAL D 218 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N PHE D 220 " --> pdb=" O VAL D 189 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N PHE D 191 " --> pdb=" O PHE D 220 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N ASN D 222 " --> pdb=" O PHE D 191 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N ALA D 193 " --> pdb=" O ASN D 222 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N HIS D 252 " --> pdb=" O ALA D 188 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N VAL D 190 " --> pdb=" O HIS D 252 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N LEU D 254 " --> pdb=" O VAL D 190 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N ALA D 192 " --> pdb=" O LEU D 254 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N ILE D 256 " --> pdb=" O ALA D 192 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N MET D 194 " --> pdb=" O ILE D 256 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N SER D 307 " --> pdb=" O VAL D 253 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N VAL D 255 " --> pdb=" O SER D 307 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N THR D 309 " --> pdb=" O VAL D 255 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N LEU D 257 " --> pdb=" O THR D 309 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N ILE D 311 " --> pdb=" O LEU D 257 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'D' and resid 336 through 338 Processing sheet with id= X, first strand: chain 'E' and resid 11 through 15 removed outlier: 6.482A pdb=" N PHE E 20 " --> pdb=" O THR E 12 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N ILE E 14 " --> pdb=" O LEU E 18 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N LEU E 18 " --> pdb=" O ILE E 14 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N GLN E 58 " --> pdb=" O VAL E 47 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N VAL E 47 " --> pdb=" O GLN E 58 " (cutoff:3.500A) removed outlier: 5.614A pdb=" N ASP E 34 " --> pdb=" O LEU E 75 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N LEU E 75 " --> pdb=" O ASP E 34 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N LYS E 36 " --> pdb=" O VAL E 73 " (cutoff:3.500A) removed outlier: 5.633A pdb=" N VAL E 73 " --> pdb=" O LYS E 36 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'E' and resid 81 through 84 removed outlier: 3.621A pdb=" N LYS E 110 " --> pdb=" O VAL E 84 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'E' and resid 91 through 93 removed outlier: 3.953A pdb=" N ARG E 91 " --> pdb=" O SER E 217 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU E 219 " --> pdb=" O ARG E 91 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N VAL E 189 " --> pdb=" O VAL E 218 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N PHE E 220 " --> pdb=" O VAL E 189 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N PHE E 191 " --> pdb=" O PHE E 220 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N ASN E 222 " --> pdb=" O PHE E 191 " (cutoff:3.500A) removed outlier: 5.628A pdb=" N ALA E 193 " --> pdb=" O ASN E 222 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N MET E 194 " --> pdb=" O THR E 258 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N SER E 307 " --> pdb=" O VAL E 253 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N VAL E 255 " --> pdb=" O SER E 307 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N THR E 309 " --> pdb=" O VAL E 255 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N LEU E 257 " --> pdb=" O THR E 309 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N ILE E 311 " --> pdb=" O LEU E 257 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N ILE E 152 " --> pdb=" O LEU E 314 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'F' and resid 11 through 15 removed outlier: 6.412A pdb=" N PHE F 20 " --> pdb=" O THR F 12 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N ILE F 14 " --> pdb=" O LEU F 18 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N LEU F 18 " --> pdb=" O ILE F 14 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N GLN F 58 " --> pdb=" O VAL F 47 " (cutoff:3.500A) removed outlier: 5.770A pdb=" N VAL F 47 " --> pdb=" O GLN F 58 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N ASP F 34 " --> pdb=" O LEU F 75 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N LEU F 75 " --> pdb=" O ASP F 34 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N LYS F 36 " --> pdb=" O VAL F 73 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N VAL F 73 " --> pdb=" O LYS F 36 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'F' and resid 81 through 84 removed outlier: 3.512A pdb=" N LYS F 110 " --> pdb=" O VAL F 84 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'F' and resid 91 through 94 removed outlier: 3.805A pdb=" N ARG F 91 " --> pdb=" O SER F 217 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL F 189 " --> pdb=" O VAL F 218 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N PHE F 220 " --> pdb=" O VAL F 189 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N PHE F 191 " --> pdb=" O PHE F 220 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N ASN F 222 " --> pdb=" O PHE F 191 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N ALA F 193 " --> pdb=" O ASN F 222 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N SER F 307 " --> pdb=" O VAL F 253 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N VAL F 255 " --> pdb=" O SER F 307 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N THR F 309 " --> pdb=" O VAL F 255 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N LEU F 257 " --> pdb=" O THR F 309 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N ILE F 311 " --> pdb=" O LEU F 257 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'F' and resid 336 through 338 Processing sheet with id= AE, first strand: chain 'G' and resid 90 through 96 removed outlier: 3.778A pdb=" N GLU G 92 " --> pdb=" O ARG G 103 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'H' and resid 19 through 22 removed outlier: 3.674A pdb=" N ALA H 46 " --> pdb=" O ALA H 2 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N VAL H 70 " --> pdb=" O VAL H 45 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N VAL H 47 " --> pdb=" O VAL H 70 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N LEU H 72 " --> pdb=" O VAL H 47 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'J' and resid 141 through 144 removed outlier: 3.601A pdb=" N GLU J 141 " --> pdb=" O LYS J 119 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N VAL J 155 " --> pdb=" O LYS J 119 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N LEU J 121 " --> pdb=" O ARG J 153 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N ARG J 153 " --> pdb=" O LEU J 121 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'L' and resid 120 through 123 1235 hydrogen bonds defined for protein. 3363 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: 9.97 Time building geometry restraints manager: 12.80 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: 9954 1.34 - 1.46: 4260 1.46 - 1.57: 15643 1.57 - 1.69: 5 1.69 - 1.81: 194 Bond restraints: 30056 Sorted by residual: bond pdb=" O4 SO4 A 600 " pdb=" S SO4 A 600 " ideal model delta sigma weight residual 1.499 1.448 0.051 2.00e-02 2.50e+03 6.40e+00 bond pdb=" O1 SO4 A 600 " pdb=" S SO4 A 600 " ideal model delta sigma weight residual 1.498 1.449 0.049 2.00e-02 2.50e+03 6.05e+00 bond pdb=" O2 SO4 A 600 " pdb=" S SO4 A 600 " ideal model delta sigma weight residual 1.498 1.449 0.049 2.00e-02 2.50e+03 5.98e+00 bond pdb=" O3 SO4 A 600 " pdb=" S SO4 A 600 " ideal model delta sigma weight residual 1.499 1.450 0.049 2.00e-02 2.50e+03 5.95e+00 bond pdb=" O3 SO4 C 600 " pdb=" S SO4 C 600 " ideal model delta sigma weight residual 1.499 1.452 0.047 2.00e-02 2.50e+03 5.47e+00 ... (remaining 30051 not shown) Histogram of bond angle deviations from ideal: 98.98 - 107.14: 1038 107.14 - 115.31: 18098 115.31 - 123.47: 20715 123.47 - 131.64: 832 131.64 - 139.81: 39 Bond angle restraints: 40722 Sorted by residual: angle pdb=" N VAL H 59 " pdb=" CA VAL H 59 " pdb=" C VAL H 59 " ideal model delta sigma weight residual 112.29 108.76 3.53 9.40e-01 1.13e+00 1.41e+01 angle pdb=" N ILE F 96 " pdb=" CA ILE F 96 " pdb=" C ILE F 96 " ideal model delta sigma weight residual 111.77 108.58 3.19 1.04e+00 9.25e-01 9.41e+00 angle pdb=" N PRO C 420 " pdb=" CA PRO C 420 " pdb=" C PRO C 420 " ideal model delta sigma weight residual 112.10 119.54 -7.44 2.60e+00 1.48e-01 8.18e+00 angle pdb=" N PRO A 420 " pdb=" CA PRO A 420 " pdb=" C PRO A 420 " ideal model delta sigma weight residual 112.10 118.88 -6.78 2.60e+00 1.48e-01 6.80e+00 angle pdb=" N ASP B 177 " pdb=" CA ASP B 177 " pdb=" C ASP B 177 " ideal model delta sigma weight residual 113.01 110.08 2.93 1.20e+00 6.94e-01 5.96e+00 ... (remaining 40717 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.73: 16505 17.73 - 35.45: 1412 35.45 - 53.18: 308 53.18 - 70.91: 72 70.91 - 88.64: 41 Dihedral angle restraints: 18338 sinusoidal: 7516 harmonic: 10822 Sorted by residual: dihedral pdb=" CA LEU D 257 " pdb=" C LEU D 257 " pdb=" N THR D 258 " pdb=" CA THR D 258 " ideal model delta harmonic sigma weight residual -180.00 -154.36 -25.64 0 5.00e+00 4.00e-02 2.63e+01 dihedral pdb=" CA TYR F 8 " pdb=" C TYR F 8 " pdb=" N THR F 9 " pdb=" CA THR F 9 " ideal model delta harmonic sigma weight residual 180.00 156.72 23.28 0 5.00e+00 4.00e-02 2.17e+01 dihedral pdb=" CA ARG E 372 " pdb=" C ARG E 372 " pdb=" N GLU E 373 " pdb=" CA GLU E 373 " ideal model delta harmonic sigma weight residual -180.00 -156.89 -23.11 0 5.00e+00 4.00e-02 2.14e+01 ... (remaining 18335 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 3732 0.058 - 0.117: 762 0.117 - 0.175: 66 0.175 - 0.234: 1 0.234 - 0.292: 3 Chirality restraints: 4564 Sorted by residual: chirality pdb=" C2' ATP B 601 " pdb=" C1' ATP B 601 " pdb=" C3' ATP B 601 " pdb=" O2' ATP B 601 " both_signs ideal model delta sigma weight residual False -2.68 -2.97 0.29 2.00e-01 2.50e+01 2.14e+00 chirality pdb=" C3' ATP B 601 " pdb=" C2' ATP B 601 " pdb=" C4' ATP B 601 " pdb=" O3' ATP B 601 " both_signs ideal model delta sigma weight residual False -2.63 -2.90 0.27 2.00e-01 2.50e+01 1.77e+00 chirality pdb=" C4' ATP B 601 " pdb=" C3' ATP B 601 " pdb=" C5' ATP B 601 " pdb=" O4' ATP B 601 " both_signs ideal model delta sigma weight residual False -2.49 -2.76 0.27 2.00e-01 2.50e+01 1.76e+00 ... (remaining 4561 not shown) Planarity restraints: 5331 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY B 228 " 0.056 5.00e-02 4.00e+02 8.62e-02 1.19e+01 pdb=" N PRO B 229 " -0.149 5.00e-02 4.00e+02 pdb=" CA PRO B 229 " 0.046 5.00e-02 4.00e+02 pdb=" CD PRO B 229 " 0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 364 " -0.228 9.50e-02 1.11e+02 1.02e-01 6.88e+00 pdb=" NE ARG A 364 " 0.018 2.00e-02 2.50e+03 pdb=" CZ ARG A 364 " -0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG A 364 " 0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG A 364 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET A 294 " -0.038 5.00e-02 4.00e+02 5.78e-02 5.34e+00 pdb=" N PRO A 295 " 0.100 5.00e-02 4.00e+02 pdb=" CA PRO A 295 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 295 " -0.032 5.00e-02 4.00e+02 ... (remaining 5328 not shown) Histogram of nonbonded interaction distances: 1.85 - 2.46: 100 2.46 - 3.07: 20529 3.07 - 3.68: 43876 3.68 - 4.29: 68437 4.29 - 4.90: 114259 Nonbonded interactions: 247201 Sorted by model distance: nonbonded pdb=" OH TYR F 8 " pdb=" OD1 ASP F 26 " model vdw 1.855 2.440 nonbonded pdb=" O MET A 220 " pdb=" OG1 THR A 379 " model vdw 1.923 2.440 nonbonded pdb=" O MET C 220 " pdb=" OG1 THR C 379 " model vdw 1.946 2.440 nonbonded pdb=" OD2 ASP C 410 " pdb=" OG SER C 412 " model vdw 1.947 2.440 nonbonded pdb=" NH2 ARG D 91 " pdb=" O PRO D 104 " model vdw 2.007 2.520 ... (remaining 247196 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: 6.