Starting phenix.real_space_refine on Tue Jul 23 21:33:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uto_42544/07_2024/8uto_42544_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uto_42544/07_2024/8uto_42544.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uto_42544/07_2024/8uto_42544.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uto_42544/07_2024/8uto_42544.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uto_42544/07_2024/8uto_42544_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uto_42544/07_2024/8uto_42544_neut.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 19 5.49 5 Mg 4 5.21 5 S 153 5.16 5 C 14863 2.51 5 N 4070 2.21 5 O 4683 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "K PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 87": "OE1" <-> "OE2" Residue "K TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 180": "OD1" <-> "OD2" Residue "K PHE 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 308": "OD1" <-> "OD2" Residue "N GLU 80": "OE1" <-> "OE2" Residue "N GLU 87": "OE1" <-> "OE2" Residue "N ASP 289": "OD1" <-> "OD2" Residue "N GLU 317": "OE1" <-> "OE2" Residue "N TYR 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 69": "OD1" <-> "OD2" Residue "A PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 279": "OE1" <-> "OE2" Residue "A GLU 290": "OE1" <-> "OE2" Residue "A ASP 345": "OD1" <-> "OD2" Residue "A GLU 420": "OE1" <-> "OE2" Residue "A GLU 429": "OE1" <-> "OE2" Residue "A ASP 438": "OD1" <-> "OD2" Residue "B ASP 26": "OD1" <-> "OD2" Residue "B ASP 31": "OD1" <-> "OD2" Residue "B GLU 123": "OE1" <-> "OE2" Residue "B PHE 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 288": "OE1" <-> "OE2" Residue "B GLU 412": "OE1" <-> "OE2" Residue "B ASP 417": "OD1" <-> "OD2" Residue "E TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 411": "OE1" <-> "OE2" Residue "E GLU 417": "OE1" <-> "OE2" Residue "E TYR 432": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 434": "OE1" <-> "OE2" Residue "E ASP 438": "OD1" <-> "OD2" Residue "E GLU 447": "OE1" <-> "OE2" Residue "I GLU 3": "OE1" <-> "OE2" Residue "I ASP 118": "OD1" <-> "OD2" Residue "I ASP 161": "OD1" <-> "OD2" Residue "I PHE 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 355": "OD1" <-> "OD2" Residue "I GLU 383": "OE1" <-> "OE2" Residue "S TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 33": "OD1" <-> "OD2" Residue "S PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 55": "OE1" <-> "OE2" Residue "S GLU 77": "OE1" <-> "OE2" Residue "S TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 113": "OE1" <-> "OE2" Residue "S PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 218": "OD1" <-> "OD2" Residue "S TYR 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 319": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 386": "OE1" <-> "OE2" Residue "S PHE 395": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 414": "OE1" <-> "OE2" Residue "S ASP 424": "OD1" <-> "OD2" Residue "S ASP 431": "OD1" <-> "OD2" Residue "S GLU 434": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 23792 Number of models: 1 Model: "" Number of chains: 16 Chain: "K" Number of atoms: 3038 Number of conformers: 1 Conformer: "" Number of residues, atoms: 386, 3038 Classifications: {'peptide': 386} Link IDs: {'PTRANS': 13, 'TRANS': 372} Chain: "N" Number of atoms: 3055 Number of conformers: 1 Conformer: "" Number of residues, atoms: 389, 3055 Classifications: {'peptide': 389} Link IDs: {'PTRANS': 13, 'TRANS': 375} Chain: "A" Number of atoms: 3437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3437 Classifications: {'peptide': 440} Link IDs: {'PTRANS': 20, 'TRANS': 419} Chain: "B" Number of atoms: 3427 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 432, 3398 Classifications: {'peptide': 432} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 411} Conformer: "B" Number of residues, atoms: 432, 3398 Classifications: {'peptide': 432} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 411} bond proxies already assigned to first conformer: 3444 Chain: "E" Number of atoms: 3524 Number of conformers: 1 Conformer: "" Number of residues, atoms: 451, 3524 Classifications: {'peptide': 451} Link IDs: {'PTRANS': 20, 'TRANS': 430} Chain: "I" Number of atoms: 3445 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 433, 3407 Classifications: {'peptide': 433} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 412} Conformer: "B" Number of residues, atoms: 433, 3407 Classifications: {'peptide': 433} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 412} bond proxies already assigned to first conformer: 3444 Chain: "S" Number of atoms: 3524 Number of conformers: 1 Conformer: "" Number of residues, atoms: 451, 3524 Classifications: {'peptide': 451} Link IDs: {'PTRANS': 20, 'TRANS': 430} Chain: "K" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "N" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 62 Unusual residues: {'TA1': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 62 Unusual residues: {'TA1': 1} Classifications: {'undetermined': 1} Chain: "S" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 9 residue: pdb=" N ATHR B 429 " occ=0.45 ... (12 atoms not shown) pdb=" CG2BTHR B 429 " occ=0.55 residue: pdb=" N AALA B 430 " occ=0.45 ... (8 atoms not shown) pdb=" CB BALA B 430 " occ=0.55 residue: pdb=" N AASP B 431 " occ=0.45 ... (14 atoms not shown) pdb=" OD2BASP B 431 " occ=0.55 residue: pdb=" N AGLU B 432 " occ=0.45 ... (16 atoms not shown) pdb=" OE2BGLU B 432 " occ=0.55 residue: pdb=" N ATHR I 429 " occ=0.54 ... (12 atoms not shown) pdb=" CG2BTHR I 429 " occ=0.46 residue: pdb=" N AALA I 430 " occ=0.54 ... (8 atoms not shown) pdb=" CB BALA I 430 " occ=0.46 residue: pdb=" N AASP I 431 " occ=0.54 ... (14 atoms not shown) pdb=" OD2BASP I 431 " occ=0.46 residue: pdb=" N AGLU I 432 " occ=0.54 ... (16 atoms not shown) pdb=" OE2BGLU I 432 " occ=0.46 residue: pdb=" N AGLN I 433 " occ=0.54 ... (16 atoms not shown) pdb=" NE2BGLN I 433 " occ=0.46 Time building chain proxies: 18.32, per 1000 atoms: 0.77 Number of scatterers: 23792 At special positions: 0 Unit cell: (81.024, 113.096, 241.384, 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 153 16.00 P 19 15.00 Mg 4 11.99 O 4683 8.00 N 4070 7.00 C 14863 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: 9.64 Conformation dependent library (CDL) restraints added in 5.4 seconds 5954 Ramachandran restraints generated. 2977 Oldfield, 0 Emsley, 2977 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5554 Finding SS restraints... Secondary structure from input PDB file: 129 helices and 24 sheets defined 49.5% alpha, 18.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.88 Creating SS restraints... Processing helix chain 'K' and resid 16 through 22 Processing helix chain 'K' and resid 69 through 77 Processing helix chain 'K' and resid 77 through 87 Processing helix chain 'K' and resid 102 through 108 Processing helix chain 'K' and resid 117 through 133 Processing helix chain 'K' and resid 188 through 203 Processing helix chain 'K' and resid 254 through 259 Processing helix chain 'K' and resid 262 through 295 removed outlier: 3.761A pdb=" N LEU K 278 " --> pdb=" O SER K 274 " (cutoff:3.500A) Proline residue: K 292 - end of helix Processing helix chain 'K' and resid 305 through 308 removed outlier: 3.742A pdb=" N ASP K 308 " --> pdb=" O PRO K 305 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 305 through 308' Processing helix chain 'K' and resid 309 through 315 Processing helix chain 'K' and resid 315 through 320 removed outlier: 3.598A pdb=" N GLY K 320 " --> pdb=" O ARG K 316 " (cutoff:3.500A) Processing helix chain 'K' and resid 334 through 336 No H-bonds generated for 'chain 'K' and resid 334 through 336' Processing helix chain 'K' and resid 337 through 352 removed outlier: 4.310A pdb=" N SER K 343 " --> pdb=" O ASP K 339 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N THR K 344 " --> pdb=" O GLU K 340 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS K 352 " --> pdb=" O ALA K 348 " (cutoff:3.500A) Processing helix chain 'K' and resid 363 through 386 Processing helix chain 'N' and resid 16 through 22 Processing helix chain 'N' and resid 69 through 77 Processing helix chain 'N' and resid 77 through 88 removed outlier: 3.602A pdb=" N GLY N 88 " --> pdb=" O HIS N 84 " (cutoff:3.500A) Processing helix chain 'N' and resid 102 through 109 removed outlier: 4.050A pdb=" N THR N 106 " --> pdb=" O GLY N 102 " (cutoff:3.500A) Processing helix chain 'N' and resid 117 through 132 removed outlier: 3.832A pdb=" N GLN N 121 " --> pdb=" O GLY N 117 " (cutoff:3.500A) Processing helix chain 'N' and resid 188 through 201 Processing helix chain 'N' and resid 262 through 296 Proline residue: N 292 - end of helix Processing helix chain 'N' and resid 305 through 308 removed outlier: 3.765A pdb=" N ASP N 308 " --> pdb=" O PRO N 305 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 305 through 308' Processing helix chain 'N' and resid 309 through 315 Processing helix chain 'N' and resid 315 through 320 Processing helix chain 'N' and resid 337 through 349 removed outlier: 3.511A pdb=" N SER N 343 " --> pdb=" O ASP N 339 " (cutoff:3.500A) Processing helix chain 'N' and resid 363 through 386 Processing helix chain 'A' and resid 10 through 29 Processing helix chain 'A' and resid 36 through 43 removed outlier: 4.286A pdb=" N LYS A 40 " --> pdb=" O MET A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 80 removed outlier: 3.811A pdb=" N VAL A 78 " --> pdb=" O VAL A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 108 Processing helix chain 'A' and resid 114 through 129 Processing helix chain 'A' and resid 143 through 161 removed outlier: 4.117A pdb=" N THR A 150 " --> pdb=" O GLY A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 189 removed outlier: 3.569A pdb=" N ASN A 186 " --> pdb=" O VAL A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 197 Processing helix chain 'A' and resid 205 through 216 Processing helix chain 'A' and resid 223 through 240 removed outlier: 3.752A pdb=" N LEU A 227 " --> pdb=" O THR A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 243 No H-bonds generated for 'chain 'A' and resid 241 through 243' Processing helix chain 'A' and resid 251 through 258 removed outlier: 3.568A pdb=" N ASN A 258 " --> pdb=" O GLU A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 266 removed outlier: 4.256A pdb=" N HIS A 266 " --> pdb=" O PRO A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 282 removed outlier: 4.088A pdb=" N TYR A 282 " --> pdb=" O ALA A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 296 removed outlier: 3.671A pdb=" N PHE A 296 " --> pdb=" O THR A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 301 Processing helix chain 'A' and resid 306 through 310 Processing helix chain 'A' and resid 324 through 338 removed outlier: 3.578A pdb=" N VAL A 328 " --> pdb=" O VAL A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 400 removed outlier: 4.063A pdb=" N ALA A 387 " --> pdb=" O ALA A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 410 removed outlier: 3.960A pdb=" N TYR A 408 " --> pdb=" O PHE A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 432 removed outlier: 4.254A pdb=" N PHE A 418 " --> pdb=" O GLU A 414 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N SER A 419 " --> pdb=" O GLU A 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 29 Processing helix chain 'B' and resid 40 through 44 removed outlier: 3.714A pdb=" N GLN B 43 " --> pdb=" O SER B 40 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LEU B 44 " --> pdb=" O ASP B 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 40 through 44' Processing helix chain 'B' and resid 46 through 49 Processing helix chain 'B' and resid 69 through 78 removed outlier: 4.603A pdb=" N MET B 73 " --> pdb=" O GLU B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 88 No H-bonds generated for 'chain 'B' and resid 86 through 88' Processing helix chain 'B' and resid 100 through 106 Processing helix chain 'B' and resid 108 through 126 removed outlier: 3.865A pdb=" N LEU B 112 " --> pdb=" O GLU B 108 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N ASP B 114 " --> pdb=" O ALA B 110 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N SER B 115 " --> pdb=" O GLU B 111 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N SER B 126 " --> pdb=" O LYS B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 159 Processing helix chain 'B' and resid 180 through 195 removed outlier: 3.589A pdb=" N ASN B 184 " --> pdb=" O VAL B 180 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N GLU B 194 " --> pdb=" O HIS B 190 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ASN B 195 " --> pdb=" O GLN B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 214 Processing helix chain 'B' and resid 221 through 237 removed outlier: 3.703A pdb=" N LEU B 225 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N THR B 237 " --> pdb=" O MET B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 258 Processing helix chain 'B' and resid 285 through 294 Processing helix chain 'B' and resid 295 through 299 Processing helix chain 'B' and resid 304 through 308 Processing helix chain 'B' and resid 322 through 337 Processing helix chain 'B' and resid 338 through 341 removed outlier: 3.835A pdb=" N PHE B 341 " --> pdb=" O SER B 338 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 338 through 341' Processing helix chain 'B' and resid 