Starting phenix.real_space_refine on Sat Aug 10 11:50:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gxz_34366/08_2024/8gxz_34366.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gxz_34366/08_2024/8gxz_34366.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gxz_34366/08_2024/8gxz_34366.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gxz_34366/08_2024/8gxz_34366.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gxz_34366/08_2024/8gxz_34366.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gxz_34366/08_2024/8gxz_34366.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 3 5.49 5 Mg 1 5.21 5 S 104 5.16 5 C 18715 2.51 5 N 5121 2.21 5 O 5555 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 331": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 408": "OD1" <-> "OD2" Residue "F TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 29499 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 4475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 578, 4475 Classifications: {'peptide': 578} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 542} Chain: "B" Number of atoms: 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: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 15.90, per 1000 atoms: 0.54 Number of scatterers: 29499 At special positions: 0 Unit cell: (147.42, 148.23, 171.72, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 104 16.00 P 3 15.00 Mg 1 11.99 O 5555 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: 12.79 Conformation dependent library (CDL) restraints added in 5.3 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... Secondary structure from input PDB file: 143 helices and 29 sheets defined 47.9% alpha, 10.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.24 Creating SS restraints... Processing helix chain 'A' and resid 90 through 98 Processing helix chain 'A' and resid 209 through 215 Processing helix chain 'A' and resid 233 through 245 Processing helix chain 'A' and resid 258 through 269 removed outlier: 4.427A pdb=" N MET A 262 " --> pdb=" O ARG A 258 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N THR A 263 " --> pdb=" O GLY A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 283 Processing helix chain 'A' and resid 297 through 317 removed outlier: 4.403A pdb=" N ALA A 301 " --> pdb=" O ALA A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 342 removed outlier: 3.921A pdb=" N TRP A 330 " --> pdb=" O SER A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 363 Processing helix chain 'A' and resid 386 through 390 removed outlier: 3.508A pdb=" N GLY A 389 " --> pdb=" O PRO A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 401 removed outlier: 3.716A pdb=" N ARG A 401 " --> pdb=" O GLN A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 410 through 416 Processing helix chain 'A' and resid 435 through 443 Processing helix chain 'A' and resid 446 through 472 removed outlier: 3.696A pdb=" N GLU A 466 " --> pdb=" O ALA A 462 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ILE A 467 " --> pdb=" O GLY A 463 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N LEU A 470 " --> pdb=" O GLU A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 494 Processing helix chain 'A' and resid 508 through 532 Processing helix chain 'A' and resid 535 through 540 Processing helix chain 'A' and resid 544 through 551 Processing helix chain 'A' and resid 558 through 577 removed outlier: 3.912A pdb=" N LEU A 577 " --> pdb=" O ALA A 573 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 99 Processing helix chain 'B' and resid 209 through 215 Processing helix chain 'B' and resid 233 through 245 Processing helix chain 'B' and resid 258 through 269 Processing helix chain 'B' and resid 280 through 283 Processing helix chain 'B' and resid 295 through 317 removed outlier: 4.760A pdb=" N ILE B 303 " --> pdb=" O ARG B 299 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N TYR B 304 " --> pdb=" O GLU B 300 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLY B 317 " --> pdb=" O PHE B 313 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 341 Processing helix chain 'B' and resid 353 through 363 Processing helix chain 'B' and resid 393 through 401 Processing helix chain 'B' and resid 410 through 416 removed outlier: 3.501A pdb=" N ALA B 414 " --> pdb=" O ASP B 410 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 443 Proline residue: B 437 - end of helix Processing helix chain 'B' and resid 446 through 464 Processing helix chain 'B' and resid 464 through 471 Processing helix chain 'B' and resid 472 through 476 Processing helix chain 'B' and resid 477 through 494 removed outlier: 3.503A pdb=" N VAL B 483 " --> pdb=" O ALA B 479 " (cutoff:3.500A) Processing helix chain 'B' and resid 508 through 533 Processing helix chain 'B' and resid 535 through 540 Processing helix chain 'B' and resid 543 through 550 Processing helix chain 'B' and resid 558 through 576 removed outlier: 4.261A pdb=" N GLN B 571 " --> pdb=" O MET B 567 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLY B 572 " --> pdb=" O LYS B 568 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N PHE B 574 " --> pdb=" O ILE B 570 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ALA B 576 " --> pdb=" O GLY B 572 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 98 Processing helix chain 'C' and resid 209 through 215 Processing helix chain 'C' and resid 233 through 245 Processing helix chain 'C' and resid 258 through 269 removed outlier: 4.039A pdb=" N MET C 262 " --> pdb=" O ARG C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 283 Processing helix chain 'C' and resid 297 through 316 removed outlier: 4.254A pdb=" N ALA C 301 " --> pdb=" O ALA C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 326 through 342 removed outlier: 3.986A pdb=" N TRP C 330 " --> pdb=" O SER C 326 " (cutoff:3.500A) Processing helix chain 'C' and resid 353 through 364 removed outlier: 3.776A pdb=" N ARG C 364 " --> pdb=" O ALA C 360 " (cutoff:3.500A) Processing helix chain 'C' and resid 386 through 390 Processing helix chain 'C' and resid 393 through 401 Processing helix chain 'C' and resid 410 through 416 removed outlier: 3.565A pdb=" N ARG C 416 " --> pdb=" O SER C 412 " (cutoff:3.500A) Processing helix chain 'C' and resid 431 through 443 removed outlier: 3.566A pdb=" N ASP C 436 " --> pdb=" O THR C 432 " (cutoff:3.500A) Proline residue: C 437 - end of helix removed outlier: 3.584A pdb=" N GLU C 441 " --> pdb=" O PRO C 437 " (cutoff:3.500A) Processing helix chain 'C' and resid 446 through 472 removed outlier: 3.992A pdb=" N GLU C 466 " --> pdb=" O ALA C 462 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ILE C 467 " --> pdb=" O GLY C 463 " (cutoff:3.500A) Processing helix chain 'C' and resid 477 through 494 Processing helix chain 'C' and resid 508 through 532 Processing helix chain 'C' and resid 535 through 541 removed outlier: 3.515A pdb=" N ILE C 539 " --> pdb=" O SER C 535 " (cutoff:3.500A) Processing helix chain 'C' and resid 543 through 549 removed outlier: 3.872A pdb=" N ARG C 547 " --> pdb=" O PRO C 543 " (cutoff:3.500A) Processing helix chain 'C' and resid 550 through 554 Processing helix chain 'C' and resid 558 through 578 removed outlier: 4.096A pdb=" N GLU C 564 " --> pdb=" O PRO C 560 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N PHE C 574 " --> pdb=" O ILE C 570 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N LYS C 575 " --> pdb=" O GLN C 571 " (cutoff:3.500A) Processing helix chain 'D' and resid 85 through 89 Processing helix chain 'D' and resid 120 through 124 Processing helix chain 'D' and resid 135 through 140 Processing helix chain 'D' and resid 159 through 171 Processing helix chain 'D' and resid 175 through 178 Processing helix chain 'D' and resid 197 through 211 removed outlier: 4.161A pdb=" N THR D 211 " --> pdb=" O GLU D 207 " (cutoff:3.500A) Processing helix chain 'D' and resid 212 through 215 Processing helix chain 'D' and resid 227 through 250 Proline residue: D 235 - end of helix Processing helix chain 'D' and resid 259 through 274 removed outlier: 3.520A pdb=" N TYR D 263 " --> pdb=" O ASP D 259 " (cutoff:3.500A) Processing helix chain 'D' and resid 279 through 283 removed