Starting phenix.real_space_refine on Tue Apr 9 17:52:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x5i_38070/04_2024/8x5i_38070_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x5i_38070/04_2024/8x5i_38070.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.01 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x5i_38070/04_2024/8x5i_38070.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x5i_38070/04_2024/8x5i_38070.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x5i_38070/04_2024/8x5i_38070_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x5i_38070/04_2024/8x5i_38070_updated.pdb" } resolution = 3.01 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= 0.001 sd= 0.023 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 12 5.49 5 Mg 4 5.21 5 S 55 5.16 5 C 10851 2.51 5 N 2808 2.21 5 O 3276 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 315": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 471": "OE1" <-> "OE2" Residue "A ASP 472": "OD1" <-> "OD2" Residue "B ARG 12": "NH1" <-> "NH2" Residue "B PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 315": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 315": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 493": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 17006 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 477, 3904 Classifications: {'peptide': 477} Link IDs: {'PTRANS': 8, 'TRANS': 468} Chain breaks: 1 Chain: "B" Number of atoms: 4537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 555, 4537 Classifications: {'peptide': 555} Link IDs: {'PTRANS': 8, 'TRANS': 546} Chain breaks: 1 Chain: "C" Number of atoms: 3888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 474, 3888 Classifications: {'peptide': 474} Link IDs: {'PTRANS': 8, 'TRANS': 465} Chain breaks: 1 Chain: "D" Number of atoms: 4549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 557, 4549 Classifications: {'peptide': 557} Link IDs: {'PTRANS': 10, 'TRANS': 546} Chain breaks: 1 Chain: "A" 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} Chain: "B" 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} 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} Chain: "D" 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: 9.14, per 1000 atoms: 0.54 Number of scatterers: 17006 At special positions: 0 Unit cell: (87.36, 112.56, 193.2, 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 55 16.00 P 12 15.00 Mg 4 11.99 O 3276 8.00 N 2808 7.00 C 10851 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: 6.35 Conformation dependent library (CDL) restraints added in 3.1 seconds 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3896 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 83 helices and 16 sheets defined 38.5% alpha, 16.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.49 Creating SS restraints... Processing helix chain 'A' and resid 35 through 45 removed outlier: 3.573A pdb=" N LEU A 39 " --> pdb=" O LYS A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 53 removed outlier: 5.013A pdb=" N PHE A 53 " --> pdb=" O GLU A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 63 No H-bonds generated for 'chain 'A' and resid 61 through 63' Processing helix chain 'A' and resid 84 through 96 removed outlier: 4.202A pdb=" N VAL A 92 " --> pdb=" O LYS A 88 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N GLY A 95 " --> pdb=" O SER A 91 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N ALA A 96 " --> pdb=" O VAL A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 101 No H-bonds generated for 'chain 'A' and resid 99 through 101' Processing helix chain 'A' and resid 261 through 276 Processing helix chain 'A' and resid 296 through 308 Processing helix chain 'A' and resid 323 through 325 No H-bonds generated for 'chain 'A' and resid 323 through 325' Processing helix chain 'A' and resid 359 through 371 removed outlier: 3.674A pdb=" N SER A 368 " --> pdb=" O LYS A 364 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA A 369 " --> pdb=" O ALA A 365 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N PHE A 371 " --> pdb=" O SER A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 393 Processing helix chain 'A' and resid 414 through 422 Processing helix chain 'A' and resid 448 through 457 Processing helix chain 'A' and resid 476 through 492 Processing helix chain 'A' and resid 495 through 502 Processing helix chain 'A' and resid 512 through 528 removed outlier: 3.658A pdb=" N ALA A 519 " --> pdb=" O ASP A 515 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N GLU A 522 " --> pdb=" O SER A 518 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N SER A 523 " --> pdb=" O ALA A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 533 through 537 Processing helix chain 'A' and resid 541 through 549 removed outlier: 3.507A pdb=" N MET A 545 " --> pdb=" O LYS A 541 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N VAL A 546 " --> pdb=" O LEU A 542 " (cutoff:3.500A) Processing helix chain 'A' and resid 557 through 561 Processing helix chain 'A' and resid 567 through 573 Processing helix chain 'B' and resid 35 through 46 removed outlier: 3.835A pdb=" N LEU B 42 " --> pdb=" O PHE B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 48 through 53 removed outlier: 4.875A pdb=" N PHE B 53 " --> pdb=" O GLU B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 63 No H-bonds generated for 'chain 'B' and resid 61 through 63' Processing helix chain 'B' and resid 84 through 90 Processing helix chain 'B' and resid 94 through 96 No H-bonds generated for 'chain 'B' and resid 94 through 96' Processing helix chain 'B' and resid 160 through 176 removed outlier: 3.856A pdb=" N GLN B 166 " --> pdb=" O LYS B 162 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N LYS B 169 " --> pdb=" O ALA B 165 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N PHE B 172 " --> pdb=" O LYS B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 186 through 195 removed outlier: 3.519A pdb=" N SER B 190 " --> pdb=" O ASN B 186 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU B 191 " --> pdb=" O ASN B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 218 removed outlier: 3.824A pdb=" N PHE B 208 " --> pdb=" O ILE B 204 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N THR B 213 " --> pdb=" O GLN B 209 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N SER B 218 " --> pdb=" O SER B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 261 through 276 removed outlier: 3.628A pdb=" N SER B 268 " --> pdb=" O MET B 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 278 through 280 No H-bonds generated for 'chain 'B' and resid 278 through 280' Processing helix chain 'B' and resid 296 through 307 Processing helix chain 'B' and resid 322 through 325 Processing helix chain 'B' and resid 356 through 371 removed outlier: 3.936A pdb=" N LYS B 359 " --> pdb=" O GLY B 356 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N LYS B 360 " --> pdb=" O SER B 357 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ASN B 363 " --> pdb=" O LYS B 360 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LYS B 364 " --> pdb=" O LYS B 361 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N SER B 367 " --> pdb=" O LYS B 364 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N SER B 368 " --> pdb=" O ALA B 365 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N LEU B 370 " --> pdb=" O SER B 367 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N PHE B 371 " --> pdb=" O SER B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 393 Processing helix chain 'B' and resid 398 through 401 No H-bonds generated for 'chain 'B' and resid 398 through 401' Processing helix chain 'B' and resid 413 through 422 Processing helix chain 'B' and resid 449 through 456 Processing helix chain 'B' and resid 477 through 492 Processing helix chain 'B' and resid 494 through 503 Processing helix chain 'B' and resid 512 through 528 removed outlier: 7.150A pdb=" N GLU B 522 " --> pdb=" O SER B 518 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N SER B 523 " --> pdb=" O ALA B 519 " (cutoff:3.500A) Processing helix chain 'B' and resid 533 through 539 Processing helix chain 'B' and resid 544 through 549 Processing helix chain 'B' and resid 554 through 561 Processing helix chain 'B' and resid 567 through 573 Processing helix chain 'C' and resid 37 through 46 removed outlier: 3.519A pdb=" N LEU C 42 " --> pdb=" O PHE C 38 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 53 removed outlier: 5.104A pdb=" N PHE C 53 " --> pdb=" O GLU C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 61 through 63 No H-bonds generated for 'chain 'C' and resid 61 through 63' Processing helix chain 'C' and resid 84 through 93 removed outlier: 4.195A pdb=" N VAL C 92 " --> pdb=" O LYS C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 262 through 277 removed outlier: 3.661A pdb=" N TYR C 270 " --> pdb=" O SER C 266 " (cutoff:3.500A) Processing helix chain 'C' and resid 296 through 307 Processing helix chain 'C' and resid 322 through 325 Processing helix chain 'C' and resid 359 through 371 removed outlier: 4.695A pdb=" N SER C 368 " --> pdb=" O LYS C 364 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ALA C 369 " --> pdb=" O ALA C 365 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N PHE C 371 " --> pdb=" O SER C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 381 through 393 Processing helix chain 'C' and resid 414 through 423 Processing helix chain 'C' and resid 448 through 457 removed outlier: 4.274A pdb=" N LEU C 456 " --> pdb=" O ARG C 452 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N LEU C 457 " --> pdb=" O CYS C 453 " (cutoff:3.500A) Processing helix chain 'C' and resid 477 through 492 Processing helix chain 'C' and resid 494 through 502 Processing helix chain 'C' and resid 512 through 519 Processing helix chain 'C' and resid 522 through 528 Processing helix chain 'C' and resid 533 through 537 Processing helix chain 'C' and resid 541 through 550 removed outlier: 3.617A pdb=" N MET C 545 " --> pdb=" O LYS C 541 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N VAL C 546 " --> pdb=" O LEU C 542 " (cutoff:3.500A) Processing helix chain 'C' and resid 556 through 561 Processing helix chain 'C' and resid 564 through 573 removed outlier: 4.063A pdb=" N ALA C 567 " --> pdb=" O GLU C 564 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N CYS C 568 " --> pdb=" O LYS C 565 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LEU C 569 " --> pdb=" O PHE C 566 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N VAL C 573 " --> pdb=" O LYS C 570 " (cutoff:3.500A) Processing helix chain 'D' and resid 35 through 46 removed outlier: 3.746A pdb=" N LEU D 42 " --> pdb=" O PHE D 38 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 53 removed outlier: 3.761A pdb=" N LYS D 52 " --> pdb=" O LYS D 48 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N PHE D 53 " --> pdb=" O GLU D 49 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 48 through 53' Processing helix chain 'D' and resid 61 through 63 No H-bonds generated for 'chain 'D' and resid 61 through 63' Processing helix chain 'D' and resid 84 through 90 Processing helix chain 'D' and resid 160 through 167 Processing helix chain 'D' and resid 182 through 191 Processing helix chain 'D' and resid 206 through 210 Processing helix chain 'D' and resid 259 through 276 removed outlier: 3.608A pdb=" N LYS D 263 " --> pdb=" O ASP D 259 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N MET D 264 " --> pdb=" O GLY D 260 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N SER D 266 " --> pdb=" O ARG D 262 " (cutoff:3.500A) Processing helix chain 'D' and resid 296 through 307 Processing helix chain 'D' and resid 322 through 325 Processing helix chain 'D' and resid 359 through 371 removed outlier: 4.637A pdb=" N SER D 368 " --> pdb=" O LYS D 364 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ALA D 369 " --> pdb=" O ALA D 365 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N PHE D 371 " --> pdb=" O SER D 367 " (cutoff:3.500A) Processing helix chain 'D' and resid 381 through 393 Processing helix chain 'D' and resid 413 through 422 removed outlier: 3.670A pdb=" N VAL D 417 " --> pdb=" O PHE D 413 " (cutoff:3.500A) Processing helix chain 'D' and resid 449 through 456 Processing helix chain 'D' and resid 476 through 492 Processing helix chain 'D' and resid 494 through 503 removed outlier: 3.796A pdb=" N GLU D 503 " --> pdb=" O GLU D 499 " (cutoff:3.500A) Processing helix chain 'D' and resid 512 through 528 removed outlier: 3.544A pdb=" N ALA D 519 " --> pdb=" O ASP D 515 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N GLU D 522 " --> pdb=" O SER D 518 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N SER D 523 " --> pdb=" O ALA D 519 " (cutoff:3.500A) Processing helix chain 'D' and resid 533 through 539 Processing helix chain 'D' and resid 543 through 551 removed outlier: 3.572A pdb=" N ASN D 551 " --> pdb=" O GLU D 547 " (cutoff:3.500A) Processing helix chain 'D' and resid 554 through 561 Processing helix chain 'D' and resid 567 through 573 Processing sheet with id= A, first strand: chain 'A' and resid 17 through 20 removed outlier: 6.721A pdb=" N THR A 74 " --> pdb=" O SER A 4 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N ILE A 6 " --> pdb=" O ILE A 72 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ILE A 72 " --> pdb=" O ILE A 6 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N ILE A 8 " --> pdb=" O GLU A 70 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N GLU A 70 " --> pdb=" O ILE A 8 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N LYS A 112 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ASN A 121 " --> pdb=" O LYS A 112 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 344 through 349 removed outlier: 8.321A pdb=" N PHE A 316 " --> pdb=" O VAL A 283 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N TYR A 285 " --> pdb=" O PHE A 316 " (cutoff:3.500A) removed outlier: 8.088A pdb=" N SER A 318 " --> pdb=" O TYR A 285 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N ILE A 287 " --> pdb=" O SER A 318 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 403 through 407 removed outlier: 6.676A pdb=" N ARG A 374 " --> pdb=" O PHE A 404 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N LEU A 406 " --> pdb=" O ARG A 374 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N LEU A 376 " --> pdb=" O LEU A 406 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N THR A 426 " --> pdb=" O VAL A 375 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N LEU A 377 " --> pdb=" O THR A 426 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N ILE A 428 " --> pdb=" O LEU A 377 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 435 through 437 Processing sheet with id= E, first strand: chain 'B' and resid 16 through 20 removed outlier: 6.617A pdb=" N THR B 74 " --> pdb=" O SER B 4 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N ILE B 6 " --> pdb=" O ILE B 72 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ILE B 72 " --> pdb=" O ILE B 6 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N ILE B 8 " --> pdb=" O GLU B 70 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N GLU B 70 " --> pdb=" O ILE B 8 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LYS B 112 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ASN B 121 " --> pdb=" O LYS B 112 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 342 through 349 removed outlier: 6.233A pdb=" N PHE B 315 " --> pdb=" O ASN B 25 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N ILE B 27 " --> pdb=" O PHE B 315 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N LEU B 317 " --> pdb=" O ILE B 27 " (cutoff:3.500A) removed outlier: 8.419A pdb=" N GLY B 29 " --> pdb=" O LEU B 317 " (cutoff:3.500A) removed outlier: 8.256A pdb=" N PHE B 316 " --> pdb=" O VAL B 283 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N TYR B 285 " --> pdb=" O PHE B 316 " (cutoff:3.500A) removed outlier: 8.034A pdb=" N SER B 318 " --> pdb=" O TYR B 285 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N ILE B 287 " --> pdb=" O SER B 318 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 403 through 407 removed outlier: 6.659A pdb=" N ARG B 374 " --> pdb=" O PHE B 404 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N LEU B 406 " --> pdb=" O ARG B 374 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N LEU B 376 " --> pdb=" O LEU B 406 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N THR B 426 " --> pdb=" O VAL B 375 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N LEU B 377 " --> pdb=" O THR B 426 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N ILE B 428 " --> pdb=" O LEU B 377 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 435 through 437 Processing sheet with id= I, first strand: chain 'C' and resid 17 through 20 removed outlier: 6.805A pdb=" N THR C 74 " --> pdb=" O SER C 4 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N ILE C 6 " --> pdb=" O ILE C 72 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N ILE C 72 " --> pdb=" O ILE C 6 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N ILE C 8 " --> pdb=" O GLU C 70 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N GLU C 70 " --> pdb=" O ILE C 8 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LYS C 112 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ASN C 121 " --> pdb=" O LYS C 112 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 344 through 349 removed outlier: 4.466A pdb=" N TYR C 314 " --> pdb=" O VAL C 283 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 403 through 407 removed outlier: 6.659A pdb=" N ARG C 374 " --> pdb=" O PHE C 404 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N LEU C 406 " --> pdb=" O ARG C 374 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N LEU C 376 " --> pdb=" O LEU C 406 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N THR C 426 " --> pdb=" O VAL C 375 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N LEU C 377 " --> pdb=" O THR C 426 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N ILE C 428 " --> pdb=" O LEU C 377 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 435 through 437 Processing sheet with id= M, first strand: chain 'D' and resid 16 through 20 removed outlier: 6.763A pdb=" N THR D 74 " --> pdb=" O SER D 4 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N ILE D 6 " --> pdb=" O ILE D 72 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ILE D 72 " --> pdb=" O ILE D 6 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N ILE D 8 " --> pdb=" O GLU D 70 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N GLU D 70 " --> pdb=" O ILE D 8 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LYS D 112 " --> pdb=" O ASN D 121 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ASN D 121 " --> pdb=" O LYS D 112 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 342 through 349 removed outlier: 6.315A pdb=" N PHE D 315 " --> pdb=" O ASN D 25 " (cutoff:3.500A) removed outlier: 7.975A pdb=" N ILE D 27 " --> pdb=" O PHE D 315 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N LEU D 317 " --> pdb=" O ILE D 27 " (cutoff:3.500A) removed outlier: 8.506A pdb=" N GLY D 29 " --> pdb=" O LEU D 317 " (cutoff:3.500A) removed outlier: 8.213A pdb=" N PHE D 316 " --> pdb=" O VAL D 283 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N TYR D 285 " --> pdb=" O PHE D 316 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N SER D 318 " --> pdb=" O TYR D 285 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ILE D 287 " --> pdb=" O SER D 318 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'D' and resid 403 through 407 removed outlier: 6.596A pdb=" N ARG D 374 " --> pdb=" O PHE D 404 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N LEU D 406 " --> pdb=" O ARG D 374 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N LEU D 376 " --> pdb=" O LEU D 406 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N THR D 426 " --> pdb=" O VAL D 375 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N LEU D 377 " --> pdb=" O THR D 426 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N ILE D 428 " --> pdb=" O LEU D 377 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 435 through 437 593 hydrogen bonds defined for protein. 1692 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: 5.09 Time building geometry restraints manager: 6.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4319 1.33 - 1.45: 3116 1.45 - 1.57: 9752 1.57 - 1.69: 17 1.69 - 1.81: 90 Bond restraints: 17294 Sorted by residual: bond pdb=" N VAL A 358 " pdb=" CA VAL A 358 " ideal model delta sigma weight residual 1.459 1.501 -0.042 1.25e-02 6.40e+03 1.15e+01 bond pdb=" N ILE A 467 " pdb=" CA ILE A 467 " ideal model delta sigma weight residual 1.456 1.494 -0.038 1.14e-02 7.69e+03 1.10e+01 bond pdb=" C VAL A 358 " pdb=" O VAL A 358 " ideal model delta sigma weight residual 1.236 1.274 -0.037 1.19e-02 7.06e+03 9.91e+00 bond pdb=" N VAL D 93 " pdb=" CA VAL D 93 " ideal model delta sigma weight residual 1.459 1.498 -0.039 1.25e-02 6.40e+03 9.59e+00 bond pdb=" N VAL B 93 " pdb=" CA VAL B 93 " ideal model delta sigma weight residual 1.459 1.498 -0.039 1.25e-02 6.40e+03 9.58e+00 ... (remaining 17289 not shown) Histogram of bond angle deviations from ideal: 97.68 - 106.09: 232 106.09 - 114.50: 10036 114.50 - 122.91: 11303 122.91 - 131.32: 1640 131.32 - 139.72: 28 Bond angle restraints: 23239 Sorted by residual: angle pdb=" C GLU C 471 " pdb=" N ASP C 472 " pdb=" CA ASP C 472 " ideal model delta sigma weight residual 121.54 134.62 -13.08 1.91e+00 2.74e-01 4.69e+01 angle pdb=" C THR C 554 " pdb=" N LYS C 555 " pdb=" CA LYS C 555 " ideal model delta sigma weight residual 121.54 133.91 -12.37 1.91e+00 2.74e-01 4.19e+01 angle pdb=" C PHE A 528 " pdb=" N GLU A 529 " pdb=" CA GLU A 529 " ideal model delta sigma weight residual 122.08 131.48 -9.40 1.47e+00 4.63e-01 4.09e+01 angle pdb=" C ASP C 64 " pdb=" N THR C 65 " pdb=" CA THR C 65 " ideal model delta sigma weight residual 122.61 132.44 -9.83 1.56e+00 4.11e-01 3.97e+01 angle pdb=" N ASP A 32 " pdb=" CA ASP A 32 " pdb=" C ASP A 32 " ideal model delta sigma weight residual 111.52 119.96 -8.44 1.40e+00 5.10e-01 3.63e+01 ... (remaining 23234 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 9413 17.90 - 35.79: 966 35.79 - 53.69: 202 53.69 - 71.58: 35 71.58 - 89.48: 15 Dihedral angle restraints: 10631 sinusoidal: 4574 harmonic: 6057 Sorted by residual: dihedral pdb=" CA GLN B 198 " pdb=" C GLN B 198 " pdb=" N ILE B 199 " pdb=" CA ILE B 199 " ideal model delta harmonic sigma weight residual 180.00 152.10 27.90 0 5.00e+00 4.00e-02 3.11e+01 dihedral pdb=" CA GLU B 201 " pdb=" C GLU B 201 " pdb=" N MET B 202 " pdb=" CA MET B 202 " ideal model delta harmonic sigma weight residual 180.00 152.81 27.19 0 5.00e+00 4.00e-02 2.96e+01 dihedral pdb=" CA LYS C 35 " pdb=" C LYS C 35 " pdb=" N THR C 36 " pdb=" CA THR C 36 " ideal model delta harmonic sigma weight residual 180.00 154.58 25.42 0 5.00e+00 4.00e-02 2.58e+01 ... (remaining 10628 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.114: 2358 0.114 - 0.228: 177 0.228 - 0.342: 12 0.342 - 0.456: 3 0.456 - 0.570: 1 Chirality restraints: 2551 Sorted by residual: chirality pdb=" CB VAL B 549 " pdb=" CA VAL B 549 " pdb=" CG1 VAL B 549 " pdb=" CG2 VAL B 549 " both_signs ideal model delta sigma weight residual False -2.63 -2.06 -0.57 2.00e-01 2.50e+01 8.11e+00 chirality pdb=" CB ILE D 199 " pdb=" CA ILE D 199 " pdb=" CG1 ILE D 199 " pdb=" CG2 ILE D 199 " both_signs ideal model delta sigma weight residual False 2.64 2.22 0.43 2.00e-01 2.50e+01 4.62e+00 chirality pdb=" CA ASP A 32 " pdb=" N ASP A 32 " pdb=" C ASP A 32 " pdb=" CB ASP A 32 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.44e+00 ... (remaining 2548 not shown) Planarity restraints: 2940 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL C 358 " -0.018 2.00e-02 2.50e+03 3.54e-02 1.25e+01 pdb=" C VAL C 358 " 0.061 2.00e-02 2.50e+03 pdb=" O VAL C 358 " -0.023 2.00e-02 2.50e+03 pdb=" N LYS C 359 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE D 90 " 0.014 2.00e-02 2.50e+03 2.81e-02 7.88e+00 pdb=" C ILE D 90 " -0.049 2.00e-02 2.50e+03 pdb=" O ILE D 90 " 0.018 2.00e-02 2.50e+03 pdb=" N SER D 91 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 90 " -0.014 2.00e-02 2.50e+03 2.80e-02 7.86e+00 pdb=" C ILE B 90 " 0.048 2.00e-02 2.50e+03 pdb=" O ILE B 90 " -0.018 2.00e-02 2.50e+03 pdb=" N SER B 91 " -0.016 2.00e-02 2.50e+03 ... (remaining 2937 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 192 2.67 - 3.23: 13806 3.23 - 3.79: 24261 3.79 - 4.34: 36475 4.34 - 4.90: 58794 Nonbonded interactions: 133528 Sorted by model distance: nonbonded pdb=" O1G ATP A 601 " pdb="MG MG A 602 " model vdw 2.113 2.170 nonbonded pdb=" OG1 THR D 36 " pdb="MG MG D 602 " model vdw 2.127 2.170 nonbonded pdb=" OG1 THR B 36 " pdb="MG MG B 602 " model vdw 2.130 2.170 nonbonded pdb=" OG1 THR A 36 " pdb="MG MG A 602 " model vdw 2.160 2.170 nonbonded pdb=" O2B ATP A 601 " pdb="MG MG A 602 " model vdw 2.197 2.170 ... (remaining 133523 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 156 or resid 261 through 578 or resid 601 throug \ h 602)) selection = (chain 'B' and (resid 1 through 156 or resid 261 through 578 or resid 601 throug \ h 602)) selection = chain 'C' selection = (chain 'D' and (resid 1 through 156 or resid 261 through 578 or resid 601 throug \ h 602)) } 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: 4.810 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: 0.000 Extract box with map and model: 12.030 Check model and map are aligned: 0.230 Set scattering table: 0.150 Process input model: 46.730 Find NCS groups from input model: 1.250 Set up NCS constraints: 0.090 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: 0.000 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 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 0.062 17294 Z= 0.430 Angle : 1.045 13.081 23239 Z= 0.595 Chirality : 0.064 0.570 2551 Planarity : 0.006 0.059 2940 Dihedral : 15.256 89.476 6735 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.79 % Favored : 95.16 % Rotamer: Outliers : 0.64 % Allowed : 0.95 % Favored : 98.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.57 (0.15), residues: 2047 helix: -3.88 (0.08), residues: 807 sheet: 0.41 (0.26), residues: 393 loop : -2.00 (0.18), residues: 847 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 126 HIS 0.012 0.002 HIS C 320 PHE 0.038 0.003 PHE C 315 TYR 0.021 0.002 TYR B 272 ARG 0.007 0.001 ARG C 51 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 1889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 322 time to evaluate : 1.956 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 70 GLU cc_start: 0.8163 (tt0) cc_final: 0.7821 (tp30) REVERT: A 143 ASN cc_start: 0.8520 (p0) cc_final: 0.8312 (p0) REVERT: A 480 GLU cc_start: 0.7159 (mp0) cc_final: 0.6626 (tp30) REVERT: A 481 ARG cc_start: 0.7940 (tpp80) cc_final: 0.7569 (tpp80) REVERT: A 511 ASP cc_start: 0.7775 (m-30) cc_final: 0.7559 (m-30) REVERT: B 132 ASN cc_start: 0.8754 (t0) cc_final: 0.8527 (t0) REVERT: B 197 GLN cc_start: 0.8395 (tm-30) cc_final: 0.7888 (tm-30) REVERT: B 211 GLU cc_start: 0.8163 (mt-10) cc_final: 0.7600 (mt-10) REVERT: B 229 LYS cc_start: 0.8178 (ptpt) cc_final: 0.7944 (ptpt) REVERT: B 232 MET cc_start: 0.8234 (ppp) cc_final: 0.7987 (ptm) REVERT: B 422 ASP cc_start: 0.8446 (m-30) cc_final: 0.8093 (m-30) REVERT: B 476 LYS cc_start: 0.7322 (tttt) cc_final: 0.6949 (mptt) REVERT: B 492 GLN cc_start: 0.8152 (tt0) cc_final: 0.7929 (tt0) REVERT: C 62 LYS cc_start: 0.8370 (mttt) cc_final: 0.7661 (mmtt) REVERT: C 70 GLU cc_start: 0.7994 (tt0) cc_final: 0.7765 (tt0) REVERT: C 94 LYS cc_start: 0.7863 (OUTLIER) cc_final: 0.7659 (tppt) REVERT: C 464 GLU cc_start: 0.7646 (pp20) cc_final: 0.6922 (pp20) REVERT: C 465 ILE cc_start: 0.8434 (pt) cc_final: 0.7948 (tp) REVERT: C 477 LYS cc_start: 0.8652 (mmmm) cc_final: 0.7733 (pttm) REVERT: C 481 ARG cc_start: 0.7719 (mtp180) cc_final: 0.7433 (ttp-170) REVERT: D 67 LYS cc_start: 0.8110 (mmpt) cc_final: 0.7366 (mtmm) REVERT: D 87 LYS cc_start: 0.8100 (mttt) cc_final: 0.7615 (mtmt) REVERT: D 114 ASP cc_start: 0.7668 (t0) cc_final: 0.7377 (t0) REVERT: D 278 TYR cc_start: 0.8749 (m-80) cc_final: 0.8459 (m-80) REVERT: D 279 GLU cc_start: 0.8001 (tm-30) cc_final: 0.7730 (tm-30) REVERT: D 280 ASP cc_start: 0.7533 (m-30) cc_final: 0.7266 (m-30) REVERT: D 434 ASP cc_start: 0.8406 (m-30) cc_final: 0.8134 (m-30) REVERT: D 438 LYS cc_start: 0.8255 (pttm) cc_final: 0.8008 (pttm) REVERT: D 526 ARG cc_start: 0.7863 (ttp-170) cc_final: 0.7505 (ttp-170) outliers start: 12 outliers final: 2 residues processed: 332 average time/residue: 0.3631 time to fit residues: 171.1621 Evaluate side-chains 219 residues out of total 1889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 216 time to evaluate : 1.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain C residue 94 LYS Chi-restraints excluded: chain C residue 103 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 172 optimal weight: 3.9990 chunk 154 optimal weight: 0.9980 chunk 85 optimal weight: 0.4980 chunk 52 optimal weight: 1.9990 chunk 104 optimal weight: 0.9980 chunk 82 optimal weight: 0.9980 chunk 159 optimal weight: 0.7980 chunk 61 optimal weight: 0.8980 chunk 97 optimal weight: 5.9990 chunk 119 optimal weight: 0.7980 chunk 185 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 492 GLN B 186 ASN B 455 ASN C 13 ASN C 56 ASN C 563 HIS D 186 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.1583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 17294 Z= 0.186 Angle : 0.510 8.584 23239 Z= 0.277 Chirality : 0.043 0.149 2551 Planarity : 0.003 0.037 2940 Dihedral : 8.746 85.019 2378 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.62 % Favored : 96.34 % Rotamer: Outliers : 1.16 % Allowed : 7.25 % Favored : 91.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.94 (0.16), residues: 2047 helix: -1.61 (0.15), residues: 823 sheet: 0.55 (0.26), residues: 391 loop : -1.73 (0.19), residues: 833 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 126 HIS 0.011 0.001 HIS A 535 PHE 0.023 0.001 PHE C 315 TYR 0.013 0.001 TYR B 272 ARG 0.004 0.000 ARG D 139 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 236 time to evaluate : 2.070 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 GLU cc_start: 0.8252 (tt0) cc_final: 0.7971 (tp30) REVERT: A 143 ASN cc_start: 0.8508 (p0) cc_final: 0.8288 (p0) REVERT: A 530 ASN cc_start: 0.7565 (t0) cc_final: 0.6654 (t0) REVERT: B 30 MET cc_start: 0.8053 (mmm) cc_final: 0.7800 (tpt) REVERT: B 106 TYR cc_start: 0.8821 (m-80) cc_final: 0.8203 (m-80) REVERT: B 129 GLU cc_start: 0.7355 (mm-30) cc_final: 0.6965 (mm-30) REVERT: B 132 ASN cc_start: 0.8712 (t0) cc_final: 0.8498 (t0) REVERT: B 197 GLN cc_start: 0.8504 (tm-30) cc_final: 0.7973 (tm-30) REVERT: B 211 GLU cc_start: 0.8079 (mt-10) cc_final: 0.7787 (mt-10) REVERT: B 217 ARG cc_start: 0.8020 (mtp85) cc_final: 0.7716 (mtp85) REVERT: B 221 LYS cc_start: 0.8862 (mtmm) cc_final: 0.8384 (mppt) REVERT: B 232 MET cc_start: 0.8394 (ppp) cc_final: 0.8068 (ptm) REVERT: B 446 GLU cc_start: 0.7754 (tt0) cc_final: 0.7419 (tt0) REVERT: B 571 GLU cc_start: 0.8134 (mm-30) cc_final: 0.7929 (tp30) REVERT: C 70 GLU cc_start: 0.8036 (tt0) cc_final: 0.7826 (tt0) REVERT: C 94 LYS cc_start: 0.8402 (ttpp) cc_final: 0.7885 (tppt) REVERT: C 278 TYR cc_start: 0.7788 (m-80) cc_final: 0.7431 (m-80) REVERT: C 464 GLU cc_start: 0.7801 (pp20) cc_final: 0.6973 (pp20) REVERT: C 465 ILE cc_start: 0.8307 (pt) cc_final: 0.7903 (tp) REVERT: C 480 GLU cc_start: 0.7333 (pm20) cc_final: 0.6932 (pm20) REVERT: C 481 ARG cc_start: 0.7865 (mtp180) cc_final: 0.7583 (ttp-170) REVERT: D 30 MET cc_start: 0.8201 (mmt) cc_final: 0.7848 (tpt) REVERT: D 67 LYS cc_start: 0.8113 (mmpt) cc_final: 0.7311 (mtmm) REVERT: D 87 LYS cc_start: 0.8010 (mttt) cc_final: 0.7699 (mtmt) REVERT: D 114 ASP cc_start: 0.7912 (t0) cc_final: 0.7574 (t0) REVERT: D 202 MET cc_start: 0.3786 (mpp) cc_final: 0.3571 (mpp) REVERT: D 279 GLU cc_start: 0.8065 (tm-30) cc_final: 0.7763 (tm-30) REVERT: D 280 ASP cc_start: 0.7527 (m-30) cc_final: 0.7245 (m-30) REVERT: D 379 GLU cc_start: 0.7838 (tp30) cc_final: 0.7498 (tp30) REVERT: D 434 ASP cc_start: 0.8397 (m-30) cc_final: 0.8134 (m-30) REVERT: D 526 ARG cc_start: 0.7989 (ttp-170) cc_final: 0.7649 (ttp-170) REVERT: D 564 GLU cc_start: 0.7772 (tp30) cc_final: 0.7530 (tp30) outliers start: 22 outliers final: 17 residues processed: 250 average time/residue: 0.3629 time to fit residues: 130.3746 Evaluate side-chains 223 residues out of total 1889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 206 time to evaluate : 2.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 LYS Chi-restraints excluded: chain A residue 318 SER Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain A residue 495 ASN Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 186 ASN Chi-restraints excluded: chain B residue 432 ASP Chi-restraints excluded: chain C residue 25 ASN Chi-restraints excluded: chain C residue 103 ASP Chi-restraints excluded: chain C residue 346 SER Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain D residue 142 ILE Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain D residue 305 GLN Chi-restraints excluded: chain D residue 418 CYS Chi-restraints excluded: chain D residue 455 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 102 optimal weight: 3.9990 chunk 57 optimal weight: 0.5980 chunk 154 optimal weight: 3.9990 chunk 126 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 185 optimal weight: 1.9990 chunk 200 optimal weight: 0.0020 chunk 165 optimal weight: 0.8980 chunk 184 optimal weight: 0.7980 chunk 63 optimal weight: 0.8980 chunk 148 optimal weight: 0.7980 overall best weight: 0.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 535 HIS B 147 ASN B 178 ASN C 56 ASN ** C 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 198 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.2028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 17294 Z= 0.153 Angle : 0.457 6.868 23239 Z= 0.249 Chirality : 0.042 0.141 2551 Planarity : 0.002 0.028 2940 Dihedral : 7.775 78.186 2374 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.62 % Favored : 96.34 % Rotamer: Outliers : 1.69 % Allowed : 8.58 % Favored : 89.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.90 (0.18), residues: 2047 helix: -0.26 (0.17), residues: 819 sheet: 0.78 (0.27), residues: 374 loop : -1.52 (0.19), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 126 HIS 0.007 0.001 HIS A 535 PHE 0.020 0.001 PHE C 315 TYR 0.011 0.001 TYR B 272 ARG 0.003 0.000 ARG A 481 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 228 time to evaluate : 2.335 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 70 GLU cc_start: 0.8267 (tt0) cc_final: 0.7960 (tp30) REVERT: A 530 ASN cc_start: 0.7614 (t0) cc_final: 0.6788 (t0) REVERT: B 129 GLU cc_start: 0.7355 (mm-30) cc_final: 0.7105 (mp0) REVERT: B 197 GLN cc_start: 0.8571 (tm-30) cc_final: 0.7974 (tm-30) REVERT: B 211 GLU cc_start: 0.8271 (mt-10) cc_final: 0.7809 (mt-10) REVERT: B 217 ARG cc_start: 0.8040 (mtp85) cc_final: 0.7822 (mtp85) REVERT: B 221 LYS cc_start: 0.8846 (mtmm) cc_final: 0.8414 (mppt) REVERT: B 232 MET cc_start: 0.8414 (ppp) cc_final: 0.8053 (ptm) REVERT: B 446 GLU cc_start: 0.7832 (tt0) cc_final: 0.7579 (tt0) REVERT: B 494 LYS cc_start: 0.7783 (ttpp) cc_final: 0.7356 (pttm) REVERT: B 547 GLU cc_start: 0.8021 (tt0) cc_final: 0.7773 (tt0) REVERT: C 70 GLU cc_start: 0.8029 (tt0) cc_final: 0.7813 (tt0) REVERT: C 94 LYS cc_start: 0.8501 (ttpp) cc_final: 0.7843 (tppt) REVERT: C 278 TYR cc_start: 0.7864 (m-80) cc_final: 0.7514 (m-80) REVERT: C 397 GLU cc_start: 0.7751 (mt-10) cc_final: 0.7525 (mt-10) REVERT: C 464 GLU cc_start: 0.7807 (pp20) cc_final: 0.6980 (pp20) REVERT: C 465 ILE cc_start: 0.8227 (pt) cc_final: 0.7848 (tt) REVERT: C 481 ARG cc_start: 0.7826 (mtp180) cc_final: 0.7464 (ttp-170) REVERT: C 538 GLN cc_start: 0.8253 (mm110) cc_final: 0.7995 (mm110) REVERT: D 30 MET cc_start: 0.8154 (mmt) cc_final: 0.7849 (tpt) REVERT: D 67 LYS cc_start: 0.8151 (mmpt) cc_final: 0.7208 (mtmm) REVERT: D 87 LYS cc_start: 0.7998 (mttt) cc_final: 0.7661 (mtmt) REVERT: D 114 ASP cc_start: 0.7927 (t0) cc_final: 0.7601 (t0) REVERT: D 198 GLN cc_start: 0.6273 (OUTLIER) cc_final: 0.5600 (pm20) REVERT: D 279 GLU cc_start: 0.8110 (tm-30) cc_final: 0.7840 (tm-30) REVERT: D 280 ASP cc_start: 0.7524 (m-30) cc_final: 0.7235 (m-30) REVERT: D 379 GLU cc_start: 0.7877 (tp30) cc_final: 0.7618 (tp30) REVERT: D 392 ASP cc_start: 0.8333 (t0) cc_final: 0.8076 (t0) REVERT: D 434 ASP cc_start: 0.8331 (m-30) cc_final: 0.8082 (m-30) REVERT: D 526 ARG cc_start: 0.8022 (ttp-170) cc_final: 0.7444 (ttt-90) REVERT: D 564 GLU cc_start: 0.7756 (tp30) cc_final: 0.7446 (tp30) outliers start: 32 outliers final: 24 residues processed: 250 average time/residue: 0.3624 time to fit residues: 130.2536 Evaluate side-chains 234 residues out of total 1889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 209 time to evaluate : 2.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 318 SER Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 367 SER Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain A residue 495 ASN Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 432 ASP Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 320 HIS Chi-restraints excluded: chain C residue 346 SER Chi-restraints excluded: chain C residue 357 SER Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 362 LEU Chi-restraints excluded: chain D residue 142 ILE Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain D residue 154 ILE Chi-restraints excluded: chain D residue 198 GLN Chi-restraints excluded: chain D residue 418 CYS Chi-restraints excluded: chain D residue 461 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 183 optimal weight: 0.3980 chunk 139 optimal weight: 7.9990 chunk 96 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 88 optimal weight: 7.9990 chunk 124 optimal weight: 3.9990 chunk 186 optimal weight: 2.9990 chunk 197 optimal weight: 3.9990 chunk 97 optimal weight: 0.8980 chunk 176 optimal weight: 1.9990 chunk 53 optimal weight: 0.0980 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 535 HIS B 209 GLN C 56 ASN C 551 ASN D 198 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.2314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 17294 Z= 0.269 Angle : 0.521 7.034 23239 Z= 0.278 Chirality : 0.044 0.244 2551 Planarity : 0.003 0.033 2940 Dihedral : 7.824 79.290 2372 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.45 % Favored : 95.51 % Rotamer: Outliers : 2.06 % Allowed : 10.59 % Favored : 87.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.63 (0.18), residues: 2047 helix: 0.07 (0.18), residues: 834 sheet: 0.68 (0.26), residues: 380 loop : -1.40 (0.20), residues: 833 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 126 HIS 0.006 0.001 HIS A 535 PHE 0.027 0.001 PHE C 315 TYR 0.011 0.001 TYR A 517 ARG 0.003 0.000 ARG A 481 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 215 time to evaluate : 2.224 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 70 GLU cc_start: 0.8330 (tt0) cc_final: 0.7950 (tp30) REVERT: A 530 ASN cc_start: 0.7581 (t0) cc_final: 0.6708 (t0) REVERT: B 106 TYR cc_start: 0.8847 (m-80) cc_final: 0.8193 (m-80) REVERT: B 129 GLU cc_start: 0.7422 (mm-30) cc_final: 0.7214 (mm-30) REVERT: B 197 GLN cc_start: 0.8657 (tm-30) cc_final: 0.8161 (tm-30) REVERT: B 206 LYS cc_start: 0.8218 (mmtt) cc_final: 0.7956 (mmtt) REVERT: B 211 GLU cc_start: 0.8300 (mt-10) cc_final: 0.7639 (mt-10) REVERT: B 221 LYS cc_start: 0.8869 (mtmm) cc_final: 0.8605 (mppt) REVERT: B 232 MET cc_start: 0.8476 (ppp) cc_final: 0.8095 (ptm) REVERT: B 446 GLU cc_start: 0.8035 (tt0) cc_final: 0.7792 (tt0) REVERT: B 494 LYS cc_start: 0.7880 (ttpp) cc_final: 0.7418 (pttm) REVERT: B 511 ASP cc_start: 0.8864 (m-30) cc_final: 0.8595 (m-30) REVERT: C 70 GLU cc_start: 0.8039 (tt0) cc_final: 0.7807 (tt0) REVERT: C 94 LYS cc_start: 0.8602 (ttpp) cc_final: 0.7832 (tppt) REVERT: C 278 TYR cc_start: 0.7867 (m-80) cc_final: 0.7530 (m-80) REVERT: C 464 GLU cc_start: 0.7903 (pp20) cc_final: 0.6950 (pp20) REVERT: C 465 ILE cc_start: 0.8224 (pt) cc_final: 0.7913 (tt) REVERT: C 477 LYS cc_start: 0.8609 (mmmm) cc_final: 0.8014 (ptmm) REVERT: C 481 ARG cc_start: 0.7789 (mtp180) cc_final: 0.7423 (ttp-170) REVERT: D 30 MET cc_start: 0.8261 (mmt) cc_final: 0.7926 (tpt) REVERT: D 67 LYS cc_start: 0.8065 (mmpt) cc_final: 0.7165 (mtmm) REVERT: D 87 LYS cc_start: 0.8014 (mttt) cc_final: 0.7653 (mtmt) REVERT: D 168 LYS cc_start: 0.8339 (mtmm) cc_final: 0.8024 (mtpt) REVERT: D 198 GLN cc_start: 0.6275 (OUTLIER) cc_final: 0.5734 (pm20) REVERT: D 379 GLU cc_start: 0.7964 (tp30) cc_final: 0.7733 (tp30) REVERT: D 434 ASP cc_start: 0.8341 (m-30) cc_final: 0.8096 (m-30) REVERT: D 526 ARG cc_start: 0.8063 (ttp-170) cc_final: 0.7354 (ttt-90) REVERT: D 564 GLU cc_start: 0.7782 (tp30) cc_final: 0.7443 (tp30) outliers start: 39 outliers final: 34 residues processed: 242 average time/residue: 0.3726 time to fit residues: 128.7181 Evaluate side-chains 236 residues out of total 1889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 201 time to evaluate : 2.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 318 SER Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 367 SER Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain A residue 495 ASN Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 535 HIS Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 432 ASP Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain C residue 25 ASN Chi-restraints excluded: chain C residue 103 ASP Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 320 HIS Chi-restraints excluded: chain C residue 346 SER Chi-restraints excluded: chain C residue 357 SER Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 362 LEU Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain D residue 66 SER Chi-restraints excluded: chain D residue 142 ILE Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain D residue 154 ILE Chi-restraints excluded: chain D residue 161 ASP Chi-restraints excluded: chain D residue 198 GLN Chi-restraints excluded: chain D residue 248 ASP Chi-restraints excluded: chain D residue 305 GLN Chi-restraints excluded: chain D residue 341 LYS Chi-restraints excluded: chain D residue 418 CYS Chi-restraints excluded: chain D residue 461 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 164 optimal weight: 2.9990 chunk 111 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 chunk 146 optimal weight: 4.9990 chunk 81 optimal weight: 0.6980 chunk 168 optimal weight: 20.0000 chunk 136 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 chunk 100 optimal weight: 0.8980 chunk 176 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 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 535 HIS B 210 GLN C 56 ASN D 198 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.2485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 17294 Z= 0.265 Angle : 0.516 7.213 23239 Z= 0.275 Chirality : 0.045 0.494 2551 Planarity : 0.003 0.033 2940 Dihedral : 7.700 78.510 2372 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.30 % Favored : 95.65 % Rotamer: Outliers : 2.44 % Allowed : 11.65 % Favored : 85.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.18), residues: 2047 helix: 0.33 (0.18), residues: 826 sheet: 0.57 (0.26), residues: 389 loop : -1.25 (0.20), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 126 HIS 0.012 0.001 HIS A 535 PHE 0.025 0.001 PHE C 315 TYR 0.010 0.001 TYR A 517 ARG 0.006 0.000 ARG A 481 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 209 time to evaluate : 1.996 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 276 LYS cc_start: 0.8036 (ttpt) cc_final: 0.7631 (mtpt) REVERT: A 479 LYS cc_start: 0.5901 (mptt) cc_final: 0.5540 (ttpt) REVERT: A 530 ASN cc_start: 0.7603 (t0) cc_final: 0.6705 (t0) REVERT: B 106 TYR cc_start: 0.8858 (m-80) cc_final: 0.8144 (m-80) REVERT: B 129 GLU cc_start: 0.7437 (mm-30) cc_final: 0.7140 (mm-30) REVERT: B 197 GLN cc_start: 0.8731 (tm-30) cc_final: 0.8260 (tm-30) REVERT: B 211 GLU cc_start: 0.8194 (OUTLIER) cc_final: 0.7856 (mt-10) REVERT: B 221 LYS cc_start: 0.8867 (mtmm) cc_final: 0.8597 (mppt) REVERT: B 232 MET cc_start: 0.8435 (ppp) cc_final: 0.7932 (ptm) REVERT: B 379 GLU cc_start: 0.8210 (tm-30) cc_final: 0.7814 (tp30) REVERT: B 446 GLU cc_start: 0.8053 (tt0) cc_final: 0.7847 (tt0) REVERT: C 70 GLU cc_start: 0.8034 (tt0) cc_final: 0.7813 (tt0) REVERT: C 278 TYR cc_start: 0.7860 (m-80) cc_final: 0.7513 (m-80) REVERT: C 464 GLU cc_start: 0.7860 (pp20) cc_final: 0.7016 (pp20) REVERT: C 465 ILE cc_start: 0.8168 (pt) cc_final: 0.7866 (tt) REVERT: C 477 LYS cc_start: 0.8611 (mmmm) cc_final: 0.7984 (ptmm) REVERT: C 481 ARG cc_start: 0.7777 (mtp180) cc_final: 0.7543 (ttp-170) REVERT: D 30 MET cc_start: 0.8268 (mmt) cc_final: 0.7937 (tpt) REVERT: D 67 LYS cc_start: 0.8046 (mmpt) cc_final: 0.7118 (mtmm) REVERT: D 87 LYS cc_start: 0.8038 (mttt) cc_final: 0.7660 (mtmt) REVERT: D 168 LYS cc_start: 0.8393 (mtmm) cc_final: 0.8092 (mtpt) REVERT: D 198 GLN cc_start: 0.6585 (OUTLIER) cc_final: 0.6305 (pm20) REVERT: D 379 GLU cc_start: 0.7948 (tp30) cc_final: 0.7329 (mp0) REVERT: D 434 ASP cc_start: 0.8337 (m-30) cc_final: 0.8093 (m-30) REVERT: D 526 ARG cc_start: 0.8011 (ttp-170) cc_final: 0.7317 (ttt-90) REVERT: D 564 GLU cc_start: 0.7787 (tp30) cc_final: 0.7443 (tp30) outliers start: 46 outliers final: 31 residues processed: 242 average time/residue: 0.3665 time to fit residues: 126.9005 Evaluate side-chains 234 residues out of total 1889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 201 time to evaluate : 2.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ILE Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 318 SER Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 367 SER Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 211 GLU Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 432 ASP Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain C residue 25 ASN Chi-restraints excluded: chain C residue 103 ASP Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 320 HIS Chi-restraints excluded: chain C residue 346 SER Chi-restraints excluded: chain C residue 357 SER Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 362 LEU Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain D residue 66 SER Chi-restraints excluded: chain D residue 142 ILE Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain D residue 154 ILE Chi-restraints excluded: chain D residue 161 ASP Chi-restraints excluded: chain D residue 198 GLN Chi-restraints excluded: chain D residue 305 GLN Chi-restraints excluded: chain D residue 341 LYS Chi-restraints excluded: chain D residue 418 CYS Chi-restraints excluded: chain D residue 461 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 66 optimal weight: 9.9990 chunk 177 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 115 optimal weight: 0.8980 chunk 48 optimal weight: 2.9990 chunk 197 optimal weight: 2.9990 chunk 163 optimal weight: 0.9980 chunk 91 optimal weight: 8.9990 chunk 16 optimal weight: 5.9990 chunk 65 optimal weight: 20.0000 chunk 103 optimal weight: 1.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 167 ASN B 210 GLN C 13 ASN C 56 ASN D 198 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.2693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 17294 Z= 0.357 Angle : 0.576 7.366 23239 Z= 0.302 Chirality : 0.046 0.430 2551 Planarity : 0.003 0.035 2940 Dihedral : 7.949 86.626 2372 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.89 % Favored : 95.07 % Rotamer: Outliers : 2.86 % Allowed : 12.07 % Favored : 85.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.18), residues: 2047 helix: 0.31 (0.18), residues: 828 sheet: 0.61 (0.26), residues: 372 loop : -1.25 (0.20), residues: 847 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP D 126 HIS 0.007 0.001 HIS C 320 PHE 0.029 0.002 PHE C 315 TYR 0.012 0.001 TYR A 517 ARG 0.005 0.000 ARG A 481 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 202 time to evaluate : 2.118 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 276 LYS cc_start: 0.8008 (ttpt) cc_final: 0.7509 (mtpt) REVERT: A 479 LYS cc_start: 0.5895 (mptt) cc_final: 0.5532 (ttpt) REVERT: A 530 ASN cc_start: 0.7644 (t0) cc_final: 0.7360 (t0) REVERT: B 106 TYR cc_start: 0.8885 (m-80) cc_final: 0.8171 (m-80) REVERT: B 129 GLU cc_start: 0.7458 (mm-30) cc_final: 0.7083 (mm-30) REVERT: B 197 GLN cc_start: 0.8824 (tm-30) cc_final: 0.8411 (tm-30) REVERT: B 211 GLU cc_start: 0.8193 (OUTLIER) cc_final: 0.7992 (mt-10) REVERT: B 221 LYS cc_start: 0.8870 (mtmm) cc_final: 0.8585 (mppt) REVERT: B 232 MET cc_start: 0.8453 (ppp) cc_final: 0.7922 (ptm) REVERT: C 278 TYR cc_start: 0.7870 (m-80) cc_final: 0.7501 (m-80) REVERT: C 464 GLU cc_start: 0.7937 (pp20) cc_final: 0.7088 (pp20) REVERT: C 465 ILE cc_start: 0.8161 (pt) cc_final: 0.7739 (tt) REVERT: C 481 ARG cc_start: 0.7775 (mtp180) cc_final: 0.7533 (ttp-170) REVERT: D 30 MET cc_start: 0.8353 (mmt) cc_final: 0.8016 (tpt) REVERT: D 67 LYS cc_start: 0.7963 (mmpt) cc_final: 0.7079 (mtmm) REVERT: D 87 LYS cc_start: 0.8051 (mttt) cc_final: 0.7748 (mttp) REVERT: D 168 LYS cc_start: 0.8437 (mtmm) cc_final: 0.8144 (mtpt) REVERT: D 379 GLU cc_start: 0.7986 (tp30) cc_final: 0.7329 (mp0) REVERT: D 434 ASP cc_start: 0.8354 (m-30) cc_final: 0.8134 (m-30) REVERT: D 526 ARG cc_start: 0.8033 (ttp-170) cc_final: 0.7420 (ttt-90) REVERT: D 564 GLU cc_start: 0.7839 (tp30) cc_final: 0.7480 (tp30) outliers start: 54 outliers final: 40 residues processed: 241 average time/residue: 0.3613 time to fit residues: 124.0011 Evaluate side-chains 235 residues out of total 1889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 194 time to evaluate : 2.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ILE Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 318 SER Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 367 SER Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain A residue 495 ASN Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 210 GLN Chi-restraints excluded: chain B residue 211 GLU Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 397 GLU Chi-restraints excluded: chain B residue 432 ASP Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 25 ASN Chi-restraints excluded: chain C residue 103 ASP Chi-restraints excluded: chain C residue 287 ILE Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 320 HIS Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain C residue 346 SER Chi-restraints excluded: chain C residue 357 SER Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 362 LEU Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain D residue 142 ILE Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain D residue 154 ILE Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 161 ASP Chi-restraints excluded: chain D residue 280 ASP Chi-restraints excluded: chain D residue 341 LYS Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 418 CYS Chi-restraints excluded: chain D residue 461 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 190 optimal weight: 7.9990 chunk 22 optimal weight: 0.5980 chunk 112 optimal weight: 0.8980 chunk 144 optimal weight: 0.8980 chunk 111 optimal weight: 1.9990 chunk 166 optimal weight: 0.8980 chunk 110 optimal weight: 0.9980 chunk 196 optimal weight: 0.8980 chunk 123 optimal weight: 0.6980 chunk 119 optimal weight: 0.8980 chunk 90 optimal weight: 0.2980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 132 ASN B 210 GLN C 13 ASN C 56 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.2702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 17294 Z= 0.169 Angle : 0.483 7.450 23239 Z= 0.260 Chirality : 0.043 0.299 2551 Planarity : 0.002 0.031 2940 Dihedral : 7.408 81.814 2372 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.76 % Favored : 96.19 % Rotamer: Outliers : 2.22 % Allowed : 13.55 % Favored : 84.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.19), residues: 2047 helix: 0.61 (0.19), residues: 830 sheet: 0.66 (0.26), residues: 380 loop : -1.15 (0.21), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 126 HIS 0.004 0.001 HIS C 415 PHE 0.019 0.001 PHE C 315 TYR 0.009 0.001 TYR A 314 ARG 0.005 0.000 ARG C 526 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 199 time to evaluate : 2.108 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 276 LYS cc_start: 0.8005 (ttpt) cc_final: 0.7550 (mtpt) REVERT: A 479 LYS cc_start: 0.5860 (mptt) cc_final: 0.5513 (ttpt) REVERT: A 530 ASN cc_start: 0.7593 (t0) cc_final: 0.7303 (t0) REVERT: B 106 TYR cc_start: 0.8847 (m-80) cc_final: 0.8154 (m-80) REVERT: B 197 GLN cc_start: 0.8877 (tm-30) cc_final: 0.8527 (tm-30) REVERT: B 211 GLU cc_start: 0.8218 (OUTLIER) cc_final: 0.7649 (mt-10) REVERT: B 221 LYS cc_start: 0.8840 (mtmm) cc_final: 0.8558 (mppt) REVERT: B 232 MET cc_start: 0.8416 (ppp) cc_final: 0.7929 (ptm) REVERT: B 379 GLU cc_start: 0.8179 (tm-30) cc_final: 0.7774 (tp30) REVERT: B 511 ASP cc_start: 0.8790 (m-30) cc_final: 0.8486 (m-30) REVERT: C 278 TYR cc_start: 0.7874 (m-80) cc_final: 0.7508 (m-80) REVERT: C 464 GLU cc_start: 0.7955 (pp20) cc_final: 0.7091 (pp20) REVERT: C 465 ILE cc_start: 0.8113 (pt) cc_final: 0.7657 (tt) REVERT: C 481 ARG cc_start: 0.7689 (mtp180) cc_final: 0.7456 (ttp-170) REVERT: D 30 MET cc_start: 0.8274 (mmt) cc_final: 0.7936 (tpt) REVERT: D 67 LYS cc_start: 0.8027 (mmpt) cc_final: 0.7082 (mtmm) REVERT: D 87 LYS cc_start: 0.8051 (mttt) cc_final: 0.7636 (mtmt) REVERT: D 168 LYS cc_start: 0.8298 (mtmm) cc_final: 0.7990 (mtpp) REVERT: D 379 GLU cc_start: 0.7858 (tp30) cc_final: 0.7246 (mp0) REVERT: D 434 ASP cc_start: 0.8334 (m-30) cc_final: 0.8090 (m-30) REVERT: D 526 ARG cc_start: 0.7995 (ttp-170) cc_final: 0.7270 (ttt-90) REVERT: D 564 GLU cc_start: 0.7798 (tp30) cc_final: 0.7457 (tp30) outliers start: 42 outliers final: 38 residues processed: 231 average time/residue: 0.3594 time to fit residues: 119.1208 Evaluate side-chains 233 residues out of total 1889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 194 time to evaluate : 2.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ILE Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 318 SER Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 367 SER Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain A residue 495 ASN Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain B residue 27 ILE Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 198 GLN Chi-restraints excluded: chain B residue 211 GLU Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 397 GLU Chi-restraints excluded: chain B residue 432 ASP Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain C residue 25 ASN Chi-restraints excluded: chain C residue 103 ASP Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 320 HIS Chi-restraints excluded: chain C residue 346 SER Chi-restraints excluded: chain C residue 357 SER Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 362 LEU Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain D residue 142 ILE Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain D residue 154 ILE Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 161 ASP Chi-restraints excluded: chain D residue 280 ASP Chi-restraints excluded: chain D residue 289 GLU Chi-restraints excluded: chain D residue 305 GLN Chi-restraints excluded: chain D residue 341 LYS Chi-restraints excluded: chain D residue 418 CYS Chi-restraints excluded: chain D residue 461 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 121 optimal weight: 0.7980 chunk 78 optimal weight: 3.9990 chunk 117 optimal weight: 3.9990 chunk 59 optimal weight: 0.3980 chunk 38 optimal weight: 1.9990 chunk 125 optimal weight: 4.9990 chunk 133 optimal weight: 0.6980 chunk 97 optimal weight: 5.9990 chunk 18 optimal weight: 0.8980 chunk 154 optimal weight: 0.0370 chunk 178 optimal weight: 2.9990 overall best weight: 0.5658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 544 ASN ** B 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 56 ASN ** C 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.2758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 17294 Z= 0.149 Angle : 0.461 7.553 23239 Z= 0.248 Chirality : 0.042 0.269 2551 Planarity : 0.002 0.030 2940 Dihedral : 7.034 82.572 2372 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.91 % Favored : 96.04 % Rotamer: Outliers : 2.28 % Allowed : 13.39 % Favored : 84.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.05 (0.19), residues: 2047 helix: 0.87 (0.19), residues: 831 sheet: 0.66 (0.26), residues: 388 loop : -1.11 (0.21), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 126 HIS 0.004 0.001 HIS A 535 PHE 0.017 0.001 PHE C 315 TYR 0.009 0.001 TYR A 314 ARG 0.004 0.000 ARG A 481 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 204 time to evaluate : 2.119 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 GLU cc_start: 0.8270 (tt0) cc_final: 0.7933 (tp30) REVERT: A 276 LYS cc_start: 0.7995 (ttpt) cc_final: 0.7522 (mtpt) REVERT: A 277 LYS cc_start: 0.8199 (mtpt) cc_final: 0.7933 (mtpt) REVERT: A 479 LYS cc_start: 0.5852 (mptt) cc_final: 0.5512 (ttpt) REVERT: B 106 TYR cc_start: 0.8827 (m-80) cc_final: 0.8174 (m-80) REVERT: B 129 GLU cc_start: 0.7366 (mm-30) cc_final: 0.7127 (mt-10) REVERT: B 197 GLN cc_start: 0.8899 (tm-30) cc_final: 0.8557 (tm-30) REVERT: B 206 LYS cc_start: 0.8208 (mmtt) cc_final: 0.7826 (mmtt) REVERT: B 210 GLN cc_start: 0.8035 (mt0) cc_final: 0.7799 (mp10) REVERT: B 211 GLU cc_start: 0.8235 (OUTLIER) cc_final: 0.7657 (mt-10) REVERT: B 221 LYS cc_start: 0.8838 (mtmm) cc_final: 0.8539 (mppt) REVERT: B 232 MET cc_start: 0.8354 (ppp) cc_final: 0.8076 (ptm) REVERT: B 379 GLU cc_start: 0.8145 (tm-30) cc_final: 0.7809 (tp30) REVERT: B 511 ASP cc_start: 0.8740 (m-30) cc_final: 0.8458 (m-30) REVERT: C 278 TYR cc_start: 0.7874 (m-80) cc_final: 0.7526 (m-80) REVERT: C 352 GLU cc_start: 0.8066 (mp0) cc_final: 0.7596 (mp0) REVERT: C 464 GLU cc_start: 0.7980 (pp20) cc_final: 0.7130 (pp20) REVERT: C 465 ILE cc_start: 0.8059 (pt) cc_final: 0.7586 (tt) REVERT: C 481 ARG cc_start: 0.7669 (mtp180) cc_final: 0.7433 (ttp-170) REVERT: D 30 MET cc_start: 0.8283 (mmt) cc_final: 0.7959 (tpt) REVERT: D 67 LYS cc_start: 0.8041 (mmpt) cc_final: 0.7273 (mtmt) REVERT: D 87 LYS cc_start: 0.8014 (mttt) cc_final: 0.7450 (mtmt) REVERT: D 168 LYS cc_start: 0.8195 (mtmm) cc_final: 0.7946 (mtpp) REVERT: D 379 GLU cc_start: 0.7869 (tp30) cc_final: 0.7236 (mp0) REVERT: D 434 ASP cc_start: 0.8307 (m-30) cc_final: 0.8074 (m-30) REVERT: D 526 ARG cc_start: 0.7984 (ttp-170) cc_final: 0.7374 (ttt-90) REVERT: D 564 GLU cc_start: 0.7813 (tp30) cc_final: 0.7475 (tp30) outliers start: 43 outliers final: 38 residues processed: 236 average time/residue: 0.3607 time to fit residues: 121.7812 Evaluate side-chains 237 residues out of total 1889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 198 time to evaluate : 2.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 318 SER Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 367 SER Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain A residue 495 ASN Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 564 GLU Chi-restraints excluded: chain B residue 27 ILE Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 198 GLN Chi-restraints excluded: chain B residue 211 GLU Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 397 GLU Chi-restraints excluded: chain B residue 432 ASP Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain C residue 25 ASN Chi-restraints excluded: chain C residue 103 ASP Chi-restraints excluded: chain C residue 287 ILE Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 320 HIS Chi-restraints excluded: chain C residue 346 SER Chi-restraints excluded: chain C residue 357 SER Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 362 LEU Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain D residue 154 ILE Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 161 ASP Chi-restraints excluded: chain D residue 280 ASP Chi-restraints excluded: chain D residue 289 GLU Chi-restraints excluded: chain D residue 305 GLN Chi-restraints excluded: chain D residue 341 LYS Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 418 CYS Chi-restraints excluded: chain D residue 461 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 188 optimal weight: 0.7980 chunk 171 optimal weight: 3.9990 chunk 183 optimal weight: 1.9990 chunk 110 optimal weight: 2.9990 chunk 79 optimal weight: 3.9990 chunk 143 optimal weight: 4.9990 chunk 56 optimal weight: 0.5980 chunk 165 optimal weight: 0.9980 chunk 173 optimal weight: 1.9990 chunk 182 optimal weight: 0.9980 chunk 120 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 544 ASN B 196 ASN C 56 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.2790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 17294 Z= 0.189 Angle : 0.484 9.002 23239 Z= 0.258 Chirality : 0.043 0.269 2551 Planarity : 0.002 0.029 2940 Dihedral : 7.071 84.341 2372 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.10 % Favored : 95.85 % Rotamer: Outliers : 2.33 % Allowed : 13.87 % Favored : 83.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.09 (0.19), residues: 2047 helix: 0.92 (0.19), residues: 827 sheet: 0.72 (0.26), residues: 380 loop : -1.09 (0.21), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 126 HIS 0.004 0.001 HIS C 320 PHE 0.020 0.001 PHE C 315 TYR 0.009 0.001 TYR A 517 ARG 0.006 0.000 ARG C 526 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 195 time to evaluate : 2.065 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 276 LYS cc_start: 0.8037 (ttpt) cc_final: 0.7502 (mtpt) REVERT: A 479 LYS cc_start: 0.5867 (mptt) cc_final: 0.5524 (ttpt) REVERT: B 106 TYR cc_start: 0.8836 (m-80) cc_final: 0.8158 (m-80) REVERT: B 129 GLU cc_start: 0.7370 (mm-30) cc_final: 0.7123 (mt-10) REVERT: B 197 GLN cc_start: 0.8909 (tm-30) cc_final: 0.8588 (tm-30) REVERT: B 211 GLU cc_start: 0.8243 (OUTLIER) cc_final: 0.7661 (mt-10) REVERT: B 221 LYS cc_start: 0.8828 (mtmm) cc_final: 0.8551 (mppt) REVERT: B 232 MET cc_start: 0.8385 (ppp) cc_final: 0.8066 (ptm) REVERT: B 379 GLU cc_start: 0.8143 (tm-30) cc_final: 0.7768 (tp30) REVERT: B 511 ASP cc_start: 0.8664 (m-30) cc_final: 0.8409 (m-30) REVERT: C 278 TYR cc_start: 0.7869 (m-80) cc_final: 0.7517 (m-80) REVERT: C 352 GLU cc_start: 0.8088 (mp0) cc_final: 0.7609 (mp0) REVERT: C 464 GLU cc_start: 0.7996 (pp20) cc_final: 0.7140 (pp20) REVERT: C 465 ILE cc_start: 0.8036 (pt) cc_final: 0.7571 (tt) REVERT: C 481 ARG cc_start: 0.7675 (mtp180) cc_final: 0.7438 (ttp-170) REVERT: D 30 MET cc_start: 0.8306 (mmt) cc_final: 0.7981 (tpt) REVERT: D 67 LYS cc_start: 0.8046 (mmpt) cc_final: 0.7277 (mtmt) REVERT: D 87 LYS cc_start: 0.8019 (mttt) cc_final: 0.7615 (mtmt) REVERT: D 168 LYS cc_start: 0.8205 (mtmm) cc_final: 0.7952 (mtpp) REVERT: D 379 GLU cc_start: 0.7893 (tp30) cc_final: 0.7268 (mp0) REVERT: D 434 ASP cc_start: 0.8320 (m-30) cc_final: 0.8083 (m-30) REVERT: D 526 ARG cc_start: 0.7958 (ttp-170) cc_final: 0.7255 (ttt-90) REVERT: D 564 GLU cc_start: 0.7808 (tp30) cc_final: 0.7469 (tp30) outliers start: 44 outliers final: 42 residues processed: 226 average time/residue: 0.3604 time to fit residues: 116.3802 Evaluate side-chains 233 residues out of total 1889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 190 time to evaluate : 2.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 318 SER Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 367 SER Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain A residue 495 ASN Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 511 ASP Chi-restraints excluded: chain A residue 564 GLU Chi-restraints excluded: chain B residue 27 ILE Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 198 GLN Chi-restraints excluded: chain B residue 211 GLU Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 397 GLU Chi-restraints excluded: chain B residue 432 ASP Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain C residue 25 ASN Chi-restraints excluded: chain C residue 103 ASP Chi-restraints excluded: chain C residue 287 ILE Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 320 HIS Chi-restraints excluded: chain C residue 346 SER Chi-restraints excluded: chain C residue 357 SER Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 362 LEU Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain D residue 154 ILE Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 161 ASP Chi-restraints excluded: chain D residue 280 ASP Chi-restraints excluded: chain D residue 289 GLU Chi-restraints excluded: chain D residue 305 GLN Chi-restraints excluded: chain D residue 341 LYS Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 418 CYS Chi-restraints excluded: chain D residue 461 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 193 optimal weight: 4.9990 chunk 118 optimal weight: 5.9990 chunk 91 optimal weight: 0.3980 chunk 134 optimal weight: 0.9990 chunk 203 optimal weight: 0.9990 chunk 187 optimal weight: 2.9990 chunk 161 optimal weight: 3.9990 chunk 16 optimal weight: 0.2980 chunk 125 optimal weight: 6.9990 chunk 99 optimal weight: 0.1980 chunk 128 optimal weight: 0.9980 overall best weight: 0.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 544 ASN B 551 ASN C 56 ASN C 147 ASN ** D 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.2841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 17294 Z= 0.150 Angle : 0.472 8.634 23239 Z= 0.250 Chirality : 0.042 0.253 2551 Planarity : 0.002 0.030 2940 Dihedral : 6.896 84.772 2372 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.76 % Favored : 96.19 % Rotamer: Outliers : 2.28 % Allowed : 14.03 % Favored : 83.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.19), residues: 2047 helix: 1.05 (0.19), residues: 824 sheet: 0.69 (0.26), residues: 388 loop : -1.05 (0.21), residues: 835 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP D 126 HIS 0.004 0.001 HIS C 415 PHE 0.017 0.001 PHE C 315 TYR 0.009 0.001 TYR A 314 ARG 0.006 0.000 ARG C 526 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 199 time to evaluate : 2.215 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 GLU cc_start: 0.8272 (tt0) cc_final: 0.7938 (tp30) REVERT: A 479 LYS cc_start: 0.5838 (mptt) cc_final: 0.5561 (ttpt) REVERT: B 106 TYR cc_start: 0.8829 (m-80) cc_final: 0.8185 (m-80) REVERT: B 129 GLU cc_start: 0.7340 (mm-30) cc_final: 0.7096 (mt-10) REVERT: B 197 GLN cc_start: 0.8916 (tm-30) cc_final: 0.8599 (tm-30) REVERT: B 211 GLU cc_start: 0.8232 (OUTLIER) cc_final: 0.7642 (mt-10) REVERT: B 221 LYS cc_start: 0.8831 (mtmm) cc_final: 0.8554 (mppt) REVERT: B 232 MET cc_start: 0.8394 (ppp) cc_final: 0.8099 (ptm) REVERT: B 379 GLU cc_start: 0.8155 (tm-30) cc_final: 0.7869 (tp30) REVERT: B 511 ASP cc_start: 0.8658 (m-30) cc_final: 0.8392 (m-30) REVERT: C 278 TYR cc_start: 0.7862 (m-80) cc_final: 0.7515 (m-80) REVERT: C 352 GLU cc_start: 0.8093 (mp0) cc_final: 0.7629 (mp0) REVERT: C 464 GLU cc_start: 0.8007 (pp20) cc_final: 0.7126 (pp20) REVERT: C 465 ILE cc_start: 0.8025 (pt) cc_final: 0.7542 (tt) REVERT: C 481 ARG cc_start: 0.7675 (mtp180) cc_final: 0.7434 (ttp-170) REVERT: C 485 ARG cc_start: 0.7790 (tpp80) cc_final: 0.7573 (tpt170) REVERT: D 30 MET cc_start: 0.8281 (mmt) cc_final: 0.7961 (tpt) REVERT: D 67 LYS cc_start: 0.8048 (mmpt) cc_final: 0.7296 (mtmt) REVERT: D 87 LYS cc_start: 0.8035 (mttt) cc_final: 0.7575 (mtmt) REVERT: D 168 LYS cc_start: 0.8133 (mtmm) cc_final: 0.7856 (mtpp) REVERT: D 379 GLU cc_start: 0.7888 (tp30) cc_final: 0.7269 (mp0) REVERT: D 434 ASP cc_start: 0.8309 (m-30) cc_final: 0.8073 (m-30) REVERT: D 526 ARG cc_start: 0.7900 (ttp-170) cc_final: 0.7579 (ttp-170) REVERT: D 564 GLU cc_start: 0.7789 (tp30) cc_final: 0.7455 (tp30) outliers start: 43 outliers final: 39 residues processed: 229 average time/residue: 0.3361 time to fit residues: 112.4960 Evaluate side-chains 235 residues out of total 1889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 195 time to evaluate : 2.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 318 SER Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 367 SER Chi-restraints excluded: chain A residue 495 ASN Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 564 GLU Chi-restraints excluded: chain B residue 27 ILE Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 198 GLN Chi-restraints excluded: chain B residue 211 GLU Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 397 GLU Chi-restraints excluded: chain B residue 432 ASP Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain C residue 25 ASN Chi-restraints excluded: chain C residue 103 ASP Chi-restraints excluded: chain C residue 287 ILE Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 320 HIS Chi-restraints excluded: chain C residue 346 SER Chi-restraints excluded: chain C residue 357 SER Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 362 LEU Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain D residue 154 ILE Chi-restraints excluded: chain D residue 161 ASP Chi-restraints excluded: chain D residue 280 ASP Chi-restraints excluded: chain D residue 289 GLU Chi-restraints excluded: chain D residue 305 GLN Chi-restraints excluded: chain D residue 341 LYS Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 418 CYS Chi-restraints excluded: chain D residue 461 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 172 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 149 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 162 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 166 optimal weight: 0.0980 chunk 20 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 142 optimal weight: 6.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 544 ASN B 209 GLN C 56 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.152487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.110664 restraints weight = 20872.369| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 2.81 r_work: 0.3109 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2950 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.2902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 17294 Z= 0.294 Angle : 0.549 9.577 23239 Z= 0.288 Chirality : 0.045 0.252 2551 Planarity : 0.003 0.031 2940 Dihedral : 7.351 88.304 2372 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.69 % Favored : 95.26 % Rotamer: Outliers : 2.17 % Allowed : 14.45 % Favored : 83.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.02 (0.19), residues: 2047 helix: 0.84 (0.19), residues: 828 sheet: 0.56 (0.26), residues: 383 loop : -1.13 (0.20), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 126 HIS 0.006 0.001 HIS C 320 PHE 0.023 0.001 PHE C 315 TYR 0.022 0.001 TYR D 253 ARG 0.006 0.000 ARG C 526 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4151.72 seconds wall clock time: 76 minutes 49.50 seconds (4609.50 seconds total)