373 through 390 removed outlier: 4.323A pdb=" N LEU B 377 " --> pdb=" O ALA B 373 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N PHE B 378 " --> pdb=" O ILE B 374 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 400 removed outlier: 4.153A pdb=" N TYR B 398 " --> pdb=" O PHE B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 427 removed outlier: 3.845A pdb=" N PHE B 408 " --> pdb=" O ASP B 404 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N TYR B 425 " --> pdb=" O GLU B 421 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLN B 426 " --> pdb=" O TYR B 422 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ASP B 427 " --> pdb=" O GLN B 423 " (cutoff:3.500A) Processing helix chain 'E' and resid 10 through 28 Processing helix chain 'E' and resid 36 through 43 removed outlier: 4.101A pdb=" N LYS E 40 " --> pdb=" O MET E 36 " (cutoff:3.500A) Processing helix chain 'E' and resid 71 through 80 removed outlier: 4.578A pdb=" N ILE E 75 " --> pdb=" O GLU E 71 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N VAL E 78 " --> pdb=" O VAL E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 102 through 108 Processing helix chain 'E' and resid 114 through 129 removed outlier: 3.578A pdb=" N GLN E 128 " --> pdb=" O LYS E 124 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N CYS E 129 " --> pdb=" O LEU E 125 " (cutoff:3.500A) Processing helix chain 'E' and resid 143 through 161 removed outlier: 4.236A pdb=" N THR E 150 " --> pdb=" O GLY E 146 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 190 removed outlier: 3.593A pdb=" N ASN E 186 " --> pdb=" O VAL E 182 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N THR E 190 " --> pdb=" O ASN E 186 " (cutoff:3.500A) Processing helix chain 'E' and resid 190 through 197 Processing helix chain 'E' and resid 206 through 216 Processing helix chain 'E' and resid 223 through 240 removed outlier: 3.794A pdb=" N LEU E 227 " --> pdb=" O THR E 223 " (cutoff:3.500A) Processing helix chain 'E' and resid 241 through 243 No H-bonds generated for 'chain 'E' and resid 241 through 243' Processing helix chain 'E' and resid 251 through 260 removed outlier: 3.808A pdb=" N GLN E 256 " --> pdb=" O LEU E 252 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N VAL E 260 " --> pdb=" O GLN E 256 " (cutoff:3.500A) Processing helix chain 'E' and resid 277 through 282 removed outlier: 4.065A pdb=" N TYR E 282 " --> pdb=" O ALA E 278 " (cutoff:3.500A) Processing helix chain 'E' and resid 287 through 296 removed outlier: 3.857A pdb=" N PHE E 296 " --> pdb=" O THR E 292 " (cutoff:3.500A) Processing helix chain 'E' and resid 297 through 301 Processing helix chain 'E' and resid 306 through 310 Processing helix chain 'E' and resid 324 through 337 removed outlier: 3.608A pdb=" N VAL E 328 " --> pdb=" O VAL E 324 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N THR E 337 " --> pdb=" O ALA E 333 " (cutoff:3.500A) Processing helix chain 'E' and resid 383 through 400 removed outlier: 4.067A pdb=" N ALA E 387 " --> pdb=" O ALA E 383 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N LEU E 391 " --> pdb=" O ALA E 387 " (cutoff:3.500A) Processing helix chain 'E' and resid 404 through 410 removed outlier: 4.172A pdb=" N TYR E 408 " --> pdb=" O PHE E 404 " (cutoff:3.500A) Processing helix chain 'E' and resid 415 through 436 removed outlier: 3.955A pdb=" N ALA E 421 " --> pdb=" O GLU E 417 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ARG E 422 " --> pdb=" O PHE E 418 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLY E 436 " --> pdb=" O TYR E 432 " (cutoff:3.500A) Processing helix chain 'I' and resid 10 through 29 Processing helix chain 'I' and resid 40 through 44 removed outlier: 3.651A pdb=" N GLN I 43 " --> pdb=" O SER I 40 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LEU I 44 " --> pdb=" O ASP I 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 40 through 44' Processing helix chain 'I' and resid 46 through 49 Processing helix chain 'I' and resid 70 through 78 Processing helix chain 'I' and resid 81 through 85 removed outlier: 3.505A pdb=" N PHE I 85 " --> pdb=" O GLY I 82 " (cutoff:3.500A) Processing helix chain 'I' and resid 86 through 88 No H-bonds generated for 'chain 'I' and resid 86 through 88' Processing helix chain 'I' and resid 100 through 106 Processing helix chain 'I' and resid 108 through 126 removed outlier: 3.771A pdb=" N LEU I 112 " --> pdb=" O GLU I 108 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N ASP I 114 " --> pdb=" O ALA I 110 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N SER I 115 " --> pdb=" O GLU I 111 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N SER I 126 " --> pdb=" O LYS I 122 " (cutoff:3.500A) Processing helix chain 'I' and resid 142 through 159 removed outlier: 3.501A pdb=" N GLY I 146 " --> pdb=" O GLY I 142 " (cutoff:3.500A) Processing helix chain 'I' and resid 180 through 196 removed outlier: 3.549A pdb=" N ASN I 184 " --> pdb=" O VAL I 180 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLN I 191 " --> pdb=" O LEU I 187 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N GLU I 194 " --> pdb=" O HIS I 190 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N THR I 196 " --> pdb=" O LEU I 192 " (cutoff:3.500A) Processing helix chain 'I' and resid 203 through 214 removed outlier: 3.536A pdb=" N LEU I 207 " --> pdb=" O ASP I 203 " (cutoff:3.500A) Processing helix chain 'I' and resid 221 through 237 removed outlier: 3.590A pdb=" N LEU I 225 " --> pdb=" O THR I 221 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N THR I 237 " --> pdb=" O MET I 233 " (cutoff:3.500A) Processing helix chain 'I' and resid 238 through 241 Processing helix chain 'I' and resid 249 through 258 Processing helix chain 'I' and resid 275 through 282 removed outlier: 4.142A pdb=" N GLN I 280 " --> pdb=" O GLY I 277 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ARG I 282 " --> pdb=" O GLN I 279 " (cutoff:3.500A) Processing helix chain 'I' and resid 285 through 294 Processing helix chain 'I' and resid 295 through 299 removed outlier: 3.730A pdb=" N MET I 299 " --> pdb=" O SER I 296 " (cutoff:3.500A) Processing helix chain 'I' and resid 304 through 308 Processing helix chain 'I' and resid 322 through 337 Processing helix chain 'I' and resid 338 through 341 removed outlier: 3.751A pdb=" N PHE I 341 " --> pdb=" O SER I 338 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 338 through 341' Processing helix chain 'I' and resid 373 through 390 removed outlier: 4.263A pdb=" N LEU I 377 " --> pdb=" O ALA I 373 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N PHE I 378 " --> pdb=" O ILE I 374 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N ALA I 387 " --> pdb=" O GLU I 383 " (cutoff:3.500A) Processing helix chain 'I' and resid 395 through 400 Processing helix chain 'I' and resid 404 through 425 removed outlier: 4.073A pdb=" N PHE I 408 " --> pdb=" O ASP I 404 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N THR I 409 " --> pdb=" O GLU I 405 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N TYR I 425 " --> pdb=" O GLU I 421 " (cutoff:3.500A) Processing helix chain 'S' and resid 10 through 29 Processing helix chain 'S' and resid 36 through 43 removed outlier: 4.053A pdb=" N LYS S 40 " --> pdb=" O MET S 36 " (cutoff:3.500A) Processing helix chain 'S' and resid 71 through 80 removed outlier: 4.408A pdb=" N ILE S 75 " --> pdb=" O GLU S 71 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N VAL S 78 " --> pdb=" O VAL S 74 " (cutoff:3.500A) Processing helix chain 'S' and resid 102 through 108 Processing helix chain 'S' and resid 114 through 129 Processing helix chain 'S' and resid 143 through 161 removed outlier: 4.051A pdb=" N THR S 150 " --> pdb=" O GLY S 146 " (cutoff:3.500A) Processing helix chain 'S' and resid 182 through 197 removed outlier: 4.555A pdb=" N HIS S 192 " --> pdb=" O ILE S 188 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N THR S 193 " --> pdb=" O LEU S 189 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLU S 196 " --> pdb=" O HIS S 192 " (cutoff:3.500A) Processing helix chain 'S' and resid 205 through 217 Processing helix chain 'S' and resid 223 through 240 removed outlier: 3.809A pdb=" N LEU S 227 " --> pdb=" O THR S 223 " (cutoff:3.500A) Processing helix chain 'S' and resid 241 through 243 No H-bonds generated for 'chain 'S' and resid 241 through 243' Processing helix chain 'S' and resid 251 through 260 removed outlier: 3.779A pdb=" N GLN S 256 " --> pdb=" O LEU S 252 " (cutoff:3.500A) Processing helix chain 'S' and resid 277 through 282 removed outlier: 4.054A pdb=" N TYR S 282 " --> pdb=" O ALA S 278 " (cutoff:3.500A) Processing helix chain 'S' and resid 287 through 297 removed outlier: 3.712A pdb=" N PHE S 296 " --> pdb=" O THR S 292 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLU S 297 " --> pdb=" O ASN S 293 " (cutoff:3.500A) Processing helix chain 'S' and resid 298 through 301 Processing helix chain 'S' and resid 306 through 310 Processing helix chain 'S' and resid 324 through 337 removed outlier: 3.712A pdb=" N VAL S 328 " --> pdb=" O VAL S 324 " (cutoff:3.500A) Processing helix chain 'S' and resid 383 through 400 removed outlier: 3.939A pdb=" N ALA S 387 " --> pdb=" O ALA S 383 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N LEU S 391 " --> pdb=" O ALA S 387 " (cutoff:3.500A) Processing helix chain 'S' and resid 404 through 411 removed outlier: 4.113A pdb=" N TYR S 408 " --> pdb=" O PHE S 404 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N GLU S 411 " --> pdb=" O TRP S 407 " (cutoff:3.500A) Processing helix chain 'S' and resid 414 through 436 removed outlier: 4.362A pdb=" N PHE S 418 " --> pdb=" O GLU S 414 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N SER S 419 " --> pdb=" O GLU S 415 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N GLY S 436 " --> pdb=" O TYR S 432 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'K' and resid 54 through 57 Processing sheet with id=AA2, first strand: chain 'K' and resid 54 through 57 Processing sheet with id=AA3, first strand: chain 'K' and resid 28 through 31 Processing sheet with id=AA4, first strand: chain 'K' and resid 167 through 171 removed outlier: 4.163A pdb=" N ARG K 167 " --> pdb=" O GLU K 179 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'K' and resid 205 through 206 Processing sheet with id=AA6, first strand: chain 'N' and resid 54 through 57 removed outlier: 8.563A pdb=" N TYR N 54 " --> pdb=" O VAL N 6 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N VAL N 8 " --> pdb=" O TYR N 54 " (cutoff:3.500A) removed outlier: 8.133A pdb=" N TYR N 56 " --> pdb=" O VAL N 8 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL N 10 " --> pdb=" O TYR N 56 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N CYS N 92 " --> pdb=" O ALA N 326 " (cutoff:3.500A) removed outlier: 8.048A pdb=" N VAL N 328 " --> pdb=" O CYS N 92 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N PHE N 94 " --> pdb=" O VAL N 328 " (cutoff:3.500A) removed outlier: 8.071A pdb=" N ALA N 330 " --> pdb=" O PHE N 94 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N TYR N 96 " --> pdb=" O ALA N 330 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N VAL N 91 " --> pdb=" O SER N 245 " (cutoff:3.500A) removed outlier: 7.784A pdb=" N VAL N 247 " --> pdb=" O VAL N 91 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N ILE N 93 " --> pdb=" O VAL N 247 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N THR N 238 " --> pdb=" O ARG N 229 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N ARG N 229 " --> pdb=" O THR N 238 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LYS N 240 " --> pdb=" O GLN N 227 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'N' and resid 54 through 57 removed outlier: 8.563A pdb=" N TYR N 54 " --> pdb=" O VAL N 6 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N VAL N 8 " --> pdb=" O TYR N 54 " (cutoff:3.500A) removed outlier: 8.133A pdb=" N TYR N 56 " --> pdb=" O VAL N 8 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL N 10 " --> pdb=" O TYR N 56 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N CYS N 92 " --> pdb=" O ALA N 326 " (cutoff:3.500A) removed outlier: 8.048A pdb=" N VAL N 328 " --> pdb=" O CYS N 92 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N PHE N 94 " --> pdb=" O VAL N 328 " (cutoff:3.500A) removed outlier: 8.071A pdb=" N ALA N 330 " --> pdb=" O PHE N 94 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N TYR N 96 " --> pdb=" O ALA N 330 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N VAL N 91 " --> pdb=" O SER N 245 " (cutoff:3.500A) removed outlier: 7.784A pdb=" N VAL N 247 " --> pdb=" O VAL N 91 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N ILE N 93 " --> pdb=" O VAL N 247 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N THR N 238 " --> pdb=" O ARG N 229 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N ARG N 229 " --> pdb=" O THR N 238 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LYS N 240 " --> pdb=" O GLN N 227 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'N' and resid 28 through 31 Processing sheet with id=AA9, first strand: chain 'N' and resid 168 through 171 Processing sheet with id=AB1, first strand: chain 'N' and resid 205 through 206 Processing sheet with id=AB2, first strand: chain 'A' and resid 65 through 68 removed outlier: 7.597A pdb=" N GLU A 3 " --> pdb=" O GLN A 133 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N PHE A 135 " --> pdb=" O