outlier: 3.742A pdb=" N GLY D 282 " --> pdb=" O GLY D 279 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 296 Processing helix chain 'D' and resid 323 through 333 Processing helix chain 'D' and resid 340 through 346 Processing helix chain 'D' and resid 361 through 365 Processing helix chain 'D' and resid 374 through 400 removed outlier: 3.819A pdb=" N ALA D 397 " --> pdb=" O ARG D 393 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N ILE D 398 " --> pdb=" O LYS D 394 " (cutoff:3.500A) Processing helix chain 'D' and resid 401 through 404 Processing helix chain 'D' and resid 405 through 422 removed outlier: 3.593A pdb=" N ASP D 416 " --> pdb=" O LEU D 412 " (cutoff:3.500A) Processing helix chain 'D' and resid 431 through 446 removed outlier: 3.645A pdb=" N MET D 445 " --> pdb=" O ALA D 441 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N LEU D 446 " --> pdb=" O LEU D 442 " (cutoff:3.500A) Processing helix chain 'D' and resid 455 through 463 Processing helix chain 'D' and resid 467 through 472 Processing helix chain 'E' and resid 23 through 27 removed outlier: 4.590A pdb=" N ASP E 26 " --> pdb=" O ASN E 23 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 89 removed outlier: 3.623A pdb=" N LEU E 89 " --> pdb=" O LYS E 86 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 124 Processing helix chain 'E' and resid 135 through 142 Processing helix chain 'E' and resid 159 through 171 removed outlier: 3.516A pdb=" N ILE E 163 " --> pdb=" O PRO E 159 " (cutoff:3.500A) Processing helix chain 'E' and resid 175 through 179 removed outlier: 3.604A pdb=" N GLY E 179 " --> pdb=" O ASP E 176 " (cutoff:3.500A) Processing helix chain 'E' and resid 197 through 210 Processing helix chain 'E' and resid 212 through 215 Processing helix chain 'E' and resid 227 through 250 removed outlier: 3.815A pdb=" N ARG E 231 " --> pdb=" O PRO E 227 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ILE E 232 " --> pdb=" O THR E 228 " (cutoff:3.500A) Proline residue: E 235 - end of helix Processing helix chain 'E' and resid 259 through 274 removed outlier: 3.650A pdb=" N TYR E 263 " --> pdb=" O ASP E 259 " (cutoff:3.500A) Processing helix chain 'E' and resid 286 through 296 Processing helix chain 'E' and resid 317 through 320 Processing helix chain 'E' and resid 323 through 333 removed outlier: 3.557A pdb=" N ILE E 332 " --> pdb=" O LEU E 328 " (cutoff:3.500A) Processing helix chain 'E' and resid 340 through 346 Processing helix chain 'E' and resid 361 through 366 removed outlier: 3.557A pdb=" N GLY E 365 " --> pdb=" O LEU E 361 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL E 366 " --> pdb=" O MET E 362 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 361 through 366' Processing helix chain 'E' and resid 374 through 400 removed outlier: 3.569A pdb=" N ALA E 397 " --> pdb=" O ARG E 393 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N ILE E 398 " --> pdb=" O LYS E 394 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ILE E 399 " --> pdb=" O LEU E 395 " (cutoff:3.500A) Processing helix chain 'E' and resid 401 through 404 removed outlier: 3.791A pdb=" N LEU E 404 " --> pdb=" O GLU E 401 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 401 through 404' Processing helix chain 'E' and resid 405 through 422 Processing helix chain 'E' and resid 431 through 444 Processing helix chain 'E' and resid 455 through 463 Processing helix chain 'F' and resid 85 through 89 removed outlier: 3.511A pdb=" N MET F 88 " --> pdb=" O SER F 85 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N LEU F 89 " --> pdb=" O LYS F 86 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 85 through 89' Processing helix chain 'F' and resid 135 through 140 Processing helix chain 'F' and resid 159 through 171 Processing helix chain 'F' and resid 174 through 179 removed outlier: 3.551A pdb=" N SER F 178 " --> pdb=" O ARG F 174 " (cutoff:3.500A) Processing helix chain 'F' and resid 197 through 211 Processing helix chain 'F' and resid 212 through 215 removed outlier: 3.831A pdb=" N SER F 215 " --> pdb=" O GLY F 212 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 212 through 215' Processing helix chain 'F' and resid 228 through 232 Processing helix chain 'F' and resid 233 through 250 Processing helix chain 'F' and resid 259 through 274 removed outlier: 3.669A pdb=" N TYR F 263 " --> pdb=" O ASP F 259 " (cutoff:3.500A) Processing helix chain 'F' and resid 286 through 296 removed outlier: 3.541A pdb=" N ILE F 294 " --> pdb=" O ASP F 290 " (cutoff:3.500A) Processing helix chain 'F' and resid 323 through 333 Processing helix chain 'F' and resid 340 through 346 Processing helix chain 'F' and resid 361 through 365 Processing helix chain 'F' and resid 374 through 400 removed outlier: 3.596A pdb=" N ALA F 397 " --> pdb=" O ARG F 393 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ILE F 398 " --> pdb=" O LYS F 394 " (cutoff:3.500A) Processing helix chain 'F' and resid 401 through 404 Processing helix chain 'F' and resid 405 through 422 Processing helix chain 'F' and resid 431 through 444 Processing helix chain 'F' and resid 445 through 446 No H-bonds generated for 'chain 'F' and resid 445 through 446' Processing helix chain 'F' and resid 447 through 451 removed outlier: 3.577A pdb=" N LEU F 451 " --> pdb=" O GLN F 448 " (cutoff:3.500A) Processing helix chain 'F' and resid 455 through 463 Processing helix chain 'F' and resid 466 through 471 removed outlier: 3.970A pdb=" N ILE F 470 " --> pdb=" O LYS F 466 " (cutoff:3.500A) Processing helix chain 'G' and resid 7 through 71 removed outlier: 3.726A pdb=" N GLY G 41 " --> pdb=" O ALA G 37 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ARG G 44 " --> pdb=" O PHE G 40 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA G 69 " --> pdb=" O LEU G 65 " (cutoff:3.500A) Processing helix chain 'G' and resid 72 through 83 Processing helix chain 'G' and resid 109 through 113 removed outlier: 3.595A pdb=" N LEU G 113 " --> pdb=" O ASP G 110 " (cutoff:3.500A) Processing helix chain 'G' and resid 120 through 167 removed outlier: 3.822A pdb=" N GLU G 125 " --> pdb=" O ALA G 121 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ALA G 126 " --> pdb=" O TYR G 122 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ARG G 128 " --> pdb=" O LEU G 124 " (cutoff:3.500A) Processing helix chain 'G' and resid 167 through 209 Processing helix chain 'H' and resid 6 through 16 Processing helix chain 'H' and resid 25 through 39 Processing helix chain 'H' and resid 54 through 59 Processing helix chain 'H' and resid 59 through 66 Processing helix chain 'H' and resid 78 through 83 Processing helix chain 'H' and resid 85 through 98 Processing helix chain 'I' and resid 82 through 106 removed outlier: 3.568A pdb=" N ALA I 105 " --> pdb=" O GLU I 101 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ARG I 106 " --> pdb=" O LYS I 102 " (cutoff:3.500A) Processing helix chain 'I' and resid 106 through 119 Processing helix chain 'J' and resid 62 through 94 Processing helix chain 'J' and resid 95 through 97 No H-bonds generated for 'chain 'J' and resid 95 through 97' Processing helix chain 'J' and resid 99 through 115 removed outlier: 3.807A pdb=" N VAL J 103 " --> pdb=" O GLU J 99 " (cutoff:3.500A) Processing helix chain 'J' and resid 127 through 139 removed outlier: 4.282A pdb=" N ALA J 133 " --> pdb=" O PRO J 129 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N LEU J 134 " --> pdb=" O HIS J 130 " (cutoff:3.500A) Processing helix chain 'J' and resid 166 through 187 removed outlier: 3.741A pdb=" N LEU J 171 " --> pdb=" O LEU J 167 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N ASP J 172 " --> pdb=" O LEU J 168 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ARG J 173 " --> pdb=" O ALA J 169 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N ASP J 176 " --> pdb=" O ASP J 172 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N ALA J 177 " --> pdb=" O ARG J 173 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N SER J 180 " --> pdb=" O ASP J 176 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N LYS J 181 " --> pdb=" O ALA J 177 " (cutoff:3.500A) Processing helix chain 'K' and resid 81 through 83 No H-bonds generated for 