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 14.870 Check model and map are aligned: 0.460 Set scattering table: 0.290 Process input model: 78.810 Find NCS groups from input model: 1.960 Set up NCS constraints: 0.220 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 115.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.090 30056 Z= 0.457 Angle : 0.575 7.435 40722 Z= 0.302 Chirality : 0.046 0.292 4564 Planarity : 0.005 0.102 5331 Dihedral : 14.574 88.636 11420 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 0.00 % Allowed : 7.75 % Favored : 92.25 % 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: 0.82 (0.14), residues: 3764 helix: 1.48 (0.13), residues: 1576 sheet: -0.30 (0.21), residues: 574 loop : 0.05 (0.16), residues: 1614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 119 HIS 0.016 0.002 HIS C 283 PHE 0.018 0.002 PHE D 418 TYR 0.020 0.002 TYR C 428 ARG 0.014 0.001 ARG E 146 *********************** 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 796 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 796 time to evaluate : 3.619 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 33 GLU cc_start: 0.6981 (pt0) cc_final: 0.6676 (pt0) REVERT: A 79 MET cc_start: 0.8721 (mtm) cc_final: 0.8288 (mtp) REVERT: A 158 LYS cc_start: 0.7400 (ttpp) cc_final: 0.6336 (tttm) REVERT: A 172 VAL cc_start: 0.7681 (t) cc_final: 0.7395 (m) REVERT: A 197 ARG cc_start: 0.7702 (ptm-80) cc_final: 0.7270 (ptm160) REVERT: A 264 ASP cc_start: 0.6882 (m-30) cc_final: 0.6571 (m-30) REVERT: A 294 MET cc_start: 0.8199 (mtp) cc_final: 0.7912 (mtp) REVERT: A 340 ARG cc_start: 0.7312 (tpp-160) cc_final: 0.6720 (tpp-160) REVERT: A 410 ASP cc_start: 0.7691 (t0) cc_final: 0.7365 (t0) REVERT: A 412 SER cc_start: 0.8443 (p) cc_final: 0.8216 (p) REVERT: A 488 ARG cc_start: 0.7488 (ttp80) cc_final: 0.7270 (ttp80) REVERT: B 7 GLN cc_start: 0.7909 (tt0) cc_final: 0.7472 (tm130) REVERT: B 19 MET cc_start: 0.8083 (mmm) cc_final: 0.7815 (mmm) REVERT: B 53 GLU cc_start: 0.6890 (mp0) cc_final: 0.6157 (pm20) REVERT: B 109 HIS cc_start: 0.7460 (m170) cc_final: 0.7223 (m170) REVERT: B 122 MET cc_start: 0.7131 (mtt) cc_final: 0.5872 (tpp) REVERT: B 162 PRO cc_start: 0.7470 (Cg_endo) cc_final: 0.7156 (Cg_exo) REVERT: B 243 LYS cc_start: 0.7261 (mtpt) cc_final: 0.6667 (mtpt) REVERT: B 264 ASP cc_start: 0.6955 (m-30) cc_final: 0.6754 (m-30) REVERT: B 325 ASP cc_start: 0.7556 (t0) cc_final: 0.7337 (t0) REVERT: B 339 SER cc_start: 0.8139 (m) cc_final: 0.7711 (t) REVERT: B 374 GLU cc_start: 0.6982 (mt-10) cc_final: 0.6733 (mm-30) REVERT: B 391 MET cc_start: 0.6999 (mmp) cc_final: 0.6714 (mmt) REVERT: B 393 GLU cc_start: 0.6936 (tt0) cc_final: 0.6375 (pt0) REVERT: B 432 THR cc_start: 0.7586 (m) cc_final: 0.7124 (p) REVERT: B 439 TYR cc_start: 0.7924 (m-80) cc_final: 0.7722 (m-80) REVERT: B 460 ARG cc_start: 0.7292 (mmm-85) cc_final: 0.6970 (mtp180) REVERT: B 467 ILE cc_start: 0.8128 (tp) cc_final: 0.7801 (tt) REVERT: B 469 GLN cc_start: 0.6662 (mt0) cc_final: 0.6357 (mm110) REVERT: B 500 TYR cc_start: 0.7079 (m-80) cc_final: 0.6815 (m-80) REVERT: B 501 HIS cc_start: 0.7633 (t-90) cc_final: 0.7415 (t70) REVERT: C 19 MET cc_start: 0.8586 (mmm) cc_final: 0.8219 (mmm) REVERT: C 103 THR cc_start: 0.7843 (m) cc_final: 0.7641 (p) REVERT: C 133 MET cc_start: 0.7992 (mtm) cc_final: 0.7768 (mtp) REVERT: C 200 ASP cc_start: 0.7792 (m-30) cc_final: 0.7580 (m-30) REVERT: C 264 ASP cc_start: 0.7423 (t0) cc_final: 0.7193 (t0) REVERT: C 342 GLU cc_start: 0.7567 (mm-30) cc_final: 0.6955 (mm-30) REVERT: C 391 MET cc_start: 0.8293 (mmt) cc_final: 0.7961 (mmt) REVERT: C 459 GLN cc_start: 0.7024 (mt0) cc_final: 0.6764 (mt0) REVERT: D 22 GLU cc_start: 0.7514 (mt-10) cc_final: 0.7287 (mt-10) REVERT: D 98 LYS cc_start: 0.7299 (mmmm) cc_final: 0.7037 (ttpt) REVERT: D 126 LYS cc_start: 0.8105 (mtpp) cc_final: 0.7783 (mtmt) REVERT: D 274 ARG cc_start: 0.7050 (mtt-85) cc_final: 0.6713 (mtp85) REVERT: D 280 ARG cc_start: 0.7328 (mtp85) cc_final: 0.7064 (mtm180) REVERT: D 305 LYS cc_start: 0.7459 (mttt) cc_final: 0.7246 (mmtt) REVERT: D 331 TYR cc_start: 0.6496 (m-80) cc_final: 0.6215 (t80) REVERT: D 363 ASN cc_start: 0.8304 (m-40) cc_final: 0.8067 (m110) REVERT: D 398 ILE cc_start: 0.7909 (mt) cc_final: 0.7670 (mm) REVERT: D 456 LYS cc_start: 0.5914 (mmtt) cc_final: 0.5626 (mmtt) REVERT: E 81 ARG cc_start: 0.7357 (mtt-85) cc_final: 0.7100 (mtt90) REVERT: E 98 LYS cc_start: 0.7461 (mmmt) cc_final: 0.7227 (mptt) REVERT: E 198 GLN cc_start: 0.8396 (mm-40) cc_final: 0.8093 (tp40) REVERT: E 209 GLU cc_start: 0.7197 (mt-10) cc_final: 0.6972 (mt-10) REVERT: E 216 ARG cc_start: 0.7982 (ptt90) cc_final: 0.7501 (ptp90) REVERT: E 251 TYR cc_start: 0.8404 (m-80) cc_final: 0.8053 (m-80) REVERT: E 274 ARG cc_start: 0.7044 (mtp180) cc_final: 0.6631 (mmm160) REVERT: E 276 GLU cc_start: 0.6969 (mt-10) cc_final: 0.6674 (mt-10) REVERT: E 318 ASP cc_start: 0.7141 (t0) cc_final: 0.6743 (t0) REVERT: E 404 LEU cc_start: 0.7243 (mt) cc_final: 0.6958 (mt) REVERT: E 453 ARG cc_start: 0.7912 (mmt90) cc_final: 0.7384 (mpt180) REVERT: F 36 LYS cc_start: 0.8133 (ttpt) cc_final: 0.7678 (ttpp) REVERT: F 92 ARG cc_start: 0.7915 (mtm-85) cc_final: 0.7468 (mtt-85) REVERT: F 109 GLU cc_start: 0.6649 (mt-10) cc_final: 0.6147 (tp30) REVERT: F 126 LYS cc_start: 0.8228 (tttm) cc_final: 0.7904 (tttp) REVERT: F 129 GLN cc_start: 0.7867 (mm110) cc_final: 0.7582 (mm-40) REVERT: F 200 GLU cc_start: 0.7442 (mt-10) cc_final: 0.7131 (mt-10) REVERT: F 248 GLU cc_start: 0.7278 (mt-10) cc_final: 0.6740 (tt0) REVERT: F 413 GLN cc_start: 0.7466 (mt0) cc_final: 0.7167 (mt0) REVERT: F 421 PHE cc_start: 0.8127 (m-80) cc_final: 0.7917 (m-80) REVERT: G 10 ASN cc_start: 0.8055 (m-40) cc_final: 0.7659 (m-40) REVERT: G 22 GLN cc_start: 0.7986 (mt0) cc_final: 0.7705 (mt0) REVERT: G 23 LYS cc_start: 0.7744 (mttm) cc_final: 0.7438 (mtpm) REVERT: G 30 LYS cc_start: 0.8076 (mttm) cc_final: 0.7840 (mtmm) REVERT: G 38 GLU cc_start: 0.7452 (tt0) cc_final: 0.7235 (tt0) REVERT: G 97 TRP cc_start: 0.5702 (m100) cc_final: 0.5502 (m100) REVERT: G 181 GLN cc_start: 0.7168 (mm-40) cc_final: 0.6599 (tp-100) REVERT: J 81 GLU cc_start: 0.5513 (mm-30) cc_final: 0.5043 (tm-30) REVERT: J 178 LEU cc_start: 0.5529 (mt) cc_final: 0.5283 (mt) REVERT: L 86 ARG cc_start: 0.5337 (mtp180) cc_final: 0.5092 (ttp-170) REVERT: L 88 ARG cc_start: 0.5491 (ttp80) cc_final: 0.4785 (ttp-110) REVERT: L 141 GLU cc_start: 0.5088 (tm-30) cc_final: 0.4532 (mp0) REVERT: L 150 LEU cc_start: 0.6036 (mt) cc_final: 0.5764 (tp) outliers start: 0 outliers final: 1 residues processed: 796 average time/residue: 1.9113 time to fit residues: 1709.6115 Evaluate side-chains 463 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 462 time to evaluate : 3.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 277 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 314 optimal weight: 3.9990 chunk 282 optimal weight: 2.9990 chunk 156 optimal weight: 0.1980 chunk 96 optimal weight: 3.9990 chunk 190 optimal weight: 0.7980 chunk 151 optimal weight: 3.9990 chunk 292 optimal weight: 0.5980 chunk 113 optimal weight: 0.5980 chunk 177 optimal weight: 2.9990 chunk 217 optimal weight: 0.7980 chunk 338 optimal weight: 10.0000 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 469 GLN A 498 ASN B 397 GLN B 418 HIS B 496 GLN C 238 GLN C 397 GLN C 496 GLN C 571 GLN D 129 GLN D 166 GLN D 206 GLN ** D 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 413 GLN E 142 ASN E 364 ASN E 427 GLN E 428 GLN E 437 GLN G 180 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.2057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 30056 Z= 0.178 Angle : 0.530 7.486 40722 Z= 0.276 Chirality : 0.043 0.147 4564 Planarity : 0.005 0.059 5331 Dihedral : 5.189 71.235 4216 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 2.37 % Allowed : 13.30 % Favored : 84.33 % 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: 1.19 (0.14), residues: 3764 helix: 1.73 (0.14), residues: 1582 sheet: -0.01 (0.22), residues: 548 loop : 0.26 (0.16), residues: 1634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP J 100 HIS 0.006 0.001 HIS C 283 PHE 0.013 0.001 PHE E 93 TYR 0.013 0.001 TYR B 439 ARG 0.008 0.001 ARG E 210 *********************** 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 547 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 474 time to evaluate : 3.189 Fit side-chains REVERT: A 54 ASP cc_start: 0.7391 (t70) cc_final: 0.7111 (t0) REVERT: A 79 MET cc_start: 0.8653 (mtm) cc_final: 0.8204 (mtp) REVERT: A 156 ARG cc_start: 0.6278 (OUTLIER) cc_final: 0.5921 (ttp80) REVERT: A 197 ARG cc_start: 0.7698 (ptm-80) cc_final: 0.7229 (ptm160) REVERT: A 340 ARG cc_start: 0.7229 (tpp-160) cc_final: 0.6669 (tpp-160) REVERT: A 343 GLU cc_start: 0.7290 (mt-10) cc_final: 0.6905 (mt-10) REVERT: A 410 ASP cc_start: 0.7683 (t0) cc_final: 0.7258 (t0) REVERT: A 412 SER cc_start: 0.8389 (p) cc_final: 0.8141 (p) REVERT: A 488 ARG cc_start: 0.7456 (ttp80) cc_final: 0.7226 (ttp80) REVERT: A 491 ARG cc_start: 0.8081 (OUTLIER) cc_final: 0.7203 (mpt90) REVERT: A 517 LYS cc_start: 0.8176 (OUTLIER) cc_final: 0.7601 (ttpt) REVERT: A 527 GLU cc_start: 0.7219 (OUTLIER) cc_final: 0.6728 (mt-10) REVERT: A 530 ILE cc_start: 0.7518 (OUTLIER) cc_final: 0.7200 (mt) REVERT: B 7 GLN cc_start: 0.8095 (tt0) cc_final: 0.7647 (tm130) REVERT: B 53 GLU cc_start: 0.6934 (mp0) cc_final: 0.6047 (pm20) REVERT: B 122 MET cc_start: 0.7124 (mtt) cc_final: 0.6882 (mtp) REVERT: B 162 PRO cc_start: 0.7484 (Cg_endo) cc_final: 0.7169 (Cg_exo) REVERT: B 197 ARG cc_start: 0.7376 (ttp-110) cc_final: 0.6998 (ttp80) REVERT: B 243 LYS cc_start: 0.7331 (mtpt) cc_final: 0.6741 (mtpt) REVERT: B 391 MET cc_start: 0.6945 (mmp) cc_final: 0.6624 (mmt) REVERT: B 393 GLU cc_start: 0.6976 (tt0) cc_final: 0.6367 (pt0) REVERT: B 417 ARG cc_start: 0.6661 (mmm160) cc_final: 0.6167 (mmm160) REVERT: B 432 THR cc_start: 0.7586 (m) cc_final: 0.7058 (p) REVERT: B 467 ILE cc_start: 0.8150 (tp) cc_final: 0.7778 (tt) REVERT: B 481 ARG cc_start: 0.6261 (ttt-90) cc_final: 0.6052 (tpt90) REVERT: B 500 TYR cc_start: 0.7187 (m-80) cc_final: 0.6937 (m-80) REVERT: C 19 MET cc_start: 0.8654 (mmm) cc_final: 0.8295 (mmm) REVERT: C 92 GLU cc_start: 0.7472 (OUTLIER) cc_final: 0.6983 (mp0) REVERT: C 103 THR cc_start: 0.7721 (m) cc_final: 0.7507 (p) REVERT: C 133 MET cc_start: 0.8016 (mtm) cc_final: 0.7757 (mtp) REVERT: C 264 ASP cc_start: 0.7308 (t0) cc_final: 0.7072 (t0) REVERT: C 323 MET cc_start: 0.8728 (mmm) cc_final: 0.8443 (mpp) REVERT: C 342 GLU cc_start: 0.7453 (mm-30) cc_final: 0.6889 (mm-30) REVERT: C 391 MET cc_start: 0.8322 (mmt) cc_final: 0.8069 (mmt) REVERT: C 459 GLN cc_start: 0.7027 (mt0) cc_final: 0.6759 (mt0) REVERT: C 547 ARG cc_start: 0.7094 (tpp-160) cc_final: 0.6551 (ttm-80) REVERT: D 6 LYS cc_start: 0.6447 (tttm) cc_final: 0.5865 (ttmt) REVERT: D 22 GLU cc_start: 0.7523 (mt-10) cc_final: 0.7301 (mt-10) REVERT: D 98 LYS cc_start: 0.7233 (mmmm) cc_final: 0.6984 (ttpt) REVERT: D 274 ARG cc_start: 0.7083 (mtt-85) cc_final: 0.6718 (mtp85) REVERT: D 280 ARG cc_start: 0.7388 (mtp85) cc_final: 0.7048 (mtm110) REVERT: D 305 LYS cc_start: 0.7493 (mttt) cc_final: 0.7277 (mmtt) REVERT: D 327 ASP cc_start: 0.7466 (OUTLIER) cc_final: 0.7163 (m-30) REVERT: D 363 ASN cc_start: 0.8373 (m-40) cc_final: 0.8038 (m110) REVERT: D 398 ILE cc_start: 0.7822 (mt) cc_final: 0.7610 (mm) REVERT: D 456 LYS cc_start: 0.5908 (mmtt) cc_final: 0.5621 (mtpt) REVERT: E 78 ASP cc_start: 0.7268 (OUTLIER) cc_final: 0.7061 (m-30) REVERT: E 81 ARG cc_start: 0.7393 (mtt-85) cc_final: 0.7085 (mtt90) REVERT: E 198 GLN cc_start: 0.8330 (mm-40) cc_final: 0.8042 (mm-40) REVERT: E 216 ARG cc_start: 0.8005 (ptt90) cc_final: 0.7344 (ptp90) REVERT: E 251 TYR cc_start: 0.8348 (m-80) cc_final: 0.8089 (m-80) REVERT: E 274 ARG cc_start: 0.6950 (mtp180) cc_final: 0.6495 (mmp-170) REVERT: E 276 GLU cc_start: 0.6979 (mt-10) cc_final: 0.6689 (mt-10) REVERT: E 318 ASP cc_start: 0.7428 (t0) cc_final: 0.6933 (t0) REVERT: E 353 ASP cc_start: 0.7598 (t0) cc_final: 0.7282 (t0) REVERT: E 416 ASP cc_start: 0.7500 (t70) cc_final: 0.7221 (t0) REVERT: E 453 ARG cc_start: 0.7783 (mmt90) cc_final: 0.6967 (mpt180) REVERT: F 36 LYS cc_start: 0.8045 (ttpt) cc_final: 0.7658 (ttpp) REVERT: F 67 ASP cc_start: 0.7676 (p0) cc_final: 0.7305 (p0) REVERT: F 92 ARG cc_start: 0.7819 (mtm-85) cc_final: 0.7572 (mtt-85) REVERT: F 109 GLU cc_start: 0.6656 (mt-10) cc_final: 0.6189 (tp30) REVERT: F 129 GLN cc_start: 0.7942 (mm110) cc_final: 0.7620 (mm-40) REVERT: F 200 GLU cc_start: 0.7545 (mt-10) cc_final: 0.7227 (mt-10) REVERT: F 223 LYS cc_start: 0.7942 (OUTLIER) cc_final: 0.7580 (mtmt) REVERT: F 248 GLU cc_start: 0.7256 (mt-10) cc_final: 0.6761 (tt0) REVERT: F 376 LYS cc_start: 0.7814 (OUTLIER) cc_final: 0.7437 (tptt) REVERT: F 421 PHE cc_start: 0.8044 (m-80) cc_final: 0.7767 (m-80) REVERT: G 10 ASN cc_start: 0.8007 (m-40) cc_final: 0.7619 (m-40) REVERT: G 22 GLN cc_start: 0.7969 (mt0) cc_final: 0.7693 (mt0) REVERT: G 23 LYS cc_start: 0.7744 (mttm) cc_final: 0.7446 (mtpm) REVERT: G 30 LYS cc_start: 0.8069 (mttm) cc_final: 0.7816 (mtmm) REVERT: G 97 TRP cc_start: 0.5919 (m100) cc_final: 0.5703 (m100) REVERT: G 181 GLN cc_start: 0.7214 (mm-40) cc_final: 0.6746 (tp-100) REVERT: J 81 GLU cc_start: 0.5651 (mm-30) cc_final: 0.5113 (tm-30) REVERT: J 178 LEU cc_start: 0.5530 (mt) cc_final: 0.5300 (mt) REVERT: L 86 ARG cc_start: 0.5358 (mtp180) cc_final: 0.5087 (ttp-170) REVERT: L 88 ARG cc_start: 0.5249 (ttp80) cc_final: 0.4779 (ttm110) REVERT: L 141 GLU cc_start: 0.5131 (tm-30) cc_final: 0.4475 (mp0) outliers start: 73 outliers final: 17 residues processed: 525 average time/residue: 1.8424 time to fit residues: 1092.3434 Evaluate side-chains 434 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 407 time to evaluate : 3.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 ARG Chi-restraints excluded: chain A residue 198 LYS Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 220 MET Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 491 ARG Chi-restraints excluded: chain A residue 517 LYS Chi-restraints excluded: chain A residue 527 GLU Chi-restraints excluded: chain A residue 530 ILE Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 327 ASP Chi-restraints excluded: chain E residue 78 ASP Chi-restraints excluded: chain E residue 258 THR Chi-restraints excluded: chain F residue 178 SER Chi-restraints excluded: chain F residue 223 LYS Chi-restraints excluded: chain F residue 259 ASP Chi-restraints excluded: chain F residue 300 VAL Chi-restraints excluded: chain F residue 373 GLU Chi-restraints excluded: chain F residue 376 LYS Chi-restraints excluded: chain F residue 406 GLU Chi-restraints excluded: chain L residue 122 VAL Chi-restraints excluded: chain L residue 152 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 188 optimal weight: 0.0470 chunk 105 optimal weight: 4.9990 chunk 281 optimal weight: 6.9990 chunk 230 optimal weight: 1.9990 chunk 93 optimal weight: 6.9990 chunk 339 optimal weight: 4.9990 chunk 366 optimal weight: 4.9990 chunk 302 optimal weight: 5.9990 chunk 336 optimal weight: 8.9990 chunk 115 optimal weight: 3.9990 chunk 272 optimal weight: 0.0570 overall best weight: 2.2202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 469 GLN B 501 HIS C 283 HIS C 541 GLN C 571 GLN D 206 GLN ** D 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 413 GLN E 58 GLN E 428 GLN E 458 HIS ** F 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.2778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.088 30056 Z= 0.354 Angle : 0.672 9.660 40722 Z= 0.350 Chirality : 0.049 0.270 4564 Planarity : 0.007 0.060 5331 Dihedral : 5.652 73.945 4214 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 3.15 % Allowed : 13.88 % Favored : 82.97 % 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: 0.77 (0.14), residues: 3764 helix: 1.28 (0.13), residues: 1575 sheet: -0.15 (0.21), residues: 567 loop : 0.15 (0.16), residues: 1622 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP B 119 HIS 0.013 0.002 HIS C 283 PHE 0.019 0.003 PHE A 313 TYR 0.019 0.002 TYR E 463 ARG 0.008 0.001 ARG L 105 *********************** 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 506 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 409 time to evaluate : 3.006 Fit side-chains revert: symmetry clash REVERT: A 85 ASP cc_start: 0.7332 (t0) cc_final: 0.7103 (t70) REVERT: A 156 ARG cc_start: 0.6443 (OUTLIER) cc_final: 0.6014 (ttp80) REVERT: A 197 ARG cc_start: 0.7665 (ptm-80) cc_final: 0.7184 (ptm160) REVERT: A 340 ARG cc_start: 0.7357 (tpp-160) cc_final: 0.6825 (tpp-160) REVERT: A 343 GLU cc_start: 0.7378 (mt-10) cc_final: 0.7069 (mt-10) REVERT: A 410 ASP cc_start: 0.7862 (t0) cc_final: 0.7382 (t0) REVERT: A 491 ARG cc_start: 0.7997 (OUTLIER) cc_final: 0.7156 (mpt90) REVERT: A 517 LYS cc_start: 0.8343 (OUTLIER) cc_final: 0.7771 (ttpp) REVERT: A 527 GLU cc_start: 0.7216 (OUTLIER) cc_final: 0.6639 (mt-10) REVERT: A 530 ILE cc_start: 0.7573 (OUTLIER) cc_final: 0.7304 (mt) REVERT: B 243 LYS cc_start: 0.7320 (OUTLIER) cc_final: 0.6563 (mttm) REVERT: B 393 GLU cc_start: 0.6900 (tt0) cc_final: 0.6184 (pt0) REVERT: B 467 ILE cc_start: 0.8122 (tp) cc_final: 0.7733 (tt) REVERT: B 481 ARG cc_start: 0.6292 (ttt-90) cc_final: 0.6005 (tpt90) REVERT: B 489 ILE cc_start: 0.6843 (OUTLIER) cc_final: 0.6432 (mt) REVERT: B 510 LYS cc_start: 0.6595 (mmtp) cc_final: 0.6391 (mttp) REVERT: B 552 ARG cc_start: 0.6609 (mtp180) cc_final: 0.6264 (mtm180) REVERT: C 92 GLU cc_start: 0.7691 (OUTLIER) cc_final: 0.7123 (mp0) REVERT: C 133 MET cc_start: 0.7971 (mtm) cc_final: 0.7634 (mtp) REVERT: C 154 ARG cc_start: 0.7492 (OUTLIER) cc_final: 0.7191 (ttm-80) REVERT: C 161 LYS cc_start: 0.8080 (mtpp) cc_final: 0.7823 (ttmt) REVERT: C 177 ASP cc_start: 0.7843 (p0) cc_final: 0.7463 (p0) REVERT: C 264 ASP cc_start: 0.7449 (t0) cc_final: 0.7197 (t0) REVERT: C 342 GLU cc_start: 0.7724 (mm-30) cc_final: 0.6924 (mm-30) REVERT: C 363 GLU cc_start: 0.8032 (mm-30) cc_final: 0.7743 (tp30) REVERT: C 433 SER cc_start: 0.8118 (p) cc_final: 0.7905 (m) REVERT: C 459 GLN cc_start: 0.7058 (mt0) cc_final: 0.6773 (mt0) REVERT: C 547 ARG cc_start: 0.6909 (tpp-160) cc_final: 0.6420 (ttm-80) REVERT: D 22 GLU cc_start: 0.7488 (mt-10) cc_final: 0.7272 (pt0) REVERT: D 70 THR cc_start: 0.8219 (m) cc_final: 0.7963 (p) REVERT: D 98 LYS cc_start: 0.7367 (mmmm) cc_final: 0.7084 (ttpm) REVERT: D 162 GLU cc_start: 0.7186 (OUTLIER) cc_final: 0.6892 (mt-10) REVERT: D 177 LEU cc_start: 0.7580 (OUTLIER) cc_final: 0.7179 (mp) REVERT: D 274 ARG cc_start: 0.7107 (OUTLIER) cc_final: 0.6825 (mtp85) REVERT: D 280 ARG cc_start: 0.7475 (mtp85) cc_final: 0.7223 (mtm180) REVERT: D 342 GLU cc_start: 0.7865 (tm-30) cc_final: 0.7603 (tm-30) REVERT: E 78 ASP cc_start: 0.7317 (OUTLIER) cc_final: 0.7095 (m-30) REVERT: E 81 ARG cc_start: 0.7582 (mtt-85) cc_final: 0.7301 (mtt90) REVERT: E 103 LEU cc_start: 0.7270 (OUTLIER) cc_final: 0.6831 (tp) REVERT: E 198 GLN cc_start: 0.8367 (OUTLIER) cc_final: 0.8036 (mm-40) REVERT: E 216 ARG cc_start: 0.7967 (ptt90) cc_final: 0.7605 (ptt90) REVERT: E 249 HIS cc_start: 0.8302 (m-70) cc_final: 0.8061 (m170) REVERT: E 274 ARG cc_start: 0.6855 (mtp180) cc_final: 0.6396 (mmp-170) REVERT: E 318 ASP cc_start: 0.7634 (t0) cc_final: 0.7176 (t0) REVERT: E 364 ASN cc_start: 0.7158 (m110) cc_final: 0.6755 (m110) REVERT: E 393 ARG cc_start: 0.8141 (OUTLIER) cc_final: 0.7676 (ttp-170) REVERT: E 409 ARG cc_start: 0.7143 (ttm110) cc_final: 0.6850 (mtt90) REVERT: E 416 ASP cc_start: 0.7459 (t70) cc_final: 0.7194 (t0) REVERT: E 453 ARG cc_start: 0.7726 (mmt90) cc_final: 0.7131 (mmt-90) REVERT: F 36 LYS cc_start: 0.8092 (ttpt) cc_final: 0.7862 (ttpp) REVERT: F 67 ASP cc_start: 0.8060 (p0) cc_final: 0.7633 (p0) REVERT: F 109 GLU cc_start: 0.6754 (mt-10) cc_final: 0.6365 (tp30) REVERT: F 110 LYS cc_start: 0.8085 (OUTLIER) cc_final: 0.7871 (mttt) REVERT: F 129 GLN cc_start: 0.7877 (mm110) cc_final: 0.7508 (mm-40) REVERT: F 210 ARG cc_start: 0.7634 (ttp-110) cc_final: 0.7365 (ttp-110) REVERT: F 342 GLU cc_start: 0.7702 (OUTLIER) cc_final: 0.7352 (mt-10) REVERT: F 421 PHE cc_start: 0.8182 (m-80) cc_final: 0.7924 (m-80) REVERT: F 452 LYS cc_start: 0.7841 (mttp) cc_final: 0.7597 (mttt) REVERT: G 10 ASN cc_start: 0.8091 (m-40) cc_final: 0.7666 (m-40) REVERT: G 22 GLN cc_start: 0.8115 (mt0) cc_final: 0.7853 (mt0) REVERT: G 23 LYS cc_start: 0.7680 (mttm) cc_final: 0.7429 (mtpm) REVERT: G 30 LYS cc_start: 0.8215 (mttm) cc_final: 0.7952 (mtmm) REVERT: G 175 GLN cc_start: 0.8674 (mt0) cc_final: 0.8378 (mt0) REVERT: G 181 GLN cc_start: 0.7276 (mm-40) cc_final: 0.6810 (tp-100) REVERT: G 184 GLU cc_start: 0.7602 (OUTLIER) cc_final: 0.7080 (tp30) REVERT: G 187 GLU cc_start: 0.7769 (OUTLIER) cc_final: 0.7541 (tt0) REVERT: H 86 VAL cc_start: 0.4292 (OUTLIER) cc_final: 0.3953 (t) REVERT: I 119 LEU cc_start: 0.4480 (OUTLIER) cc_final: 0.4223 (tp) REVERT: J 81 GLU cc_start: 0.5532 (mm-30) cc_final: 0.5007 (tm-30) REVERT: J 141 GLU cc_start: 0.4546 (tp30) cc_final: 0.4329 (tp30) REVERT: J 142 LEU cc_start: 0.3464 (OUTLIER) cc_final: 0.3118 (pp) REVERT: L 88 ARG cc_start: 0.5567 (ttp80) cc_final: 0.4631 (mtp85) REVERT: L 141 GLU cc_start: 0.5250 (tm-30) cc_final: 0.4521 (mt-10) outliers start: 97 outliers final: 39 residues processed: 470 average time/residue: 1.8618 time to fit residues: 990.1082 Evaluate side-chains 453 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 391 time to evaluate : 3.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 ARG Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 198 LYS Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain A residue 433 SER Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 491 ARG Chi-restraints excluded: chain A residue 517 LYS Chi-restraints excluded: chain A residue 527 GLU Chi-restraints excluded: chain A residue 530 ILE Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 243 LYS Chi-restraints excluded: chain B residue 433 SER Chi-restraints excluded: chain B residue 459 GLN Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain B residue 489 ILE Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 154 ARG Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 235 SER Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain D residue 162 GLU Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 248 GLU Chi-restraints excluded: chain D residue 274 ARG Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 396 VAL Chi-restraints excluded: chain D residue 450 GLU Chi-restraints excluded: chain E residue 37 ASP Chi-restraints excluded: chain E residue 78 ASP Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain E residue 198 GLN Chi-restraints excluded: chain E residue 258 THR Chi-restraints excluded: chain E residue 393 ARG Chi-restraints excluded: chain F residue 110 LYS Chi-restraints excluded: chain F residue 178 SER Chi-restraints excluded: chain F residue 300 VAL Chi-restraints excluded: chain F residue 342 GLU Chi-restraints excluded: chain F residue 373 GLU Chi-restraints excluded: chain F residue 376 LYS Chi-restraints excluded: chain F residue 396 VAL Chi-restraints excluded: chain F residue 406 GLU Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 184 GLU Chi-restraints excluded: chain G residue 187 GLU Chi-restraints excluded: chain H residue 36 LEU Chi-restraints excluded: chain H residue 81 PHE Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain J residue 142 LEU Chi-restraints excluded: chain K residue 114 VAL Chi-restraints excluded: chain L residue 122 VAL Chi-restraints excluded: chain L residue 152 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 335 optimal weight: 9.9990 chunk 255 optimal weight: 1.9990 chunk 176 optimal weight: 0.5980 chunk 37 optimal weight: 8.9990 chunk 161 optimal weight: 0.0170 chunk 227 optimal weight: 1.9990 chunk 340 optimal weight: 9.9990 chunk 360 optimal weight: 6.9990 chunk 177 optimal weight: 4.9990 chunk 322 optimal weight: 6.9990 chunk 97 optimal weight: 5.9990 overall best weight: 1.9224 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 469 GLN C 571 GLN D 206 GLN ** D 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 413 GLN E 58 GLN E 428 GLN ** F 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.2982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 30056 Z= 0.298 Angle : 0.619 8.796 40722 Z= 0.322 Chirality : 0.046 0.253 4564 Planarity : 0.006 0.064 5331 Dihedral : 5.593 72.557 4214 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 3.80 % Allowed : 14.17 % Favored : 82.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.14), residues: 3764 helix: 1.17 (0.13), residues: 1582 sheet: -0.24 (0.21), residues: 566 loop : 0.09 (0.16), residues: 1616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP J 100 HIS 0.006 0.001 HIS F 375 PHE 0.016 0.002 PHE A 230 TYR 0.019 0.002 TYR C 25 ARG 0.007 0.001 ARG B 340 *********************** 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 518 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 401 time to evaluate : 3.437 Fit side-chains revert: symmetry clash REVERT: A 83 ILE cc_start: 0.8621 (OUTLIER) cc_final: 0.8316 (tp) REVERT: A 85 ASP cc_start: 0.7404 (t0) cc_final: 0.7164 (t70) REVERT: A 197 ARG cc_start: 0.7689 (ptm-80) cc_final: 0.7438 (ptm-80) REVERT: A 274 ASP cc_start: 0.7478 (t0) cc_final: 0.7227 (t0) REVERT: A 332 GLU cc_start: 0.7895 (OUTLIER) cc_final: 0.7680 (mt-10) REVERT: A 340 ARG cc_start: 0.7312 (tpp-160) cc_final: 0.6751 (ttp-170) REVERT: A 410 ASP cc_start: 0.7939 (t0) cc_final: 0.7437 (t0) REVERT: A 491 ARG cc_start: 0.8050 (OUTLIER) cc_final: 0.7171 (mpt90) REVERT: A 517 LYS cc_start: 0.8331 (OUTLIER) cc_final: 0.7767 (ttpp) REVERT: A 527 GLU cc_start: 0.7232 (OUTLIER) cc_final: 0.6693 (mt-10) REVERT: A 530 ILE cc_start: 0.7548 (OUTLIER) cc_final: 0.7277 (mt) REVERT: B 161 LYS cc_start: 0.7635 (OUTLIER) cc_final: 0.7379 (mttm) REVERT: B 393 GLU cc_start: 0.6864 (tt0) cc_final: 0.6106 (pt0) REVERT: B 467 ILE cc_start: 0.8106 (tp) cc_final: 0.7713 (tt) REVERT: B 552 ARG cc_start: 0.6576 (mtp180) cc_final: 0.6230 (mtm180) REVERT: B 567 MET cc_start: 0.5871 (OUTLIER) cc_final: 0.5640 (mmm) REVERT: C 92 GLU cc_start: 0.7648 (OUTLIER) cc_final: 0.7087 (mp0) REVERT: C 133 MET cc_start: 0.7980 (mtm) cc_final: 0.7659 (mtp) REVERT: C 154 ARG cc_start: 0.7516 (OUTLIER) cc_final: 0.7209 (ttm-80) REVERT: C 161 LYS cc_start: 0.8054 (mtpp) cc_final: 0.7718 (mttp) REVERT: C 170 GLU cc_start: 0.7019 (OUTLIER) cc_final: 0.6684 (tp30) REVERT: C 177 ASP cc_start: 0.7869 (p0) cc_final: 0.7506 (p0) REVERT: C 264 ASP cc_start: 0.7400 (t0) cc_final: 0.7199 (t0) REVERT: C 363 GLU cc_start: 0.8032 (mm-30) cc_final: 0.7739 (tp30) REVERT: C 433 SER cc_start: 0.8101 (p) cc_final: 0.7896 (m) REVERT: C 461 GLU cc_start: 0.7479 (OUTLIER) cc_final: 0.7184 (tm-30) REVERT: C 547 ARG cc_start: 0.6847 (tpp-160) cc_final: 0.6345 (ttm-80) REVERT: C 565 GLU cc_start: 0.6320 (tm-30) cc_final: 0.5988 (tm-30) REVERT: D 22 GLU cc_start: 0.7537 (mt-10) cc_final: 0.7315 (pt0) REVERT: D 67 ASP cc_start: 0.6946 (p0) cc_final: 0.6680 (p0) REVERT: D 70 THR cc_start: 0.8211 (m) cc_final: 0.7908 (p) REVERT: D 98 LYS cc_start: 0.7399 (mmmm) cc_final: 0.7083 (tttm) REVERT: D 162 GLU cc_start: 0.7200 (OUTLIER) cc_final: 0.6867 (mt-10) REVERT: D 177 LEU cc_start: 0.7529 (OUTLIER) cc_final: 0.7168 (mp) REVERT: D 274 ARG cc_start: 0.7079 (OUTLIER) cc_final: 0.6786 (mtp85) REVERT: D 342 GLU cc_start: 0.7843 (tm-30) cc_final: 0.7582 (tm-30) REVERT: D 362 MET cc_start: 0.8566 (OUTLIER) cc_final: 0.8341 (ttp) REVERT: E 4 LEU cc_start: 0.5752 (OUTLIER) cc_final: 0.5224 (pp) REVERT: E 81 ARG cc_start: 0.7535 (mtt-85) cc_final: 0.7261 (mtt90) REVERT: E 198 GLN cc_start: 0.8417 (OUTLIER) cc_final: 0.8084 (mm-40) REVERT: E 216 ARG cc_start: 0.7892 (ptt90) cc_final: 0.7530 (ptt90) REVERT: E 249 HIS cc_start: 0.8336 (m-70) cc_final: 0.8118 (m170) REVERT: E 274 ARG cc_start: 0.6859 (mtp180) cc_final: 0.6400 (mmp-170) REVERT: E 318 ASP cc_start: 0.7655 (t0) cc_final: 0.7197 (t0) REVERT: E 393 ARG cc_start: 0.8142 (OUTLIER) cc_final: 0.7647 (ttp-170) REVERT: E 409 ARG cc_start: 0.7132 (ttm110) cc_final: 0.6837 (mtt90) REVERT: E 416 ASP cc_start: 0.7560 (t70) cc_final: 0.7279 (t0) REVERT: E 453 ARG cc_start: 0.7758 (mmt90) cc_final: 0.7437 (mmt-90) REVERT: F 41 ARG cc_start: 0.7595 (OUTLIER) cc_final: 0.5610 (tpt-90) REVERT: F 67 ASP cc_start: 0.8109 (p0) cc_final: 0.7643 (p0) REVERT: F 110 LYS cc_start: 0.8081 (OUTLIER) cc_final: 0.7824 (mttt) REVERT: F 129 GLN cc_start: 0.7858 (mm110) cc_final: 0.7505 (mm-40) REVERT: F 342 GLU cc_start: 0.7677 (OUTLIER) cc_final: 0.7339 (mt-10) REVERT: F 376 LYS cc_start: 0.7966 (OUTLIER) cc_final: 0.7536 (tptt) REVERT: F 452 LYS cc_start: 0.7807 (mttp) cc_final: 0.7564 (mttt) REVERT: F 456 LYS cc_start: 0.8275 (mttp) cc_final: 0.8033 (mtpp) REVERT: G 10 ASN cc_start: 0.8099 (m-40) cc_final: 0.7665 (m-40) REVERT: G 22 GLN cc_start: 0.8095 (mt0) cc_final: 0.7852 (mt0) REVERT: G 23 LYS cc_start: 0.7686 (mttm) cc_final: 0.7424 (mtpm) REVERT: G 30 LYS cc_start: 0.8202 (mttm) cc_final: 0.7941 (mtmm) REVERT: G 149 LYS cc_start: 0.7500 (tppt) cc_final: 0.7299 (tppt) REVERT: G 175 GLN cc_start: 0.8659 (mt0) cc_final: 0.8364 (mt0) REVERT: G 181 GLN cc_start: 0.7319 (mm-40) cc_final: 0.6900 (tp40) REVERT: G 184 GLU cc_start: 0.7669 (OUTLIER) cc_final: 0.7125 (tp30) REVERT: G 187 GLU cc_start: 0.7781 (OUTLIER) cc_final: 0.7556 (tt0) REVERT: H 86 VAL cc_start: 0.4524 (OUTLIER) cc_final: 0.4253 (t) REVERT: J 81 GLU cc_start: 0.5546 (mm-30) cc_final: 0.4964 (tm-30) REVERT: J 130 HIS cc_start: 0.3496 (OUTLIER) cc_final: 0.3256 (m-70) REVERT: J 141 GLU cc_start: 0.4463 (OUTLIER) cc_final: 0.4235 (tp30) REVERT: L 88 ARG cc_start: 0.5737 (ttp80) cc_final: 0.4621 (mtp85) REVERT: L 141 GLU cc_start: 0.5222 (tm-30) cc_final: 0.4571 (mt-10) outliers start: 117 outliers final: 45 residues processed: 479 average time/residue: 1.8820 time to fit residues: 1022.9767 Evaluate side-chains 458 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 385 time to evaluate : 3.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 198 LYS Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 332 GLU Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain A residue 433 SER Chi-restraints excluded: chain A residue 491 ARG Chi-restraints excluded: chain A residue 517 LYS Chi-restraints excluded: chain A residue 527 GLU Chi-restraints excluded: chain A residue 530 ILE Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 159 GLU Chi-restraints excluded: chain B residue 161 LYS Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 433 SER Chi-restraints excluded: chain B residue 459 GLN Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 567 MET Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 154 ARG Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 170 GLU Chi-restraints excluded: chain C residue 235 SER Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 461 GLU Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 162 GLU Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 269 GLU Chi-restraints excluded: chain D residue 274 ARG Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 321 ARG Chi-restraints excluded: chain D residue 362 MET Chi-restraints excluded: chain D residue 396 VAL Chi-restraints excluded: chain D residue 405 THR Chi-restraints excluded: chain D residue 450 GLU Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 37 ASP Chi-restraints excluded: chain E residue 176 ASP Chi-restraints excluded: chain E residue 198 GLN Chi-restraints excluded: chain E residue 258 THR Chi-restraints excluded: chain E residue 300 VAL Chi-restraints excluded: chain E residue 393 ARG Chi-restraints excluded: chain F residue 41 ARG Chi-restraints excluded: chain F residue 49 GLU Chi-restraints excluded: chain F residue 110 LYS Chi-restraints excluded: chain F residue 178 SER Chi-restraints excluded: chain F residue 259 ASP Chi-restraints excluded: chain F residue 300 VAL Chi-restraints excluded: chain F residue 342 GLU Chi-restraints excluded: chain F residue 362 MET Chi-restraints excluded: chain F residue 373 GLU Chi-restraints excluded: chain F residue 376 LYS Chi-restraints excluded: chain F residue 406 GLU Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 184 GLU Chi-restraints excluded: chain G residue 187 GLU Chi-restraints excluded: chain H residue 36 LEU Chi-restraints excluded: chain H residue 81 PHE Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain J residue 130 HIS Chi-restraints excluded: chain J residue 141 GLU Chi-restraints excluded: chain K residue 114 VAL Chi-restraints excluded: chain L residue 122 VAL Chi-restraints excluded: chain L residue 152 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 300 optimal weight: 0.0980 chunk 204 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 268 optimal weight: 3.9990 chunk 148 optimal weight: 0.9980 chunk 307 optimal weight: 2.9990 chunk 249 optimal weight: 0.2980 chunk 0 optimal weight: 1.9990 chunk 184 optimal weight: 4.9990 chunk 323 optimal weight: 5.9990 chunk 90 optimal weight: 3.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 469 GLN C 571 GLN D 206 GLN ** D 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 413 GLN E 58 GLN E 428 GLN F 323 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.3129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 30056 Z= 0.227 Angle : 0.558 8.645 40722 Z= 0.289 Chirality : 0.044 0.161 4564 Planarity : 0.005 0.062 5331 Dihedral : 5.377 73.369 4214 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 3.44 % Allowed : 14.95 % Favored : 81.61 % 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: 0.81 (0.14), residues: 3764 helix: 1.31 (0.13), residues: 1590 sheet: -0.14 (0.22), residues: 538 loop : 0.14 (0.16), residues: 1636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP J 100 HIS 0.005 0.001 HIS A 185 PHE 0.013 0.002 PHE B 574 TYR 0.016 0.002 TYR C 25 ARG 0.005 0.001 ARG B 340 *********************** 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 510 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 404 time to evaluate : 3.482 Fit side-chains revert: symmetry clash REVERT: A 83 ILE cc_start: 0.8621 (OUTLIER) cc_final: 0.8329 (tp) REVERT: A 85 ASP cc_start: 0.7276 (t0) cc_final: 0.7050 (t70) REVERT: A 156 ARG cc_start: 0.6457 (OUTLIER) cc_final: 0.6078 (ttp80) REVERT: A 197 ARG cc_start: 0.7697 (ptm-80) cc_final: 0.7341 (ptm160) REVERT: A 274 ASP cc_start: 0.7550 (t0) cc_final: 0.7301 (t0) REVERT: A 332 GLU cc_start: 0.7887 (OUTLIER) cc_final: 0.7682 (mt-10) REVERT: A 340 ARG cc_start: 0.7283 (tpp-160) cc_final: 0.6719 (ttp-170) REVERT: A 410 ASP cc_start: 0.7926 (t0) cc_final: 0.7431 (t0) REVERT: A 491 ARG cc_start: 0.8044 (OUTLIER) cc_final: 0.7146 (mpt90) REVERT: A 517 LYS cc_start: 0.8307 (OUTLIER) cc_final: 0.7732 (ttpt) REVERT: A 527 GLU cc_start: 0.7220 (OUTLIER) cc_final: 0.6628 (mt-10) REVERT: A 530 ILE cc_start: 0.7536 (OUTLIER) cc_final: 0.7236 (mt) REVERT: B 161 LYS cc_start: 0.7627 (OUTLIER) cc_final: 0.7353 (mttm) REVERT: B 393 GLU cc_start: 0.6918 (tt0) cc_final: 0.6154 (pt0) REVERT: B 417 ARG cc_start: 0.6821 (mmm160) cc_final: 0.6265 (mmm160) REVERT: B 467 ILE cc_start: 0.8024 (tp) cc_final: 0.7636 (tt) REVERT: B 501 HIS cc_start: 0.7618 (t-90) cc_final: 0.7367 (t70) REVERT: B 502 GLU cc_start: 0.6610 (mp0) cc_final: 0.5654 (pm20) REVERT: B 552 ARG cc_start: 0.6498 (mtp180) cc_final: 0.6128 (mtm110) REVERT: C 92 GLU cc_start: 0.7667 (OUTLIER) cc_final: 0.7116 (mp0) REVERT: C 133 MET cc_start: 0.7968 (mtm) cc_final: 0.7634 (mtp) REVERT: C 161 LYS cc_start: 0.8056 (mtpp) cc_final: 0.7719 (mttp) REVERT: C 177 ASP cc_start: 0.7847 (p0) cc_final: 0.7502 (p0) REVERT: C 363 GLU cc_start: 0.8044 (mm-30) cc_final: 0.7737 (tp30) REVERT: C 433 SER cc_start: 0.8059 (p) cc_final: 0.7856 (m) REVERT: C 461 GLU cc_start: 0.7425 (OUTLIER) cc_final: 0.7171 (tm-30) REVERT: C 547 ARG cc_start: 0.6853 (tpp-160) cc_final: 0.6509 (ttm-80) REVERT: C 565 GLU cc_start: 0.6307 (tm-30) cc_final: 0.6022 (tm-30) REVERT: D 22 GLU cc_start: 0.7549 (mt-10) cc_final: 0.7334 (pt0) REVERT: D 67 ASP cc_start: 0.7009 (p0) cc_final: 0.6761 (p0) REVERT: D 70 THR cc_start: 0.8172 (m) cc_final: 0.7893 (p) REVERT: D 98 LYS cc_start: 0.7457 (mmmm) cc_final: 0.7186 (tttm) REVERT: D 162 GLU cc_start: 0.7200 (OUTLIER) cc_final: 0.6868 (mt-10) REVERT: D 248 GLU cc_start: 0.8068 (OUTLIER) cc_final: 0.7623 (mm-30) REVERT: D 274 ARG cc_start: 0.7070 (OUTLIER) cc_final: 0.6772 (mtp85) REVERT: D 362 MET cc_start: 0.8562 (OUTLIER) cc_final: 0.8343 (ttp) REVERT: E 62 GLU cc_start: 0.6560 (OUTLIER) cc_final: 0.6298 (mp0) REVERT: E 81 ARG cc_start: 0.7490 (mtt-85) cc_final: 0.7222 (mtt90) REVERT: E 198 GLN cc_start: 0.8391 (OUTLIER) cc_final: 0.8109 (mm-40) REVERT: E 216 ARG cc_start: 0.7939 (ptt90) cc_final: 0.7481 (ptt90) REVERT: E 249 HIS cc_start: 0.8319 (m-70) cc_final: 0.8109 (m170) REVERT: E 274 ARG cc_start: 0.6804 (mtp180) cc_final: 0.6362 (mmm160) REVERT: E 318 ASP cc_start: 0.7645 (t0) cc_final: 0.7179 (t0) REVERT: E 342 GLU cc_start: 0.7793 (OUTLIER) cc_final: 0.7257 (tm-30) REVERT: E 409 ARG cc_start: 0.7163 (ttm110) cc_final: 0.6803 (mtt90) REVERT: E 416 ASP cc_start: 0.7546 (t70) cc_final: 0.7258 (t0) REVERT: E 453 ARG cc_start: 0.7756 (mmt90) cc_final: 0.7349 (mmt-90) REVERT: F 67 ASP cc_start: 0.8050 (p0) cc_final: 0.7585 (p0) REVERT: F 342 GLU cc_start: 0.7609 (OUTLIER) cc_final: 0.7133 (mt-10) REVERT: F 376 LYS cc_start: 0.7950 (OUTLIER) cc_final: 0.7539 (tptt) REVERT: F 452 LYS cc_start: 0.7785 (mttp) cc_final: 0.7539 (mttt) REVERT: F 456 LYS cc_start: 0.8215 (mttp) cc_final: 0.7918 (mptt) REVERT: G 10 ASN cc_start: 0.8104 (m-40) cc_final: 0.7696 (m-40) REVERT: G 23 LYS cc_start: 0.7672 (mttm) cc_final: 0.7358 (mtpm) REVERT: G 30 LYS cc_start: 0.8179 (mttm) cc_final: 0.7917 (mtmm) REVERT: G 175 GLN cc_start: 0.8661 (mt0) cc_final: 0.8353 (mt0) REVERT: G 181 GLN cc_start: 0.7284 (mm-40) cc_final: 0.6885 (tp-100) REVERT: G 184 GLU cc_start: 0.7606 (OUTLIER) cc_final: 0.7080 (tp30) REVERT: G 187 GLU cc_start: 0.7782 (OUTLIER) cc_final: 0.7555 (tt0) REVERT: H 85 ASP cc_start: 0.3810 (OUTLIER) cc_final: 0.3073 (t70) REVERT: H 86 VAL cc_start: 0.4618 (OUTLIER) cc_final: 0.4366 (t) REVERT: I 119 LEU cc_start: 0.4285 (OUTLIER) cc_final: 0.3816 (mt) REVERT: J 81 GLU cc_start: 0.5506 (mm-30) cc_final: 0.4938 (tm-30) REVERT: J 130 HIS cc_start: 0.3526 (OUTLIER) cc_final: 0.3241 (m-70) REVERT: J 141 GLU cc_start: 0.4451 (OUTLIER) cc_final: 0.4211 (tp30) REVERT: L 88 ARG cc_start: 0.5634 (ttp80) cc_final: 0.4665 (ttp-110) REVERT: L 141 GLU cc_start: 0.5279 (tm-30) cc_final: 0.4545 (mt-10) outliers start: 106 outliers final: 45 residues processed: 474 average time/residue: 1.8471 time to fit residues: 989.7742 Evaluate side-chains 450 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 379 time to evaluate : 3.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 156 ARG Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 198 LYS Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 332 GLU Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain A residue 433 SER Chi-restraints excluded: chain A residue 491 ARG Chi-restraints excluded: chain A residue 517 LYS Chi-restraints excluded: chain A residue 527 GLU Chi-restraints excluded: chain A residue 530 ILE Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 159 GLU Chi-restraints excluded: chain B residue 161 LYS Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 433 SER Chi-restraints excluded: chain B residue 459 GLN Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 461 GLU Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain C residue 548 ILE Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 162 GLU Chi-restraints excluded: chain D residue 248 GLU Chi-restraints excluded: chain D residue 274 ARG Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 316 MET Chi-restraints excluded: chain D residue 362 MET Chi-restraints excluded: chain D residue 396 VAL Chi-restraints excluded: chain D residue 450 GLU Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 37 ASP Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain E residue 176 ASP Chi-restraints excluded: chain E residue 198 GLN Chi-restraints excluded: chain E residue 258 THR Chi-restraints excluded: chain E residue 300 VAL Chi-restraints excluded: chain E residue 342 GLU Chi-restraints excluded: chain F residue 259 ASP Chi-restraints excluded: chain F residue 300 VAL Chi-restraints excluded: chain F residue 342 GLU Chi-restraints excluded: chain F residue 362 MET Chi-restraints excluded: chain F residue 373 GLU Chi-restraints excluded: chain F residue 376 LYS Chi-restraints excluded: chain F residue 406 GLU Chi-restraints excluded: chain F residue 428 GLN Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 184 GLU Chi-restraints excluded: chain G residue 187 GLU Chi-restraints excluded: chain H residue 36 LEU Chi-restraints excluded: chain H residue 81 PHE Chi-restraints excluded: chain H residue 85 ASP Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain J residue 130 HIS Chi-restraints excluded: chain J residue 141 GLU Chi-restraints excluded: chain K residue 114 VAL Chi-restraints excluded: chain L residue 122 VAL Chi-restraints excluded: chain L residue 152 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 121 optimal weight: 8.9990 chunk 324 optimal weight: 4.9990 chunk 71 optimal weight: 6.9990 chunk 211 optimal weight: 2.9990 chunk 89 optimal weight: 7.9990 chunk 360 optimal weight: 7.9990 chunk 299 optimal weight: 2.9990 chunk 167 optimal weight: 6.9990 chunk 30 optimal weight: 2.9990 chunk 119 optimal weight: 0.0970 chunk 189 optimal weight: 4.9990 overall best weight: 2.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 469 GLN C 571 GLN D 206 GLN D 323 HIS D 413 GLN ** E 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 364 ASN E 428 GLN F 252 HIS G 166 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.3349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.093 30056 Z= 0.410 Angle : 0.712 10.045 40722 Z= 0.370 Chirality : 0.050 0.198 4564 Planarity : 0.007 0.071 5331 Dihedral : 5.861 70.230 4214 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 4.12 % Allowed : 14.99 % Favored : 80.90 % 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: 0.35 (0.14), residues: 3764 helix: 0.86 (0.13), residues: 1573 sheet: -0.27 (0.21), residues: 585 loop : -0.03 (0.15), residues: 1606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP J 100 HIS 0.007 0.002 HIS C 283 PHE 0.021 0.003 PHE A 230 TYR 0.024 0.003 TYR C 25 ARG 0.007 0.001 ARG F 43 *********************** 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 514 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 387 time to evaluate : 3.122 Fit side-chains revert: symmetry clash REVERT: A 83 ILE cc_start: 0.8599 (OUTLIER) cc_final: 0.8300 (tp) REVERT: A 85 ASP cc_start: 0.7273 (t0) cc_final: 0.7070 (t70) REVERT: A 104 ARG cc_start: 0.7368 (OUTLIER) cc_final: 0.5945 (ptm160) REVERT: A 156 ARG cc_start: 0.6552 (OUTLIER) cc_final: 0.6035 (ttp80) REVERT: A 197 ARG cc_start: 0.7692 (ptm-80) cc_final: 0.7354 (ptt180) REVERT: A 274 ASP cc_start: 0.7595 (t0) cc_final: 0.7356 (t0) REVERT: A 332 GLU cc_start: 0.7930 (OUTLIER) cc_final: 0.7719 (mt-10) REVERT: A 491 ARG cc_start: 0.8061 (OUTLIER) cc_final: 0.7244 (mpt90) REVERT: A 492 GLU cc_start: 0.7753 (OUTLIER) cc_final: 0.7508 (mt-10) REVERT: A 517 LYS cc_start: 0.8347 (OUTLIER) cc_final: 0.7792 (ttpp) REVERT: A 527 GLU cc_start: 0.7229 (OUTLIER) cc_final: 0.6685 (mt-10) REVERT: A 530 ILE cc_start: 0.7555 (OUTLIER) cc_final: 0.7283 (mt) REVERT: B 161 LYS cc_start: 0.7673 (OUTLIER) cc_final: 0.7374 (mttm) REVERT: B 393 GLU cc_start: 0.6911 (tt0) cc_final: 0.6258 (pt0) REVERT: B 467 ILE cc_start: 0.8037 (tp) cc_final: 0.7640 (tt) REVERT: B 552 ARG cc_start: 0.6649 (mtp180) cc_final: 0.6319 (mtm180) REVERT: C 53 GLU cc_start: 0.8319 (OUTLIER) cc_final: 0.7844 (mt-10) REVERT: C 92 GLU cc_start: 0.7678 (OUTLIER) cc_final: 0.6860 (mp0) REVERT: C 133 MET cc_start: 0.7985 (OUTLIER) cc_final: 0.7652 (mtp) REVERT: C 154 ARG cc_start: 0.7549 (OUTLIER) cc_final: 0.7230 (ttm-80) REVERT: C 161 LYS cc_start: 0.8033 (mtpp) cc_final: 0.7664 (mttp) REVERT: C 177 ASP cc_start: 0.7787 (p0) cc_final: 0.7440 (p0) REVERT: C 209 MET cc_start: 0.7799 (OUTLIER) cc_final: 0.7493 (mtp) REVERT: C 235 SER cc_start: 0.8175 (OUTLIER) cc_final: 0.7925 (t) REVERT: C 363 GLU cc_start: 0.8037 (mm-30) cc_final: 0.7788 (tp30) REVERT: C 433 SER cc_start: 0.8109 (p) cc_final: 0.7890 (m) REVERT: C 547 ARG cc_start: 0.6858 (tpp-160) cc_final: 0.6471 (ttm-80) REVERT: C 565 GLU cc_start: 0.6395 (tm-30) cc_final: 0.6106 (tm-30) REVERT: D 6 LYS cc_start: 0.6370 (tttm) cc_final: 0.5889 (tttt) REVERT: D 22 GLU cc_start: 0.7558 (mt-10) cc_final: 0.7358 (pt0) REVERT: D 98 LYS cc_start: 0.7318 (mmmm) cc_final: 0.7077 (ttpm) REVERT: D 162 GLU cc_start: 0.7214 (OUTLIER) cc_final: 0.6925 (mt-10) REVERT: D 177 LEU cc_start: 0.7491 (OUTLIER) cc_final: 0.7106 (mp) REVERT: D 274 ARG cc_start: 0.7159 (OUTLIER) cc_final: 0.6852 (mtp85) REVERT: E 62 GLU cc_start: 0.6611 (OUTLIER) cc_final: 0.6351 (mp0) REVERT: E 78 ASP cc_start: 0.7131 (OUTLIER) cc_final: 0.6918 (m-30) REVERT: E 81 ARG cc_start: 0.7622 (mtt-85) cc_final: 0.7348 (mtt90) REVERT: E 198 GLN cc_start: 0.8473 (OUTLIER) cc_final: 0.8178 (mm-40) REVERT: E 216 ARG cc_start: 0.7904 (ptt90) cc_final: 0.7510 (ptt90) REVERT: E 237 MET cc_start: 0.8364 (OUTLIER) cc_final: 0.8099 (mtt) REVERT: E 249 HIS cc_start: 0.8335 (m-70) cc_final: 0.8124 (m170) REVERT: E 274 ARG cc_start: 0.6926 (mtp180) cc_final: 0.6447 (mmm160) REVERT: E 318 ASP cc_start: 0.7670 (t0) cc_final: 0.7216 (t0) REVERT: E 393 ARG cc_start: 0.8193 (OUTLIER) cc_final: 0.7677 (ttp-170) REVERT: E 409 ARG cc_start: 0.7278 (ttm110) cc_final: 0.6962 (mtt90) REVERT: E 416 ASP cc_start: 0.7547 (t70) cc_final: 0.7265 (t0) REVERT: E 453 ARG cc_start: 0.7712 (mmt90) cc_final: 0.7289 (mmt-90) REVERT: F 41 ARG cc_start: 0.7672 (OUTLIER) cc_final: 0.5606 (tpt-90) REVERT: F 67 ASP cc_start: 0.7966 (p0) cc_final: 0.7457 (p0) REVERT: F 109 GLU cc_start: 0.7139 (tp30) cc_final: 0.6825 (tp30) REVERT: F 210 ARG cc_start: 0.7681 (ttp-170) cc_final: 0.7465 (ttp-110) REVERT: F 342 GLU cc_start: 0.7696 (OUTLIER) cc_final: 0.7347 (mt-10) REVERT: F 452 LYS cc_start: 0.7775 (mttp) cc_final: 0.7450 (mttt) REVERT: G 10 ASN cc_start: 0.8161 (m-40) cc_final: 0.7616 (m-40) REVERT: G 23 LYS cc_start: 0.7735 (mttm) cc_final: 0.7415 (mtpm) REVERT: G 30 LYS cc_start: 0.8209 (mttm) cc_final: 0.7930 (mtmm) REVERT: G 181 GLN cc_start: 0.7316 (mm-40) cc_final: 0.6916 (tp-100) REVERT: G 184 GLU cc_start: 0.7706 (OUTLIER) cc_final: 0.7465 (tt0) REVERT: G 187 GLU cc_start: 0.7814 (OUTLIER) cc_final: 0.7579 (tt0) REVERT: H 85 ASP cc_start: 0.3743 (OUTLIER) cc_final: 0.3006 (t70) REVERT: H 86 VAL cc_start: 0.4840 (OUTLIER) cc_final: 0.4564 (t) REVERT: J 81 GLU cc_start: 0.5382 (mm-30) cc_final: 0.4903 (tm-30) REVERT: J 160 LYS cc_start: 0.5945 (mmtm) cc_final: 0.5533 (mtmm) REVERT: K 85 LEU cc_start: 0.5107 (OUTLIER) cc_final: 0.4842 (tt) REVERT: L 88 ARG cc_start: 0.5620 (ttp80) cc_final: 0.4636 (mtp85) REVERT: L 178 LEU cc_start: 0.6206 (mt) cc_final: 0.5810 (mm) outliers start: 127 outliers final: 52 residues processed: 478 average time/residue: 1.8721 time to fit residues: 1013.8317 Evaluate side-chains 460 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 377 time to evaluate : 3.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 104 ARG Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 156 ARG Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 198 LYS Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 332 GLU Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain A residue 433 SER Chi-restraints excluded: chain A residue 491 ARG Chi-restraints excluded: chain A residue 492 GLU Chi-restraints excluded: chain A residue 517 LYS Chi-restraints excluded: chain A residue 527 GLU Chi-restraints excluded: chain A residue 530 ILE Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 159 GLU Chi-restraints excluded: chain B residue 161 LYS Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 433 SER Chi-restraints excluded: chain B residue 459 GLN Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain C residue 53 GLU Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 133 MET Chi-restraints excluded: chain C residue 154 ARG Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 209 MET Chi-restraints excluded: chain C residue 235 SER Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 461 GLU Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain C residue 548 ILE Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 162 GLU Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 269 GLU Chi-restraints excluded: chain D residue 274 ARG Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 321 ARG Chi-restraints excluded: chain D residue 396 VAL Chi-restraints excluded: chain D residue 405 THR Chi-restraints excluded: chain D residue 450 GLU Chi-restraints excluded: chain E residue 21 VAL Chi-restraints excluded: chain E residue 37 ASP Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain E residue 78 ASP Chi-restraints excluded: chain E residue 198 GLN Chi-restraints excluded: chain E residue 206 GLN Chi-restraints excluded: chain E residue 237 MET Chi-restraints excluded: chain E residue 258 THR Chi-restraints excluded: chain E residue 300 VAL Chi-restraints excluded: chain E residue 393 ARG Chi-restraints excluded: chain F residue 41 ARG Chi-restraints excluded: chain F residue 49 GLU Chi-restraints excluded: chain F residue 178 SER Chi-restraints excluded: chain F residue 300 VAL Chi-restraints excluded: chain F residue 342 GLU Chi-restraints excluded: chain F residue 373 GLU Chi-restraints excluded: chain F residue 376 LYS Chi-restraints excluded: chain F residue 406 GLU Chi-restraints excluded: chain F residue 428 GLN Chi-restraints excluded: chain G residue 9 MET Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 184 GLU Chi-restraints excluded: chain G residue 187 GLU Chi-restraints excluded: chain H residue 36 LEU Chi-restraints excluded: chain H residue 81 PHE Chi-restraints excluded: chain H residue 85 ASP Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain K residue 85 LEU Chi-restraints excluded: chain K residue 114 VAL Chi-restraints excluded: chain L residue 122 VAL Chi-restraints excluded: chain L residue 152 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 347 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 205 optimal weight: 1.9990 chunk 263 optimal weight: 4.9990 chunk 204 optimal weight: 1.9990 chunk 303 optimal weight: 0.7980 chunk 201 optimal weight: 0.9990 chunk 359 optimal weight: 3.9990 chunk 224 optimal weight: 3.9990 chunk 219 optimal weight: 0.9990 chunk 165 optimal weight: 0.8980 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 GLN A 283 HIS B 469 GLN B 501 HIS C 571 GLN D 206 GLN D 413 GLN E 58 GLN E 364 ASN ** J 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.3366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 30056 Z= 0.216 Angle : 0.558 9.013 40722 Z= 0.290 Chirality : 0.044 0.177 4564 Planarity : 0.005 0.062 5331 Dihedral : 5.451 65.925 4214 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 3.18 % Allowed : 16.06 % Favored : 80.77 % 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: 0.71 (0.14), residues: 3764 helix: 1.24 (0.13), residues: 1571 sheet: -0.17 (0.22), residues: 553 loop : 0.09 (0.16), residues: 1640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP J 100 HIS 0.017 0.001 HIS J 130 PHE 0.012 0.002 PHE B 574 TYR 0.019 0.001 TYR D 29 ARG 0.006 0.000 ARG E 345 *********************** 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 482 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 384 time to evaluate : 3.679 Fit side-chains revert: symmetry clash REVERT: A 83 ILE cc_start: 0.8608 (OUTLIER) cc_final: 0.8323 (tp) REVERT: A 85 ASP cc_start: 0.7274 (t0) cc_final: 0.7063 (t70) REVERT: A 156 ARG cc_start: 0.6462 (OUTLIER) cc_final: 0.6043 (ttp80) REVERT: A 197 ARG cc_start: 0.7692 (ptm-80) cc_final: 0.7322 (ptm160) REVERT: A 274 ASP cc_start: 0.7552 (t0) cc_final: 0.7291 (t0) REVERT: A 340 ARG cc_start: 0.7376 (tpp-160) cc_final: 0.6748 (ttp-170) REVERT: A 491 ARG cc_start: 0.8046 (OUTLIER) cc_final: 0.7222 (mpt90) REVERT: A 492 GLU cc_start: 0.7714 (OUTLIER) cc_final: 0.7461 (mt-10) REVERT: A 517 LYS cc_start: 0.8307 (OUTLIER) cc_final: 0.7734 (ttpt) REVERT: A 527 GLU cc_start: 0.7228 (OUTLIER) cc_final: 0.6638 (mt-10) REVERT: A 530 ILE cc_start: 0.7553 (OUTLIER) cc_final: 0.7290 (mt) REVERT: B 128 GLU cc_start: 0.6743 (OUTLIER) cc_final: 0.6433 (mm-30) REVERT: B 161 LYS cc_start: 0.7646 (OUTLIER) cc_final: 0.7353 (mttm) REVERT: B 393 GLU cc_start: 0.6895 (tt0) cc_final: 0.6221 (pt0) REVERT: B 552 ARG cc_start: 0.6570 (mtp180) cc_final: 0.6195 (mtm110) REVERT: C 92 GLU cc_start: 0.7627 (OUTLIER) cc_final: 0.7068 (mp0) REVERT: C 133 MET cc_start: 0.7975 (mtm) cc_final: 0.7642 (mtp) REVERT: C 154 ARG cc_start: 0.7493 (OUTLIER) cc_final: 0.7179 (ttm-80) REVERT: C 161 LYS cc_start: 0.8079 (mtpp) cc_final: 0.7738 (mttp) REVERT: C 170 GLU cc_start: 0.6964 (OUTLIER) cc_final: 0.6177 (tp30) REVERT: C 177 ASP cc_start: 0.7800 (p0) cc_final: 0.7477 (p0) REVERT: C 363 GLU cc_start: 0.8033 (mm-30) cc_final: 0.7737 (tp30) REVERT: C 433 SER cc_start: 0.8057 (p) cc_final: 0.7852 (m) REVERT: C 461 GLU cc_start: 0.7410 (OUTLIER) cc_final: 0.7113 (tm-30) REVERT: C 547 ARG cc_start: 0.6882 (tpp-160) cc_final: 0.6423 (ttm-80) REVERT: C 565 GLU cc_start: 0.6323 (tm-30) cc_final: 0.5998 (tm-30) REVERT: C 569 GLU cc_start: 0.6726 (tt0) cc_final: 0.5888 (tm-30) REVERT: D 98 LYS cc_start: 0.7367 (mmmm) cc_final: 0.7106 (tttm) REVERT: D 162 GLU cc_start: 0.7201 (OUTLIER) cc_final: 0.6871 (mt-10) REVERT: D 274 ARG cc_start: 0.7098 (mtt-85) cc_final: 0.6802 (mtp85) REVERT: D 362 MET cc_start: 0.8505 (OUTLIER) cc_final: 0.8305 (ttp) REVERT: E 37 ASP cc_start: 0.7577 (OUTLIER) cc_final: 0.7300 (p0) REVERT: E 62 GLU cc_start: 0.6560 (OUTLIER) cc_final: 0.6302 (mp0) REVERT: E 81 ARG cc_start: 0.7578 (mtt-85) cc_final: 0.7294 (mtt90) REVERT: E 198 GLN cc_start: 0.8416 (OUTLIER) cc_final: 0.8106 (mm-40) REVERT: E 216 ARG cc_start: 0.7894 (ptt90) cc_final: 0.7544 (ptt90) REVERT: E 249 HIS cc_start: 0.8322 (m-70) cc_final: 0.8102 (m170) REVERT: E 274 ARG cc_start: 0.6818 (mtp180) cc_final: 0.6392 (mmm160) REVERT: E 318 ASP cc_start: 0.7581 (t0) cc_final: 0.7136 (t0) REVERT: E 393 ARG cc_start: 0.8139 (OUTLIER) cc_final: 0.7651 (ttp-170) REVERT: E 409 ARG cc_start: 0.7179 (ttm110) cc_final: 0.6821 (mtt90) REVERT: E 416 ASP cc_start: 0.7539 (t70) cc_final: 0.7246 (t0) REVERT: E 453 ARG cc_start: 0.7739 (mmt90) cc_final: 0.7347 (mmt-90) REVERT: F 67 ASP cc_start: 0.8023 (p0) cc_final: 0.7562 (p0) REVERT: F 236 ARG cc_start: 0.7785 (OUTLIER) cc_final: 0.7024 (mtt90) REVERT: F 342 GLU cc_start: 0.7636 (OUTLIER) cc_final: 0.7156 (mt-10) REVERT: F 376 LYS cc_start: 0.7950 (OUTLIER) cc_final: 0.7534 (tptt) REVERT: F 452 LYS cc_start: 0.7756 (mttp) cc_final: 0.7490 (mttt) REVERT: G 10 ASN cc_start: 0.8120 (m-40) cc_final: 0.7695 (m-40) REVERT: G 23 LYS cc_start: 0.7693 (mttm) cc_final: 0.7382 (mtpm) REVERT: G 30 LYS cc_start: 0.8187 (mttm) cc_final: 0.7914 (mtmm) REVERT: G 181 GLN cc_start: 0.7261 (mm-40) cc_final: 0.6868 (tp40) REVERT: G 184 GLU cc_start: 0.7635 (OUTLIER) cc_final: 0.7094 (tp30) REVERT: G 187 GLU cc_start: 0.7793 (OUTLIER) cc_final: 0.7563 (tt0) REVERT: J 81 GLU cc_start: 0.5404 (mm-30) cc_final: 0.4883 (tm-30) REVERT: J 160 LYS cc_start: 0.5879 (mmtm) cc_final: 0.5549 (mttp) REVERT: L 67 LEU cc_start: 0.4132 (OUTLIER) cc_final: 0.3864 (tp) REVERT: L 88 ARG cc_start: 0.5642 (ttp80) cc_final: 0.4616 (mtp85) REVERT: L 178 LEU cc_start: 0.6255 (mt) cc_final: 0.5910 (mm) outliers start: 98 outliers final: 45 residues processed: 458 average time/residue: 1.9449 time to fit residues: 1019.7675 Evaluate side-chains 448 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 378 time to evaluate : 3.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 156 ARG Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 198 LYS Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain A residue 433 SER Chi-restraints excluded: chain A residue 491 ARG Chi-restraints excluded: chain A residue 492 GLU Chi-restraints excluded: chain A residue 517 LYS Chi-restraints excluded: chain A residue 527 GLU Chi-restraints excluded: chain A residue 530 ILE Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 159 GLU Chi-restraints excluded: chain B residue 161 LYS Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 385 SER Chi-restraints excluded: chain B residue 433 SER Chi-restraints excluded: chain B residue 459 GLN Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 154 ARG Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 170 GLU Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 461 GLU Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain C residue 548 ILE Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 162 GLU Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 362 MET Chi-restraints excluded: chain D residue 396 VAL Chi-restraints excluded: chain D residue 405 THR Chi-restraints excluded: chain D residue 416 ASP Chi-restraints excluded: chain D residue 450 GLU Chi-restraints excluded: chain E residue 21 VAL Chi-restraints excluded: chain E residue 37 ASP Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain E residue 176 ASP Chi-restraints excluded: chain E residue 198 GLN Chi-restraints excluded: chain E residue 258 THR Chi-restraints excluded: chain E residue 300 VAL Chi-restraints excluded: chain E residue 393 ARG Chi-restraints excluded: chain E residue 396 VAL Chi-restraints excluded: chain F residue 49 GLU Chi-restraints excluded: chain F residue 178 SER Chi-restraints excluded: chain F residue 236 ARG Chi-restraints excluded: chain F residue 259 ASP Chi-restraints excluded: chain F residue 300 VAL Chi-restraints excluded: chain F residue 342 GLU Chi-restraints excluded: chain F residue 373 GLU Chi-restraints excluded: chain F residue 376 LYS Chi-restraints excluded: chain F residue 406 GLU Chi-restraints excluded: chain F residue 428 GLN Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 184 GLU Chi-restraints excluded: chain G residue 187 GLU Chi-restraints excluded: chain H residue 36 LEU Chi-restraints excluded: chain H residue 81 PHE Chi-restraints excluded: chain L residue 67 LEU Chi-restraints excluded: chain L residue 122 VAL Chi-restraints excluded: chain L residue 152 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 222 optimal weight: 0.9990 chunk 143 optimal weight: 4.9990 chunk 214 optimal weight: 5.9990 chunk 108 optimal weight: 7.9990 chunk 70 optimal weight: 0.7980 chunk 69 optimal weight: 4.9990 chunk 228 optimal weight: 0.0570 chunk 244 optimal weight: 1.9990 chunk 177 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 chunk 282 optimal weight: 1.9990 overall best weight: 1.1704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 GLN B 469 GLN C 571 GLN D 206 GLN D 413 GLN E 58 GLN J 130 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.3414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 30056 Z= 0.219 Angle : 0.560 9.212 40722 Z= 0.289 Chirality : 0.044 0.194 4564 Planarity : 0.005 0.063 5331 Dihedral : 5.341 64.166 4214 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.92 % Allowed : 16.38 % Favored : 80.70 % 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: 0.78 (0.14), residues: 3764 helix: 1.30 (0.13), residues: 1577 sheet: -0.15 (0.22), residues: 553 loop : 0.13 (0.16), residues: 1634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP J 100 HIS 0.013 0.001 HIS J 130 PHE 0.013 0.002 PHE A 230 TYR 0.021 0.002 TYR D 29 ARG 0.006 0.001 ARG E 345 *********************** 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 477 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 387 time to evaluate : 2.819 Fit side-chains revert: symmetry clash REVERT: A 83 ILE cc_start: 0.8617 (OUTLIER) cc_final: 0.8328 (tp) REVERT: A 85 ASP cc_start: 0.7260 (t0) cc_final: 0.7054 (t70) REVERT: A 156 ARG cc_start: 0.6463 (OUTLIER) cc_final: 0.6044 (ttp80) REVERT: A 197 ARG cc_start: 0.7684 (ptm-80) cc_final: 0.7320 (ptm160) REVERT: A 274 ASP cc_start: 0.7572 (t0) cc_final: 0.7302 (t0) REVERT: A 340 ARG cc_start: 0.7361 (tpp-160) cc_final: 0.6776 (ttp-170) REVERT: A 491 ARG cc_start: 0.8059 (OUTLIER) cc_final: 0.7163 (mpt90) REVERT: A 492 GLU cc_start: 0.7697 (OUTLIER) cc_final: 0.7458 (mt-10) REVERT: A 517 LYS cc_start: 0.8301 (OUTLIER) cc_final: 0.7729 (ttpt) REVERT: A 527 GLU cc_start: 0.7198 (OUTLIER) cc_final: 0.6594 (mt-10) REVERT: A 530 ILE cc_start: 0.7549 (OUTLIER) cc_final: 0.7245 (mt) REVERT: B 128 GLU cc_start: 0.6669 (OUTLIER) cc_final: 0.6379 (mm-30) REVERT: B 161 LYS cc_start: 0.7628 (OUTLIER) cc_final: 0.7340 (mttm) REVERT: B 393 GLU cc_start: 0.6863 (tt0) cc_final: 0.6167 (pt0) REVERT: B 502 GLU cc_start: 0.6548 (mp0) cc_final: 0.5827 (pm20) REVERT: B 552 ARG cc_start: 0.6545 (mtp180) cc_final: 0.6185 (mtm110) REVERT: C 92 GLU cc_start: 0.7649 (OUTLIER) cc_final: 0.7090 (mp0) REVERT: C 133 MET cc_start: 0.7989 (OUTLIER) cc_final: 0.7646 (mtp) REVERT: C 154 ARG cc_start: 0.7491 (OUTLIER) cc_final: 0.7174 (ttm-80) REVERT: C 161 LYS cc_start: 0.8091 (mtpp) cc_final: 0.7757 (mttp) REVERT: C 177 ASP cc_start: 0.7807 (p0) cc_final: 0.7482 (p0) REVERT: C 363 GLU cc_start: 0.8036 (mm-30) cc_final: 0.7739 (tp30) REVERT: C 433 SER cc_start: 0.8062 (p) cc_final: 0.7855 (m) REVERT: C 461 GLU cc_start: 0.7371 (OUTLIER) cc_final: 0.7060 (tm-30) REVERT: C 547 ARG cc_start: 0.6779 (tpp-160) cc_final: 0.6394 (ttm-80) REVERT: C 565 GLU cc_start: 0.6282 (tm-30) cc_final: 0.6041 (tm-30) REVERT: C 569 GLU cc_start: 0.6726 (tt0) cc_final: 0.5926 (tm-30) REVERT: D 6 LYS cc_start: 0.6341 (tttm) cc_final: 0.5839 (tttt) REVERT: D 62 GLU cc_start: 0.6658 (pm20) cc_final: 0.6229 (mm-30) REVERT: D 98 LYS cc_start: 0.7436 (mmmm) cc_final: 0.7163 (tttm) REVERT: D 162 GLU cc_start: 0.7202 (OUTLIER) cc_final: 0.6892 (mt-10) REVERT: D 248 GLU cc_start: 0.8117 (OUTLIER) cc_final: 0.7718 (mm-30) REVERT: D 274 ARG cc_start: 0.7102 (OUTLIER) cc_final: 0.6791 (mtp85) REVERT: E 37 ASP cc_start: 0.7583 (OUTLIER) cc_final: 0.7316 (p0) REVERT: E 62 GLU cc_start: 0.6543 (OUTLIER) cc_final: 0.6289 (mp0) REVERT: E 81 ARG cc_start: 0.7577 (mtt-85) cc_final: 0.7296 (mtt90) REVERT: E 198 GLN cc_start: 0.8403 (OUTLIER) cc_final: 0.8095 (mm-40) REVERT: E 216 ARG cc_start: 0.7903 (ptt90) cc_final: 0.7478 (ptt90) REVERT: E 249 HIS cc_start: 0.8320 (m-70) cc_final: 0.8091 (m170) REVERT: E 274 ARG cc_start: 0.6820 (mtp180) cc_final: 0.6391 (mmp-170) REVERT: E 318 ASP cc_start: 0.7602 (t0) cc_final: 0.7147 (t0) REVERT: E 393 ARG cc_start: 0.8137 (OUTLIER) cc_final: 0.7670 (ttp-170) REVERT: E 409 ARG cc_start: 0.7156 (ttm110) cc_final: 0.6783 (mtt90) REVERT: E 416 ASP cc_start: 0.7506 (t70) cc_final: 0.7205 (OUTLIER) REVERT: E 453 ARG cc_start: 0.7733 (mmt90) cc_final: 0.7352 (mmt-90) REVERT: F 67 ASP cc_start: 0.7973 (p0) cc_final: 0.7553 (p0) REVERT: F 236 ARG cc_start: 0.7754 (OUTLIER) cc_final: 0.7007 (mtt90) REVERT: F 342 GLU cc_start: 0.7636 (OUTLIER) cc_final: 0.7158 (mt-10) REVERT: F 376 LYS cc_start: 0.7934 (OUTLIER) cc_final: 0.7531 (tptt) REVERT: F 452 LYS cc_start: 0.7748 (mttp) cc_final: 0.7425 (mttt) REVERT: G 10 ASN cc_start: 0.8141 (m-40) cc_final: 0.7608 (m-40) REVERT: G 23 LYS cc_start: 0.7695 (mttm) cc_final: 0.7375 (mtpm) REVERT: G 30 LYS cc_start: 0.8181 (mttm) cc_final: 0.7915 (mtmm) REVERT: G 175 GLN cc_start: 0.8649 (mt0) cc_final: 0.8357 (mt0) REVERT: G 181 GLN cc_start: 0.7259 (mm-40) cc_final: 0.6864 (tp40) REVERT: G 184 GLU cc_start: 0.7613 (OUTLIER) cc_final: 0.7086 (tp30) REVERT: G 187 GLU cc_start: 0.7800 (OUTLIER) cc_final: 0.7567 (tt0) REVERT: H 85 ASP cc_start: 0.3730 (OUTLIER) cc_final: 0.2952 (t70) REVERT: J 81 GLU cc_start: 0.5390 (mm-30) cc_final: 0.4945 (tm-30) REVERT: J 160 LYS cc_start: 0.5799 (mmtm) cc_final: 0.5483 (mttp) REVERT: L 67 LEU cc_start: 0.4119 (OUTLIER) cc_final: 0.3835 (tp) REVERT: L 88 ARG cc_start: 0.5645 (ttp80) cc_final: 0.4682 (ttp-110) REVERT: L 178 LEU cc_start: 0.6145 (mt) cc_final: 0.5829 (mm) outliers start: 90 outliers final: 47 residues processed: 452 average time/residue: 1.9010 time to fit residues: 970.1400 Evaluate side-chains 450 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 377 time to evaluate : 3.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 156 ARG Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 198 LYS Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 261 GLU Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain A residue 433 SER Chi-restraints excluded: chain A residue 491 ARG Chi-restraints excluded: chain A residue 492 GLU Chi-restraints excluded: chain A residue 517 LYS Chi-restraints excluded: chain A residue 527 GLU Chi-restraints excluded: chain A residue 530 ILE Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 159 GLU Chi-restraints excluded: chain B residue 161 LYS Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 385 SER Chi-restraints excluded: chain B residue 454 ILE Chi-restraints excluded: chain B residue 459 GLN Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 133 MET Chi-restraints excluded: chain C residue 154 ARG Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 461 GLU Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 162 GLU Chi-restraints excluded: chain D residue 248 GLU Chi-restraints excluded: chain D residue 274 ARG Chi-restraints excluded: chain D residue 378 VAL Chi-restraints excluded: chain D residue 396 VAL Chi-restraints excluded: chain D residue 405 THR Chi-restraints excluded: chain D residue 450 GLU Chi-restraints excluded: chain E residue 21 VAL Chi-restraints excluded: chain E residue 37 ASP Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain E residue 176 ASP Chi-restraints excluded: chain E residue 198 GLN Chi-restraints excluded: chain E residue 206 GLN Chi-restraints excluded: chain E residue 258 THR Chi-restraints excluded: chain E residue 300 VAL Chi-restraints excluded: chain E residue 393 ARG Chi-restraints excluded: chain E residue 396 VAL Chi-restraints excluded: chain F residue 49 GLU Chi-restraints excluded: chain F residue 178 SER Chi-restraints excluded: chain F residue 236 ARG Chi-restraints excluded: chain F residue 259 ASP Chi-restraints excluded: chain F residue 300 VAL Chi-restraints excluded: chain F residue 342 GLU Chi-restraints excluded: chain F residue 373 GLU Chi-restraints excluded: chain F residue 376 LYS Chi-restraints excluded: chain F residue 406 GLU Chi-restraints excluded: chain F residue 428 GLN Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 184 GLU Chi-restraints excluded: chain G residue 187 GLU Chi-restraints excluded: chain H residue 36 LEU Chi-restraints excluded: chain H residue 81 PHE Chi-restraints excluded: chain H residue 85 ASP Chi-restraints excluded: chain L residue 67 LEU Chi-restraints excluded: chain L residue 122 VAL Chi-restraints excluded: chain L residue 152 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 327 optimal weight: 0.0670 chunk 344 optimal weight: 6.9990 chunk 314 optimal weight: 6.9990 chunk 335 optimal weight: 10.0000 chunk 201 optimal weight: 2.9990 chunk 145 optimal weight: 0.0270 chunk 263 optimal weight: 6.9990 chunk 102 optimal weight: 6.9990 chunk 302 optimal weight: 4.9990 chunk 316 optimal weight: 5.9990 chunk 333 optimal weight: 4.9990 overall best weight: 2.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 238 GLN B 469 GLN B 501 HIS C 571 GLN D 206 GLN D 413 GLN ** J 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.3525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.083 30056 Z= 0.379 Angle : 0.682 9.728 40722 Z= 0.354 Chirality : 0.048 0.183 4564 Planarity : 0.006 0.065 5331 Dihedral : 5.761 65.748 4214 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 3.21 % Allowed : 16.51 % Favored : 80.28 % 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: 0.92 (0.13), residues: 1574 sheet: -0.18 (0.22), residues: 560 loop : -0.04 (0.15), residues: 1630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP J 100 HIS 0.006 0.002 HIS E 458 PHE 0.020 0.003 PHE A 230 TYR 0.025 0.003 TYR D 29 ARG 0.006 0.001 ARG H 95 *********************** 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 482 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 383 time to evaluate : 3.728 Fit side-chains revert: symmetry clash REVERT: A 83 ILE cc_start: 0.8594 (OUTLIER) cc_final: 0.8312 (tp) REVERT: A 156 ARG cc_start: 0.6525 (OUTLIER) cc_final: 0.6250 (ttm-80) REVERT: A 197 ARG cc_start: 0.7688 (ptm-80) cc_final: 0.7367 (ptt180) REVERT: A 274 ASP cc_start: 0.7611 (t0) cc_final: 0.7365 (t0) REVERT: A 340 ARG cc_start: 0.7369 (tpp-160) cc_final: 0.6768 (ttp-170) REVERT: A 491 ARG cc_start: 0.8040 (OUTLIER) cc_final: 0.7152 (mpt90) REVERT: A 492 GLU cc_start: 0.7736 (OUTLIER) cc_final: 0.7513 (mt-10) REVERT: A 517 LYS cc_start: 0.8319 (OUTLIER) cc_final: 0.7756 (ttpp) REVERT: A 527 GLU cc_start: 0.7230 (OUTLIER) cc_final: 0.6672 (mt-10) REVERT: A 530 ILE cc_start: 0.7551 (OUTLIER) cc_final: 0.7277 (mt) REVERT: B 1 MET cc_start: 0.4946 (pp-130) cc_final: 0.4713 (pp-130) REVERT: B 128 GLU cc_start: 0.6774 (OUTLIER) cc_final: 0.6444 (mm-30) REVERT: B 161 LYS cc_start: 0.7641 (OUTLIER) cc_final: 0.7342 (mttm) REVERT: B 502 GLU cc_start: 0.6536 (mp0) cc_final: 0.5696 (pm20) REVERT: B 552 ARG cc_start: 0.6653 (mtp180) cc_final: 0.6276 (mtm110) REVERT: C 53 GLU cc_start: 0.8304 (OUTLIER) cc_final: 0.7858 (mt-10) REVERT: C 92 GLU cc_start: 0.7663 (OUTLIER) cc_final: 0.7095 (mp0) REVERT: C 133 MET cc_start: 0.7979 (OUTLIER) cc_final: 0.7654 (mtp) REVERT: C 154 ARG cc_start: 0.7514 (OUTLIER) cc_final: 0.7200 (ttm-80) REVERT: C 161 LYS cc_start: 0.8047 (mtpp) cc_final: 0.7723 (mttp) REVERT: C 170 GLU cc_start: 0.7062 (OUTLIER) cc_final: 0.6727 (tp30) REVERT: C 363 GLU cc_start: 0.8038 (mm-30) cc_final: 0.7731 (tp30) REVERT: C 433 SER cc_start: 0.8107 (p) cc_final: 0.7892 (m) REVERT: C 547 ARG cc_start: 0.6794 (tpp-160) cc_final: 0.6272 (ttm-80) REVERT: C 565 GLU cc_start: 0.6400 (tm-30) cc_final: 0.6131 (tm-30) REVERT: C 569 GLU cc_start: 0.6827 (tt0) cc_final: 0.5952 (tm-30) REVERT: D 98 LYS cc_start: 0.7373 (mmmm) cc_final: 0.7111 (ttpm) REVERT: D 162 GLU cc_start: 0.7205 (OUTLIER) cc_final: 0.6916 (mt-10) REVERT: D 248 GLU cc_start: 0.8102 (OUTLIER) cc_final: 0.7652 (mm-30) REVERT: D 274 ARG cc_start: 0.7138 (OUTLIER) cc_final: 0.6827 (mtp85) REVERT: E 37 ASP cc_start: 0.7591 (OUTLIER) cc_final: 0.7330 (p0) REVERT: E 62 GLU cc_start: 0.6563 (OUTLIER) cc_final: 0.6304 (mp0) REVERT: E 78 ASP cc_start: 0.7121 (OUTLIER) cc_final: 0.6907 (m-30) REVERT: E 81 ARG cc_start: 0.7606 (mtt-85) cc_final: 0.7347 (mtt90) REVERT: E 198 GLN cc_start: 0.8466 (OUTLIER) cc_final: 0.8163 (mm-40) REVERT: E 216 ARG cc_start: 0.7889 (ptt90) cc_final: 0.7523 (ptt90) REVERT: E 249 HIS cc_start: 0.8340 (m-70) cc_final: 0.8125 (m170) REVERT: E 274 ARG cc_start: 0.6947 (mtp180) cc_final: 0.6473 (mmm160) REVERT: E 318 ASP cc_start: 0.7549 (t0) cc_final: 0.7094 (t0) REVERT: E 393 ARG cc_start: 0.8211 (OUTLIER) cc_final: 0.7698 (ttp-170) REVERT: E 409 ARG cc_start: 0.7297 (ttm110) cc_final: 0.6924 (mtt90) REVERT: E 416 ASP cc_start: 0.7543 (t70) cc_final: 0.7255 (t0) REVERT: E 453 ARG cc_start: 0.7733 (mmt90) cc_final: 0.7354 (mmt-90) REVERT: F 41 ARG cc_start: 0.7704 (OUTLIER) cc_final: 0.5566 (tpt-90) REVERT: F 67 ASP cc_start: 0.7953 (p0) cc_final: 0.7441 (p0) REVERT: F 109 GLU cc_start: 0.7130 (tp30) cc_final: 0.6832 (tp30) REVERT: F 342 GLU cc_start: 0.7695 (OUTLIER) cc_final: 0.7346 (mt-10) REVERT: F 452 LYS cc_start: 0.7806 (mttp) cc_final: 0.7542 (mttt) REVERT: G 10 ASN cc_start: 0.8190 (m-40) cc_final: 0.7648 (m-40) REVERT: G 23 LYS cc_start: 0.7772 (mttm) cc_final: 0.7442 (mtpm) REVERT: G 30 LYS cc_start: 0.8177 (mttm) cc_final: 0.7899 (mtmm) REVERT: G 175 GLN cc_start: 0.8664 (mt0) cc_final: 0.8377 (mt0) REVERT: G 181 GLN cc_start: 0.7289 (mm-40) cc_final: 0.6903 (tp-100) REVERT: G 184 GLU cc_start: 0.7699 (OUTLIER) cc_final: 0.7150 (tp30) REVERT: G 187 GLU cc_start: 0.7821 (OUTLIER) cc_final: 0.7589 (tt0) REVERT: H 85 ASP cc_start: 0.3652 (OUTLIER) cc_final: 0.2905 (t70) REVERT: J 81 GLU cc_start: 0.5426 (mm-30) cc_final: 0.4979 (tm-30) REVERT: J 160 LYS cc_start: 0.5980 (mmtm) cc_final: 0.5584 (mttp) REVERT: K 85 LEU cc_start: 0.5242 (OUTLIER) cc_final: 0.4929 (tt) REVERT: L 88 ARG cc_start: 0.5706 (ttp80) cc_final: 0.4704 (mtp85) REVERT: L 164 GLU cc_start: 0.6260 (tt0) cc_final: 0.6054 (tt0) REVERT: L 168 LEU cc_start: 0.5864 (OUTLIER) cc_final: 0.5483 (mt) REVERT: L 178 LEU cc_start: 0.6178 (mt) cc_final: 0.5796 (mm) outliers start: 99 outliers final: 52 residues processed: 459 average time/residue: 1.8802 time to fit residues: 975.7671 Evaluate side-chains 457 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 376 time to evaluate : 3.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 156 ARG Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 198 LYS Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 261 GLU Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain A residue 433 SER Chi-restraints excluded: chain A residue 491 ARG Chi-restraints excluded: chain A residue 492 GLU Chi-restraints excluded: chain A residue 517 LYS Chi-restraints excluded: chain A residue 527 GLU Chi-restraints excluded: chain A residue 530 ILE Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 159 GLU Chi-restraints excluded: chain B residue 161 LYS Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 385 SER Chi-restraints excluded: chain B residue 433 SER Chi-restraints excluded: chain B residue 454 ILE Chi-restraints excluded: chain B residue 459 GLN Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain C residue 53 GLU Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 133 MET Chi-restraints excluded: chain C residue 154 ARG Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 170 GLU Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 162 GLU Chi-restraints excluded: chain D residue 248 GLU Chi-restraints excluded: chain D residue 274 ARG Chi-restraints excluded: chain D residue 321 ARG Chi-restraints excluded: chain D residue 396 VAL Chi-restraints excluded: chain D residue 405 THR Chi-restraints excluded: chain D residue 450 GLU Chi-restraints excluded: chain E residue 21 VAL Chi-restraints excluded: chain E residue 37 ASP Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain E residue 78 ASP Chi-restraints excluded: chain E residue 176 ASP Chi-restraints excluded: chain E residue 198 GLN Chi-restraints excluded: chain E residue 206 GLN Chi-restraints excluded: chain E residue 258 THR Chi-restraints excluded: chain E residue 300 VAL Chi-restraints excluded: chain E residue 393 ARG Chi-restraints excluded: chain E residue 396 VAL Chi-restraints excluded: chain F residue 41 ARG Chi-restraints excluded: chain F residue 49 GLU Chi-restraints excluded: chain F residue 178 SER Chi-restraints excluded: chain F residue 259 ASP Chi-restraints excluded: chain F residue 300 VAL Chi-restraints excluded: chain F residue 342 GLU Chi-restraints excluded: chain F residue 373 GLU Chi-restraints excluded: chain F residue 376 LYS Chi-restraints excluded: chain F residue 406 GLU Chi-restraints excluded: chain F residue 428 GLN Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain G residue 124 LEU Chi-restraints excluded: chain G residue 184 GLU Chi-restraints excluded: chain G residue 187 GLU Chi-restraints excluded: chain H residue 36 LEU Chi-restraints excluded: chain H residue 81 PHE Chi-restraints excluded: chain H residue 85 ASP Chi-restraints excluded: chain K residue 85 LEU Chi-restraints excluded: chain K residue 114 VAL Chi-restraints excluded: chain L residue 122 VAL Chi-restraints excluded: chain L residue 152 VAL Chi-restraints excluded: chain L residue 168 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 219 optimal weight: 0.9980 chunk 354 optimal weight: 0.0470 chunk 216 optimal weight: 4.9990 chunk 168 optimal weight: 0.0670 chunk 246 optimal weight: 0.6980 chunk 371 optimal weight: 4.9990 chunk 342 optimal weight: 0.5980 chunk 295 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 chunk 228 optimal weight: 0.0570 chunk 181 optimal weight: 2.9990 overall best weight: 0.2934 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 238 GLN B 469 GLN C 571 GLN D 166 GLN D 206 GLN D 388 ASN D 413 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.3532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 30056 Z= 0.153 Angle : 0.503 9.151 40722 Z= 0.260 Chirality : 0.042 0.145 4564 Planarity : 0.005 0.060 5331 Dihedral : 5.080 59.378 4214 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.62 % Allowed : 18.10 % Favored : 80.28 % 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: 0.94 (0.14), residues: 3764 helix: 1.45 (0.14), residues: 1578 sheet: -0.08 (0.22), residues: 559 loop : 0.20 (0.16), residues: 1627 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP J 100 HIS 0.003 0.001 HIS C 418 PHE 0.010 0.001 PHE F 191 TYR 0.024 0.001 TYR D 29 ARG 0.010 0.000 ARG E 210 ********************** 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 446 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 396 time to evaluate : 3.772 Fit side-chains revert: symmetry clash REVERT: A 156 ARG cc_start: 0.6448 (OUTLIER) cc_final: 0.5944 (ttp80) REVERT: A 197 ARG cc_start: 0.7701 (ptm-80) cc_final: 0.7338 (ptm160) REVERT: A 274 ASP cc_start: 0.7610 (t0) cc_final: 0.7350 (t0) REVERT: A 340 ARG cc_start: 0.7328 (tpp-160) cc_final: 0.6748 (ttp-170) REVERT: A 343 GLU cc_start: 0.7485 (mt-10) cc_final: 0.7244 (mt-10) REVERT: A 491 ARG cc_start: 0.8078 (OUTLIER) cc_final: 0.7161 (mpt90) REVERT: A 492 GLU cc_start: 0.7670 (OUTLIER) cc_final: 0.7417 (mt-10) REVERT: A 517 LYS cc_start: 0.8182 (OUTLIER) cc_final: 0.7626 (ttpt) REVERT: A 527 GLU cc_start: 0.7156 (OUTLIER) cc_final: 0.6549 (mt-10) REVERT: A 530 ILE cc_start: 0.7571 (OUTLIER) cc_final: 0.7256 (mt) REVERT: B 1 MET cc_start: 0.4923 (pp-130) cc_final: 0.4719 (pp-130) REVERT: B 417 ARG cc_start: 0.6704 (mmm160) cc_final: 0.6226 (mmm160) REVERT: B 425 ASN cc_start: 0.8185 (m110) cc_final: 0.7861 (m-40) REVERT: B 432 THR cc_start: 0.7736 (m) cc_final: 0.7116 (p) REVERT: B 502 GLU cc_start: 0.6463 (mp0) cc_final: 0.5685 (pm20) REVERT: B 552 ARG cc_start: 0.6484 (mtp180) cc_final: 0.6132 (mtm110) REVERT: C 54 ASP cc_start: 0.7735 (t0) cc_final: 0.7358 (t0) REVERT: C 92 GLU cc_start: 0.7550 (OUTLIER) cc_final: 0.6990 (mp0) REVERT: C 133 MET cc_start: 0.8004 (mtm) cc_final: 0.7656 (mtp) REVERT: C 154 ARG cc_start: 0.7454 (OUTLIER) cc_final: 0.6810 (ttm-80) REVERT: C 161 LYS cc_start: 0.8061 (mtpp) cc_final: 0.7723 (mttp) REVERT: C 177 ASP cc_start: 0.7853 (p0) cc_final: 0.7563 (p0) REVERT: C 363 GLU cc_start: 0.8038 (mm-30) cc_final: 0.7704 (tp30) REVERT: C 461 GLU cc_start: 0.7298 (tm-30) cc_final: 0.7019 (tm-30) REVERT: C 547 ARG cc_start: 0.6818 (tpp-160) cc_final: 0.6407 (ttm-80) REVERT: C 565 GLU cc_start: 0.6218 (tm-30) cc_final: 0.5953 (tm-30) REVERT: C 569 GLU cc_start: 0.6671 (tt0) cc_final: 0.5888 (tm-30) REVERT: D 6 LYS cc_start: 0.6256 (tttm) cc_final: 0.5744 (tttt) REVERT: D 62 GLU cc_start: 0.6635 (pm20) cc_final: 0.6207 (mm-30) REVERT: D 98 LYS cc_start: 0.7435 (mmmm) cc_final: 0.7203 (tttm) REVERT: D 274 ARG cc_start: 0.7011 (OUTLIER) cc_final: 0.6720 (mtp85) REVERT: E 37 ASP cc_start: 0.7582 (OUTLIER) cc_final: 0.7375 (p0) REVERT: E 81 ARG cc_start: 0.7471 (mtt-85) cc_final: 0.7150 (mtt90) REVERT: E 198 GLN cc_start: 0.8363 (OUTLIER) cc_final: 0.7984 (mm-40) REVERT: E 216 ARG cc_start: 0.7926 (ptt90) cc_final: 0.7516 (ptt90) REVERT: E 249 HIS cc_start: 0.8304 (m-70) cc_final: 0.8094 (m170) REVERT: E 274 ARG cc_start: 0.6890 (mtp180) cc_final: 0.6411 (mmp-170) REVERT: E 318 ASP cc_start: 0.7570 (t0) cc_final: 0.7100 (t0) REVERT: E 393 ARG cc_start: 0.8101 (OUTLIER) cc_final: 0.7618 (ttp-170) REVERT: E 409 ARG cc_start: 0.7153 (ttm110) cc_final: 0.6842 (mtt90) REVERT: E 416 ASP cc_start: 0.7483 (t70) cc_final: 0.7181 (OUTLIER) REVERT: E 453 ARG cc_start: 0.7745 (mmt90) cc_final: 0.7343 (mmt-90) REVERT: F 67 ASP cc_start: 0.7884 (p0) cc_final: 0.7504 (p0) REVERT: F 376 LYS cc_start: 0.7853 (OUTLIER) cc_final: 0.7458 (tptt) REVERT: G 10 ASN cc_start: 0.8108 (m-40) cc_final: 0.7673 (m-40) REVERT: G 23 LYS cc_start: 0.7621 (mttm) cc_final: 0.7361 (mtpm) REVERT: G 30 LYS cc_start: 0.8071 (mttm) cc_final: 0.7818 (mtmm) REVERT: G 181 GLN cc_start: 0.7230 (mm-40) cc_final: 0.6835 (tp-100) REVERT: G 184 GLU cc_start: 0.7567 (OUTLIER) cc_final: 0.6950 (tp30) REVERT: G 187 GLU cc_start: 0.7783 (OUTLIER) cc_final: 0.7564 (tt0) REVERT: H 85 ASP cc_start: 0.3602 (OUTLIER) cc_final: 0.2870 (t70) REVERT: J 81 GLU cc_start: 0.5462 (mm-30) cc_final: 0.4941 (tm-30) REVERT: J 160 LYS cc_start: 0.5857 (mmtm) cc_final: 0.5610 (mttp) REVERT: L 67 LEU cc_start: 0.4311 (mt) cc_final: 0.4074 (tp) REVERT: L 88 ARG cc_start: 0.5642 (ttp80) cc_final: 0.4681 (mtp85) outliers start: 50 outliers final: 24 residues processed: 432 average time/residue: 1.8815 time to fit residues: 917.4165 Evaluate side-chains 423 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 384 time to evaluate : 3.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 156 ARG Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain A residue 491 ARG Chi-restraints excluded: chain A residue 492 GLU Chi-restraints excluded: chain A residue 517 LYS Chi-restraints excluded: chain A residue 527 GLU Chi-restraints excluded: chain A residue 530 ILE Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 385 SER Chi-restraints excluded: chain B residue 459 GLN Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 154 ARG Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain D residue 274 ARG Chi-restraints excluded: chain E residue 37 ASP Chi-restraints excluded: chain E residue 176 ASP Chi-restraints excluded: chain E residue 198 GLN Chi-restraints excluded: chain E residue 300 VAL Chi-restraints excluded: chain E residue 393 ARG Chi-restraints excluded: chain F residue 178 SER Chi-restraints excluded: chain F residue 259 ASP Chi-restraints excluded: chain F residue 300 VAL Chi-restraints excluded: chain F residue 376 LYS Chi-restraints excluded: chain F residue 428 GLN Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 184 GLU Chi-restraints excluded: chain G residue 187 GLU Chi-restraints excluded: chain H residue 36 LEU Chi-restraints excluded: chain H residue 81 PHE Chi-restraints excluded: chain H residue 85 ASP Chi-restraints excluded: chain L residue 122 VAL 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: 0.9990 chunk 90 optimal weight: 2.9990 chunk 272 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 chunk 82 optimal weight: 10.0000 chunk 296 optimal weight: 0.4980 chunk 124 optimal weight: 3.9990 chunk 304 optimal weight: 2.9990 chunk 37 optimal weight: 6.9990 chunk 54 optimal weight: 0.7980 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 GLN B 469 GLN D 166 GLN D 206 GLN D 413 GLN E 58 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.156110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.123966 restraints weight = 34244.985| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 1.47 r_work: 0.3234 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.3135 rms_B_bonded: 2.69 restraints_weight: 0.2500 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.3535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 30056 Z= 0.230 Angle : 0.558 9.446 40722 Z= 0.289 Chirality : 0.044 0.149 4564 Planarity : 0.005 0.061 5331 Dihedral : 5.242 60.693 4214 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 1.72 % Allowed : 18.03 % Favored : 80.25 % 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: 0.92 (0.14), residues: 3764 helix: 1.39 (0.14), residues: 1576 sheet: 0.01 (0.22), residues: 547 loop : 0.18 (0.16), residues: 1641 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP J 100 HIS 0.003 0.001 HIS E 458 PHE 0.013 0.002 PHE A 230 TYR 0.023 0.002 TYR D 29 ARG 0.009 0.001 ARG E 210 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15044.05 seconds wall clock time: 264 minutes 24.23 seconds (15864.23 seconds total)