GLU A 3 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N ILE A 5 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N VAL A 137 " --> pdb=" O ILE A 5 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N ILE A 7 " --> pdb=" O VAL A 137 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N HIS A 139 " --> pdb=" O ILE A 7 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N VAL A 9 " --> pdb=" O HIS A 139 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N SER A 165 " --> pdb=" O GLN A 133 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N HIS A 139 " --> pdb=" O PHE A 169 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ILE A 171 " --> pdb=" O HIS A 139 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N LYS A 166 " --> pdb=" O CYS A 200 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N PHE A 202 " --> pdb=" O LYS A 166 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N GLU A 168 " --> pdb=" O PHE A 202 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N VAL A 204 " --> pdb=" O GLU A 168 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N SER A 170 " --> pdb=" O VAL A 204 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AB4, first strand: chain 'A' and resid 269 through 272 Processing sheet with id=AB5, first strand: chain 'B' and resid 90 through 92 removed outlier: 8.172A pdb=" N VAL B 91 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N LEU B 65 " --> pdb=" O VAL B 91 " (cutoff:3.500A) removed outlier: 8.449A pdb=" N ILE B 64 " --> pdb=" O ILE B 4 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N HIS B 6 " --> pdb=" O ILE B 64 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N VAL B 66 " --> pdb=" O HIS B 6 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N GLN B 8 " --> pdb=" O VAL B 66 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N GLU B 3 " --> pdb=" O GLN B 131 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N PHE B 133 " --> pdb=" O GLU B 3 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N VAL B 5 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N LEU B 135 " --> pdb=" O VAL B 5 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N ILE B 7 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N HIS B 137 " --> pdb=" O ILE B 7 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N ALA B 9 " --> pdb=" O HIS B 137 " (cutoff:3.500A) removed outlier: 9.592A pdb=" N ILE B 163 " --> pdb=" O CYS B 129 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N GLN B 131 " --> pdb=" O ILE B 163 " (cutoff:3.500A) removed outlier: 8.254A pdb=" N ASN B 165 " --> pdb=" O GLN B 131 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N PHE B 133 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N PHE B 167 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N LEU B 135 " --> pdb=" O PHE B 167 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N VAL B 169 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N HIS B 137 " --> pdb=" O VAL B 169 " (cutoff:3.500A) removed outlier: 8.190A pdb=" N TYR B 200 " --> pdb=" O MET B 164 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N THR B 166 " --> pdb=" O TYR B 200 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N ILE B 202 " --> pdb=" O THR B 166 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N SER B 168 " --> pdb=" O ILE B 202 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N PHE B 265 " --> pdb=" O SER B 371 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N SER B 371 " --> pdb=" O PHE B 265 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 51 through 53 Processing sheet with id=AB7, first strand: chain 'E' and resid 65 through 68 removed outlier: 6.722A pdb=" N ILE E 5 " --> pdb=" O LEU E 136 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N PHE E 138 " --> pdb=" O ILE E 5 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ILE E 7 " --> pdb=" O PHE E 138 " (cutoff:3.500A) removed outlier: 8.892A pdb=" N SER E 140 " --> pdb=" O ILE E 7 " (cutoff:3.500A) removed outlier: 8.861A pdb=" N VAL E 9 " --> pdb=" O SER E 140 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N PHE E 135 " --> pdb=" O LEU E 167 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N PHE E 169 " --> pdb=" O PHE E 135 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N VAL E 137 " --> pdb=" O PHE E 169 " (cutoff:3.500A) removed outlier: 8.144A pdb=" N ILE E 171 " --> pdb=" O VAL E 137 " (cutoff:3.500A) removed outlier: 8.035A pdb=" N HIS E 139 " --> pdb=" O ILE E 171 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N LYS E 166 " --> pdb=" O CYS E 200 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N PHE E 202 " --> pdb=" O LYS E 166 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N GLU E 168 " --> pdb=" O PHE E 202 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N VAL E 204 " --> pdb=" O GLU E 168 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N SER E 170 " --> pdb=" O VAL E 204 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 53 through 55 Processing sheet with id=AB9, first strand: chain 'E' and resid 269 through 272 Processing sheet with id=AC1, first strand: chain 'I' and resid 90 through 92 removed outlier: 8.150A pdb=" N VAL I 91 " --> pdb=" O ALA I 63 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N LEU I 65 " --> pdb=" O VAL I 91 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N GLU I 3 " --> pdb=" O GLN I 131 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N PHE I 133 " --> pdb=" O GLU I 3 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N VAL I 5 " --> pdb=" O PHE I 133 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N LEU I 135 " --> pdb=" O VAL I 5 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N ILE I 7 " --> pdb=" O LEU I 135 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N HIS I 137 " --> pdb=" O ILE I 7 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N ALA I 9 " --> pdb=" O HIS I 137 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 90 through 92 removed outlier: 8.150A pdb=" N VAL I 91 " --> pdb=" O ALA I 63 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N LEU I 65 " --> pdb=" O VAL I 91 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N GLU I 3 " --> pdb=" O GLN I 131 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N PHE I 133 " --> pdb=" O GLU I 3 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N VAL I 5 " --> pdb=" O PHE I 133 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N LEU I 135 " --> pdb=" O VAL I 5 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N ILE I 7 " --> pdb=" O LEU I 135 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N HIS I 137 " --> pdb=" O ILE I 7 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N ALA I 9 " --> pdb=" O HIS I 137 " (cutoff:3.500A) removed outlier: 7.875A pdb=" N PHE I 167 " --> pdb=" O PHE I 133 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N LEU I 135 " --> pdb=" O PHE I 167 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N VAL I 169 " --> pdb=" O LEU I 135 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N HIS I 137 " --> pdb=" O VAL I 169 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N SER I 168 " --> pdb=" O ILE I 202 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N PHE I 265 " --> pdb=" O SER I 371 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N SER I 371 " --> pdb=" O PHE I 265 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 51 through 54 Processing sheet with id=AC4, first strand: chain 'S' and resid 65 through 68 removed outlier: 8.562A pdb=" N VAL S 66 " --> pdb=" O CYS S 4 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N SER S 6 " --> pdb=" O VAL S 66 " (cutoff:3.500A) removed outlier: 7.968A pdb=" N VAL S 68 " --> pdb=" O SER S 6 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N HIS S 8 " --> pdb=" O VAL S 68 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N GLU S 3 " --> pdb=" O GLY S 134 " (cutoff:3.500A) removed outlier: 8.496A pdb=" N LEU S 136 " --> pdb=" O GLU S 3 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ILE S 5 " --> pdb=" O LEU S 136 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N PHE S 138 " --> pdb=" O ILE S 5 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ILE S 7 " --> pdb=" O PHE S 138 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N GLN S 133 " --> pdb=" O SER S 165 " (cutoff:3.500A) removed outlier: 7.940A pdb=" N LEU S 167 " --> pdb=" O GLN S 133 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N PHE S 135 " --> pdb=" O LEU S 167 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N PHE S 169 " --> pdb=" O PHE S 135 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N VAL S 137 " --> pdb=" O PHE S 169 " (cutoff:3.500A) removed outlier: 8.244A pdb=" N ILE S 171 " --> pdb=" O VAL S 137 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N LYS S 166 " --> pdb=" O CYS S 200 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N PHE S 202 " --> pdb=" O LYS S 166 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N GLU S 168 " --> pdb=" O PHE S 202 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N VAL S 204 " --> pdb=" O GLU S 168 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N SER S 170 " --> pdb=" O VAL S 204 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'S' and resid 53 through 55 Processing sheet with id=AC6, first strand: chain 'S' and resid 269 through 272 1173 hydrogen bonds defined for protein. 3357 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: 8.21 Time building geometry restraints manager: 10.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 4214 1.32 - 1.45: 6333 1.45 - 1.57: 13458 1.57 - 1.69: 43 1.69 - 1.82: 244 Bond restraints: 24292 Sorted by residual: bond pdb=" O3A ANP K 502 " pdb=" PB ANP K 502 " ideal model delta sigma weight residual 1.700 1.553 0.147 2.00e-02 2.50e+03 5.38e+01 bond pdb=" O3A ANP N 501 " pdb=" PB ANP N 501 " ideal model delta sigma weight residual 1.700 1.557 0.143 2.00e-02 2.50e+03 5.12e+01 bond pdb=" N3B ANP K 502 " pdb=" PG ANP K 502 " ideal model delta sigma weight residual 1.795 1.688 0.107 2.00e-02 2.50e+03 2.87e+01 bond pdb=" N3B ANP N 501 " pdb=" PG ANP N 501 " ideal model delta sigma weight residual 1.795 1.692 0.103 2.00e-02 2.50e+03 2.63e+01 bond pdb=" O5' ANP K 502 " pdb=" PA ANP K 502 " ideal model delta sigma weight residual 1.655 1.578 0.077 2.00e-02 2.50e+03 1.50e+01 ... (remaining 24287 not shown) Histogram of bond angle deviations from ideal: 84.01 - 94.48: 8 94.48 - 104.95: 441 104.95 - 115.42: 14827 115.42 - 125.89: 17362 125.89 - 136.36: 336 Bond angle restraints: 32974 Sorted by residual: angle pdb=" N GLU E 417 " pdb=" CA GLU E 417 " pdb=" C GLU E 417 " ideal model delta sigma weight residual 113.20 104.86 8.34 1.21e+00 6.83e-01 4.76e+01 angle pdb=" PB ANP N 501 " pdb=" N3B ANP N 501 " pdb=" PG ANP N 501 " ideal model delta sigma weight residual 126.95 109.68 17.27 3.00e+00 1.11e-01 3.32e+01 angle pdb=" PB ANP K 502 " pdb=" N3B ANP K 502 " pdb=" PG ANP K 502 " ideal model delta sigma weight residual 126.95 111.09 15.86 3.00e+00 1.11e-01 2.79e+01 angle pdb=" N TYR A 432 " pdb=" CA TYR A 432 " pdb=" C TYR A 432 " ideal model delta sigma weight residual 112.97 108.19 4.78 1.06e+00 8.90e-01 2.04e+01 angle pdb=" N ILE S 114 " pdb=" CA ILE S 114 " pdb=" C ILE S 114 " ideal model delta sigma weight residual 113.71 109.62 4.09 9.50e-01 1.11e+00 1.86e+01 ... (remaining 32969 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.96: 14109 31.96 - 63.93: 533 63.93 - 95.89: 86 95.89 - 127.85: 15 127.85 - 159.82: 21 Dihedral angle restraints: 14764 sinusoidal: 6106 harmonic: 8658 Sorted by residual: dihedral pdb=" C5' GTP E 501 " pdb=" O5' GTP E 501 " pdb=" PA GTP E 501 " pdb=" O3A GTP E 501 " ideal model delta sinusoidal sigma weight residual 69.27 -130.91 -159.82 1 2.00e+01 2.50e-03 4.65e+01 dihedral pdb=" C4' GTP A 501 " pdb=" C5' GTP A 501 " pdb=" O5' GTP A 501 " pdb=" PA GTP A 501 " ideal model delta sinusoidal sigma weight residual 260.87 111.93 148.94 1 2.00e+01 2.50e-03 4.46e+01 dihedral pdb=" C8 GTP A 501 " pdb=" C1' GTP A 501 " pdb=" N9 GTP A 501 " pdb=" O4' GTP A 501 " ideal model delta sinusoidal sigma weight residual 104.59 -39.31 143.90 1 2.00e+01 2.50e-03 4.34e+01 ... (remaining 14761 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.109: 3474 0.109 - 0.217: 139 0.217 - 0.326: 3 0.326 - 0.435: 0 0.435 - 0.543: 1 Chirality restraints: 3617 Sorted by residual: chirality pdb=" C18 TA1 B 502 " pdb=" C10 TA1 B 502 " pdb=" C17 TA1 B 502 " pdb=" C20 TA1 B 502 " both_signs ideal model delta sigma weight residual False -3.16 -2.62 -0.54 2.00e-01 2.50e+01 7.38e+00 chirality pdb=" C3' ANP N 501 " pdb=" C2' ANP N 501 " pdb=" C4' ANP N 501 " pdb=" O3' ANP N 501 " both_signs ideal model delta sigma weight residual False -2.36 -2.61 0.25 2.00e-01 2.50e+01 1.62e+00 chirality pdb=" C3' ANP K 502 " pdb=" C2' ANP K 502 " pdb=" C4' ANP K 502 " pdb=" O3' ANP K 502 " both_signs ideal model delta sigma weight residual False -2.36 -2.61 0.25 2.00e-01 2.50e+01 1.56e+00 ... (remaining 3614 not shown) Planarity restraints: 4288 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY N 291 " 0.066 5.00e-02 4.00e+02 9.97e-02 1.59e+01 pdb=" N PRO N 292 " -0.172 5.00e-02 4.00e+02 pdb=" CA PRO N 292 " 0.053 5.00e-02 4.00e+02 pdb=" CD PRO N 292 " 0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY K 291 " 0.059 5.00e-02 4.00e+02 8.85e-02 1.25e+01 pdb=" N PRO K 292 " -0.153 5.00e-02 4.00e+02 pdb=" CA PRO K 292 " 0.046 5.00e-02 4.00e+02 pdb=" CD PRO K 292 " 0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR N 46 " -0.055 5.00e-02 4.00e+02 8.46e-02 1.15e+01 pdb=" N PRO N 47 " 0.146 5.00e-02 4.00e+02 pdb=" CA PRO N 47 " -0.045 5.00e-02 4.00e+02 pdb=" CD PRO N 47 " -0.046 5.00e-02 4.00e+02 ... (remaining 4285 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 139 2.53 - 3.12: 17880 3.12 - 3.72: 35601 3.72 - 4.31: 49378 4.31 - 4.90: 85619 Nonbonded interactions: 188617 Sorted by model distance: nonbonded pdb="MG MG K 501 " pdb=" O1G ANP K 502 " model vdw 1.940 2.170 nonbonded pdb=" O1B GTP E 501 " pdb="MG MG E 502 " model vdw 1.946 2.170 nonbonded pdb=" O1B GTP A 501 " pdb="MG MG A 502 " model vdw 1.952 2.170 nonbonded pdb=" O1G GTP A 501 " pdb="MG MG A 502 " model vdw 1.954 2.170 nonbonded pdb=" O1G GTP E 501 " pdb="MG MG E 502 " model vdw 1.955 2.170 ... (remaining 188612 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' selection = (chain 'E' and (resid 1 through 440 or resid 501 through 502)) selection = (chain 'S' and (resid 1 through 440 or resid 501 through 502)) } ncs_group { reference = (chain 'B' and (resid 1 through 428 or resid 501 or resid 502)) selection = (chain 'I' and (resid 1 through 428 or resid 501 or resid 502)) } ncs_group { reference = (chain 'K' and resid 4 through 389) selection = (chain 'N' and resid 4 through 389) } 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=0.45 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.890 Check model and map are aligned: 0.180 Set scattering table: 0.200 Process input model: 69.500 Find NCS groups from input model: 1.740 Set up NCS constraints: 0.110 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:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 82.