'chain 'K' and resid 81 through 83' Processing helix chain 'K' and resid 84 through 119 removed outlier: 3.791A pdb=" N TYR K 88 " --> pdb=" O LEU K 84 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ARG K 100 " --> pdb=" O ALA K 96 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N ALA K 105 " --> pdb=" O GLU K 101 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N ARG K 106 " --> pdb=" O LYS K 102 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N ASP K 108 " --> pdb=" O MET K 104 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N GLU K 109 " --> pdb=" O ALA K 105 " (cutoff:3.500A) Processing helix chain 'L' and resid 62 through 93 removed outlier: 3.871A pdb=" N LEU L 66 " --> pdb=" O SER L 62 " (cutoff:3.500A) Processing helix chain 'L' and resid 94 through 97 Processing helix chain 'L' and resid 99 through 115 Processing helix chain 'L' and resid 128 through 130 No H-bonds generated for 'chain 'L' and resid 128 through 130' Processing helix chain 'L' and resid 131 through 139 Processing helix chain 'L' and resid 166 through 187 removed outlier: 3.799A pdb=" N ASP L 172 " --> pdb=" O LEU L 168 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ARG L 173 " --> pdb=" O ALA L 169 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N ASP L 176 " --> pdb=" O ASP L 172 " (cutoff:3.500A) removed outlier: 5.272A pdb=" N ALA L 177 " --> pdb=" O ARG L 173 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N SER L 180 " --> pdb=" O ASP L 176 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N LYS L 181 " --> pdb=" O ALA L 177 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 10 removed outlier: 6.574A pdb=" N ILE A 15 " --> pdb=" O GLN A 7 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N ILE A 9 " --> pdb=" O ALA A 13 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N ALA A 13 " --> pdb=" O ILE A 9 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 13 through 17 current: chain 'A' and resid 35 through 43 removed outlier: 5.659A pdb=" N ILE A 39 " --> pdb=" O GLN A 50 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N GLN A 50 " --> pdb=" O ILE A 39 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ARG A 41 " --> pdb=" O PHE A 48 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 46 through 51 current: chain 'B' and resid 13 through 17 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 13 through 17 current: chain 'B' and resid 35 through 43 removed outlier: 6.144A pdb=" N ILE B 39 " --> pdb=" O GLN B 50 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N GLN B 50 " --> pdb=" O ILE B 39 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ARG B 41 " --> pdb=" O PHE B 48 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 46 through 51 current: chain 'C' and resid 13 through 17 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 13 through 17 current: chain 'C' and resid 35 through 43 removed outlier: 6.467A pdb=" N PHE C 48 " --> pdb=" O ILE C 40 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N LEU C 42 " --> pdb=" O THR C 46 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N THR C 46 " --> pdb=" O LEU C 42 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 46 through 51 current: chain 'D' and resid 18 through 22 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 18 through 22 current: chain 'D' and resid 42 through 51 removed outlier: 5.590A pdb=" N VAL D 47 " --> pdb=" O GLN D 58 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N GLN D 58 " --> pdb=" O VAL D 47 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLU D 49 " --> pdb=" O VAL D 56 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N TYR D 54 " --> pdb=" O SER D 51 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 54 through 59 current: chain 'E' and resid 18 through 21 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 18 through 21 current: chain 'E' and resid 42 through 51 removed outlier: 6.087A pdb=" N VAL E 47 " --> pdb=" O GLN E 58 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N GLN E 58 " --> pdb=" O VAL E 47 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLU E 49 " --> pdb=" O VAL E 56 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 55 through 59 current: chain 'F' and resid 18 through 21 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 18 through 21 current: chain 'F' and resid 42 through 51 removed outlier: 5.969A pdb=" N VAL F 47 " --> pdb=" O GLN F 58 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N GLN F 58 " --> pdb=" O VAL F 47 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLU F 49 " --> pdb=" O VAL F 56 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 55 through 59 current: chain 'J' and resid 141 through 144 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 141 through 144 current: chain 'J' and resid 161 through 164 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 161 through 164 current: chain 'L' and resid 141 through 142 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 141 through 142 current: chain 'L' and resid 161 through 164 Processing sheet with id=AA2, first strand: chain 'A' and resid 72 through 75 Processing sheet with id=AA3, first strand: chain 'A' and resid 83 through 84 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 83 through 84 current: chain 'A' and resid 285 through 290 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 285 through 290 current: chain 'A' and resid 375 through 384 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 375 through 384 current: chain 'A' and resid 428 through 429 No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 143 through 148 removed outlier: 3.667A pdb=" N GLY A 136 " --> pdb=" O ILE A 147 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N ALA A 118 " --> pdb=" O PRO A 139 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 128 through 129 removed outlier: 6.924A pdb=" N VAL A 174 " --> pdb=" O LYS A 158 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 72 through 75 Processing sheet with id=AA7, first strand: chain 'B' and resid 83 through 84 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 83 through 84 current: chain 'B' and resid 285 through 288 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 285 through 288 current: chain 'B' and resid 375 through 384 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 375 through 384 current: chain 'B' and resid 428 through 429 No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 143 through 148 removed outlier: 3.827A pdb=" N GLY B 136 " --> pdb=" O ILE B 147 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N ALA B 118 " --> pdb=" O PRO B 139 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 128 through 129 removed outlier: 3.510A pdb=" N VAL B 173 " --> pdb=" O LEU B 181 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 72 through 75 Processing sheet with id=AB2, first strand: chain 'C' and resid 82 through 84 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 82 through 84 current: chain 'C' and resid 285 through 290 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 285 through 290 current: chain 'C' and resid 375 through 382 No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'C' and resid 117 through 119 Processing sheet with id=AB4, first strand: chain 'C' and resid 128 through 129 removed outlier: 6.682A pdb=" N VAL C 174 " --> pdb=" O LYS C 158 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N VAL C 160 " --> pdb=" O VAL C 172 " (cutoff:3.500A) removed outlier: 8.148A pdb=" N VAL C 172 " --> pdb=" O VAL C 160 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 134 through 139 removed outlier: 6.658A pdb=" N ILE C 147 " --> pdb=" O LEU C 135 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N THR C 137 " --> pdb=" O HIS C 145 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N HIS C 145 " --> pdb=" O THR C 137 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 405 through 406 Processing sheet with id=AB7, first strand: chain 'D' and resid 81 through 84 removed outlier: 3.564A pdb=" N LYS D 110 " --> pdb=" O VAL D 84 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 92 through 93 removed outlier: 5.795A pdb=" N PHE D 93 " --> pdb=" O LEU D 221 