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 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 : 0.005 0.147 24292 Z= 0.321 Angle : 0.812 17.275 32974 Z= 0.419 Chirality : 0.047 0.543 3617 Planarity : 0.006 0.100 4288 Dihedral : 18.597 159.819 9210 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.30 % Allowed : 3.84 % Favored : 95.86 % Rotamer: Outliers : 0.59 % Allowed : 13.78 % Favored : 85.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % 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: -0.12 (0.15), residues: 2977 helix: 0.97 (0.15), residues: 1217 sheet: -0.06 (0.22), residues: 538 loop : -1.11 (0.17), residues: 1222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 21 HIS 0.015 0.001 HIS I 37 PHE 0.022 0.002 PHE E 255 TYR 0.039 0.002 TYR S 24 ARG 0.015 0.001 ARG E 123 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5954 Ramachandran restraints generated. 2977 Oldfield, 0 Emsley, 2977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5954 Ramachandran restraints generated. 2977 Oldfield, 0 Emsley, 2977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 537 residues out of total 2548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 528 time to evaluate : 2.593 Fit side-chains REVERT: K 81 MET cc_start: 0.8227 (mmt) cc_final: 0.7768 (mmt) REVERT: K 189 TYR cc_start: 0.8442 (t80) cc_final: 0.8119 (t80) REVERT: N 66 ASN cc_start: 0.7761 (m-40) cc_final: 0.7376 (m110) REVERT: N 107 MET cc_start: 0.8013 (tmm) cc_final: 0.7364 (tmm) REVERT: N 346 ARG cc_start: 0.9045 (mtt90) cc_final: 0.8840 (mmm-85) REVERT: N 347 TYR cc_start: 0.8232 (t80) cc_final: 0.7841 (t80) REVERT: A 9 VAL cc_start: 0.8996 (t) cc_final: 0.8695 (m) REVERT: A 347 CYS cc_start: 0.9105 (t) cc_final: 0.8863 (t) REVERT: A 423 GLU cc_start: 0.7961 (mp0) cc_final: 0.7344 (mp0) REVERT: E 214 ARG cc_start: 0.8767 (tmm160) cc_final: 0.8465 (tmm-80) REVERT: I 31 ASP cc_start: 0.8546 (t70) cc_final: 0.8131 (t70) REVERT: I 67 ASP cc_start: 0.8314 (t0) cc_final: 0.7978 (t0) REVERT: I 100 ASN cc_start: 0.8788 (t0) cc_final: 0.8522 (t0) REVERT: S 36 MET cc_start: 0.8093 (ttp) cc_final: 0.7763 (ttt) REVERT: S 413 MET cc_start: 0.8108 (mtp) cc_final: 0.7684 (ttp) outliers start: 9 outliers final: 5 residues processed: 533 average time/residue: 0.3477 time to fit residues: 286.6210 Evaluate side-chains 508 residues out of total 2548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 503 time to evaluate : 2.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 217 SER Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain E residue 417 GLU Chi-restraints excluded: chain E residue 419 SER Chi-restraints excluded: chain S residue 101 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 249 optimal weight: 2.9990 chunk 224 optimal weight: 0.9990 chunk 124 optimal weight: 0.3980 chunk 76 optimal weight: 5.9990 chunk 151 optimal weight: 2.9990 chunk 119 optimal weight: 2.9990 chunk 232 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 141 optimal weight: 2.9990 chunk 172 optimal weight: 0.0670 chunk 268 optimal weight: 0.4980 overall best weight: 0.7922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 98 GLN ** N 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 270 ASN N 295 ASN A 192 HIS B 99 ASN B 165 ASN B 195 ASN B 423 GLN E 358 GLN I 37 HIS I 279 GLN ** I 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 197 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.1163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 24292 Z= 0.171 Angle : 0.550 10.556 32974 Z= 0.273 Chirality : 0.044 0.402 3617 Planarity : 0.005 0.090 4288 Dihedral : 12.100 155.670 3610 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.27 % Allowed : 3.17 % Favored : 96.56 % Rotamer: Outliers : 2.34 % Allowed : 13.43 % Favored : 84.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % 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: 0.47 (0.15), residues: 2977 helix: 1.65 (0.15), residues: 1219 sheet: 0.22 (0.22), residues: 541 loop : -1.03 (0.17), residues: 1217 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP S 388 HIS 0.005 0.001 HIS I 37 PHE 0.016 0.001 PHE K 94 TYR 0.025 0.001 TYR N 177 ARG 0.007 0.000 ARG K 129 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5954 Ramachandran restraints generated. 2977 Oldfield, 0 Emsley, 2977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5954 Ramachandran restraints generated. 2977 Oldfield, 0 Emsley, 2977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 588 residues out of total 2548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 534 time to evaluate : 2.714 Fit side-chains revert: symmetry clash REVERT: K 115 GLN cc_start: 0.8411 (pm20) cc_final: 0.8053 (pm20) REVERT: K 177 TYR cc_start: 0.8857 (p90) cc_final: 0.8542 (p90) REVERT: K 189 TYR cc_start: 0.8125 (t80) cc_final: 0.7889 (t80) REVERT: K 318 ASN cc_start: 0.8530 (m-40) cc_final: 0.8198 (m110) REVERT: N 66 ASN cc_start: 0.7848 (m-40) cc_final: 0.7449 (m110) REVERT: N 107 MET cc_start: 0.8060 (tmm) cc_final: 0.7779 (tpp) REVERT: N 129 ARG cc_start: 0.7887 (ttm110) cc_final: 0.7678 (ttm110) REVERT: N 143 GLU cc_start: 0.7062 (pt0) cc_final: 0.6732 (pt0) REVERT: A 9 VAL cc_start: 0.8965 (t) cc_final: 0.8630 (m) REVERT: A 24 TYR cc_start: 0.8624 (m-80) cc_final: 0.8358 (m-80) REVERT: A 258 ASN cc_start: 0.9126 (m-40) cc_final: 0.8913 (m-40) REVERT: A 322 ASP cc_start: 0.8745 (t0) cc_final: 0.8530 (t0) REVERT: A 423 GLU cc_start: 0.7829 (mt-10) cc_final: 0.7371 (mp0) REVERT: A 425 MET cc_start: 0.8686 (tpt) cc_final: 0.8411 (tpt) REVERT: A 430 LYS cc_start: 0.8148 (ttpp) cc_final: 0.7874 (ttpp) REVERT: A 434 GLU cc_start: 0.8179 (mt-10) cc_final: 0.7859 (mt-10) REVERT: B 347 ASN cc_start: 0.7609 (t0) cc_final: 0.7341 (t0) REVERT: E 214 ARG cc_start: 0.8756 (tmm160) cc_final: 0.8462 (tmm-80) REVERT: I 31 ASP cc_start: 0.8493 (t70) cc_final: 0.8070 (t70) REVERT: I 67 ASP cc_start: 0.8340 (t0) cc_final: 0.7963 (t0) REVERT: S 36 MET cc_start: 0.8163 (ttp) cc_final: 0.7762 (ttt) REVERT: S 80 THR cc_start: 0.8232 (OUTLIER) cc_final: 0.7975 (p) REVERT: S 112 LYS cc_start: 0.9022 (mmmt) cc_final: 0.8770 (mmtm) REVERT: S 392 ASP cc_start: 0.8035 (OUTLIER) cc_final: 0.7791 (t0) REVERT: S 397 LEU cc_start: 0.8857 (mt) cc_final: 0.8475 (tt) REVERT: S 413 MET cc_start: 0.8055 (mtp) cc_final: 0.7203 (ttp) REVERT: S 414 GLU cc_start: 0.7089 (pm20) cc_final: 0.6818 (pt0) outliers start: 54 outliers final: 33 residues processed: 557 average time/residue: 0.3514 time to fit residues: 302.8418 Evaluate side-chains 536 residues out of total 2548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 501 time to evaluate : 2.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 86 PHE Chi-restraints excluded: chain K residue 98 GLN Chi-restraints excluded: chain K residue 226 THR Chi-restraints excluded: chain N residue 133 THR Chi-restraints excluded: chain N residue 180 ASP Chi-restraints excluded: chain N residue 270 ASN Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 98 ASP Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain A residue 295 CYS Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain E residue 98 ASP Chi-restraints excluded: chain E residue 335 ILE Chi-restraints excluded: chain E residue 367 ASP Chi-restraints excluded: chain E residue 417 GLU Chi-restraints excluded: chain E residue 419 SER Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain I residue 143 THR Chi-restraints excluded: chain I residue 313 VAL Chi-restraints excluded: chain I residue 403 MET Chi-restraints excluded: chain S residue 80 THR Chi-restraints excluded: chain S residue 101 ASN Chi-restraints excluded: chain S residue 199 ASP Chi-restraints excluded: chain S residue 265 ILE Chi-restraints excluded: chain S residue 271 THR Chi-restraints excluded: chain S residue 334 THR Chi-restraints excluded: chain S residue 367 ASP Chi-restraints excluded: chain S residue 371 VAL Chi-restraints excluded: chain S residue 381 THR Chi-restraints excluded: chain S residue 392 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 149 optimal weight: 4.9990 chunk 83 optimal weight: 2.9990 chunk 223 optimal weight: 3.9990 chunk 183 optimal weight: 0.9980 chunk 74 optimal weight: 40.0000 chunk 269 optimal weight: 0.9990 chunk 290 optimal weight: 9.9990 chunk 239 optimal weight: 0.9990 chunk 267 optimal weight: 8.9990 chunk 91 optimal weight: 4.9990 chunk 216 optimal weight: 0.9980 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 98 GLN K 318 ASN N 98 GLN ** N 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 270 ASN N 322 ASN A 285 GLN A 309 HIS A 356 ASN B 99 ASN B 137 HIS B 423 GLN E 128 GLN ** I 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 186 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.1440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 24292 Z= 0.227 Angle : 0.536 8.322 32974 Z= 0.269 Chirality : 0.045 0.443 3617 Planarity : 0.004 0.086 4288 Dihedral : 10.134 151.658 3609 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.37 % Favored : 96.39 % Rotamer: Outliers : 2.89 % Allowed : 14.36 % Favored : 82.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % 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: 0.58 (0.16), residues: 2977 helix: 1.76 (0.15), residues: 1235 sheet: 0.35 (0.22), residues: 536 loop : -1.08 (0.17), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP S 388 HIS 0.004 0.001 HIS A 88 PHE 0.020 0.001 PHE E 255 TYR 0.024 0.001 TYR N 177 ARG 0.005 0.000 ARG E 123 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5954 Ramachandran restraints generated. 2977 Oldfield, 0 Emsley, 2977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5954 Ramachandran restraints generated. 2977 Oldfield, 0 Emsley, 2977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 582 residues out of total 2548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 514 time to evaluate : 2.378 Fit side-chains revert: symmetry clash REVERT: K 11 ARG cc_start: 0.8205 (OUTLIER) cc_final: 0.7369 (ttt-90) REVERT: K 115 GLN cc_start: 0.8379 (pm20) cc_final: 0.7978 (pm20) REVERT: K 180 ASP cc_start: 0.7252 (t0) cc_final: 0.7021 (t0) REVERT: K 318 ASN cc_start: 0.8498 (m110) cc_final: 0.8274 (m110) REVERT: N 66 ASN cc_start: 0.7820 (m-40) cc_final: 0.7427 (m110) REVERT: N 107 MET cc_start: 0.8127 (OUTLIER) cc_final: 0.7475 (tmm) REVERT: N 201 LYS cc_start: 0.8946 (tttm) cc_final: 0.8412 (mtmm) REVERT: A 9 VAL cc_start: 0.9042 (t) cc_final: 0.8716 (m) REVERT: A 322 ASP cc_start: 0.8766 (t0) cc_final: 0.8544 (t0) REVERT: A 423 GLU cc_start: 0.7867 (mt-10) cc_final: 0.7596 (mt-10) REVERT: A 434 GLU cc_start: 0.8251 (mt-10) cc_final: 0.7917 (mt-10) REVERT: B 217 LEU cc_start: 0.8774 (mt) cc_final: 0.8562 (mp) REVERT: B 347 ASN cc_start: 0.7756 (t0) cc_final: 0.7461 (t0) REVERT: I 31 ASP cc_start: 0.8498 (t70) cc_final: 0.8125 (t70) REVERT: I 67 ASP cc_start: 0.8410 (t0) cc_final: 0.8002 (t0) REVERT: S 36 MET cc_start: 0.8194 (ttp) cc_final: 0.7810 (ttt) REVERT: S 80 THR cc_start: 0.8075 (OUTLIER) cc_final: 0.7779 (p) REVERT: S 112 LYS cc_start: 0.9015 (mmmt) cc_final: 0.8742 (mmtm) REVERT: S 160 ASP cc_start: 0.7574 (m-30) cc_final: 0.7320 (m-30) REVERT: S 392 ASP cc_start: 0.8155 (OUTLIER) cc_final: 0.7763 (t0) REVERT: S 397 LEU cc_start: 0.8922 (mt) cc_final: 0.8579 (tt) REVERT: S 414 GLU cc_start: 0.7077 (pm20) cc_final: 0.6858 (pt0) REVERT: S 434 GLU cc_start: 0.8252 (tt0) cc_final: 0.7949 (tt0) outliers start: 68 outliers final: 48 residues processed: 544 average time/residue: 0.3536 time to fit residues: 296.3066 Evaluate side-chains 535 residues out of total 2548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 483 time to evaluate : 2.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 5 SER Chi-restraints excluded: chain K residue 11 ARG Chi-restraints excluded: chain K residue 86 PHE Chi-restraints excluded: chain K residue 98 GLN Chi-restraints excluded: chain K residue 118 ILE Chi-restraints excluded: chain K residue 226 THR Chi-restraints excluded: chain N residue 107 MET Chi-restraints excluded: chain N residue 116 GLN Chi-restraints excluded: chain N residue 133 THR Chi-restraints excluded: chain N residue 165 ASN Chi-restraints excluded: chain N residue 180 ASP Chi-restraints excluded: chain N residue 217 SER Chi-restraints excluded: chain N residue 241 VAL Chi-restraints excluded: chain A residue 2 ARG Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 98 ASP Chi-restraints excluded: chain A residue 129 CYS Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain A residue 295 CYS Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain E residue 93 ILE Chi-restraints excluded: chain E residue 98 ASP Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain E residue 335 ILE Chi-restraints excluded: chain E residue 367 ASP Chi-restraints excluded: chain E residue 417 GLU Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain I residue 143 THR Chi-restraints excluded: chain I residue 236 VAL Chi-restraints excluded: chain I residue 284 LEU Chi-restraints excluded: chain I residue 313 VAL Chi-restraints excluded: chain I residue 403 MET Chi-restraints excluded: chain I residue 415 MET Chi-restraints excluded: chain S residue 27 GLU Chi-restraints excluded: chain S residue 80 THR Chi-restraints excluded: chain S residue 101 ASN Chi-restraints excluded: chain S residue 130 THR Chi-restraints excluded: chain S residue 199 ASP Chi-restraints excluded: chain S residue 271 THR Chi-restraints excluded: chain S residue 334 THR Chi-restraints excluded: chain S residue 363 VAL Chi-restraints excluded: chain S residue 367 ASP Chi-restraints excluded: chain S residue 371 VAL Chi-restraints excluded: chain S residue 381 THR Chi-restraints excluded: chain S residue 392 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 266 optimal weight: 3.9990 chunk 202 optimal weight: 0.5980 chunk 139 optimal weight: 5.9990 chunk 29 optimal weight: 7.9990 chunk 128 optimal weight: 3.9990 chunk 180 optimal weight: 3.9990 chunk 270 optimal weight: 4.9990 chunk 286 optimal weight: 4.9990 chunk 141 optimal weight: 3.9990 chunk 256 optimal weight: 7.9990 chunk 77 optimal weight: 3.9990 overall best weight: 3.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 193 GLN ** N 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 285 GLN B 204 ASN ** B 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 128 GLN I 37 HIS I 204 ASN ** I 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 15 GLN S 107 HIS S 186 ASN S 301 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.1831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.077 24292 Z= 0.475 Angle : 0.640 8.595 32974 Z= 0.325 Chirality : 0.048 0.355 3617 Planarity : 0.005 0.083 4288 Dihedral : 10.358 153.062 3608 Min Nonbonded Distance : 1.820 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.45 % Favored : 95.32 % Rotamer: Outliers : 3.90 % Allowed : 14.52 % Favored : 81.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % 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: 0.31 (0.15), residues: 2977 helix: 1.53 (0.15), residues: 1226 sheet: 0.39 (0.23), residues: 531 loop : -1.27 (0.17), residues: 1220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP E 21 HIS 0.011 0.002 HIS A 88 PHE 0.023 0.002 PHE E 255 TYR 0.036 0.002 TYR N 74 ARG 0.009 0.001 ARG K 129 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5954 Ramachandran restraints generated. 2977 Oldfield, 0 Emsley, 2977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5954 Ramachandran restraints generated. 2977 Oldfield, 0 Emsley, 2977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 608 residues out of total 2548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 514 time to evaluate : 2.858 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 11 ARG cc_start: 0.8199 (OUTLIER) cc_final: 0.7537 (ttt-90) REVERT: K 81 MET cc_start: 0.8143 (mmm) cc_final: 0.7603 (mmt) REVERT: K 143 GLU cc_start: 0.8023 (tt0) cc_final: 0.7731 (tt0) REVERT: K 180 ASP cc_start: 0.7517 (t0) cc_final: 0.7305 (t0) REVERT: K 240 LYS cc_start: 0.7875 (mttm) cc_final: 0.7582 (mttm) REVERT: K 323 SER cc_start: 0.8784 (m) cc_final: 0.8567 (m) REVERT: N 66 ASN cc_start: 0.7793 (m-40) cc_final: 0.7407 (m110) REVERT: N 107 MET cc_start: 0.8101 (OUTLIER) cc_final: 0.7454 (tmm) REVERT: N 201 LYS cc_start: 0.9017 (tttm) cc_final: 0.8432 (mtmm) REVERT: N 289 ASP cc_start: 0.4389 (OUTLIER) cc_final: 0.4085 (t0) REVERT: N 340 GLU cc_start: 0.8358 (mm-30) cc_final: 0.8052 (mp0) REVERT: A 9 VAL cc_start: 0.9100 (t) cc_final: 0.8794 (m) REVERT: A 120 ASP cc_start: 0.8534 (t70) cc_final: 0.8190 (t70) REVERT: A 322 ASP cc_start: 0.8848 (t0) cc_final: 0.8481 (t0) REVERT: A 423 GLU cc_start: 0.7923 (mt-10) cc_final: 0.7549 (mt-10) REVERT: A 432 TYR cc_start: 0.8677 (OUTLIER) cc_final: 0.7851 (t80) REVERT: A 434 GLU cc_start: 0.8315 (mt-10) cc_final: 0.7986 (mt-10) REVERT: B 213 ARG cc_start: 0.8674 (mtm-85) cc_final: 0.8345 (mtm-85) REVERT: B 347 ASN cc_start: 0.7906 (t0) cc_final: 0.7606 (t0) REVERT: E 242 LEU cc_start: 0.9409 (OUTLIER) cc_final: 0.9133 (pp) REVERT: I 31 ASP cc_start: 0.8544 (t70) cc_final: 0.8189 (t70) REVERT: I 67 ASP cc_start: 0.8535 (t0) cc_final: 0.7935 (t0) REVERT: I 72 THR cc_start: 0.8921 (m) cc_final: 0.8664 (p) REVERT: I 168 SER cc_start: 0.9162 (p) cc_final: 0.8665 (m) REVERT: I 318 ARG cc_start: 0.8580 (mtp85) cc_final: 0.8321 (mtp180) REVERT: S 36 MET cc_start: 0.8315 (ttp) cc_final: 0.7921 (ttt) REVERT: S 80 THR cc_start: 0.8192 (OUTLIER) cc_final: 0.7924 (p) REVERT: S 112 LYS cc_start: 0.9016 (mmmt) cc_final: 0.8789 (mmtm) REVERT: S 199 ASP cc_start: 0.8278 (OUTLIER) cc_final: 0.7863 (t0) REVERT: S 242 LEU cc_start: 0.9027 (OUTLIER) cc_final: 0.8748 (pp) REVERT: S 392 ASP cc_start: 0.8178 (OUTLIER) cc_final: 0.7774 (t0) REVERT: S 394 LYS cc_start: 0.8241 (mttt) cc_final: 0.7801 (mmtt) REVERT: S 397 LEU cc_start: 0.8996 (mt) cc_final: 0.8666 (tt) REVERT: S 414 GLU cc_start: 0.7152 (pm20) cc_final: 0.6916 (pt0) REVERT: S 433 GLU cc_start: 0.8327 (tp30) cc_final: 0.7940 (tt0) REVERT: S 434 GLU cc_start: 0.8326 (tt0) cc_final: 0.7970 (tt0) outliers start: 94 outliers final: 65 residues processed: 564 average time/residue: 0.3540 time to fit residues: 308.1477 Evaluate side-chains 559 residues out of total 2548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 485 time to evaluate : 2.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 5 SER Chi-restraints excluded: chain K residue 11 ARG Chi-restraints excluded: chain K residue 86 PHE Chi-restraints excluded: chain K residue 118 ILE Chi-restraints excluded: chain K residue 142 VAL Chi-restraints excluded: chain K residue 186 VAL Chi-restraints excluded: chain K residue 226 THR Chi-restraints excluded: chain N residue 107 MET Chi-restraints excluded: chain N residue 116 GLN Chi-restraints excluded: chain N residue 165 ASN Chi-restraints excluded: chain N residue 180 ASP Chi-restraints excluded: chain N residue 217 SER Chi-restraints excluded: chain N residue 224 ILE Chi-restraints excluded: chain N residue 241 VAL Chi-restraints excluded: chain N residue 289 ASP Chi-restraints excluded: chain A residue 2 ARG Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 98 ASP Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain A residue 258 ASN Chi-restraints excluded: chain A residue 295 CYS Chi-restraints excluded: chain A residue 316 CYS Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 98 ASP Chi-restraints excluded: chain E residue 145 THR Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain E residue 242 LEU Chi-restraints excluded: chain E residue 259 LEU Chi-restraints excluded: chain E residue 295 CYS Chi-restraints excluded: chain E residue 300 ASN Chi-restraints excluded: chain E residue 335 ILE Chi-restraints excluded: chain E residue 367 ASP Chi-restraints excluded: chain E residue 371 VAL Chi-restraints excluded: chain E residue 417 GLU Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain I residue 88 ASP Chi-restraints excluded: chain I residue 117 LEU Chi-restraints excluded: chain I residue 143 THR Chi-restraints excluded: chain I residue 218 THR Chi-restraints excluded: chain I residue 219 THR Chi-restraints excluded: chain I residue 236 VAL Chi-restraints excluded: chain I residue 284 LEU Chi-restraints excluded: chain I residue 313 VAL Chi-restraints excluded: chain I residue 403 MET Chi-restraints excluded: chain I residue 415 MET Chi-restraints excluded: chain S residue 27 GLU Chi-restraints excluded: chain S residue 80 THR Chi-restraints excluded: chain S residue 101 ASN Chi-restraints excluded: chain S residue 130 THR Chi-restraints excluded: chain S residue 199 ASP Chi-restraints excluded: chain S residue 223 THR Chi-restraints excluded: chain S residue 242 LEU Chi-restraints excluded: chain S residue 271 THR Chi-restraints excluded: chain S residue 334 THR Chi-restraints excluded: chain S residue 363 VAL Chi-restraints excluded: chain S residue 367 ASP Chi-restraints excluded: chain S residue 371 VAL Chi-restraints excluded: chain S residue 379 SER Chi-restraints excluded: chain S residue 381 THR Chi-restraints excluded: chain S residue 392 ASP Chi-restraints excluded: chain S residue 449 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 238 optimal weight: 0.9990 chunk 162 optimal weight: 0.8980 chunk 4 optimal weight: 6.9990 chunk 213 optimal weight: 0.9990 chunk 118 optimal weight: 0.9990 chunk 244 optimal weight: 1.9990 chunk 197 optimal weight: 0.8980 chunk 0 optimal weight: 9.9990 chunk 146 optimal weight: 0.7980 chunk 256 optimal weight: 5.9990 chunk 72 optimal weight: 2.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 200 ASN K 318 ASN ** N 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 285 GLN ** B 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 128 GLN I 37 HIS I 204 ASN I 279 GLN ** I 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 396 HIS S 15 GLN S 61 HIS S 186 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.1897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 24292 Z= 0.179 Angle : 0.524 8.090 32974 Z= 0.263 Chirality : 0.043 0.283 3617 Planarity : 0.004 0.080 4288 Dihedral : 9.777 155.288 3608 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.74 % Favored : 96.02 % Rotamer: Outliers : 3.20 % Allowed : 16.08 % Favored : 80.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % 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: 0.51 (0.16), residues: 2977 helix: 1.73 (0.15), residues: 1237 sheet: 0.42 (0.23), residues: 540 loop : -1.21 (0.17), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP S 388 HIS 0.005 0.001 HIS I 37 PHE 0.018 0.001 PHE S 255 TYR 0.038 0.001 TYR N 74 ARG 0.006 0.000 ARG N 346 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5954 Ramachandran restraints generated. 2977 Oldfield, 0 Emsley, 2977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5954 Ramachandran restraints generated. 2977 Oldfield, 0 Emsley, 2977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 583 residues out of total 2548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 507 time to evaluate : 2.790 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 11 ARG cc_start: 0.8153 (OUTLIER) cc_final: 0.7452 (ttt-90) REVERT: K 138 MET cc_start: 0.7134 (tpp) cc_final: 0.6717 (mmm) REVERT: K 180 ASP cc_start: 0.7364 (t0) cc_final: 0.7161 (t0) REVERT: K 240 LYS cc_start: 0.7807 (mttm) cc_final: 0.7599 (mttm) REVERT: K 288 MET cc_start: 0.6177 (tpt) cc_final: 0.5710 (tpt) REVERT: N 66 ASN cc_start: 0.7771 (m-40) cc_final: 0.7417 (m110) REVERT: N 107 MET cc_start: 0.8036 (OUTLIER) cc_final: 0.7814 (tpp) REVERT: N 201 LYS cc_start: 0.8969 (tttm) cc_final: 0.8406 (mtmm) REVERT: N 289 ASP cc_start: 0.4393 (OUTLIER) cc_final: 0.4184 (t0) REVERT: A 9 VAL cc_start: 0.9027 (t) cc_final: 0.8702 (m) REVERT: A 24 TYR cc_start: 0.8626 (m-10) cc_final: 0.8330 (m-80) REVERT: A 322 ASP cc_start: 0.8731 (t0) cc_final: 0.8358 (t0) REVERT: A 423 GLU cc_start: 0.7890 (mt-10) cc_final: 0.7515 (mt-10) REVERT: A 432 TYR cc_start: 0.8664 (OUTLIER) cc_final: 0.8087 (t80) REVERT: A 434 GLU cc_start: 0.8295 (mt-10) cc_final: 0.7955 (mt-10) REVERT: B 125 GLU cc_start: 0.8154 (OUTLIER) cc_final: 0.7906 (mt-10) REVERT: B 213 ARG cc_start: 0.8695 (mtm-85) cc_final: 0.8334 (mtm-85) REVERT: B 217 LEU cc_start: 0.8785 (mt) cc_final: 0.8583 (mp) REVERT: B 347 ASN cc_start: 0.7766 (t0) cc_final: 0.7457 (t0) REVERT: E 242 LEU cc_start: 0.9399 (OUTLIER) cc_final: 0.9110 (pp) REVERT: E 377 MET cc_start: 0.8535 (ttp) cc_final: 0.8206 (ttt) REVERT: E 414 GLU cc_start: 0.7841 (pm20) cc_final: 0.7607 (pm20) REVERT: I 31 ASP cc_start: 0.8521 (t70) cc_final: 0.8157 (t70) REVERT: I 67 ASP cc_start: 0.8481 (t0) cc_final: 0.7916 (t0) REVERT: I 168 SER cc_start: 0.9132 (p) cc_final: 0.8691 (m) REVERT: S 36 MET cc_start: 0.8269 (ttp) cc_final: 0.7875 (ttt) REVERT: S 80 THR cc_start: 0.8066 (OUTLIER) cc_final: 0.7714 (p) REVERT: S 112 LYS cc_start: 0.8992 (mmmt) cc_final: 0.8724 (mmtm) REVERT: S 160 ASP cc_start: 0.7502 (m-30) cc_final: 0.7205 (m-30) REVERT: S 199 ASP cc_start: 0.8180 (OUTLIER) cc_final: 0.7845 (t0) REVERT: S 392 ASP cc_start: 0.8133 (OUTLIER) cc_final: 0.7785 (t0) REVERT: S 394 LYS cc_start: 0.8188 (mttt) cc_final: 0.7881 (mmtt) REVERT: S 397 LEU cc_start: 0.8954 (mt) cc_final: 0.8671 (tt) REVERT: S 433 GLU cc_start: 0.8290 (tp30) cc_final: 0.7910 (tt0) REVERT: S 434 GLU cc_start: 0.8293 (tt0) cc_final: 0.7924 (tt0) outliers start: 76 outliers final: 58 residues processed: 547 average time/residue: 0.3663 time to fit residues: 312.9301 Evaluate side-chains 545 residues out of total 2548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 478 time to evaluate : 2.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 5 SER Chi-restraints excluded: chain K residue 7 LYS Chi-restraints excluded: chain K residue 11 ARG Chi-restraints excluded: chain K residue 86 PHE Chi-restraints excluded: chain K residue 118 ILE Chi-restraints excluded: chain K residue 132 ASP Chi-restraints excluded: chain K residue 183 LYS Chi-restraints excluded: chain K residue 226 THR Chi-restraints excluded: chain K residue 253 GLU Chi-restraints excluded: chain N residue 107 MET Chi-restraints excluded: chain N residue 116 GLN Chi-restraints excluded: chain N residue 180 ASP Chi-restraints excluded: chain N residue 182 SER Chi-restraints excluded: chain N residue 210 MET Chi-restraints excluded: chain N residue 217 SER Chi-restraints excluded: chain N residue 289 ASP Chi-restraints excluded: chain A residue 2 ARG Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain A residue 258 ASN Chi-restraints excluded: chain A residue 279 GLU Chi-restraints excluded: chain A residue 295 CYS Chi-restraints excluded: chain A residue 316 CYS Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain E residue 98 ASP Chi-restraints excluded: chain E residue 242 LEU Chi-restraints excluded: chain E residue 259 LEU Chi-restraints excluded: chain E residue 295 CYS Chi-restraints excluded: chain E residue 335 ILE Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain E residue 367 ASP Chi-restraints excluded: chain E residue 371 VAL Chi-restraints excluded: chain E residue 417 GLU Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain I residue 143 THR Chi-restraints excluded: chain I residue 218 THR Chi-restraints excluded: chain I residue 236 VAL Chi-restraints excluded: chain I residue 279 GLN Chi-restraints excluded: chain I residue 284 LEU Chi-restraints excluded: chain I residue 313 VAL Chi-restraints excluded: chain I residue 348 ASN Chi-restraints excluded: chain I residue 377 LEU Chi-restraints excluded: chain I residue 403 MET Chi-restraints excluded: chain I residue 415 MET Chi-restraints excluded: chain S residue 27 GLU Chi-restraints excluded: chain S residue 55 GLU Chi-restraints excluded: chain S residue 80 THR Chi-restraints excluded: chain S residue 101 ASN Chi-restraints excluded: chain S residue 130 THR Chi-restraints excluded: chain S residue 191 THR Chi-restraints excluded: chain S residue 199 ASP Chi-restraints excluded: chain S residue 223 THR Chi-restraints excluded: chain S residue 226 ASN Chi-restraints excluded: chain S residue 239 THR Chi-restraints excluded: chain S residue 271 THR Chi-restraints excluded: chain S residue 363 VAL Chi-restraints excluded: chain S residue 367 ASP Chi-restraints excluded: chain S residue 371 VAL Chi-restraints excluded: chain S residue 381 THR Chi-restraints excluded: chain S residue 392 ASP Chi-restraints excluded: chain S residue 449 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 96 optimal weight: 3.9990 chunk 257 optimal weight: 8.9990 chunk 56 optimal weight: 6.9990 chunk 167 optimal weight: 0.0470 chunk 70 optimal weight: 10.0000 chunk 286 optimal weight: 3.9990 chunk 237 optimal weight: 4.9990 chunk 132 optimal weight: 6.9990 chunk 23 optimal weight: 5.9990 chunk 94 optimal weight: 2.9990 chunk 150 optimal weight: 0.7980 overall best weight: 2.3684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 193 GLN K 318 ASN K 337 ASN ** N 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 128 GLN I 37 HIS I 99 ASN I 204 ASN I 279 GLN ** I 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 15 GLN S 186 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.2062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 24292 Z= 0.352 Angle : 0.591 8.816 32974 Z= 0.297 Chirality : 0.045 0.270 3617 Planarity : 0.005 0.078 4288 Dihedral : 9.854 156.129 3608 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.65 % Favored : 95.11 % Rotamer: Outliers : 4.14 % Allowed : 16.32 % Favored : 79.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % 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: 0.38 (0.15), residues: 2977 helix: 1.62 (0.15), residues: 1237 sheet: 0.40 (0.23), residues: 540 loop : -1.30 (0.17), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP S 388 HIS 0.008 0.001 HIS A 88 PHE 0.021 0.002 PHE K 94 TYR 0.053 0.002 TYR N 74 ARG 0.009 0.001 ARG K 129 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5954 Ramachandran restraints generated. 2977 Oldfield, 0 Emsley, 2977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5954 Ramachandran restraints generated. 2977 Oldfield, 0 Emsley, 2977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 590 residues out of total 2548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 490 time to evaluate : 2.613 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 11 ARG cc_start: 0.8182 (OUTLIER) cc_final: 0.7535 (ttt-90) REVERT: K 138 MET cc_start: 0.7197 (tpp) cc_final: 0.6795 (mmm) REVERT: K 240 LYS cc_start: 0.7819 (mttm) cc_final: 0.7607 (mttm) REVERT: K 317 GLU cc_start: 0.8043 (mm-30) cc_final: 0.7602 (mm-30) REVERT: N 66 ASN cc_start: 0.7764 (m-40) cc_final: 0.7450 (m110) REVERT: N 80 GLU cc_start: 0.7963 (tp30) cc_final: 0.7416 (tt0) REVERT: N 107 MET cc_start: 0.8041 (OUTLIER) cc_final: 0.7397 (tmm) REVERT: N 201 LYS cc_start: 0.8992 (tttm) cc_final: 0.8395 (mtmm) REVERT: N 289 ASP cc_start: 0.4471 (OUTLIER) cc_final: 0.4179 (t0) REVERT: A 9 VAL cc_start: 0.9074 (t) cc_final: 0.8771 (m) REVERT: A 345 ASP cc_start: 0.8622 (t0) cc_final: 0.8207 (m-30) REVERT: A 423 GLU cc_start: 0.7937 (mt-10) cc_final: 0.7543 (mt-10) REVERT: A 432 TYR cc_start: 0.8751 (OUTLIER) cc_final: 0.8049 (t80) REVERT: A 434 GLU cc_start: 0.8309 (mt-10) cc_final: 0.8007 (mt-10) REVERT: B 213 ARG cc_start: 0.8704 (mtm-85) cc_final: 0.8356 (mtm-85) REVERT: B 217 LEU cc_start: 0.8810 (mt) cc_final: 0.8600 (mp) REVERT: B 347 ASN cc_start: 0.7838 (t0) cc_final: 0.7523 (t0) REVERT: B 426 GLN cc_start: 0.8766 (OUTLIER) cc_final: 0.8281 (tm-30) REVERT: E 242 LEU cc_start: 0.9412 (OUTLIER) cc_final: 0.9140 (pp) REVERT: I 31 ASP cc_start: 0.8548 (t70) cc_final: 0.8199 (t70) REVERT: I 67 ASP cc_start: 0.8344 (t0) cc_final: 0.7923 (t0) REVERT: I 168 SER cc_start: 0.9176 (p) cc_final: 0.8651 (m) REVERT: I 170 MET cc_start: 0.8394 (mtt) cc_final: 0.8183 (mtt) REVERT: I 318 ARG cc_start: 0.8570 (mtp85) cc_final: 0.8238 (mtp180) REVERT: S 36 MET cc_start: 0.8313 (ttp) cc_final: 0.7891 (ttt) REVERT: S 80 THR cc_start: 0.8129 (OUTLIER) cc_final: 0.7802 (p) REVERT: S 109 THR cc_start: 0.8616 (t) cc_final: 0.8249 (p) REVERT: S 160 ASP cc_start: 0.7536 (m-30) cc_final: 0.7228 (m-30) REVERT: S 199 ASP cc_start: 0.8235 (OUTLIER) cc_final: 0.7896 (t0) REVERT: S 392 ASP cc_start: 0.8195 (OUTLIER) cc_final: 0.7795 (t0) REVERT: S 394 LYS cc_start: 0.8193 (mttt) cc_final: 0.7796 (mmtt) REVERT: S 397 LEU cc_start: 0.8976 (mt) cc_final: 0.8676 (tt) REVERT: S 434 GLU cc_start: 0.8314 (tt0) cc_final: 0.7931 (tt0) outliers start: 100 outliers final: 78 residues processed: 545 average time/residue: 0.3495 time to fit residues: 295.7011 Evaluate side-chains 559 residues out of total 2548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 472 time to evaluate : 2.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 5 SER Chi-restraints excluded: chain K residue 11 ARG Chi-restraints excluded: chain K residue 86 PHE Chi-restraints excluded: chain K residue 118 ILE Chi-restraints excluded: chain K residue 132 ASP Chi-restraints excluded: chain K residue 183 LYS Chi-restraints excluded: chain K residue 186 VAL Chi-restraints excluded: chain K residue 193 GLN Chi-restraints excluded: chain K residue 226 THR Chi-restraints excluded: chain K residue 253 GLU Chi-restraints excluded: chain K residue 285 LEU Chi-restraints excluded: chain K residue 318 ASN Chi-restraints excluded: chain K residue 319 LEU Chi-restraints excluded: chain K residue 337 ASN Chi-restraints excluded: chain N residue 107 MET Chi-restraints excluded: chain N residue 116 GLN Chi-restraints excluded: chain N residue 165 ASN Chi-restraints excluded: chain N residue 180 ASP Chi-restraints excluded: chain N residue 182 SER Chi-restraints excluded: chain N residue 190 ASN Chi-restraints excluded: chain N residue 217 SER Chi-restraints excluded: chain N residue 241 VAL Chi-restraints excluded: chain N residue 289 ASP Chi-restraints excluded: chain A residue 2 ARG Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 258 ASN Chi-restraints excluded: chain A residue 295 CYS Chi-restraints excluded: chain A residue 316 CYS Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 426 GLN Chi-restraints excluded: chain E residue 98 ASP Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain E residue 242 LEU Chi-restraints excluded: chain E residue 259 LEU Chi-restraints excluded: chain E residue 286 LEU Chi-restraints excluded: chain E residue 295 CYS Chi-restraints excluded: chain E residue 335 ILE Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain E residue 367 ASP Chi-restraints excluded: chain E residue 371 VAL Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain I residue 117 LEU Chi-restraints excluded: chain I residue 143 THR Chi-restraints excluded: chain I residue 218 THR Chi-restraints excluded: chain I residue 219 THR Chi-restraints excluded: chain I residue 236 VAL Chi-restraints excluded: chain I residue 279 GLN Chi-restraints excluded: chain I residue 284 LEU Chi-restraints excluded: chain I residue 313 VAL Chi-restraints excluded: chain I residue 348 ASN Chi-restraints excluded: chain I residue 377 LEU Chi-restraints excluded: chain I residue 403 MET Chi-restraints excluded: chain I residue 415 MET Chi-restraints excluded: chain S residue 55 GLU Chi-restraints excluded: chain S residue 74 VAL Chi-restraints excluded: chain S residue 80 THR Chi-restraints excluded: chain S residue 101 ASN Chi-restraints excluded: chain S residue 116 ASP Chi-restraints excluded: chain S residue 130 THR Chi-restraints excluded: chain S residue 191 THR Chi-restraints excluded: chain S residue 199 ASP Chi-restraints excluded: chain S residue 223 THR Chi-restraints excluded: chain S residue 226 ASN Chi-restraints excluded: chain S residue 239 THR Chi-restraints excluded: chain S residue 271 THR Chi-restraints excluded: chain S residue 337 THR Chi-restraints excluded: chain S residue 363 VAL Chi-restraints excluded: chain S residue 367 ASP Chi-restraints excluded: chain S residue 371 VAL Chi-restraints excluded: chain S residue 381 THR Chi-restraints excluded: chain S residue 392 ASP Chi-restraints excluded: chain S residue 449 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 276 optimal weight: 0.8980 chunk 32 optimal weight: 10.0000 chunk 163 optimal weight: 0.5980 chunk 209 optimal weight: 3.9990 chunk 162 optimal weight: 3.9990 chunk 241 optimal weight: 3.9990 chunk 159 optimal weight: 0.6980 chunk 285 optimal weight: 3.9990 chunk 178 optimal weight: 0.8980 chunk 173 optimal weight: 4.9990 chunk 131 optimal weight: 2.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 193 GLN ** K 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 318 ASN K 337 ASN ** N 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 128 GLN I 37 HIS I 279 GLN ** I 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 15 GLN S 186 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.2139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 24292 Z= 0.211 Angle : 0.545 9.503 32974 Z= 0.274 Chirality : 0.043 0.241 3617 Planarity : 0.004 0.077 4288 Dihedral : 9.544 157.721 3605 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.04 % Favored : 95.72 % Rotamer: Outliers : 3.79 % Allowed : 16.86 % Favored : 79.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.16), residues: 2977 helix: 1.70 (0.15), residues: 1248 sheet: 0.37 (0.23), residues: 545 loop : -1.24 (0.17), residues: 1184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP S 388 HIS 0.007 0.001 HIS I 137 PHE 0.017 0.001 PHE K 94 TYR 0.056 0.001 TYR N 74 ARG 0.009 0.000 ARG K 129 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5954 Ramachandran restraints generated. 2977 Oldfield, 0 Emsley, 2977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5954 Ramachandran restraints generated. 2977 Oldfield, 0 Emsley, 2977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 581 residues out of total 2548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 490 time to evaluate : 2.779 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 11 ARG cc_start: 0.8120 (OUTLIER) cc_final: 0.7453 (ttt-90) REVERT: K 138 MET cc_start: 0.7124 (tpp) cc_final: 0.6730 (mmm) REVERT: K 143 GLU cc_start: 0.7993 (tt0) cc_final: 0.7768 (tt0) REVERT: K 240 LYS cc_start: 0.7807 (mttm) cc_final: 0.7579 (mttm) REVERT: K 317 GLU cc_start: 0.7947 (mm-30) cc_final: 0.7677 (mm-30) REVERT: N 66 ASN cc_start: 0.7796 (m-40) cc_final: 0.7444 (m110) REVERT: N 83 GLN cc_start: 0.8698 (tp40) cc_final: 0.8125 (tp-100) REVERT: N 107 MET cc_start: 0.8011 (OUTLIER) cc_final: 0.7793 (tpp) REVERT: N 201 LYS cc_start: 0.8953 (tttm) cc_final: 0.8290 (mtmm) REVERT: N 289 ASP cc_start: 0.4581 (OUTLIER) cc_final: 0.4286 (t0) REVERT: A 9 VAL cc_start: 0.9040 (t) cc_final: 0.8717 (m) REVERT: A 24 TYR cc_start: 0.8632 (m-10) cc_final: 0.8320 (m-80) REVERT: A 163 LYS cc_start: 0.9059 (mmmt) cc_final: 0.8766 (mmtp) REVERT: A 322 ASP cc_start: 0.8739 (t0) cc_final: 0.8378 (t0) REVERT: A 423 GLU cc_start: 0.7915 (mt-10) cc_final: 0.7527 (mt-10) REVERT: A 432 TYR cc_start: 0.8731 (OUTLIER) cc_final: 0.8121 (t80) REVERT: A 434 GLU cc_start: 0.8318 (mt-10) cc_final: 0.8018 (mt-10) REVERT: B 125 GLU cc_start: 0.8137 (OUTLIER) cc_final: 0.7893 (mt-10) REVERT: B 213 ARG cc_start: 0.8698 (mtm-85) cc_final: 0.8355 (mtm-85) REVERT: B 217 LEU cc_start: 0.8787 (mt) cc_final: 0.8580 (mp) REVERT: B 347 ASN cc_start: 0.7773 (t0) cc_final: 0.7447 (t0) REVERT: B 426 GLN cc_start: 0.8746 (OUTLIER) cc_final: 0.8260 (tm-30) REVERT: E 69 ASP cc_start: 0.8638 (t0) cc_final: 0.8367 (t70) REVERT: E 242 LEU cc_start: 0.9394 (OUTLIER) cc_final: 0.9132 (pp) REVERT: E 377 MET cc_start: 0.8529 (ttp) cc_final: 0.8165 (ttt) REVERT: I 31 ASP cc_start: 0.8528 (t70) cc_final: 0.8169 (t70) REVERT: I 67 ASP cc_start: 0.8308 (t0) cc_final: 0.7909 (t0) REVERT: I 168 SER cc_start: 0.9172 (p) cc_final: 0.8621 (m) REVERT: I 170 MET cc_start: 0.8394 (mtt) cc_final: 0.8178 (mtt) REVERT: S 36 MET cc_start: 0.8312 (ttp) cc_final: 0.7879 (ttt) REVERT: S 80 THR cc_start: 0.8090 (OUTLIER) cc_final: 0.7744 (p) REVERT: S 109 THR cc_start: 0.8562 (t) cc_final: 0.8238 (p) REVERT: S 160 ASP cc_start: 0.7514 (m-30) cc_final: 0.7188 (m-30) REVERT: S 199 ASP cc_start: 0.8205 (OUTLIER) cc_final: 0.7898 (t0) REVERT: S 392 ASP cc_start: 0.8162 (OUTLIER) cc_final: 0.7820 (t0) REVERT: S 394 LYS cc_start: 0.8167 (mttt) cc_final: 0.7884 (mmtt) REVERT: S 397 LEU cc_start: 0.8951 (mt) cc_final: 0.8657 (tt) outliers start: 91 outliers final: 72 residues processed: 540 average time/residue: 0.3692 time to fit residues: 309.6987 Evaluate side-chains 561 residues out of total 2548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 479 time to evaluate : 2.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 5 SER Chi-restraints excluded: chain K residue 11 ARG Chi-restraints excluded: chain K residue 86 PHE Chi-restraints excluded: chain K residue 118 ILE Chi-restraints excluded: chain K residue 132 ASP Chi-restraints excluded: chain K residue 183 LYS Chi-restraints excluded: chain K residue 186 VAL Chi-restraints excluded: chain K residue 226 THR Chi-restraints excluded: chain K residue 253 GLU Chi-restraints excluded: chain K residue 288 MET Chi-restraints excluded: chain K residue 319 LEU Chi-restraints excluded: chain K residue 337 ASN Chi-restraints excluded: chain N residue 107 MET Chi-restraints excluded: chain N residue 116 GLN Chi-restraints excluded: chain N residue 165 ASN Chi-restraints excluded: chain N residue 180 ASP Chi-restraints excluded: chain N residue 182 SER Chi-restraints excluded: chain N residue 190 ASN Chi-restraints excluded: chain N residue 217 SER Chi-restraints excluded: chain N residue 241 VAL Chi-restraints excluded: chain N residue 289 ASP Chi-restraints excluded: chain A residue 2 ARG Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 258 ASN Chi-restraints excluded: chain A residue 295 CYS Chi-restraints excluded: chain A residue 316 CYS Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 209 ASP Chi-restraints excluded: chain B residue 426 GLN Chi-restraints excluded: chain E residue 98 ASP Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain E residue 242 LEU Chi-restraints excluded: chain E residue 259 LEU Chi-restraints excluded: chain E residue 286 LEU Chi-restraints excluded: chain E residue 295 CYS Chi-restraints excluded: chain E residue 335 ILE Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain E residue 367 ASP Chi-restraints excluded: chain E residue 371 VAL Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain I residue 88 ASP Chi-restraints excluded: chain I residue 117 LEU Chi-restraints excluded: chain I residue 143 THR Chi-restraints excluded: chain I residue 147 MET Chi-restraints excluded: chain I residue 218 THR Chi-restraints excluded: chain I residue 219 THR Chi-restraints excluded: chain I residue 236 VAL Chi-restraints excluded: chain I residue 279 GLN Chi-restraints excluded: chain I residue 284 LEU Chi-restraints excluded: chain I residue 313 VAL Chi-restraints excluded: chain I residue 348 ASN Chi-restraints excluded: chain I residue 377 LEU Chi-restraints excluded: chain I residue 415 MET Chi-restraints excluded: chain S residue 27 GLU Chi-restraints excluded: chain S residue 55 GLU Chi-restraints excluded: chain S residue 80 THR Chi-restraints excluded: chain S residue 101 ASN Chi-restraints excluded: chain S residue 130 THR Chi-restraints excluded: chain S residue 191 THR Chi-restraints excluded: chain S residue 199 ASP Chi-restraints excluded: chain S residue 223 THR Chi-restraints excluded: chain S residue 226 ASN Chi-restraints excluded: chain S residue 239 THR Chi-restraints excluded: chain S residue 271 THR Chi-restraints excluded: chain S residue 337 THR Chi-restraints excluded: chain S residue 363 VAL Chi-restraints excluded: chain S residue 367 ASP Chi-restraints excluded: chain S residue 371 VAL Chi-restraints excluded: chain S residue 381 THR Chi-restraints excluded: chain S residue 392 ASP Chi-restraints excluded: chain S residue 449 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 176 optimal weight: 3.9990 chunk 113 optimal weight: 0.0970 chunk 170 optimal weight: 0.6980 chunk 85 optimal weight: 0.0570 chunk 56 optimal weight: 8.9990 chunk 55 optimal weight: 0.5980 chunk 181 optimal weight: 2.9990 chunk 194 optimal weight: 1.9990 chunk 141 optimal weight: 0.0970 chunk 26 optimal weight: 4.9990 chunk 224 optimal weight: 0.0270 overall best weight: 0.1752 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 337 ASN ** N 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 204 ASN ** B 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 128 GLN I 37 HIS I 204 ASN I 279 GLN ** I 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 186 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.2418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 24292 Z= 0.130 Angle : 0.513 7.169 32974 Z= 0.256 Chirality : 0.042 0.233 3617 Planarity : 0.004 0.075 4288 Dihedral : 9.002 160.395 3605 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.67 % Favored : 96.16 % Rotamer: Outliers : 2.46 % Allowed : 18.19 % Favored : 79.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % 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: 0.69 (0.16), residues: 2977 helix: 1.93 (0.15), residues: 1237 sheet: 0.54 (0.22), residues: 544 loop : -1.18 (0.17), residues: 1196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP S 388 HIS 0.005 0.001 HIS I 37 PHE 0.013 0.001 PHE K 94 TYR 0.036 0.001 TYR K 189 ARG 0.009 0.000 ARG K 129 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5954 Ramachandran restraints generated. 2977 Oldfield, 0 Emsley, 2977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5954 Ramachandran restraints generated. 2977 Oldfield, 0 Emsley, 2977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 585 residues out of total 2548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 528 time to evaluate : 2.788 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 11 ARG cc_start: 0.8104 (OUTLIER) cc_final: 0.7369 (ttt-90) REVERT: K 76 ASP cc_start: 0.8545 (t0) cc_final: 0.8143 (t0) REVERT: K 81 MET cc_start: 0.8282 (mmm) cc_final: 0.8057 (mmt) REVERT: K 115 GLN cc_start: 0.8428 (mp10) cc_final: 0.8020 (pm20) REVERT: K 138 MET cc_start: 0.7028 (tpp) cc_final: 0.6619 (mmm) REVERT: K 240 LYS cc_start: 0.7781 (mttm) cc_final: 0.7576 (mttm) REVERT: K 327 MET cc_start: 0.7831 (ttt) cc_final: 0.7416 (ttt) REVERT: N 51 SER cc_start: 0.7437 (p) cc_final: 0.6574 (m) REVERT: N 66 ASN cc_start: 0.7742 (m-40) cc_final: 0.7396 (m110) REVERT: N 201 LYS cc_start: 0.8874 (tttm) cc_final: 0.8240 (mtmm) REVERT: N 289 ASP cc_start: 0.4560 (OUTLIER) cc_final: 0.4341 (t0) REVERT: A 1 MET cc_start: 0.6841 (tpp) cc_final: 0.6514 (tpp) REVERT: A 9 VAL cc_start: 0.8937 (t) cc_final: 0.8604 (m) REVERT: A 24 TYR cc_start: 0.8615 (m-10) cc_final: 0.8272 (m-80) REVERT: A 163 LYS cc_start: 0.8982 (mmmt) cc_final: 0.8697 (mmtp) REVERT: A 322 ASP cc_start: 0.8681 (t0) cc_final: 0.8401 (t0) REVERT: A 423 GLU cc_start: 0.7881 (mt-10) cc_final: 0.7544 (mt-10) REVERT: A 430 LYS cc_start: 0.8559 (ttpp) cc_final: 0.8357 (ttpp) REVERT: A 432 TYR cc_start: 0.8724 (OUTLIER) cc_final: 0.8294 (t80) REVERT: A 434 GLU cc_start: 0.8294 (mt-10) cc_final: 0.7981 (mt-10) REVERT: B 60 VAL cc_start: 0.8893 (t) cc_final: 0.8536 (m) REVERT: B 170 MET cc_start: 0.8548 (ptp) cc_final: 0.8103 (mtt) REVERT: B 217 LEU cc_start: 0.8706 (mt) cc_final: 0.8481 (mp) REVERT: B 288 GLU cc_start: 0.8183 (mm-30) cc_final: 0.7659 (mt-10) REVERT: B 347 ASN cc_start: 0.7680 (t0) cc_final: 0.7359 (t0) REVERT: E 214 ARG cc_start: 0.8728 (tmm160) cc_final: 0.8434 (tmm-80) REVERT: E 242 LEU cc_start: 0.9366 (OUTLIER) cc_final: 0.9113 (pp) REVERT: I 31 ASP cc_start: 0.8499 (t70) cc_final: 0.8107 (t70) REVERT: I 67 ASP cc_start: 0.8234 (t0) cc_final: 0.7853 (t0) REVERT: I 168 SER cc_start: 0.9128 (p) cc_final: 0.8587 (m) REVERT: I 355 ASP cc_start: 0.8141 (m-30) cc_final: 0.7860 (m-30) REVERT: I 426 GLN cc_start: 0.8570 (tm-30) cc_final: 0.8171 (tt0) REVERT: S 36 MET cc_start: 0.8309 (ttp) cc_final: 0.7871 (ttt) REVERT: S 109 THR cc_start: 0.8506 (t) cc_final: 0.8241 (p) REVERT: S 160 ASP cc_start: 0.7468 (m-30) cc_final: 0.7172 (m-30) REVERT: S 186 ASN cc_start: 0.8649 (m110) cc_final: 0.8323 (m-40) REVERT: S 392 ASP cc_start: 0.8100 (OUTLIER) cc_final: 0.7815 (t0) REVERT: S 394 LYS cc_start: 0.8119 (mttt) cc_final: 0.7896 (mmtt) REVERT: S 397 LEU cc_start: 0.8870 (mt) cc_final: 0.8592 (tt) outliers start: 57 outliers final: 38 residues processed: 555 average time/residue: 0.3607 time to fit residues: 311.7857 Evaluate side-chains 538 residues out of total 2548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 495 time to evaluate : 2.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 5 SER Chi-restraints excluded: chain K residue 11 ARG Chi-restraints excluded: chain K residue 86 PHE Chi-restraints excluded: chain K residue 226 THR Chi-restraints excluded: chain K residue 253 GLU Chi-restraints excluded: chain K residue 288 MET Chi-restraints excluded: chain K residue 337 ASN Chi-restraints excluded: chain N residue 116 GLN Chi-restraints excluded: chain N residue 241 VAL Chi-restraints excluded: chain N residue 289 ASP Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain A residue 295 CYS Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 356 ILE Chi-restraints excluded: chain E residue 98 ASP Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 242 LEU Chi-restraints excluded: chain E residue 286 LEU Chi-restraints excluded: chain E residue 295 CYS Chi-restraints excluded: chain E residue 335 ILE Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain E residue 367 ASP Chi-restraints excluded: chain E residue 371 VAL Chi-restraints excluded: chain I residue 143 THR Chi-restraints excluded: chain I residue 279 GLN Chi-restraints excluded: chain I residue 377 LEU Chi-restraints excluded: chain S residue 55 GLU Chi-restraints excluded: chain S residue 130 THR Chi-restraints excluded: chain S residue 191 THR Chi-restraints excluded: chain S residue 226 ASN Chi-restraints excluded: chain S residue 239 THR Chi-restraints excluded: chain S residue 271 THR Chi-restraints excluded: chain S residue 324 VAL Chi-restraints excluded: chain S residue 337 THR Chi-restraints excluded: chain S residue 367 ASP Chi-restraints excluded: chain S residue 381 THR Chi-restraints excluded: chain S residue 392 ASP Chi-restraints excluded: chain S residue 449 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 259 optimal weight: 2.9990 chunk 273 optimal weight: 2.9990 chunk 249 optimal weight: 8.9990 chunk 265 optimal weight: 6.9990 chunk 160 optimal weight: 2.9990 chunk 115 optimal weight: 1.9990 chunk 208 optimal weight: 1.9990 chunk 81 optimal weight: 3.9990 chunk 240 optimal weight: 0.0970 chunk 251 optimal weight: 6.9990 chunk 264 optimal weight: 0.7980 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 115 GLN N 200 ASN A 256 GLN B 204 ASN ** B 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 128 GLN I 52 ASN I 279 GLN ** I 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 197 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.2383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 24292 Z= 0.255 Angle : 0.562 10.943 32974 Z= 0.281 Chirality : 0.044 0.290 3617 Planarity : 0.004 0.075 4288 Dihedral : 9.083 160.931 3603 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.18 % Favored : 95.65 % Rotamer: Outliers : 2.62 % Allowed : 18.15 % Favored : 79.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % 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: 0.68 (0.16), residues: 2977 helix: 1.86 (0.15), residues: 1248 sheet: 0.54 (0.23), residues: 536 loop : -1.15 (0.17), residues: 1193 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP S 388 HIS 0.006 0.001 HIS I 137 PHE 0.021 0.001 PHE B 367 TYR 0.037 0.001 TYR N 74 ARG 0.009 0.000 ARG K 129 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5954 Ramachandran restraints generated. 2977 Oldfield, 0 Emsley, 2977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5954 Ramachandran restraints generated. 2977 Oldfield, 0 Emsley, 2977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 556 residues out of total 2548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 495 time to evaluate : 2.812 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 11 ARG cc_start: 0.8118 (OUTLIER) cc_final: 0.7430 (ttt-90) REVERT: K 81 MET cc_start: 0.8388 (mmm) cc_final: 0.8056 (mmt) REVERT: K 115 GLN cc_start: 0.8351 (OUTLIER) cc_final: 0.7962 (pm20) REVERT: K 138 MET cc_start: 0.7036 (tpp) cc_final: 0.6582 (mmm) REVERT: K 240 LYS cc_start: 0.7725 (mttm) cc_final: 0.7435 (ttmm) REVERT: K 327 MET cc_start: 0.8107 (ttt) cc_final: 0.7658 (ttt) REVERT: N 51 SER cc_start: 0.7475 (p) cc_final: 0.6586 (m) REVERT: N 66 ASN cc_start: 0.7757 (m-40) cc_final: 0.7418 (m110) REVERT: N 201 LYS cc_start: 0.8929 (tttm) cc_final: 0.8274 (mtmm) REVERT: N 289 ASP cc_start: 0.4614 (OUTLIER) cc_final: 0.4283 (t0) REVERT: A 9 VAL cc_start: 0.9034 (t) cc_final: 0.8717 (m) REVERT: A 423 GLU cc_start: 0.7925 (mt-10) cc_final: 0.7504 (mt-10) REVERT: A 432 TYR cc_start: 0.8814 (OUTLIER) cc_final: 0.8249 (t80) REVERT: A 434 GLU cc_start: 0.8317 (mt-10) cc_final: 0.8025 (mt-10) REVERT: B 125 GLU cc_start: 0.8131 (OUTLIER) cc_final: 0.7867 (mt-10) REVERT: B 170 MET cc_start: 0.8579 (ptp) cc_final: 0.8134 (mtt) REVERT: B 217 LEU cc_start: 0.8778 (mt) cc_final: 0.8564 (mp) REVERT: B 288 GLU cc_start: 0.8225 (mm-30) cc_final: 0.7718 (mt-10) REVERT: B 347 ASN cc_start: 0.7781 (t0) cc_final: 0.7465 (t0) REVERT: E 3 GLU cc_start: 0.8207 (mp0) cc_final: 0.7901 (mp0) REVERT: E 31 GLN cc_start: 0.8486 (mt0) cc_final: 0.8229 (mt0) REVERT: I 31 ASP cc_start: 0.8524 (t70) cc_final: 0.8154 (t70) REVERT: I 67 ASP cc_start: 0.8297 (t0) cc_final: 0.7854 (t0) REVERT: I 168 SER cc_start: 0.9180 (p) cc_final: 0.8632 (m) REVERT: I 355 ASP cc_start: 0.8129 (m-30) cc_final: 0.7882 (m-30) REVERT: S 36 MET cc_start: 0.8315 (ttp) cc_final: 0.7875 (ttt) REVERT: S 109 THR cc_start: 0.8485 (t) cc_final: 0.8234 (p) REVERT: S 160 ASP cc_start: 0.7517 (m-30) cc_final: 0.7204 (m-30) REVERT: S 199 ASP cc_start: 0.8197 (OUTLIER) cc_final: 0.7933 (t0) REVERT: S 392 ASP cc_start: 0.8209 (OUTLIER) cc_final: 0.7894 (t0) REVERT: S 394 LYS cc_start: 0.8144 (mttt) cc_final: 0.7874 (mmtt) REVERT: S 397 LEU cc_start: 0.8911 (mt) cc_final: 0.8637 (tt) REVERT: S 413 MET cc_start: 0.7840 (mmm) cc_final: 0.7364 (mtp) REVERT: S 433 GLU cc_start: 0.8293 (tp30) cc_final: 0.7915 (tt0) outliers start: 61 outliers final: 47 residues processed: 529 average time/residue: 0.3527 time to fit residues: 288.8631 Evaluate side-chains 532 residues out of total 2548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 478 time to evaluate : 2.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 5 SER Chi-restraints excluded: chain K residue 11 ARG Chi-restraints excluded: chain K residue 86 PHE Chi-restraints excluded: chain K residue 115 GLN Chi-restraints excluded: chain K residue 132 ASP Chi-restraints excluded: chain K residue 186 VAL Chi-restraints excluded: chain K residue 226 THR Chi-restraints excluded: chain K residue 253 GLU Chi-restraints excluded: chain N residue 116 GLN Chi-restraints excluded: chain N residue 165 ASN Chi-restraints excluded: chain N residue 241 VAL Chi-restraints excluded: chain N residue 289 ASP Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain A residue 295 CYS Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 195 ASN Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain E residue 98 ASP Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 286 LEU Chi-restraints excluded: chain E residue 295 CYS Chi-restraints excluded: chain E residue 334 THR Chi-restraints excluded: chain E residue 335 ILE Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain E residue 367 ASP Chi-restraints excluded: chain E residue 371 VAL Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain I residue 143 THR Chi-restraints excluded: chain I residue 279 GLN Chi-restraints excluded: chain I residue 313 VAL Chi-restraints excluded: chain I residue 348 ASN Chi-restraints excluded: chain I residue 377 LEU Chi-restraints excluded: chain I residue 403 MET Chi-restraints excluded: chain S residue 55 GLU Chi-restraints excluded: chain S residue 130 THR Chi-restraints excluded: chain S residue 191 THR Chi-restraints excluded: chain S residue 199 ASP Chi-restraints excluded: chain S residue 226 ASN Chi-restraints excluded: chain S residue 239 THR Chi-restraints excluded: chain S residue 271 THR Chi-restraints excluded: chain S residue 324 VAL Chi-restraints excluded: chain S residue 337 THR Chi-restraints excluded: chain S residue 363 VAL Chi-restraints excluded: chain S residue 367 ASP Chi-restraints excluded: chain S residue 381 THR Chi-restraints excluded: chain S residue 392 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 174 optimal weight: 4.9990 chunk 281 optimal weight: 0.8980 chunk 171 optimal weight: 0.6980 chunk 133 optimal weight: 0.8980 chunk 195 optimal weight: 2.9990 chunk 294 optimal weight: 6.9990 chunk 271 optimal weight: 3.9990 chunk 234 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 181 optimal weight: 1.9990 chunk 143 optimal weight: 4.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 98 GLN A 256 GLN B 204 ASN ** B 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 128 GLN I 279 GLN ** I 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 18 ASN S 186 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.2456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 24292 Z= 0.191 Angle : 0.541 9.832 32974 Z= 0.270 Chirality : 0.043 0.284 3617 Planarity : 0.004 0.074 4288 Dihedral : 8.985 161.579 3603 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.94 % Favored : 95.89 % Rotamer: Outliers : 2.50 % Allowed : 18.42 % Favored : 79.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % 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: 0.68 (0.16), residues: 2977 helix: 1.87 (0.15), residues: 1248 sheet: 0.59 (0.23), residues: 537 loop : -1.19 (0.17), residues: 1192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP S 388 HIS 0.006 0.001 HIS I 137 PHE 0.020 0.001 PHE B 367 TYR 0.036 0.001 TYR N 74 ARG 0.006 0.000 ARG A 123 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5954 Ramachandran restraints generated. 2977 Oldfield, 0 Emsley, 2977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5954 Ramachandran restraints generated. 2977 Oldfield, 0 Emsley, 2977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 549 residues out of total 2548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 491 time to evaluate : 2.458 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 11 ARG cc_start: 0.8124 (OUTLIER) cc_final: 0.7434 (ttt-90) REVERT: K 76 ASP cc_start: 0.8559 (t0) cc_final: 0.8303 (t0) REVERT: K 81 MET cc_start: 0.8372 (mmm) cc_final: 0.8057 (mmt) REVERT: K 115 GLN cc_start: 0.8371 (mp10) cc_final: 0.8153 (pm20) REVERT: K 138 MET cc_start: 0.7046 (tpp) cc_final: 0.6563 (mmm) REVERT: K 240 LYS cc_start: 0.7749 (mttm) cc_final: 0.7464 (ttmm) REVERT: N 51 SER cc_start: 0.7485 (p) cc_final: 0.6570 (m) REVERT: N 66 ASN cc_start: 0.7754 (m-40) cc_final: 0.7413 (m110) REVERT: N 201 LYS cc_start: 0.8909 (tttm) cc_final: 0.8254 (mtmm) REVERT: N 289 ASP cc_start: 0.4617 (OUTLIER) cc_final: 0.4332 (t0) REVERT: A 9 VAL cc_start: 0.9012 (t) cc_final: 0.8690 (m) REVERT: A 24 TYR cc_start: 0.8635 (m-10) cc_final: 0.8266 (m-80) REVERT: A 163 LYS cc_start: 0.9010 (mmmt) cc_final: 0.8713 (mmtm) REVERT: A 423 GLU cc_start: 0.7907 (mt-10) cc_final: 0.7514 (mt-10) REVERT: A 432 TYR cc_start: 0.8824 (OUTLIER) cc_final: 0.8239 (t80) REVERT: A 434 GLU cc_start: 0.8308 (mt-10) cc_final: 0.8013 (mt-10) REVERT: B 125 GLU cc_start: 0.8111 (OUTLIER) cc_final: 0.7843 (mt-10) REVERT: B 217 LEU cc_start: 0.8791 (mt) cc_final: 0.8591 (mp) REVERT: B 288 GLU cc_start: 0.8219 (mm-30) cc_final: 0.7760 (mm-30) REVERT: B 347 ASN cc_start: 0.7725 (t0) cc_final: 0.7417 (t0) REVERT: E 3 GLU cc_start: 0.8207 (mp0) cc_final: 0.7899 (mp0) REVERT: E 31 GLN cc_start: 0.8452 (mt0) cc_final: 0.8198 (mt0) REVERT: E 214 ARG cc_start: 0.8722 (tmm160) cc_final: 0.8435 (tmm-80) REVERT: I 31 ASP cc_start: 0.8522 (t70) cc_final: 0.8150 (t70) REVERT: I 67 ASP cc_start: 0.8291 (t0) cc_final: 0.7898 (t0) REVERT: I 168 SER cc_start: 0.9150 (p) cc_final: 0.8626 (m) REVERT: I 355 ASP cc_start: 0.8116 (m-30) cc_final: 0.7864 (m-30) REVERT: I 388 MET cc_start: 0.8551 (mtp) cc_final: 0.8245 (ttm) REVERT: S 36 MET cc_start: 0.8315 (ttp) cc_final: 0.7867 (ttt) REVERT: S 109 THR cc_start: 0.8457 (t) cc_final: 0.8211 (p) REVERT: S 160 ASP cc_start: 0.7487 (m-30) cc_final: 0.7174 (m-30) REVERT: S 339 ARG cc_start: 0.8431 (mtp-110) cc_final: 0.8219 (mtm110) REVERT: S 392 ASP cc_start: 0.8183 (OUTLIER) cc_final: 0.7884 (t0) REVERT: S 394 LYS cc_start: 0.8145 (mttt) cc_final: 0.7873 (mmtt) REVERT: S 397 LEU cc_start: 0.8882 (mt) cc_final: 0.8584 (tt) REVERT: S 413 MET cc_start: 0.7808 (mmm) cc_final: 0.7324 (mtp) REVERT: S 433 GLU cc_start: 0.8278 (tp30) cc_final: 0.7915 (tt0) outliers start: 58 outliers final: 49 residues processed: 521 average time/residue: 0.3500 time to fit residues: 280.7202 Evaluate side-chains 540 residues out of total 2548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 486 time to evaluate : 2.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 5 SER Chi-restraints excluded: chain K residue 11 ARG Chi-restraints excluded: chain K residue 86 PHE Chi-restraints excluded: chain K residue 186 VAL Chi-restraints excluded: chain K residue 226 THR Chi-restraints excluded: chain K residue 253 GLU Chi-restraints excluded: chain K residue 319 LEU Chi-restraints excluded: chain N residue 165 ASN Chi-restraints excluded: chain N residue 217 SER Chi-restraints excluded: chain N residue 241 VAL Chi-restraints excluded: chain N residue 289 ASP Chi-restraints excluded: chain A residue 2 ARG Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 295 CYS Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 195 ASN Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain E residue 98 ASP Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain E residue 286 LEU Chi-restraints excluded: chain E residue 295 CYS Chi-restraints excluded: chain E residue 334 THR Chi-restraints excluded: chain E residue 335 ILE Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain E residue 367 ASP Chi-restraints excluded: chain E residue 371 VAL Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain I residue 143 THR Chi-restraints excluded: chain I residue 279 GLN Chi-restraints excluded: chain I residue 313 VAL Chi-restraints excluded: chain I residue 348 ASN Chi-restraints excluded: chain I residue 377 LEU Chi-restraints excluded: chain I residue 403 MET Chi-restraints excluded: chain S residue 55 GLU Chi-restraints excluded: chain S residue 130 THR Chi-restraints excluded: chain S residue 191 THR Chi-restraints excluded: chain S residue 226 ASN Chi-restraints excluded: chain S residue 239 THR Chi-restraints excluded: chain S residue 271 THR Chi-restraints excluded: chain S residue 324 VAL Chi-restraints excluded: chain S residue 337 THR Chi-restraints excluded: chain S residue 367 ASP Chi-restraints excluded: chain S residue 381 THR Chi-restraints excluded: chain S residue 392 ASP Chi-restraints excluded: chain S residue 429 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 186 optimal weight: 0.9990 chunk 250 optimal weight: 0.9990 chunk 71 optimal weight: 9.9990 chunk 216 optimal weight: 0.9980 chunk 34 optimal weight: 4.9990 chunk 65 optimal weight: 0.0770 chunk 235 optimal weight: 0.9980 chunk 98 optimal weight: 3.9990 chunk 241 optimal weight: 2.9990 chunk 29 optimal weight: 20.0000 chunk 43 optimal weight: 0.2980 overall best weight: 0.6740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 115 GLN A 256 GLN ** B 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 128 GLN I 279 GLN ** I 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 186 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.128884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.098673 restraints weight = 36579.811| |-----------------------------------------------------------------------------| r_work (start): 0.3471 rms_B_bonded: 2.41 r_work: 0.3338 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3179 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3182 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3182 r_free = 0.3182 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3182 r_free = 0.3182 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3182 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.2558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 24292 Z= 0.157 Angle : 0.534 11.123 32974 Z= 0.263 Chirality : 0.042 0.278 3617 Planarity : 0.004 0.074 4288 Dihedral : 8.838 162.758 3603 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.98 % Favored : 95.86 % Rotamer: Outliers : 2.50 % Allowed : 18.58 % Favored : 78.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.16), residues: 2977 helix: 1.92 (0.15), residues: 1255 sheet: 0.66 (0.23), residues: 534 loop : -1.14 (0.17), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP S 388 HIS 0.005 0.001 HIS I 137 PHE 0.019 0.001 PHE B 367 TYR 0.034 0.001 TYR K 189 ARG 0.007 0.000 ARG N 346 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6638.38 seconds wall clock time: 118 minutes 9.36 seconds (7089.36 seconds total)