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N LYS D 223 " --> pdb=" O PHE D 93 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N VAL D 253 " --> pdb=" O THR D 309 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 144 through 145 removed outlier: 4.533A pdb=" N LEU D 144 " --> pdb=" O ILE D 131 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 152 through 154 removed outlier: 3.515A pdb=" N LEU D 314 " --> pdb=" O ILE D 152 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 81 through 84 Processing sheet with id=AC3, first strand: chain 'E' and resid 92 through 93 removed outlier: 3.583A pdb=" N MET E 194 " --> pdb=" O THR E 258 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 130 through 131 removed outlier: 4.560A pdb=" N LEU E 144 " --> pdb=" O ILE E 131 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 313 through 315 Processing sheet with id=AC6, first strand: chain 'F' and resid 81 through 82 Processing sheet with id=AC7, first strand: chain 'F' and resid 91 through 94 removed outlier: 6.587A pdb=" N ARG F 91 " --> pdb=" O LEU F 219 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N LEU F 221 " --> pdb=" O ARG F 91 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N PHE F 93 " --> pdb=" O LEU F 221 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ALA F 188 " --> pdb=" O LEU F 254 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N ILE F 256 " --> pdb=" O ALA F 188 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N VAL F 190 " --> pdb=" O ILE F 256 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 144 through 145 removed outlier: 4.598A pdb=" N LEU F 144 " --> pdb=" O ILE F 131 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N THR F 172 " --> pdb=" O GLN F 132 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 313 through 315 removed outlier: 6.480A pdb=" N ILE F 337 " --> pdb=" O PHE F 153 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 91 through 96 removed outlier: 3.508A pdb=" N SER G 99 " --> pdb=" O VAL G 96 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 19 through 22 removed outlier: 6.800A pdb=" N VAL H 3 " --> pdb=" O TYR H 21 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N VAL H 45 " --> pdb=" O LEU H 72 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N ILE H 74 " --> pdb=" O VAL H 45 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N VAL H 47 " --> pdb=" O ILE H 74 " (cutoff:3.500A) 1303 hydrogen bonds defined for protein. 3738 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 10.35 Time building geometry restraints manager: 13.76 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: 9960 1.34 - 1.46: 4580 1.46 - 1.57: 15313 1.57 - 1.69: 5 1.69 - 1.81: 194 Bond restraints: 30052 Sorted by residual: bond pdb=" CB ARG C 95 " pdb=" CG ARG C 95 " ideal model delta sigma weight residual 1.520 1.399 0.121 3.00e-02 1.11e+03 1.62e+01 bond pdb=" CG ARG C 95 " pdb=" CD ARG C 95 " ideal model delta sigma weight residual 1.520 1.405 0.115 3.00e-02 1.11e+03 1.47e+01 bond pdb=" O4 SO4 A 600 " pdb=" S SO4 A 600 " ideal model delta sigma weight residual 1.499 1.455 0.044 2.00e-02 2.50e+03 4.90e+00 bond pdb=" O3 SO4 A 600 " pdb=" S SO4 A 600 " ideal model delta sigma weight residual 1.499 1.455 0.044 2.00e-02 2.50e+03 4.82e+00 bond pdb=" CA ARG C 95 " pdb=" CB ARG C 95 " ideal model delta sigma weight residual 1.531 1.498 0.034 1.57e-02 4.06e+03 4.60e+00 ... (remaining 30047 not shown) Histogram of bond angle deviations from ideal: 99.81 - 107.78: 1258 107.78 - 115.76: 18399 115.76 - 123.74: 20356 123.74 - 131.72: 664 131.72 - 139.70: 39 Bond angle restraints: 40716 Sorted by residual: angle pdb=" CG ARG C 95 " pdb=" CD ARG C 95 " pdb=" NE ARG C 95 " ideal model delta sigma weight residual 112.00 104.50 7.50 2.20e+00 2.07e-01 1.16e+01 angle pdb=" N HIS E 375 " pdb=" CA HIS E 375 " pdb=" C HIS E 375 " ideal model delta sigma weight residual 111.07 114.08 -3.01 1.07e+00 8.73e-01 7.89e+00 angle pdb=" N ILE F 100 " pdb=" CA ILE F 100 " pdb=" C ILE F 100 " ideal model delta sigma weight residual 113.20 110.56 2.64 9.60e-01 1.09e+00 7.54e+00 angle pdb=" C2' ATP C 601 " pdb=" C3' ATP C 601 " pdb=" O3' ATP C 601 " ideal model delta sigma weight residual 111.83 104.97 6.86 2.67e+00 1.40e-01 6.61e+00 angle pdb=" C GLU B 347 " pdb=" CA GLU B 347 " pdb=" CB GLU B 347 " ideal model delta sigma weight residual 110.42 115.22 -4.80 1.99e+00 2.53e-01 5.81e+00 ... (remaining 40711 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 16690 17.91 - 35.82: 1335 35.82 - 53.73: 217 53.73 - 71.63: 57 71.63 - 89.54: 39 Dihedral angle restraints: 18338 sinusoidal: 7516 harmonic: 10822 Sorted by residual: dihedral pdb=" CA LEU F 257 " pdb=" C LEU F 257 " pdb=" N THR F 258 " pdb=" CA THR F 258 " ideal model delta harmonic sigma weight residual 180.00 -157.61 -22.39 0 5.00e+00 4.00e-02 2.00e+01 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 -159.58 -20.42 0 5.00e+00 4.00e-02 1.67e+01 dihedral pdb=" CA LEU L 128 " pdb=" C LEU L 128 " pdb=" N PRO L 129 " pdb=" CA PRO L 129 " ideal model delta harmonic sigma weight residual -180.00 -160.85 -19.15 0 5.00e+00 4.00e-02 1.47e+01 ... (remaining 18335 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 3899 0.058 - 0.116: 593 0.116 - 0.174: 69 0.174 - 0.232: 0 0.232 - 0.290: 3 Chirality restraints: 4564 Sorted by residual: chirality pdb=" C2' ATP C 601 " pdb=" C1' ATP C 601 " pdb=" C3' ATP C 601 " pdb=" O2' ATP C 601 " both_signs ideal model delta sigma weight residual False -2.68 -2.97 0.29 2.00e-01 2.50e+01 2.10e+00 chirality pdb=" C3' ATP C 601 " pdb=" C2' ATP C 601 " pdb=" C4' ATP C 601 " pdb=" O3' ATP C 601 " both_signs ideal model delta sigma weight residual False -2.63 -2.92 0.29 2.00e-01 2.50e+01 2.04e+00 chirality pdb=" C4' ATP C 601 " pdb=" C3' ATP C 601 " pdb=" C5' ATP C 601 " pdb=" O4' ATP C 601 " both_signs ideal model delta sigma weight residual False -2.49 -2.73 0.24 2.00e-01 2.50e+01 1.41e+00 ... (remaining 4561 not shown) Planarity restraints: 5331 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU A 393 " -0.029 5.00e-02 4.00e+02 4.31e-02 2.97e+00 pdb=" N PRO A 394 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO A 394 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 394 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU D 355 " 0.028 5.00e-02 4.00e+02 4.24e-02 2.87e+00 pdb=" N PRO D 356 " -0.073 5.00e-02 4.00e+02 pdb=" CA PRO D 356 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO D 356 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B 228 " 0.027 5.00e-02 4.00e+02 4.02e-02 2.59e+00 pdb=" N PRO B 229 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO B 229 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 229 " 0.022 5.00e-02 4.00e+02 ... (remaining 5328 not shown) Histogram of nonbonded interaction distances: 1.83 - 2.44: 117 2.44 - 3.06: 20498 3.06 - 3.67: 42898 3.67 - 4.29: 64431 4.29 - 4.90: 111267 Nonbonded interactions: 239211 Sorted by model distance: nonbonded pdb=" O1G ATP C 601 " pdb="MG MG C 602 " model vdw 1.826 2.170 nonbonded pdb=" O1B ATP C 601 " pdb="MG MG C 602 " model vdw 1.888 2.170 nonbonded pdb=" O3B ATP C 601 " pdb="MG MG C 602 " model vdw 1.893 2.170 nonbonded pdb=" OG SER H 24 " pdb=" OE1 GLU H 28 " model vdw 1.939 3.040 nonbonded pdb=" O LYS D 370 " pdb=" OG1 THR D 371 " model vdw 1.953 3.040 ... (remaining 239206 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 1 through 578) selection = chain 'B' 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: 1.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.140 Check model and map are aligned: 0.190 Set scattering table: 0.250 Process input model: 77.240 Find NCS groups from input model: 1.240 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 84.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7106 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 : 0.006 0.121 30052 Z= 0.361 Angle : 0.536 7.501 40716 Z= 0.283 Chirality : 0.043 0.290 4564 Planarity : 0.004 0.058 5331 Dihedral : 13.924 89.543 11420 Min Nonbonded Distance : 1.826 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.17 % Favored : 95.80 % Rotamer: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % 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: 0.46 (0.14), residues: 3764 helix: 1.46 (0.13), residues: 1571 sheet: -1.06 (0.21), residues: 594 loop : -0.19 (0.16), residues: 1599 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP L 175 HIS 0.004 0.001 HIS B 145 PHE 0.018 0.001 PHE A 269 TYR 0.021 0.001 TYR D 331 ARG 0.004 0.000 ARG E 174 *********************** 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 823 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 823 time to evaluate : 3.688 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 GLU cc_start: 0.7931 (mt-10) cc_final: 0.7517 (mt-10) REVERT: A 95 ARG cc_start: 0.6391 (tpt-90) cc_final: 0.6012 (tpt-90) REVERT: A 96 GLU cc_start: 0.6996 (mt-10) cc_final: 0.6398 (pt0) REVERT: A 129 VAL cc_start: 0.7083 (t) cc_final: 0.6662 (m) REVERT: A 143 PHE cc_start: 0.7299 (m-80) cc_final: 0.6979 (m-80) REVERT: A 156 ARG cc_start: 0.5953 (mtp-110) cc_final: 0.5209 (ttp-170) REVERT: A 174 VAL cc_start: 0.7585 (t) cc_final: 0.7216 (p) REVERT: A 182 LYS cc_start: 0.6738 (mtmm) cc_final: 0.6368 (mptt) REVERT: A 323 MET cc_start: 0.8377 (mmt) cc_final: 0.8068 (mmm) REVERT: A 337 ILE cc_start: 0.7042 (mm) cc_final: 0.6587 (mt) REVERT: A 340 ARG cc_start: 0.6537 (tpp-160) cc_final: 0.5995 (mpt180) REVERT: A 348 GLU cc_start: 0.7167 (mt-10) cc_final: 0.5920 (tt0) REVERT: A 374 GLU cc_start: 0.7015 (mt-10) cc_final: 0.6043 (tt0) REVERT: A 375 GLU cc_start: 0.6368 (tt0) cc_final: 0.6057 (tt0) REVERT: A 416 ARG cc_start: 0.7283 (mtm-85) cc_final: 0.6309 (mtp85) REVERT: A 481 ARG cc_start: 0.7125 (mtm-85) cc_final: 0.6650 (mtp-110) REVERT: A 492 GLU cc_start: 0.7222 (mt-10) cc_final: 0.6996 (tt0) REVERT: A 517 LYS cc_start: 0.6952 (mmtp) cc_final: 0.6710 (mtpt) REVERT: A 518 MET cc_start: 0.8303 (mtp) cc_final: 0.8051 (mtm) REVERT: A 541 GLN cc_start: 0.6311 (mt0) cc_final: 0.5858 (pt0) REVERT: A 546 GLU cc_start: 0.6922 (mt-10) cc_final: 0.6170 (mm-30) REVERT: A 550 ARG cc_start: 0.6935 (mtm-85) cc_final: 0.6555 (tpp-160) REVERT: A 557 GLU cc_start: 0.7214 (pm20) cc_final: 0.6413 (tp30) REVERT: A 558 GLU cc_start: 0.7353 (mt-10) cc_final: 0.7085 (mt-10) REVERT: A 565 GLU cc_start: 0.7347 (tp30) cc_final: 0.6834 (mt-10) REVERT: A 567 MET cc_start: 0.6993 (mmm) cc_final: 0.6690 (mmm) REVERT: B 3 GLN cc_start: 0.7514 (tt0) cc_final: 0.6932 (mt0) REVERT: B 29 LYS cc_start: 0.7039 (mtpt) cc_final: 0.6664 (mttt) REVERT: B 59 LYS cc_start: 0.7602 (mtpp) cc_final: 0.7089 (mttp) REVERT: B 93 ARG cc_start: 0.6342 (mtm-85) cc_final: 0.6125 (mtm180) REVERT: B 130 ARG cc_start: 0.5639 (ttm-80) cc_final: 0.5288 (tpt170) REVERT: B 133 MET cc_start: 0.6094 (mmm) cc_final: 0.5823 (mmt) REVERT: B 134 VAL cc_start: 0.7311 (m) cc_final: 0.7072 (t) REVERT: B 159 GLU cc_start: 0.7268 (tt0) cc_final: 0.6060 (tp30) REVERT: B 166 TYR cc_start: 0.7004 (m-10) cc_final: 0.5893 (m-80) REVERT: B 197 ARG cc_start: 0.6468 (ttp80) cc_final: 0.6115 (ttp-110) REVERT: B 200 ASP cc_start: 0.6602 (m-30) cc_final: 0.6366 (m-30) REVERT: B 220 MET cc_start: 0.7641 (tpp) cc_final: 0.7379 (ttm) REVERT: B 236 VAL cc_start: 0.7230 (t) cc_final: 0.7006 (p) REVERT: B 243 LYS cc_start: 0.7176 (mtpp) cc_final: 0.6917 (mtpp) REVERT: B 264 ASP cc_start: 0.6515 (m-30) cc_final: 0.6230 (m-30) REVERT: B 340 ARG cc_start: 0.6820 (tpp-160) cc_final: 0.6513 (tpt-90) REVERT: B 374 GLU cc_start: 0.6185 (mt-10) cc_final: 0.5722 (mm-30) REVERT: B 480 GLU cc_start: 0.6331 (mp0) cc_final: 0.5936 (mt-10) REVERT: B 481 ARG cc_start: 0.6785 (mmm-85) cc_final: 0.5968 (mmm160) REVERT: B 553 TYR cc_start: 0.7670 (m-10) cc_final: 0.7419 (m-10) REVERT: C 5 VAL cc_start: 0.8148 (t) cc_final: 0.7911 (m) REVERT: C 24 MET cc_start: 0.8053 (mtp) cc_final: 0.7730 (mmm) REVERT: C 69 LEU cc_start: 0.7718 (mt) cc_final: 0.7448 (mp) REVERT: C 84 TYR cc_start: 0.8652 (m-80) cc_final: 0.8437 (m-80) REVERT: C 124 LYS cc_start: 0.7262 (mttt) cc_final: 0.6930 (mtmm) REVERT: C 125 PRO cc_start: 0.7245 (Cg_exo) cc_final: 0.6763 (Cg_endo) REVERT: C 183 MET cc_start: 0.8416 (mtp) cc_final: 0.8203 (mtm) REVERT: C 191 ARG cc_start: 0.7840 (mtp180) cc_final: 0.7503 (ttp80) REVERT: C 197 ARG cc_start: 0.7495 (mtm110) cc_final: 0.7275 (ptm-80) REVERT: C 198 LYS cc_start: 0.7288 (mmtp) cc_final: 0.7047 (mmmt) REVERT: C 268 GLU cc_start: 0.6702 (mt-10) cc_final: 0.5867 (tp30) REVERT: C 272 LEU cc_start: 0.7520 (mt) cc_final: 0.7316 (mt) REVERT: C 338 SER cc_start: 0.7704 (t) cc_final: 0.7232 (p) REVERT: C 344 MET cc_start: 0.7786 (mmm) cc_final: 0.7529 (mmt) REVERT: C 367 LYS cc_start: 0.7633 (ttpp) cc_final: 0.7269 (ttpp) REVERT: C 374 GLU cc_start: 0.7318 (mt-10) cc_final: 0.6663 (mm-30) REVERT: C 393 GLU cc_start: 0.6565 (tm-30) cc_final: 0.6317 (tm-30) REVERT: C 416 ARG cc_start: 0.7325 (mtm110) cc_final: 0.6653 (mtm180) REVERT: C 442 ASN cc_start: 0.8212 (m-40) cc_final: 0.7812 (m-40) REVERT: C 452 ASP cc_start: 0.7241 (m-30) cc_final: 0.6879 (m-30) REVERT: C 460 ARG cc_start: 0.7080 (mtm180) cc_final: 0.6850 (mtm-85) REVERT: C 513 TYR cc_start: 0.7369 (t80) cc_final: 0.6959 (t80) REVERT: C 518 MET cc_start: 0.7998 (mtp) cc_final: 0.7693 (mtm) REVERT: C 524 LYS cc_start: 0.6951 (mtpp) cc_final: 0.6547 (ttpp) REVERT: C 525 GLU cc_start: 0.6628 (mm-30) cc_final: 0.6234 (mt-10) REVERT: C 547 ARG cc_start: 0.6217 (mtp85) cc_final: 0.5803 (mtp85) REVERT: C 550 ARG cc_start: 0.6744 (ttm-80) cc_final: 0.6400 (mtm110) REVERT: D 22 GLU cc_start: 0.7253 (mt-10) cc_final: 0.6928 (mt-10) REVERT: D 51 SER cc_start: 0.7670 (t) cc_final: 0.7406 (p) REVERT: D 52 GLU cc_start: 0.7610 (mm-30) cc_final: 0.7075 (mt-10) REVERT: D 92 ARG cc_start: 0.7576 (mtm110) cc_final: 0.6990 (mtm-85) REVERT: D 111 ARG cc_start: 0.7359 (mtp-110) cc_final: 0.7026 (mmm-85) REVERT: D 199 ARG cc_start: 0.6475 (ttp80) cc_final: 0.6116 (ttp80) REVERT: D 231 ARG cc_start: 0.7450 (ttm170) cc_final: 0.7236 (ttm170) REVERT: D 232 ILE cc_start: 0.7456 (mm) cc_final: 0.7174 (mt) REVERT: D 250 ASP cc_start: 0.7756 (m-30) cc_final: 0.7547 (m-30) REVERT: D 269 GLU cc_start: 0.6088 (tt0) cc_final: 0.5757 (mt-10) REVERT: D 280 ARG cc_start: 0.7016 (mtp85) cc_final: 0.6387 (mtp-110) REVERT: D 302 GLU cc_start: 0.6876 (mt-10) cc_final: 0.6552 (mm-30) REVERT: D 305 LYS cc_start: 0.6868 (mtmm) cc_final: 0.6115 (mtpp) REVERT: D 337 ILE cc_start: 0.8288 (mt) cc_final: 0.8076 (mm) REVERT: D 338 GLN cc_start: 0.8540 (tt0) cc_final: 0.8031 (tp40) REVERT: D 376 LYS cc_start: 0.6549 (tppt) cc_final: 0.5787 (tttm) REVERT: D 406 GLU cc_start: 0.6061 (tp30) cc_final: 0.5379 (pm20) REVERT: D 409 ARG cc_start: 0.6647 (ttm-80) cc_final: 0.6269 (mtt90) REVERT: D 416 ASP cc_start: 0.7040 (t0) cc_final: 0.6240 (m-30) REVERT: D 461 LYS cc_start: 0.6961 (tttt) cc_final: 0.6754 (ttmt) REVERT: D 463 TYR cc_start: 0.7646 (t80) cc_final: 0.7394 (t80) REVERT: D 465 GLN cc_start: 0.6690 (mm-40) cc_final: 0.6374 (mp10) REVERT: E 25 LYS cc_start: 0.7336 (ttmm) cc_final: 0.7055 (mtpp) REVERT: E 128 GLU cc_start: 0.7079 (pt0) cc_final: 0.6701 (pt0) REVERT: E 228 THR cc_start: 0.8009 (t) cc_final: 0.7392 (m) REVERT: E 251 TYR cc_start: 0.7793 (m-80) cc_final: 0.7274 (m-80) REVERT: E 252 HIS cc_start: 0.8169 (m-70) cc_final: 0.7881 (m170) REVERT: E 302 GLU cc_start: 0.6980 (tt0) cc_final: 0.5904 (tp30) REVERT: E 345 ARG cc_start: 0.6305 (mtm110) cc_final: 0.6068 (mtm-85) REVERT: E 394 LYS cc_start: 0.6768 (tptp) cc_final: 0.6283 (tttm) REVERT: E 410 ARG cc_start: 0.4761 (mtm180) cc_final: 0.4097 (mmp80) REVERT: E 420 ARG cc_start: 0.7440 (mtm110) cc_final: 0.7236 (mtm-85) REVERT: E 445 MET cc_start: 0.7298 (mtp) cc_final: 0.7016 (mtt) REVERT: E 450 GLU cc_start: 0.5914 (mm-30) cc_final: 0.5698 (mt-10) REVERT: F 6 LYS cc_start: 0.6096 (tptm) cc_final: 0.5689 (mtpp) REVERT: F 7 GLU cc_start: 0.7237 (mt-10) cc_final: 0.6813 (mt-10) REVERT: F 13 TYR cc_start: 0.8585 (t80) cc_final: 0.8252 (t80) REVERT: F 53 GLU cc_start: 0.6863 (mt-10) cc_final: 0.6390 (mm-30) REVERT: F 77 GLU cc_start: 0.7454 (mt-10) cc_final: 0.6940 (pt0) REVERT: F 81 ARG cc_start: 0.7387 (mtt-85) cc_final: 0.6880 (mtm-85) REVERT: F 98 LYS cc_start: 0.7429 (mttt) cc_final: 0.7055 (mmtm) REVERT: F 207 GLU cc_start: 0.6592 (mm-30) cc_final: 0.5996 (tm-30) REVERT: F 209 GLU cc_start: 0.7120 (mt-10) cc_final: 0.6725 (mt-10) REVERT: F 210 ARG cc_start: 0.6282 (ttp80) cc_final: 0.5322 (ttm110) REVERT: F 230 GLU cc_start: 0.7137 (mt-10) cc_final: 0.6928 (mt-10) REVERT: F 280 ARG cc_start: 0.7680 (mtp85) cc_final: 0.7365 (mtt180) REVERT: F 302 GLU cc_start: 0.7292 (tt0) cc_final: 0.6717 (mm-30) REVERT: F 305 LYS cc_start: 0.7994 (mttt) cc_final: 0.7787 (mttm) REVERT: F 362 MET cc_start: 0.8007 (ttp) cc_final: 0.7771 (ttt) REVERT: F 409 ARG cc_start: 0.6795 (ttm110) cc_final: 0.6117 (mtt90) REVERT: F 412 LEU cc_start: 0.7402 (tp) cc_final: 0.7183 (tp) REVERT: F 453 ARG cc_start: 0.6971 (mmt90) cc_final: 0.6716 (mmm-85) REVERT: G 17 GLN cc_start: 0.6886 (mm-40) cc_final: 0.6570 (mm-40) REVERT: G 38 GLU cc_start: 0.6675 (mt-10) cc_final: 0.6467 (tp30) REVERT: G 47 MET cc_start: 0.5255 (mmm) cc_final: 0.4213 (ttm) REVERT: G 177 ARG cc_start: 0.6645 (mtp85) cc_final: 0.6267 (mtm-85) REVERT: G 180 GLN cc_start: 0.7189 (mt0) cc_final: 0.6964 (mt0) REVERT: G 198 LYS cc_start: 0.6461 (tttm) cc_final: 0.6256 (ttmm) REVERT: H 63 MET cc_start: 0.3761 (mmm) cc_final: 0.2141 (ttp) REVERT: J 65 GLU cc_start: 0.4107 (mt-10) cc_final: 0.3655 (mm-30) REVERT: J 86 ARG cc_start: 0.4035 (mmp80) cc_final: 0.3396 (ttm-80) REVERT: J 105 ARG cc_start: 0.3493 (mtt-85) cc_final: 0.3235 (mtt-85) REVERT: J 112 LEU cc_start: 0.4601 (mp) cc_final: 0.4061 (tt) REVERT: J 158 GLU cc_start: 0.5277 (mp0) cc_final: 0.4537 (mt-10) REVERT: J 182 VAL cc_start: 0.3334 (t) cc_final: 0.3066 (p) REVERT: L 86 ARG cc_start: 0.5163 (mtt180) cc_final: 0.4852 (mtp180) REVERT: L 102 GLU cc_start: 0.5661 (mp0) cc_final: 0.4687 (tp30) REVERT: L 153 ARG cc_start: 0.3855 (ttm170) cc_final: 0.3545 (ttp-170) outliers start: 0 outliers final: 0 residues processed: 823 average time/residue: 0.5143 time to fit residues: 617.5054 Evaluate side-chains 506 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 506 time to evaluate : 3.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 314 optimal weight: 4.9990 chunk 282 optimal weight: 3.9990 chunk 156 optimal weight: 0.7980 chunk 96 optimal weight: 0.4980 chunk 190 optimal weight: 6.9990 chunk 151 optimal weight: 3.9990 chunk 292 optimal weight: 1.9990 chunk 113 optimal weight: 10.0000 chunk 177 optimal weight: 5.9990 chunk 217 optimal weight: 0.9980 chunk 338 optimal weight: 6.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 316 GLN A 442 ASN A 571 GLN B 145 HIS B 185 HIS B 571 GLN C 81 ASN C 145 HIS C 283 HIS C 316 GLN C 397 GLN C 418 HIS C 459 GLN C 496 GLN D 252 HIS ** D 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 375 HIS D 448 GLN E 58 GLN E 148 GLN ** E 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 249 HIS ** E 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 142 ASN F 206 GLN F 388 ASN F 413 GLN F 427 GLN G 180 GLN L 130 HIS Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7184 moved from start: 0.2153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.129 30052 Z= 0.231 Angle : 0.570 10.127 40716 Z= 0.296 Chirality : 0.045 0.212 4564 Planarity : 0.005 0.041 5331 Dihedral : 5.120 82.881 4214 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.42 % Favored : 97.53 % Rotamer: Outliers : 1.49 % Allowed : 9.80 % Favored : 88.71 % 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: 0.87 (0.14), residues: 3764 helix: 1.68 (0.13), residues: 1597 sheet: -0.72 (0.22), residues: 570 loop : 0.06 (0.16), residues: 1597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP L 175 HIS 0.005 0.001 HIS C 283 PHE 0.017 0.002 PHE F 130 TYR 0.016 0.001 TYR H 89 ARG 0.014 0.001 ARG C 95 *********************** 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 573 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 527 time to evaluate : 3.317 Fit side-chains REVERT: A 62 GLU cc_start: 0.7810 (mt-10) cc_final: 0.7586 (mt-10) REVERT: A 95 ARG cc_start: 0.6488 (tpt-90) cc_final: 0.5861 (tpt-90) REVERT: A 154 ARG cc_start: 0.7045 (mtp85) cc_final: 0.6746 (mtp180) REVERT: A 156 ARG cc_start: 0.6080 (mtp-110) cc_final: 0.5409 (ttp-170) REVERT: A 169 GLU cc_start: 0.7358 (mm-30) cc_final: 0.6943 (mm-30) REVERT: A 174 VAL cc_start: 0.7652 (t) cc_final: 0.7319 (p) REVERT: A 200 ASP cc_start: 0.7261 (m-30) cc_final: 0.6841 (m-30) REVERT: A 243 LYS cc_start: 0.7761 (mtmt) cc_final: 0.7412 (mtpt) REVERT: A 257 GLU cc_start: 0.7621 (mm-30) cc_final: 0.7342 (mm-30) REVERT: A 262 MET cc_start: 0.7595 (mmp) cc_final: 0.6944 (mmt) REVERT: A 323 MET cc_start: 0.8275 (mmt) cc_final: 0.8067 (mpp) REVERT: A 340 ARG cc_start: 0.6613 (tpp-160) cc_final: 0.5821 (mmp80) REVERT: A 348 GLU cc_start: 0.7123 (mt-10) cc_final: 0.5725 (tt0) REVERT: A 374 GLU cc_start: 0.6955 (mt-10) cc_final: 0.6056 (tt0) REVERT: A 375 GLU cc_start: 0.6572 (tt0) cc_final: 0.6142 (mt-10) REVERT: A 393 GLU cc_start: 0.6731 (pt0) cc_final: 0.6377 (pt0) REVERT: A 416 ARG cc_start: 0.7174 (mtm-85) cc_final: 0.6251 (mtp85) REVERT: A 481 ARG cc_start: 0.7237 (mtm-85) cc_final: 0.6509 (mtp-110) REVERT: A 492 GLU cc_start: 0.7152 (mt-10) cc_final: 0.6300 (pt0) REVERT: A 517 LYS cc_start: 0.6960 (mmtp) cc_final: 0.6751 (mtpt) REVERT: A 518 MET cc_start: 0.8320 (mtp) cc_final: 0.7980 (mtm) REVERT: A 541 GLN cc_start: 0.6533 (mt0) cc_final: 0.5924 (pt0) REVERT: A 546 GLU cc_start: 0.6993 (mt-10) cc_final: 0.6084 (mm-30) REVERT: A 550 ARG cc_start: 0.6995 (mtm-85) cc_final: 0.6636 (tpp-160) REVERT: A 557 GLU cc_start: 0.7155 (pm20) cc_final: 0.6414 (tp30) REVERT: A 558 GLU cc_start: 0.7303 (mt-10) cc_final: 0.7071 (mt-10) REVERT: B 29 LYS cc_start: 0.7023 (mtpt) cc_final: 0.6704 (mttt) REVERT: B 93 ARG cc_start: 0.6579 (mtm-85) cc_final: 0.6272 (mtm180) REVERT: B 130 ARG cc_start: 0.5973 (ttm-80) cc_final: 0.5733 (tpt90) REVERT: B 156 ARG cc_start: 0.6548 (ttp-170) cc_final: 0.5588 (mpt-90) REVERT: B 159 GLU cc_start: 0.7248 (tt0) cc_final: 0.6127 (tp30) REVERT: B 166 TYR cc_start: 0.7073 (m-10) cc_final: 0.5960 (m-80) REVERT: B 197 ARG cc_start: 0.6493 (ttp80) cc_final: 0.6179 (ttp-110) REVERT: B 220 MET cc_start: 0.7699 (tpp) cc_final: 0.7375 (ttm) REVERT: B 241 LEU cc_start: 0.7508 (mp) cc_final: 0.7138 (tt) REVERT: B 243 LYS cc_start: 0.7170 (mtpp) cc_final: 0.6884 (mtpt) REVERT: B 374 GLU cc_start: 0.6447 (mt-10) cc_final: 0.5877 (mm-30) REVERT: B 397 GLN cc_start: 0.6500 (mm-40) cc_final: 0.6085 (tt0) REVERT: B 449 GLU cc_start: 0.6179 (mm-30) cc_final: 0.5685 (mp0) REVERT: B 452 ASP cc_start: 0.7652 (m-30) cc_final: 0.7270 (m-30) REVERT: B 480 GLU cc_start: 0.6530 (mp0) cc_final: 0.5767 (mt-10) REVERT: B 481 ARG cc_start: 0.6873 (mmm-85) cc_final: 0.6266 (ttt-90) REVERT: C 8 LYS cc_start: 0.7631 (ttpp) cc_final: 0.7235 (tttt) REVERT: C 84 TYR cc_start: 0.8729 (m-80) cc_final: 0.8455 (m-80) REVERT: C 101 TYR cc_start: 0.7955 (m-80) cc_final: 0.7300 (m-80) REVERT: C 124 LYS cc_start: 0.7409 (mttt) cc_final: 0.7196 (mtmm) REVERT: C 183 MET cc_start: 0.8566 (mtp) cc_final: 0.8300 (mtm) REVERT: C 191 ARG cc_start: 0.7792 (mtp180) cc_final: 0.7421 (ttp80) REVERT: C 197 ARG cc_start: 0.7420 (mtm110) cc_final: 0.7066 (ptm-80) REVERT: C 198 LYS cc_start: 0.7334 (mmtp) cc_final: 0.7116 (mmmt) REVERT: C 338 SER cc_start: 0.7779 (t) cc_final: 0.7416 (p) REVERT: C 367 LYS cc_start: 0.7655 (ttpp) cc_final: 0.7246 (ttpp) REVERT: C 374 GLU cc_start: 0.7425 (mt-10) cc_final: 0.6631 (mm-30) REVERT: C 415 PHE cc_start: 0.7460 (m-10) cc_final: 0.7259 (m-10) REVERT: C 416 ARG cc_start: 0.7294 (mtm110) cc_final: 0.6530 (mtm180) REVERT: C 442 ASN cc_start: 0.8147 (m-40) cc_final: 0.7618 (m-40) REVERT: C 452 ASP cc_start: 0.7305 (m-30) cc_final: 0.6997 (m-30) REVERT: C 518 MET cc_start: 0.7987 (mtp) cc_final: 0.7699 (mtm) REVERT: C 524 LYS cc_start: 0.7055 (mtpp) cc_final: 0.6790 (ttpp) REVERT: C 547 ARG cc_start: 0.6272 (mtp85) cc_final: 0.5742 (mtp85) REVERT: C 550 ARG cc_start: 0.6720 (ttm-80) cc_final: 0.6236 (mtm110) REVERT: D 22 GLU cc_start: 0.7199 (mt-10) cc_final: 0.6902 (mt-10) REVERT: D 34 ASP cc_start: 0.7219 (m-30) cc_final: 0.6776 (t0) REVERT: D 52 GLU cc_start: 0.7558 (mm-30) cc_final: 0.6705 (mt-10) REVERT: D 231 ARG cc_start: 0.7475 (ttm170) cc_final: 0.7273 (ttp-110) REVERT: D 250 ASP cc_start: 0.7724 (m-30) cc_final: 0.7507 (m-30) REVERT: D 269 GLU cc_start: 0.6266 (tt0) cc_final: 0.5875 (mt-10) REVERT: D 280 ARG cc_start: 0.6941 (mtp85) cc_final: 0.6219 (mtp-110) REVERT: D 305 LYS cc_start: 0.7025 (mtmm) cc_final: 0.5658 (tttt) REVERT: D 322 THR cc_start: 0.7787 (p) cc_final: 0.7487 (p) REVERT: D 327 ASP cc_start: 0.6690 (t0) cc_final: 0.6425 (m-30) REVERT: D 338 GLN cc_start: 0.8452 (tt0) cc_final: 0.7872 (tp40) REVERT: D 376 LYS cc_start: 0.6410 (tppt) cc_final: 0.5962 (tttm) REVERT: D 406 GLU cc_start: 0.5581 (tp30) cc_final: 0.5223 (pm20) REVERT: D 409 ARG cc_start: 0.6571 (ttm-80) cc_final: 0.6140 (mtt90) REVERT: D 437 GLN cc_start: 0.7646 (tt0) cc_final: 0.7358 (tt0) REVERT: D 461 LYS cc_start: 0.7032 (tttt) cc_final: 0.6710 (tttp) REVERT: D 463 TYR cc_start: 0.7635 (t80) cc_final: 0.7141 (t80) REVERT: E 49 GLU cc_start: 0.7482 (tt0) cc_final: 0.7087 (mt-10) REVERT: E 128 GLU cc_start: 0.7206 (pt0) cc_final: 0.6772 (pt0) REVERT: E 194 MET cc_start: 0.8572 (mtm) cc_final: 0.8301 (mtm) REVERT: E 209 GLU cc_start: 0.5828 (mt-10) cc_final: 0.5447 (mm-30) REVERT: E 252 HIS cc_start: 0.8273 (m-70) cc_final: 0.8012 (m170) REVERT: E 259 ASP cc_start: 0.6307 (m-30) cc_final: 0.5812 (m-30) REVERT: E 278 PRO cc_start: 0.8004 (Cg_endo) cc_final: 0.7706 (Cg_exo) REVERT: E 302 GLU cc_start: 0.6919 (tt0) cc_final: 0.5813 (tp30) REVERT: E 360 ARG cc_start: 0.7087 (mtm-85) cc_final: 0.6807 (mtt90) REVERT: E 420 ARG cc_start: 0.7395 (mtm110) cc_final: 0.7156 (mtm-85) REVERT: E 445 MET cc_start: 0.7312 (mtp) cc_final: 0.7007 (mtt) REVERT: E 450 GLU cc_start: 0.5894 (mm-30) cc_final: 0.5633 (mt-10) REVERT: F 6 LYS cc_start: 0.6133 (tptm) cc_final: 0.5426 (mtpp) REVERT: F 7 GLU cc_start: 0.7239 (mt-10) cc_final: 0.6622 (mt-10) REVERT: F 53 GLU cc_start: 0.7003 (mt-10) cc_final: 0.6622 (pt0) REVERT: F 74 SER cc_start: 0.8011 (p) cc_final: 0.7426 (t) REVERT: F 77 GLU cc_start: 0.7471 (mt-10) cc_final: 0.6990 (pt0) REVERT: F 86 LYS cc_start: 0.7492 (tptp) cc_final: 0.7267 (tptm) REVERT: F 98 LYS cc_start: 0.7418 (mttt) cc_final: 0.7094 (mmtm) REVERT: F 109 GLU cc_start: 0.6797 (mt-10) cc_final: 0.6276 (mm-30) REVERT: F 207 GLU cc_start: 0.6787 (mm-30) cc_final: 0.6154 (tm-30) REVERT: F 209 GLU cc_start: 0.6698 (mt-10) cc_final: 0.6453 (mt-10) REVERT: F 210 ARG cc_start: 0.6142 (ttp80) cc_final: 0.5194 (ttm110) REVERT: F 280 ARG cc_start: 0.7599 (mtp85) cc_final: 0.7339 (mtt180) REVERT: F 302 GLU cc_start: 0.7350 (tt0) cc_final: 0.6723 (mm-30) REVERT: F 399 ILE cc_start: 0.6401 (mm) cc_final: 0.5924 (mt) REVERT: G 47 MET cc_start: 0.5079 (mmm) cc_final: 0.4558 (ttm) REVERT: G 59 GLU cc_start: 0.5495 (pp20) cc_final: 0.4420 (tp30) REVERT: G 177 ARG cc_start: 0.6548 (mtp85) cc_final: 0.6231 (mtm-85) REVERT: G 180 GLN cc_start: 0.7061 (mt0) cc_final: 0.6796 (mt0) REVERT: G 197 ILE cc_start: 0.5224 (pt) cc_final: 0.4950 (mm) REVERT: H 63 MET cc_start: 0.4016 (mmm) cc_final: 0.2332 (ttp) REVERT: J 65 GLU cc_start: 0.4081 (mt-10) cc_final: 0.3719 (tt0) REVERT: J 81 GLU cc_start: 0.4431 (tt0) cc_final: 0.4044 (tp30) REVERT: J 86 ARG cc_start: 0.4086 (mmp80) cc_final: 0.3423 (ttm-80) REVERT: J 112 LEU cc_start: 0.4461 (mp) cc_final: 0.3910 (tt) REVERT: J 162 GLN cc_start: 0.5877 (tt0) cc_final: 0.5564 (tt0) REVERT: J 164 GLU cc_start: 0.5227 (tp30) cc_final: 0.4666 (mt-10) REVERT: J 173 ARG cc_start: 0.3641 (mtp180) cc_final: 0.3426 (ttt-90) REVERT: K 102 LYS cc_start: 0.5821 (tptp) cc_final: 0.4247 (mmtt) REVERT: L 86 ARG cc_start: 0.5403 (mtt180) cc_final: 0.4946 (mtp180) REVERT: L 102 GLU cc_start: 0.5546 (mp0) cc_final: 0.4671 (tp30) REVERT: L 141 GLU cc_start: 0.5024 (tt0) cc_final: 0.4230 (mm-30) REVERT: L 153 ARG cc_start: 0.4014 (ttm170) cc_final: 0.3399 (ttm-80) outliers start: 46 outliers final: 27 residues processed: 552 average time/residue: 0.5282 time to fit residues: 428.7264 Evaluate side-chains 492 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 465 time to evaluate : 4.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 273 THR Chi-restraints excluded: chain C residue 433 SER Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 130 PHE Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 259 ASP Chi-restraints excluded: chain D residue 309 THR Chi-restraints excluded: chain E residue 21 VAL Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 131 ILE Chi-restraints excluded: chain E residue 143 THR Chi-restraints excluded: chain E residue 237 MET Chi-restraints excluded: chain E residue 309 THR Chi-restraints excluded: chain F residue 85 SER Chi-restraints excluded: chain F residue 107 THR Chi-restraints excluded: chain F residue 410 ARG Chi-restraints excluded: chain F residue 413 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 188 optimal weight: 4.9990 chunk 105 optimal weight: 0.9990 chunk 281 optimal weight: 7.9990 chunk 230 optimal weight: 0.6980 chunk 93 optimal weight: 8.9990 chunk 339 optimal weight: 9.9990 chunk 366 optimal weight: 30.0000 chunk 302 optimal weight: 9.9990 chunk 336 optimal weight: 10.0000 chunk 115 optimal weight: 9.9990 chunk 272 optimal weight: 6.9990 overall best weight: 4.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 397 GLN A 423 ASN A 498 ASN B 290 ASN D 170 GLN D 310 GLN D 323 HIS D 364 ASN ** E 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 364 ASN ** E 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 458 HIS F 249 HIS F 381 GLN G 68 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7231 moved from start: 0.3343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.161 30052 Z= 0.420 Angle : 0.701 14.153 40716 Z= 0.363 Chirality : 0.050 0.244 4564 Planarity : 0.006 0.075 5331 Dihedral : 5.714 77.975 4214 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.00 % Favored : 96.97 % Rotamer: Outliers : 2.66 % Allowed : 11.58 % Favored : 85.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.14), residues: 3764 helix: 1.07 (0.13), residues: 1570 sheet: -0.97 (0.20), residues: 570 loop : -0.25 (0.16), residues: 1624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP J 175 HIS 0.011 0.002 HIS D 375 PHE 0.026 0.003 PHE F 414 TYR 0.020 0.002 TYR C 562 ARG 0.014 0.001 ARG C 95 *********************** 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 547 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 465 time to evaluate : 4.243 Fit side-chains REVERT: A 53 GLU cc_start: 0.7706 (OUTLIER) cc_final: 0.7475 (mt-10) REVERT: A 93 ARG cc_start: 0.7028 (mmm160) cc_final: 0.6393 (mpt180) REVERT: A 95 ARG cc_start: 0.6464 (tpt-90) cc_final: 0.5720 (tpt-90) REVERT: A 96 GLU cc_start: 0.6481 (mt-10) cc_final: 0.6132 (pt0) REVERT: A 119 TRP cc_start: 0.8170 (OUTLIER) cc_final: 0.7915 (t-100) REVERT: A 154 ARG cc_start: 0.7122 (mtp85) cc_final: 0.6830 (mtp180) REVERT: A 156 ARG cc_start: 0.6079 (mtp-110) cc_final: 0.5381 (ttp-170) REVERT: A 174 VAL cc_start: 0.7594 (t) cc_final: 0.7211 (p) REVERT: A 257 GLU cc_start: 0.7744 (mm-30) cc_final: 0.7474 (mm-30) REVERT: A 323 MET cc_start: 0.8173 (mmt) cc_final: 0.7755 (mmm) REVERT: A 332 GLU cc_start: 0.6590 (mt-10) cc_final: 0.6216 (mt-10) REVERT: A 340 ARG cc_start: 0.6724 (tpp-160) cc_final: 0.5963 (mpt180) REVERT: A 374 GLU cc_start: 0.7010 (mt-10) cc_final: 0.6203 (tt0) REVERT: A 393 GLU cc_start: 0.6658 (pt0) cc_final: 0.6412 (pt0) REVERT: A 416 ARG cc_start: 0.7251 (mtm-85) cc_final: 0.6171 (mtp85) REVERT: A 481 ARG cc_start: 0.7224 (mtm-85) cc_final: 0.6651 (mtp-110) REVERT: A 518 MET cc_start: 0.8275 (mtp) cc_final: 0.8015 (mtm) REVERT: A 541 GLN cc_start: 0.6435 (mt0) cc_final: 0.5927 (pt0) REVERT: A 546 GLU cc_start: 0.6853 (mt-10) cc_final: 0.6054 (mm-30) REVERT: A 550 ARG cc_start: 0.7040 (mtm-85) cc_final: 0.6568 (tpp-160) REVERT: A 557 GLU cc_start: 0.7166 (pm20) cc_final: 0.6531 (tp30) REVERT: A 558 GLU cc_start: 0.7365 (mt-10) cc_final: 0.7106 (mt-10) REVERT: B 29 LYS cc_start: 0.7008 (mtpt) cc_final: 0.6678 (mttt) REVERT: B 33 GLU cc_start: 0.7810 (mt-10) cc_final: 0.7601 (mt-10) REVERT: B 93 ARG cc_start: 0.6508 (mtm-85) cc_final: 0.6081 (mtm180) REVERT: B 119 TRP cc_start: 0.6891 (t60) cc_final: 0.6550 (t60) REVERT: B 166 TYR cc_start: 0.7251 (m-80) cc_final: 0.6056 (m-80) REVERT: B 197 ARG cc_start: 0.6672 (ttp80) cc_final: 0.6209 (ttp-110) REVERT: B 268 GLU cc_start: 0.7234 (mt-10) cc_final: 0.7025 (mt-10) REVERT: B 284 ARG cc_start: 0.8369 (OUTLIER) cc_final: 0.8062 (ptt90) REVERT: B 397 GLN cc_start: 0.6654 (mm-40) cc_final: 0.6396 (mt0) REVERT: B 449 GLU cc_start: 0.6281 (mm-30) cc_final: 0.5751 (mp0) REVERT: B 477 GLN cc_start: 0.6506 (pm20) cc_final: 0.6262 (mp10) REVERT: B 480 GLU cc_start: 0.6568 (mp0) cc_final: 0.5780 (mt-10) REVERT: B 481 ARG cc_start: 0.6916 (mmm-85) cc_final: 0.6178 (ttt-90) REVERT: C 8 LYS cc_start: 0.7795 (ttpp) cc_final: 0.7483 (tttt) REVERT: C 93 ARG cc_start: 0.6130 (mmm-85) cc_final: 0.5895 (mmm-85) REVERT: C 115 LYS cc_start: 0.7163 (OUTLIER) cc_final: 0.6867 (tttm) REVERT: C 124 LYS cc_start: 0.7299 (mttt) cc_final: 0.7089 (mtmm) REVERT: C 125 PRO cc_start: 0.7090 (Cg_exo) cc_final: 0.6624 (Cg_endo) REVERT: C 183 MET cc_start: 0.8527 (mtp) cc_final: 0.8306 (mtm) REVERT: C 197 ARG cc_start: 0.7383 (mtm110) cc_final: 0.6795 (mtm110) REVERT: C 198 LYS cc_start: 0.7658 (mmtp) cc_final: 0.7284 (mmmt) REVERT: C 262 MET cc_start: 0.6979 (mmm) cc_final: 0.6708 (mmm) REVERT: C 338 SER cc_start: 0.7823 (t) cc_final: 0.7355 (p) REVERT: C 416 ARG cc_start: 0.7126 (mtm110) cc_final: 0.6424 (mtm180) REVERT: C 442 ASN cc_start: 0.8285 (m-40) cc_final: 0.7692 (m110) REVERT: C 460 ARG cc_start: 0.7072 (mtp180) cc_final: 0.6851 (mtm-85) REVERT: C 518 MET cc_start: 0.8210 (mtp) cc_final: 0.7932 (mtm) REVERT: C 524 LYS cc_start: 0.6949 (mtpp) cc_final: 0.6721 (tttm) REVERT: C 547 ARG cc_start: 0.6256 (mtp85) cc_final: 0.5886 (mtp180) REVERT: C 550 ARG cc_start: 0.6995 (ttm-80) cc_final: 0.6021 (mtm110) REVERT: D 22 GLU cc_start: 0.7136 (mt-10) cc_final: 0.6917 (mt-10) REVERT: D 34 ASP cc_start: 0.7199 (m-30) cc_final: 0.6725 (t0) REVERT: D 52 GLU cc_start: 0.7554 (mm-30) cc_final: 0.6796 (mt-10) REVERT: D 206 GLN cc_start: 0.6324 (tp40) cc_final: 0.5929 (mm-40) REVERT: D 269 GLU cc_start: 0.6286 (tt0) cc_final: 0.5814 (mt-10) REVERT: D 305 LYS cc_start: 0.7335 (OUTLIER) cc_final: 0.6622 (mtpp) REVERT: D 338 GLN cc_start: 0.8654 (tt0) cc_final: 0.8145 (tp40) REVERT: D 342 GLU cc_start: 0.7410 (tt0) cc_final: 0.7142 (tt0) REVERT: D 362 MET cc_start: 0.7493 (ttp) cc_final: 0.7044 (ttt) REVERT: D 376 LYS cc_start: 0.6608 (tppt) cc_final: 0.6239 (tttm) REVERT: D 406 GLU cc_start: 0.5473 (tp30) cc_final: 0.5206 (pm20) REVERT: D 409 ARG cc_start: 0.6465 (ttm-80) cc_final: 0.5954 (mtt90) REVERT: D 437 GLN cc_start: 0.7650 (tt0) cc_final: 0.7286 (tt0) REVERT: D 461 LYS cc_start: 0.7092 (tttt) cc_final: 0.6765 (tttp) REVERT: D 463 TYR cc_start: 0.7784 (t80) cc_final: 0.7238 (t80) REVERT: E 26 ASP cc_start: 0.7201 (t0) cc_final: 0.6851 (t0) REVERT: E 132 GLN cc_start: 0.7486 (tt0) cc_final: 0.7251 (tt0) REVERT: E 209 GLU cc_start: 0.5995 (mt-10) cc_final: 0.5624 (mm-30) REVERT: E 219 LEU cc_start: 0.7520 (mt) cc_final: 0.7244 (mp) REVERT: E 259 ASP cc_start: 0.6546 (m-30) cc_final: 0.6077 (m-30) REVERT: E 278 PRO cc_start: 0.8091 (Cg_endo) cc_final: 0.7755 (Cg_exo) REVERT: E 302 GLU cc_start: 0.6987 (tt0) cc_final: 0.5703 (tp30) REVERT: E 316 MET cc_start: 0.7823 (mtm) cc_final: 0.7620 (mtp) REVERT: E 410 ARG cc_start: 0.5586 (mtm-85) cc_final: 0.4356 (mmp80) REVERT: E 420 ARG cc_start: 0.7612 (mtm110) cc_final: 0.7161 (mtm-85) REVERT: E 445 MET cc_start: 0.7192 (mtp) cc_final: 0.6673 (mtt) REVERT: E 448 GLN cc_start: 0.5710 (OUTLIER) cc_final: 0.4961 (mm110) REVERT: E 450 GLU cc_start: 0.6167 (mm-30) cc_final: 0.5812 (mt-10) REVERT: F 7 GLU cc_start: 0.7305 (mt-10) cc_final: 0.6947 (mt-10) REVERT: F 53 GLU cc_start: 0.6851 (mt-10) cc_final: 0.6440 (pt0) REVERT: F 77 GLU cc_start: 0.7359 (mt-10) cc_final: 0.6901 (pt0) REVERT: F 86 LYS cc_start: 0.7562 (tptp) cc_final: 0.7358 (tttt) REVERT: F 98 LYS cc_start: 0.7281 (mttt) cc_final: 0.7029 (mmtm) REVERT: F 109 GLU cc_start: 0.6828 (mt-10) cc_final: 0.6311 (mm-30) REVERT: F 207 GLU cc_start: 0.6635 (mm-30) cc_final: 0.5935 (tm-30) REVERT: F 209 GLU cc_start: 0.6961 (mt-10) cc_final: 0.6710 (mt-10) REVERT: F 210 ARG cc_start: 0.6100 (ttp80) cc_final: 0.5645 (ttp80) REVERT: F 280 ARG cc_start: 0.7502 (mtp85) cc_final: 0.7270 (mtt180) REVERT: F 302 GLU cc_start: 0.7401 (tt0) cc_final: 0.7100 (tt0) REVERT: F 362 MET cc_start: 0.8229 (ttm) cc_final: 0.7936 (ttt) REVERT: F 405 THR cc_start: 0.6535 (OUTLIER) cc_final: 0.6234 (t) REVERT: F 406 GLU cc_start: 0.5886 (tm-30) cc_final: 0.5511 (pm20) REVERT: F 410 ARG cc_start: 0.6499 (OUTLIER) cc_final: 0.5984 (mtm-85) REVERT: G 47 MET cc_start: 0.5360 (mmm) cc_final: 0.4847 (ttm) REVERT: G 59 GLU cc_start: 0.5554 (pp20) cc_final: 0.4284 (tp30) REVERT: G 139 ARG cc_start: 0.5398 (ttp80) cc_final: 0.4639 (ptm160) REVERT: H 63 MET cc_start: 0.3886 (mmm) cc_final: 0.2499 (ttp) REVERT: H 77 LEU cc_start: 0.4239 (mm) cc_final: 0.3940 (mp) REVERT: J 65 GLU cc_start: 0.4382 (mt-10) cc_final: 0.3898 (tt0) REVERT: J 86 ARG cc_start: 0.4220 (mmp80) cc_final: 0.3389 (ttm-80) REVERT: J 112 LEU cc_start: 0.4529 (OUTLIER) cc_final: 0.3990 (tt) REVERT: J 162 GLN cc_start: 0.5555 (tt0) cc_final: 0.5266 (tt0) REVERT: J 173 ARG cc_start: 0.4025 (mtp180) cc_final: 0.3792 (mtp85) REVERT: K 102 LYS cc_start: 0.5548 (tptp) cc_final: 0.4008 (mmtt) REVERT: L 86 ARG cc_start: 0.5481 (mtt180) cc_final: 0.4935 (mtp180) REVERT: L 102 GLU cc_start: 0.5529 (mp0) cc_final: 0.4600 (tp30) REVERT: L 153 ARG cc_start: 0.4058 (ttm170) cc_final: 0.3515 (ttm-80) outliers start: 82 outliers final: 56 residues processed: 523 average time/residue: 0.5050 time to fit residues: 389.0594 Evaluate side-chains 492 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 427 time to evaluate : 3.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 119 TRP Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 326 SER Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 412 SER Chi-restraints excluded: chain A residue 466 GLU Chi-restraints excluded: chain A residue 538 GLU Chi-restraints excluded: chain B residue 2 ILE Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 284 ARG Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain B residue 570 ILE Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 115 LYS Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 273 THR Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 433 SER Chi-restraints excluded: chain C residue 484 ILE Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 76 VAL Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 130 PHE Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 259 ASP Chi-restraints excluded: chain D residue 305 LYS Chi-restraints excluded: chain D residue 348 ILE Chi-restraints excluded: chain D residue 399 ILE Chi-restraints excluded: chain E residue 21 VAL Chi-restraints excluded: chain E residue 37 ASP Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 130 PHE Chi-restraints excluded: chain E residue 131 ILE Chi-restraints excluded: chain E residue 200 GLU Chi-restraints excluded: chain E residue 228 THR Chi-restraints excluded: chain E residue 237 MET Chi-restraints excluded: chain E residue 275 GLU Chi-restraints excluded: chain E residue 309 THR Chi-restraints excluded: chain E residue 362 MET Chi-restraints excluded: chain E residue 390 VAL Chi-restraints excluded: chain E residue 448 GLN Chi-restraints excluded: chain F residue 85 SER Chi-restraints excluded: chain F residue 107 THR Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 314 LEU Chi-restraints excluded: chain F residue 405 THR Chi-restraints excluded: chain F residue 410 ARG Chi-restraints excluded: chain J residue 105 ARG Chi-restraints excluded: chain J residue 112 LEU Chi-restraints excluded: chain L residue 134 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 335 optimal weight: 10.0000 chunk 255 optimal weight: 6.9990 chunk 176 optimal weight: 1.9990 chunk 37 optimal weight: 7.9990 chunk 161 optimal weight: 9.9990 chunk 227 optimal weight: 5.9990 chunk 340 optimal weight: 8.9990 chunk 360 optimal weight: 9.9990 chunk 177 optimal weight: 1.9990 chunk 322 optimal weight: 9.9990 chunk 97 optimal weight: 4.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 498 ASN B 145 HIS B 316 GLN D 388 ASN E 161 ASN ** E 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 429 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7242 moved from start: 0.3632 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: