Starting phenix.real_space_refine on Tue Jul 23 20:53:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8utn_42543/07_2024/8utn_42543_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8utn_42543/07_2024/8utn_42543.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8utn_42543/07_2024/8utn_42543.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8utn_42543/07_2024/8utn_42543.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8utn_42543/07_2024/8utn_42543_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8utn_42543/07_2024/8utn_42543_neut.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 19 5.49 5 Mg 4 5.21 5 S 152 5.16 5 C 14858 2.51 5 N 4069 2.21 5 O 4682 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "K TYR 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 124": "OE1" <-> "OE2" Residue "K ASP 125": "OD1" <-> "OD2" Residue "K GLU 143": "OE1" <-> "OE2" Residue "K GLU 170": "OE1" <-> "OE2" Residue "K GLU 212": "OE1" <-> "OE2" Residue "K ASP 231": "OD1" <-> "OD2" Residue "K ASP 248": "OD1" <-> "OD2" Residue "K ASP 256": "OD1" <-> "OD2" Residue "K TYR 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 231": "OD1" <-> "OD2" Residue "N GLU 287": "OE1" <-> "OE2" Residue "N ASP 289": "OD1" <-> "OD2" Residue "N ASP 339": "OD1" <-> "OD2" Residue "N GLU 340": "OE1" <-> "OE2" Residue "A ASP 69": "OD1" <-> "OD2" Residue "A GLU 196": "OE1" <-> "OE2" Residue "A TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 290": "OE1" <-> "OE2" Residue "A ASP 306": "OD1" <-> "OD2" Residue "A TYR 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 319": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 22": "OE1" <-> "OE2" Residue "B ASP 31": "OD1" <-> "OD2" Residue "B TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 111": "OE1" <-> "OE2" Residue "B TYR 398": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 196": "OE1" <-> "OE2" Residue "E ASP 199": "OD1" <-> "OD2" Residue "E GLU 220": "OE1" <-> "OE2" Residue "E GLU 284": "OE1" <-> "OE2" Residue "E TYR 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 411": "OE1" <-> "OE2" Residue "E GLU 434": "OE1" <-> "OE2" Residue "E GLU 445": "OE1" <-> "OE2" Residue "E GLU 450": "OE1" <-> "OE2" Residue "E TYR 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 111": "OE1" <-> "OE2" Residue "I ASP 161": "OD1" <-> "OD2" Residue "I PHE 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 209": "OD1" <-> "OD2" Residue "I PHE 394": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 431": "OD1" <-> "OD2" Residue "S GLU 22": "OE1" <-> "OE2" Residue "S ASP 46": "OD1" <-> "OD2" Residue "S GLU 77": "OE1" <-> "OE2" Residue "S GLU 97": "OE1" <-> "OE2" Residue "S ASP 199": "OD1" <-> "OD2" Residue "S TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 218": "OD1" <-> "OD2" Residue "S PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 319": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 345": "OD1" <-> "OD2" Residue "S PHE 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 386": "OE1" <-> "OE2" Residue "S ASP 392": "OD1" <-> "OD2" Residue "S ASP 396": "OD1" <-> "OD2" Residue "S TYR 399": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 420": "OE1" <-> "OE2" Residue "S ASP 424": "OD1" <-> "OD2" Residue "S GLU 429": "OE1" <-> "OE2" Residue "S GLU 433": "OE1" <-> "OE2" Residue "S GLU 434": "OE1" <-> "OE2" Residue "S ASP 438": "OD1" <-> "OD2" Residue "S GLU 441": "OE1" <-> "OE2" Residue "S GLU 449": "OE1" <-> "OE2" Residue "S TYR 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 23784 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: 3047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3047 Classifications: {'peptide': 388} Link IDs: {'PTRANS': 13, 'TRANS': 374} 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=0.51 ... (12 atoms not shown) pdb=" CG2BTHR B 429 " occ=0.49 residue: pdb=" N AALA B 430 " occ=0.51 ... (8 atoms not shown) pdb=" CB BALA B 430 " occ=0.49 residue: pdb=" N AASP B 431 " occ=0.51 ... (14 atoms not shown) pdb=" OD2BASP B 431 " occ=0.49 residue: pdb=" N AGLU B 432 " occ=0.51 ... (16 atoms not shown) pdb=" OE2BGLU B 432 " occ=0.49 residue: pdb=" N ATHR I 429 " occ=0.51 ... (12 atoms not shown) pdb=" CG2BTHR I 429 " occ=0.49 residue: pdb=" N AALA I 430 " occ=0.51 ... (8 atoms not shown) pdb=" CB BALA I 430 " occ=0.49 residue: pdb=" N AASP I 431 " occ=0.51 ... (14 atoms not shown) pdb=" OD2BASP I 431 " occ=0.49 residue: pdb=" N AGLU I 432 " occ=0.51 ... (16 atoms not shown) pdb=" OE2BGLU I 432 " occ=0.49 residue: pdb=" N AGLN I 433 " occ=0.51 ... (16 atoms not shown) pdb=" NE2BGLN I 433 " occ=0.49 Time building chain proxies: 16.70, per 1000 atoms: 0.70 Number of scatterers: 23784 At special positions: 0 Unit cell: (80.18, 116.472, 238.008, 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 152 16.00 P 19 15.00 Mg 4 11.99 O 4682 8.00 N 4069 7.00 C 14858 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: 9.11 Conformation dependent library (CDL) restraints added in 5.6 seconds 5952 Ramachandran restraints generated. 2976 Oldfield, 0 Emsley, 2976 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5552 Finding SS restraints... Secondary structure from input PDB file: 127 helices and 24 sheets defined 49.4% alpha, 18.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.10 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 159 through 163 removed outlier: 3.904A pdb=" N ASN K 162 " --> pdb=" O ASN K 159 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LYS K 163 " --> pdb=" O PRO K 160 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 159 through 163' 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 294 Proline residue: K 292 - end of helix Processing helix chain 'K' and resid 305 through 308 removed outlier: 3.865A 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 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 354 removed outlier: 3.978A pdb=" N SER K 343 " --> pdb=" O ASP K 339 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLN K 353 " --> pdb=" O ASP K 349 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ILE K 354 " --> pdb=" O ARG K 350 " (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 87 removed outlier: 4.604A pdb=" N GLU N 79 " --> pdb=" O ARG N 75 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N GLU N 80 " --> pdb=" O ASP N 76 " (cutoff:3.500A) Processing helix chain 'N' and resid 102 through 108 Processing helix chain 'N' and resid 117 through 133 removed outlier: 3.894A 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: 3.753A 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: 3.908A 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: 4.232A pdb=" N LYS A 40 " --> pdb=" O MET A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 80 removed outlier: 3.731A 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 113 through 129 removed outlier: 4.252A pdb=" N LEU A 117 " --> pdb=" O GLU A 113 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLN A 128 " --> pdb=" O LYS A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 161 removed outlier: 4.177A pdb=" N THR A 150 " --> pdb=" O GLY A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 190 removed outlier: 3.514A 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: 3.801A 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: 3.659A pdb=" N ASN A 258 " --> pdb=" O GLU A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 266 removed outlier: 3.692A pdb=" N ILE A 265 " --> pdb=" O TYR A 262 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N HIS A 266 " --> pdb=" O PRO A 263 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 262 through 266' Processing helix chain 'A' and resid 277 through 282 removed outlier: 3.919A pdb=" N TYR A 282 " --> pdb=" O ALA A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 296 removed outlier: 3.781A 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: 3.525A pdb=" N VAL A 328 " --> pdb=" O VAL A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 400 removed outlier: 3.820A pdb=" N ALA A 387 " --> pdb=" O ALA A 383 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N LEU A 391 " --> pdb=" O ALA A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 410 removed outlier: 4.133A pdb=" N TYR A 408 " --> pdb=" O PHE A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 436 removed outlier: 4.044A pdb=" N SER A 419 " --> pdb=" O GLU A 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 28 Processing helix chain 'B' and resid 46 through 49 removed outlier: 3.520A pdb=" N VAL B 49 " --> pdb=" O ARG B 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 46 through 49' Processing helix chain 'B' and resid 69 through 78 removed outlier: 4.545A 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: 3.810A pdb=" N LEU B 112 " --> pdb=" O GLU B 108 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N ASP B 114 " --> pdb=" O ALA B 110 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N SER B 115 " --> pdb=" O GLU B 111 " (cutoff:3.500A) removed outlier: 3.784A 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: 3.650A pdb=" N ASN B 184 " --> pdb=" O VAL B 180 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N GLU B 194 " --> pdb=" O HIS B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 214 Processing helix chain 'B' and resid 221 through 237 removed outlier: 3.683A pdb=" N LEU B 225 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N THR B 237 " --> pdb=" O MET B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 241 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: 4.081A 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: 4.258A pdb=" N LEU B 377 " --> pdb=" O ALA B 373 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N PHE B 378 " --> pdb=" O ILE B 374 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 400 removed outlier: 4.170A pdb=" N TYR B 398 " --> pdb=" O PHE B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 425 removed outlier: 3.810A pdb=" N PHE B 408 " --> pdb=" O ASP B 404 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N TYR B 425 " --> pdb=" O GLU B 421 " (cutoff:3.500A) Processing helix chain 'E' and resid 10 through 28 Processing helix chain 'E' and resid 36 through 43 removed outlier: 3.904A pdb=" N LYS E 40 " --> pdb=" O MET E 36 " (cutoff:3.500A) Processing helix chain 'E' and resid 71 through 80 removed outlier: 4.637A pdb=" N ILE E 75 " --> pdb=" O GLU E 71 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N VAL E 78 " --> pdb=" O VAL E 74 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N THR E 80 " --> pdb=" O ASP E 76 " (cutoff:3.500A) Processing helix chain 'E' and resid 102 through 108 Processing helix chain 'E' and resid 114 through 128 Processing helix chain 'E' and resid 143 through 161 removed outlier: 3.510A pdb=" N SER E 147 " --> pdb=" O GLY E 143 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N THR E 150 " --> pdb=" O GLY E 146 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 198 removed outlier: 3.703A pdb=" N ASN E 186 " --> pdb=" O VAL E 182 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N HIS E 192 " --> pdb=" O ILE E 188 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N THR E 193 " --> pdb=" O LEU E 189 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N GLU E 196 " --> pdb=" O HIS E 192 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N SER E 198 " --> pdb=" O THR E 194 " (cutoff:3.500A) Processing helix chain 'E' and resid 205 through 216 Processing helix chain 'E' and resid 223 through 240 removed outlier: 3.837A 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: 3.670A pdb=" N GLN E 256 " --> pdb=" O LEU E 252 " (cutoff:3.500A) Processing helix chain 'E' and resid 277 through 282 removed outlier: 3.973A pdb=" N TYR E 282 " --> pdb=" O ALA E 278 " (cutoff:3.500A) Processing helix chain 'E' and resid 287 through 296 removed outlier: 3.762A 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: 3.633A pdb=" N VAL E 328 " --> pdb=" O VAL E 324 " (cutoff:3.500A) Processing helix chain 'E' and resid 383 through 400 removed outlier: 3.930A pdb=" N ALA E 387 " --> pdb=" O ALA E 383 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N LEU E 391 " --> pdb=" O ALA E 387 " (cutoff:3.500A) Processing helix chain 'E' and resid 404 through 410 removed outlier: 4.317A pdb=" N TYR E 408 " --> pdb=" O PHE E 404 " (cutoff:3.500A) Processing helix chain 'E' and resid 414 through 436 removed outlier: 4.398A pdb=" N PHE E 418 " --> pdb=" O GLU E 414 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N SER E 419 " --> pdb=" O GLU E 415 " (cutoff:3.500A) Processing helix chain 'I' and resid 10 through 25 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: 3.701A 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: 3.738A pdb=" N LEU I 112 " --> pdb=" O GLU I 108 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N ASP I 114 " --> pdb=" O ALA I 110 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N SER I 115 " --> pdb=" O GLU I 111 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N SER I 126 " --> pdb=" O LYS I 122 " (cutoff:3.500A) Processing helix chain 'I' and resid 142 through 159 Processing helix chain 'I' and resid 180 through 193 removed outlier: 3.522A pdb=" N ASN I 184 " --> pdb=" O VAL I 180 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLN I 191 " --> pdb=" O LEU I 187 " (cutoff:3.500A) Processing helix chain 'I' and resid 203 through 214 removed outlier: 3.505A pdb=" N LEU I 207 " --> pdb=" O ASP I 203 " (cutoff:3.500A) Processing helix chain 'I' and resid 221 through 237 removed outlier: 3.649A pdb=" N LEU I 225 " --> pdb=" O THR I 221 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N THR I 237 " --> pdb=" O MET I 233 " (cutoff:3.500A) Processing helix chain 'I' and resid 237 through 242 removed outlier: 4.089A pdb=" N ARG I 241 " --> pdb=" O THR I 237 " (cutoff:3.500A) Processing helix chain 'I' and resid 249 through 258 Processing helix chain 'I' and resid 275 through 282 removed outlier: 4.361A pdb=" N GLN I 280 " --> pdb=" O GLY I 277 " (cutoff:3.500A) Processing helix chain 'I' and resid 285 through 294 Processing helix chain 'I' and resid 295 through 299 removed outlier: 3.609A 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: 3.623A 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: 4.278A pdb=" N LEU I 377 " --> pdb=" O ALA I 373 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N PHE I 378 " --> pdb=" O ILE I 374 " (cutoff:3.500A) Processing helix chain 'I' and resid 394 through 400 removed outlier: 4.152A pdb=" N TYR I 398 " --> pdb=" O PHE I 394 " (cutoff:3.500A) Processing helix chain 'I' and resid 404 through 427 removed outlier: 4.337A pdb=" N PHE I 408 " --> pdb=" O ASP I 404 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N THR I 409 " --> pdb=" O GLU I 405 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLU I 421 " --> pdb=" O ASP I 417 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N TYR I 422 " --> pdb=" O LEU I 418 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ASP I 427 " --> pdb=" O GLN I 423 " (cutoff:3.500A) Processing helix chain 'S' and resid 10 through 29 Processing helix chain 'S' and resid 36 through 43 removed outlier: 3.970A pdb=" N LYS S 40 " --> pdb=" O MET S 36 " (cutoff:3.500A) Processing helix chain 'S' and resid 71 through 80 removed outlier: 4.407A pdb=" N ILE S 75 " --> pdb=" O GLU S 71 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N VAL S 78 " --> pdb=" O VAL S 74 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N THR S 80 " --> pdb=" O ASP S 76 " (cutoff:3.500A) Processing helix chain 'S' and resid 102 through 108 Processing helix chain 'S' and resid 114 through 128 Processing helix chain 'S' and resid 143 through 161 removed outlier: 4.105A pdb=" N THR S 150 " --> pdb=" O GLY S 146 " (cutoff:3.500A) Processing helix chain 'S' and resid 182 through 198 removed outlier: 3.606A pdb=" N ASN S 186 " --> pdb=" O VAL S 182 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N HIS S 192 " --> pdb=" O ILE S 188 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N THR S 193 " --> pdb=" O LEU S 189 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLU S 196 " --> pdb=" O HIS S 192 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N SER S 198 " --> pdb=" O THR S 194 " (cutoff:3.500A) Processing helix chain 'S' and resid 205 through 216 Processing helix chain 'S' and resid 223 through 240 removed outlier: 3.812A 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: 3.717A pdb=" N GLN S 256 " --> pdb=" O LEU S 252 " (cutoff:3.500A) Processing helix chain 'S' and resid 277 through 282 removed outlier: 4.020A pdb=" N TYR S 282 " --> pdb=" O ALA S 278 " (cutoff:3.500A) Processing helix chain 'S' and resid 287 through 297 removed outlier: 3.684A pdb=" N PHE S 296 " --> pdb=" O THR S 292 " (cutoff:3.500A) removed outlier: 3.560A 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: 3.707A pdb=" N VAL S 328 " --> pdb=" O VAL S 324 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR S 337 " --> pdb=" O ALA S 333 " (cutoff:3.500A) Processing helix chain 'S' and resid 383 through 400 removed outlier: 4.019A pdb=" N ALA S 387 " --> pdb=" O ALA S 383 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N LEU S 391 " --> pdb=" O ALA S 387 " (cutoff:3.500A) Processing helix chain 'S' and resid 404 through 410 removed outlier: 4.296A pdb=" N TYR S 408 " --> pdb=" O PHE S 404 " (cutoff:3.500A) Processing helix chain 'S' and resid 414 through 436 removed outlier: 4.313A pdb=" N PHE S 418 " --> pdb=" O GLU S 414 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N SER S 419 " --> pdb=" O GLU S 415 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'K' and resid 54 through 57 removed outlier: 6.576A pdb=" N LYS K 7 " --> pdb=" O MET K 327 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N ALA K 329 " --> pdb=" O LYS K 7 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N ALA K 9 " --> pdb=" O ALA K 329 " (cutoff:3.500A) removed outlier: 8.007A pdb=" N LEU K 331 " --> pdb=" O ALA K 9 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N ARG K 11 " --> pdb=" O LEU K 331 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N VAL K 91 " --> pdb=" O SER K 245 " (cutoff:3.500A) removed outlier: 8.165A pdb=" N VAL K 247 " --> pdb=" O VAL K 91 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ILE K 93 " --> pdb=" O VAL K 247 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'K' and resid 54 through 57 removed outlier: 6.576A pdb=" N LYS K 7 " --> pdb=" O MET K 327 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N ALA K 329 " --> pdb=" O LYS K 7 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N ALA K 9 " --> pdb=" O ALA K 329 " (cutoff:3.500A) removed outlier: 8.007A pdb=" N LEU K 331 " --> pdb=" O ALA K 9 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N ARG K 11 " --> pdb=" O LEU K 331 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N VAL K 91 " --> pdb=" O SER K 245 " (cutoff:3.500A) removed outlier: 8.165A pdb=" N VAL K 247 " --> pdb=" O VAL K 91 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ILE K 93 " --> pdb=" O VAL K 247 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N VAL K 142 " --> pdb=" O VAL K 186 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL K 186 " --> pdb=" O VAL K 142 " (cutoff:3.500A) 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 168 through 171 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 56 removed outlier: 8.901A pdb=" N TYR N 54 " --> pdb=" O VAL N 6 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N VAL N 8 " --> pdb=" O TYR N 54 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N TYR N 56 " --> pdb=" O VAL N 8 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N VAL N 10 " --> pdb=" O TYR N 56 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA N 326 " --> pdb=" O CYS N 92 " (cutoff:3.500A) removed outlier: 3.866A 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 56 removed outlier: 8.901A pdb=" N TYR N 54 " --> pdb=" O VAL N 6 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N VAL N 8 " --> pdb=" O TYR N 54 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N TYR N 56 " --> pdb=" O VAL N 8 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N VAL N 10 " --> pdb=" O TYR N 56 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA N 326 " --> pdb=" O CYS N 92 " (cutoff:3.500A) removed outlier: 3.866A 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: 8.766A pdb=" N VAL A 66 " --> pdb=" O CYS A 4 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N SER A 6 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 7.947A pdb=" N VAL A 68 " --> pdb=" O SER A 6 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N HIS A 8 " --> pdb=" O VAL A 68 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N GLU A 3 " --> pdb=" O GLN A 133 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N PHE A 135 " --> pdb=" O GLU A 3 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N ILE A 5 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N VAL A 137 " --> pdb=" O ILE A 5 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ILE A 7 " --> pdb=" O VAL A 137 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N HIS A 139 " --> pdb=" O ILE A 7 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N VAL A 9 " --> pdb=" O HIS A 139 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N GLN A 133 " --> pdb=" O SER A 165 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N LEU A 167 " --> pdb=" O GLN A 133 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N PHE A 135 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N PHE A 169 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N VAL A 137 " --> pdb=" O PHE A 169 " (cutoff:3.500A) removed outlier: 7.973A pdb=" N ILE A 171 " --> pdb=" O VAL A 137 " (cutoff:3.500A) removed outlier: 8.028A pdb=" N HIS A 139 " --> pdb=" O ILE A 171 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N LYS A 166 " --> pdb=" O CYS A 200 " (cutoff:3.500A) removed outlier: 7.975A pdb=" N PHE A 202 " --> pdb=" O LYS A 166 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N GLU A 168 " --> pdb=" O PHE A 202 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N VAL A 204 " --> pdb=" O GLU A 168 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N SER A 170 " --> pdb=" O VAL A 204 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 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 removed outlier: 6.722A pdb=" N ALA A 374 " --> pdb=" O TYR A 319 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N TYR A 319 " --> pdb=" O ALA A 374 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N CYS A 376 " --> pdb=" O LEU A 317 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N LEU A 317 " --> pdb=" O CYS A 376 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N LEU A 378 " --> pdb=" O CYS A 315 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N CYS A 315 " --> pdb=" O LEU A 378 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ASN A 380 " --> pdb=" O MET A 313 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 90 through 91 removed outlier: 8.098A pdb=" N VAL B 91 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N LEU B 65 " --> pdb=" O VAL B 91 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N GLU B 3 " --> pdb=" O GLN B 131 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N PHE B 133 " --> pdb=" O GLU B 3 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N VAL B 5 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N LEU B 135 " --> pdb=" O VAL B 5 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ILE B 7 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N HIS B 137 " --> pdb=" O ILE B 7 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N ALA B 9 " --> pdb=" O HIS B 137 " (cutoff:3.500A) removed outlier: 9.620A pdb=" N ILE B 163 " --> pdb=" O CYS B 129 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N GLN B 131 " --> pdb=" O ILE B 163 " (cutoff:3.500A) removed outlier: 7.969A pdb=" N ASN B 165 " --> pdb=" O GLN B 131 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N PHE B 133 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N PHE B 167 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N LEU B 135 " --> pdb=" O PHE B 167 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N VAL B 169 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N HIS B 137 " --> pdb=" O VAL B 169 " (cutoff:3.500A) removed outlier: 7.982A pdb=" N TYR B 200 " --> pdb=" O MET B 164 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N THR B 166 " --> pdb=" O TYR B 200 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N ILE B 202 " --> pdb=" O THR B 166 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N SER B 168 " --> pdb=" O ILE B 202 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N PHE B 265 " --> pdb=" O SER B 371 " (cutoff:3.500A) removed outlier: 4.942A 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 54 Processing sheet with id=AB7, first strand: chain 'E' and resid 65 through 68 removed outlier: 7.634A pdb=" N GLU E 3 " --> pdb=" O GLN E 133 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N PHE E 135 " --> pdb=" O GLU E 3 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ILE E 5 " --> pdb=" O PHE E 135 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N VAL E 137 " --> pdb=" O ILE E 5 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N ILE E 7 " --> pdb=" O VAL E 137 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N HIS E 139 " --> pdb=" O ILE E 7 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N VAL E 9 " --> pdb=" O HIS E 139 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N GLN E 133 " --> pdb=" O SER E 165 " (cutoff:3.500A) removed outlier: 7.808A pdb=" N LEU E 167 " --> pdb=" O GLN E 133 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N PHE E 135 " --> pdb=" O LEU E 167 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N PHE E 169 " --> pdb=" O PHE E 135 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N VAL E 137 " --> pdb=" O PHE E 169 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N ILE E 171 " --> pdb=" O VAL E 137 " (cutoff:3.500A) removed outlier: 7.994A pdb=" N HIS E 139 " --> pdb=" O ILE E 171 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N LYS E 166 " --> pdb=" O CYS E 200 " (cutoff:3.500A) removed outlier: 8.071A pdb=" N PHE E 202 " --> pdb=" O LYS E 166 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N GLU E 168 " --> pdb=" O PHE E 202 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N VAL E 204 " --> pdb=" O GLU E 168 " (cutoff:3.500A) removed outlier: 6.521A 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: 8.110A pdb=" N VAL I 91 " --> pdb=" O ALA I 63 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N LEU I 65 " --> pdb=" O VAL I 91 " (cutoff:3.500A) removed outlier: 8.792A pdb=" N ILE I 64 " --> pdb=" O ILE I 4 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N HIS I 6 " --> pdb=" O ILE I 64 " (cutoff:3.500A) removed outlier: 8.061A pdb=" N VAL I 66 " --> pdb=" O HIS I 6 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N GLN I 8 " --> pdb=" O VAL I 66 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N GLU I 3 " --> pdb=" O GLN I 131 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N PHE I 133 " --> pdb=" O GLU I 3 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N VAL I 5 " --> pdb=" O PHE I 133 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N LEU I 135 " --> pdb=" O VAL I 5 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N ILE I 7 " --> pdb=" O LEU I 135 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N HIS I 137 " --> pdb=" O ILE I 7 " (cutoff:3.500A) removed outlier: 7.559A 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: 8.110A pdb=" N VAL I 91 " --> pdb=" O ALA I 63 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N LEU I 65 " --> pdb=" O VAL I 91 " (cutoff:3.500A) removed outlier: 8.792A pdb=" N ILE I 64 " --> pdb=" O ILE I 4 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N HIS I 6 " --> pdb=" O ILE I 64 " (cutoff:3.500A) removed outlier: 8.061A pdb=" N VAL I 66 " --> pdb=" O HIS I 6 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N GLN I 8 " --> pdb=" O VAL I 66 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N GLU I 3 " --> pdb=" O GLN I 131 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N PHE I 133 " --> pdb=" O GLU I 3 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N VAL I 5 " --> pdb=" O PHE I 133 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N LEU I 135 " --> pdb=" O VAL I 5 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N ILE I 7 " --> pdb=" O LEU I 135 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N HIS I 137 " --> pdb=" O ILE I 7 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N ALA I 9 " --> pdb=" O HIS I 137 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N PHE I 167 " --> pdb=" O PHE I 133 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N LEU I 135 " --> pdb=" O PHE I 167 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N VAL I 169 " --> pdb=" O LEU I 135 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N HIS I 137 " --> pdb=" O VAL I 169 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N PHE I 265 " --> pdb=" O SER I 371 " (cutoff:3.500A) removed outlier: 4.938A 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: 8.390A pdb=" N VAL S 66 " --> pdb=" O CYS S 4 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N SER S 6 " --> pdb=" O VAL S 66 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N VAL S 68 " --> pdb=" O SER S 6 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N HIS S 8 " --> pdb=" O VAL S 68 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N GLU S 3 " --> pdb=" O LEU S 132 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N GLY S 134 " --> pdb=" O GLU S 3 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N SER S 140 " --> pdb=" O VAL S 9 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N GLN S 133 " --> pdb=" O SER S 165 " (cutoff:3.500A) removed outlier: 7.971A pdb=" N LEU S 167 " --> pdb=" O GLN S 133 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N PHE S 135 " --> pdb=" O LEU S 167 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N PHE S 169 " --> pdb=" O PHE S 135 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N VAL S 137 " --> pdb=" O PHE S 169 " (cutoff:3.500A) removed outlier: 8.016A pdb=" N ILE S 171 " --> pdb=" O VAL S 137 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N HIS S 139 " --> pdb=" O ILE S 171 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N LYS S 166 " --> pdb=" O CYS S 200 " (cutoff:3.500A) removed outlier: 7.962A pdb=" N PHE S 202 " --> pdb=" O LYS S 166 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N GLU S 168 " --> pdb=" O PHE S 202 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N VAL S 204 " --> pdb=" O GLU S 168 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N SER S 170 " --> pdb=" O VAL S 204 " (cutoff:3.500A) 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 1165 hydrogen bonds defined for protein. 3351 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: 8.56 Time building geometry restraints manager: 9.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 4082 1.32 - 1.44: 6432 1.44 - 1.57: 13488 1.57 - 1.69: 40 1.69 - 1.82: 242 Bond restraints: 24284 Sorted by residual: bond pdb=" N3B ANP N 501 " pdb=" PG ANP N 501 " ideal model delta sigma weight residual 1.795 1.613 0.182 2.00e-02 2.50e+03 8.32e+01 bond pdb=" O3A ANP K 502 " pdb=" PB ANP K 502 " ideal model delta sigma weight residual 1.700 1.555 0.145 2.00e-02 2.50e+03 5.28e+01 bond pdb=" C ASN K 293 " pdb=" O ASN K 293 " ideal model delta sigma weight residual 1.235 1.303 -0.068 1.10e-02 8.26e+03 3.79e+01 bond pdb=" O3A ANP N 501 " pdb=" PB ANP N 501 " ideal model delta sigma weight residual 1.700 1.588 0.112 2.00e-02 2.50e+03 3.12e+01 bond pdb=" N ASP I 427 " pdb=" CA ASP I 427 " ideal model delta sigma weight residual 1.457 1.529 -0.071 1.29e-02 6.01e+03 3.06e+01 ... (remaining 24279 not shown) Histogram of bond angle deviations from ideal: 83.69 - 94.17: 8 94.17 - 104.65: 432 104.65 - 115.14: 14624 115.14 - 125.62: 17535 125.62 - 136.11: 365 Bond angle restraints: 32964 Sorted by residual: angle pdb=" N GLU I 27 " pdb=" CA GLU I 27 " pdb=" C GLU I 27 " ideal model delta sigma weight residual 113.88 101.64 12.24 1.23e+00 6.61e-01 9.90e+01 angle pdb=" C ASN K 293 " pdb=" N LYS K 294 " pdb=" CA LYS K 294 " ideal model delta sigma weight residual 121.81 109.46 12.35 1.83e+00 2.99e-01 4.56e+01 angle pdb=" C PRO N 333 " pdb=" CA PRO N 333 " pdb=" CB PRO N 333 " ideal model delta sigma weight residual 111.56 101.39 10.17 1.65e+00 3.67e-01 3.80e+01 angle pdb=" PB ANP K 502 " pdb=" N3B ANP K 502 " pdb=" PG ANP K 502 " ideal model delta sigma weight residual 126.95 109.31 17.64 3.00e+00 1.11e-01 3.46e+01 angle pdb=" N ASP K 114 " pdb=" CA ASP K 114 " pdb=" C ASP K 114 " ideal model delta sigma weight residual 113.02 106.38 6.64 1.20e+00 6.94e-01 3.06e+01 ... (remaining 32959 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.39: 13975 30.39 - 60.77: 651 60.77 - 91.16: 95 91.16 - 121.55: 11 121.55 - 151.93: 26 Dihedral angle restraints: 14758 sinusoidal: 6103 harmonic: 8655 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 -138.80 -151.93 1 2.00e+01 2.50e-03 4.52e+01 dihedral pdb=" C5' GTP S 501 " pdb=" O5' GTP S 501 " pdb=" PA GTP S 501 " pdb=" O3A GTP S 501 " ideal model delta sinusoidal sigma weight residual 69.27 -141.99 -148.74 1 2.00e+01 2.50e-03 4.45e+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 260.87 113.35 147.52 1 2.00e+01 2.50e-03 4.42e+01 ... (remaining 14755 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.115: 3490 0.115 - 0.231: 120 0.231 - 0.346: 5 0.346 - 0.461: 0 0.461 - 0.577: 1 Chirality restraints: 3616 Sorted by residual: chirality pdb=" C18 TA1 I 502 " pdb=" C10 TA1 I 502 " pdb=" C17 TA1 I 502 " pdb=" C20 TA1 I 502 " both_signs ideal model delta sigma weight residual False -3.16 -2.59 -0.58 2.00e-01 2.50e+01 8.32e+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 -2.67 0.32 2.00e-01 2.50e+01 2.50e+00 chirality pdb=" CA ILE N 27 " pdb=" N ILE N 27 " pdb=" C ILE N 27 " pdb=" CB ILE N 27 " both_signs ideal model delta sigma weight residual False 2.43 2.72 -0.29 2.00e-01 2.50e+01 2.12e+00 ... (remaining 3613 not shown) Planarity restraints: 4287 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS K 296 " 0.022 2.00e-02 2.50e+03 4.65e-02 2.16e+01 pdb=" C LYS K 296 " -0.080 2.00e-02 2.50e+03 pdb=" O LYS K 296 " 0.029 2.00e-02 2.50e+03 pdb=" N LYS K 297 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG N 11 " -0.023 2.00e-02 2.50e+03 4.59e-02 2.11e+01 pdb=" C ARG N 11 " 0.079 2.00e-02 2.50e+03 pdb=" O ARG N 11 " -0.030 2.00e-02 2.50e+03 pdb=" N VAL N 12 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP I 21 " -0.023 2.00e-02 2.50e+03 4.44e-02 1.97e+01 pdb=" C TRP I 21 " 0.077 2.00e-02 2.50e+03 pdb=" O TRP I 21 " -0.028 2.00e-02 2.50e+03 pdb=" N GLU I 22 " -0.026 2.00e-02 2.50e+03 ... (remaining 4284 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.52: 141 2.52 - 3.11: 17365 3.11 - 3.71: 35131 3.71 - 4.30: 50377 4.30 - 4.90: 86969 Nonbonded interactions: 189983 Sorted by model distance: nonbonded pdb=" O1G GTP A 501 " pdb="MG MG A 502 " model vdw 1.920 2.170 nonbonded pdb=" O1B GTP S 501 " pdb="MG MG S 502 " model vdw 1.944 2.170 nonbonded pdb=" O1B GTP E 501 " pdb="MG MG E 502 " model vdw 1.950 2.170 nonbonded pdb=" OE1 GLU S 71 " pdb="MG MG S 502 " model vdw 1.959 2.170 nonbonded pdb=" O1G GTP S 501 " pdb="MG MG S 502 " model vdw 1.967 2.170 ... (remaining 189978 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=0.49 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: 6.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.000 Check model and map are aligned: 0.170 Set scattering table: 0.240 Process input model: 69.790 Find NCS groups from input model: 1.840 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 81.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.182 24284 Z= 0.398 Angle : 0.892 17.641 32964 Z= 0.484 Chirality : 0.050 0.577 3616 Planarity : 0.006 0.086 4287 Dihedral : 18.882 151.934 9206 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.84 % Allowed : 3.67 % Favored : 95.48 % Rotamer: Outliers : 1.64 % Allowed : 16.48 % Favored : 81.88 % Cbeta Deviations : 0.07 % 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: -0.26 (0.15), residues: 2976 helix: 0.97 (0.15), residues: 1216 sheet: -0.09 (0.22), residues: 527 loop : -1.35 (0.16), residues: 1233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP K 57 HIS 0.013 0.001 HIS I 28 PHE 0.034 0.002 PHE S 255 TYR 0.015 0.002 TYR K 74 ARG 0.015 0.001 ARG K 75 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5952 Ramachandran restraints generated. 2976 Oldfield, 0 Emsley, 2976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5952 Ramachandran restraints generated. 2976 Oldfield, 0 Emsley, 2976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 522 residues out of total 2547 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 485 time to evaluate : 2.775 Fit side-chains revert: symmetry clash REVERT: K 19 GLU cc_start: 0.7864 (mt-10) cc_final: 0.7114 (mp0) REVERT: K 56 TYR cc_start: 0.7932 (m-80) cc_final: 0.7509 (m-10) REVERT: K 116 GLN cc_start: 0.7535 (OUTLIER) cc_final: 0.7193 (mt0) REVERT: N 107 MET cc_start: 0.7588 (mmm) cc_final: 0.6927 (tpp) REVERT: N 274 SER cc_start: 0.8769 (t) cc_final: 0.8263 (p) REVERT: N 333 PRO cc_start: 0.8570 (OUTLIER) cc_final: 0.8349 (Cg_endo) REVERT: N 352 LYS cc_start: 0.6008 (OUTLIER) cc_final: 0.5619 (pttp) REVERT: A 254 GLU cc_start: 0.4542 (mm-30) cc_final: 0.3057 (pt0) REVERT: B 195 ASN cc_start: 0.8235 (m-40) cc_final: 0.7850 (m110) REVERT: B 239 CYS cc_start: 0.8586 (m) cc_final: 0.8371 (m) REVERT: E 195 LEU cc_start: 0.7892 (tt) cc_final: 0.7691 (tt) REVERT: I 1 MET cc_start: 0.6078 (mmp) cc_final: 0.5760 (mmp) REVERT: I 417 ASP cc_start: 0.7533 (m-30) cc_final: 0.7038 (m-30) REVERT: S 108 TYR cc_start: 0.8565 (m-80) cc_final: 0.8073 (m-10) REVERT: S 401 LYS cc_start: 0.8972 (mtpp) cc_final: 0.8341 (mtmt) REVERT: S 451 TYR cc_start: 0.0947 (OUTLIER) cc_final: 0.0345 (p90) outliers start: 37 outliers final: 12 residues processed: 513 average time/residue: 0.3667 time to fit residues: 294.5524 Evaluate side-chains 488 residues out of total 2547 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 472 time to evaluate : 2.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 116 GLN Chi-restraints excluded: chain K residue 236 ILE Chi-restraints excluded: chain K residue 283 SER Chi-restraints excluded: chain K residue 288 MET Chi-restraints excluded: chain N residue 28 ILE Chi-restraints excluded: chain N residue 222 ASN Chi-restraints excluded: chain N residue 261 LYS Chi-restraints excluded: chain N residue 289 ASP Chi-restraints excluded: chain N residue 295 ASN Chi-restraints excluded: chain N residue 297 LYS Chi-restraints excluded: chain N residue 333 PRO Chi-restraints excluded: chain N residue 352 LYS Chi-restraints excluded: chain E residue 449 GLU Chi-restraints excluded: chain I residue 26 ASP Chi-restraints excluded: chain I residue 359 ARG Chi-restraints excluded: chain S residue 451 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 249 optimal weight: 0.9990 chunk 224 optimal weight: 0.5980 chunk 124 optimal weight: 0.7980 chunk 76 optimal weight: 4.9990 chunk 151 optimal weight: 1.9990 chunk 119 optimal weight: 0.5980 chunk 232 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 141 optimal weight: 3.9990 chunk 172 optimal weight: 0.9990 chunk 268 optimal weight: 10.0000 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 98 GLN K 116 GLN K 293 ASN A 256 GLN B 165 ASN ** B 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 424 GLN B 426 GLN E 15 GLN E 107 HIS E 128 GLN E 197 HIS I 195 ASN I 416 ASN I 426 GLN I 433 GLN A S 285 GLN S 358 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.1133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 24284 Z= 0.199 Angle : 0.588 10.464 32964 Z= 0.291 Chirality : 0.044 0.402 3616 Planarity : 0.004 0.055 4287 Dihedral : 12.188 154.697 3643 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.74 % Favored : 96.02 % Rotamer: Outliers : 3.28 % Allowed : 14.76 % Favored : 81.96 % 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: 0.30 (0.15), residues: 2976 helix: 1.55 (0.15), residues: 1247 sheet: 0.18 (0.22), residues: 537 loop : -1.28 (0.17), residues: 1192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP E 388 HIS 0.005 0.001 HIS I 137 PHE 0.017 0.001 PHE E 255 TYR 0.015 0.001 TYR K 74 ARG 0.005 0.000 ARG B 320 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5952 Ramachandran restraints generated. 2976 Oldfield, 0 Emsley, 2976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5952 Ramachandran restraints generated. 2976 Oldfield, 0 Emsley, 2976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 558 residues out of total 2547 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 479 time to evaluate : 2.545 Fit side-chains revert: symmetry clash REVERT: K 19 GLU cc_start: 0.7851 (mt-10) cc_final: 0.7109 (mp0) REVERT: K 340 GLU cc_start: 0.7845 (mp0) cc_final: 0.7386 (mp0) REVERT: N 82 LEU cc_start: 0.6154 (OUTLIER) cc_final: 0.5916 (mt) REVERT: N 107 MET cc_start: 0.7648 (mmm) cc_final: 0.6941 (tpp) REVERT: N 274 SER cc_start: 0.8740 (t) cc_final: 0.8207 (p) REVERT: N 299 LYS cc_start: 0.3039 (OUTLIER) cc_final: 0.2832 (ptpt) REVERT: A 9 VAL cc_start: 0.8708 (t) cc_final: 0.8383 (m) REVERT: A 254 GLU cc_start: 0.4491 (mm-30) cc_final: 0.3110 (pt0) REVERT: A 256 GLN cc_start: 0.7913 (mt0) cc_final: 0.7709 (mt0) REVERT: B 195 ASN cc_start: 0.8344 (m-40) cc_final: 0.8003 (m-40) REVERT: B 226 ASN cc_start: 0.8077 (m-40) cc_final: 0.7828 (m-40) REVERT: B 237 THR cc_start: 0.8786 (p) cc_final: 0.8541 (t) REVERT: B 406 MET cc_start: 0.7492 (ttm) cc_final: 0.7276 (ttm) REVERT: B 426 GLN cc_start: 0.8056 (OUTLIER) cc_final: 0.7849 (tt0) REVERT: E 449 GLU cc_start: 0.4638 (OUTLIER) cc_final: 0.4296 (pp20) REVERT: I 306 ARG cc_start: 0.8521 (mtm180) cc_final: 0.8116 (mtm180) REVERT: S 108 TYR cc_start: 0.8584 (m-80) cc_final: 0.8063 (m-10) REVERT: S 129 CYS cc_start: 0.7726 (m) cc_final: 0.7467 (m) REVERT: S 401 LYS cc_start: 0.8976 (mtpp) cc_final: 0.8292 (mtmt) outliers start: 79 outliers final: 44 residues processed: 520 average time/residue: 0.3436 time to fit residues: 281.2612 Evaluate side-chains 502 residues out of total 2547 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 454 time to evaluate : 2.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 36 THR Chi-restraints excluded: chain K residue 98 GLN Chi-restraints excluded: chain K residue 158 LEU Chi-restraints excluded: chain K residue 236 ILE Chi-restraints excluded: chain K residue 283 SER Chi-restraints excluded: chain K residue 319 LEU Chi-restraints excluded: chain K residue 336 ILE Chi-restraints excluded: chain N residue 28 ILE Chi-restraints excluded: chain N residue 82 LEU Chi-restraints excluded: chain N residue 182 SER Chi-restraints excluded: chain N residue 252 SER Chi-restraints excluded: chain N residue 261 LYS Chi-restraints excluded: chain N residue 289 ASP Chi-restraints excluded: chain N residue 295 ASN Chi-restraints excluded: chain N residue 297 LYS Chi-restraints excluded: chain N residue 299 LYS Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 313 VAL 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 191 THR Chi-restraints excluded: chain E residue 245 ASP Chi-restraints excluded: chain E residue 334 THR Chi-restraints excluded: chain E residue 417 GLU Chi-restraints excluded: chain E residue 449 GLU Chi-restraints excluded: chain I residue 4 ILE Chi-restraints excluded: chain I residue 26 ASP Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain I residue 230 SER Chi-restraints excluded: chain I residue 313 VAL Chi-restraints excluded: chain I residue 407 GLU Chi-restraints excluded: chain S residue 26 LEU Chi-restraints excluded: chain S residue 68 VAL Chi-restraints excluded: chain S residue 98 ASP Chi-restraints excluded: chain S residue 125 LEU Chi-restraints excluded: chain S residue 191 THR Chi-restraints excluded: chain S residue 362 VAL Chi-restraints excluded: chain S residue 367 ASP Chi-restraints excluded: chain S residue 377 MET Chi-restraints excluded: chain S residue 413 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 149 optimal weight: 0.8980 chunk 83 optimal weight: 5.9990 chunk 223 optimal weight: 1.9990 chunk 183 optimal weight: 0.8980 chunk 74 optimal weight: 2.9990 chunk 269 optimal weight: 8.9990 chunk 290 optimal weight: 3.9990 chunk 239 optimal weight: 3.9990 chunk 267 optimal weight: 5.9990 chunk 91 optimal weight: 0.6980 chunk 216 optimal weight: 3.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 98 GLN K 200 ASN K 361 ASN N 227 GLN A 128 GLN B 165 ASN B 279 GLN ** B 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 426 GLN I 57 ASN I 195 ASN I 375 GLN I 423 GLN S 8 HIS S 15 GLN S 197 HIS S 301 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.1520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 24284 Z= 0.292 Angle : 0.575 8.287 32964 Z= 0.290 Chirality : 0.046 0.433 3616 Planarity : 0.004 0.059 4287 Dihedral : 9.847 151.282 3622 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.88 % Favored : 95.89 % Rotamer: Outliers : 3.67 % Allowed : 15.19 % Favored : 81.14 % 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: 0.45 (0.15), residues: 2976 helix: 1.75 (0.15), residues: 1236 sheet: 0.38 (0.22), residues: 531 loop : -1.30 (0.17), residues: 1209 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP E 21 HIS 0.007 0.001 HIS A 88 PHE 0.017 0.002 PHE E 141 TYR 0.018 0.002 TYR K 74 ARG 0.006 0.001 ARG B 320 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5952 Ramachandran restraints generated. 2976 Oldfield, 0 Emsley, 2976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5952 Ramachandran restraints generated. 2976 Oldfield, 0 Emsley, 2976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 573 residues out of total 2547 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 485 time to evaluate : 3.242 Fit side-chains revert: symmetry clash REVERT: K 19 GLU cc_start: 0.7893 (mt-10) cc_final: 0.7097 (mp0) REVERT: K 340 GLU cc_start: 0.7806 (mp0) cc_final: 0.7148 (mp0) REVERT: N 13 ARG cc_start: 0.8028 (OUTLIER) cc_final: 0.7028 (ppt170) REVERT: N 82 LEU cc_start: 0.6209 (OUTLIER) cc_final: 0.5957 (mt) REVERT: N 107 MET cc_start: 0.7663 (mmm) cc_final: 0.6917 (tpp) REVERT: N 274 SER cc_start: 0.8774 (t) cc_final: 0.8237 (p) REVERT: A 9 VAL cc_start: 0.8756 (t) cc_final: 0.8462 (m) REVERT: A 191 THR cc_start: 0.8339 (m) cc_final: 0.8018 (p) REVERT: A 254 GLU cc_start: 0.4534 (mm-30) cc_final: 0.3519 (tp30) REVERT: B 75 SER cc_start: 0.8657 (t) cc_final: 0.8389 (t) REVERT: B 226 ASN cc_start: 0.8137 (m-40) cc_final: 0.7809 (m110) REVERT: B 237 THR cc_start: 0.8862 (p) cc_final: 0.8514 (t) REVERT: B 426 GLN cc_start: 0.8304 (OUTLIER) cc_final: 0.8091 (tt0) REVERT: E 203 MET cc_start: 0.8551 (OUTLIER) cc_final: 0.8186 (mtt) REVERT: I 1 MET cc_start: 0.6200 (mmp) cc_final: 0.5852 (mmp) REVERT: I 213 ARG cc_start: 0.8068 (mtp85) cc_final: 0.7862 (mtp180) REVERT: I 321 MET cc_start: 0.9115 (ptp) cc_final: 0.8904 (ptp) REVERT: S 108 TYR cc_start: 0.8610 (m-80) cc_final: 0.8025 (m-10) REVERT: S 129 CYS cc_start: 0.7636 (m) cc_final: 0.7408 (m) REVERT: S 302 MET cc_start: 0.8126 (mmm) cc_final: 0.7659 (mtm) REVERT: S 401 LYS cc_start: 0.8975 (mtpp) cc_final: 0.8283 (mtmt) outliers start: 88 outliers final: 68 residues processed: 530 average time/residue: 0.3269 time to fit residues: 272.3680 Evaluate side-chains 533 residues out of total 2547 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 461 time to evaluate : 2.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 31 SER Chi-restraints excluded: chain K residue 36 THR Chi-restraints excluded: chain K residue 49 SER Chi-restraints excluded: chain K residue 118 ILE Chi-restraints excluded: chain K residue 158 LEU Chi-restraints excluded: chain K residue 165 ASN Chi-restraints excluded: chain K residue 204 THR Chi-restraints excluded: chain K residue 234 THR Chi-restraints excluded: chain K residue 236 ILE Chi-restraints excluded: chain K residue 270 ASN Chi-restraints excluded: chain K residue 312 THR Chi-restraints excluded: chain K residue 336 ILE Chi-restraints excluded: chain K residue 361 ASN Chi-restraints excluded: chain N residue 8 VAL Chi-restraints excluded: chain N residue 13 ARG Chi-restraints excluded: chain N residue 38 VAL Chi-restraints excluded: chain N residue 82 LEU Chi-restraints excluded: chain N residue 182 SER Chi-restraints excluded: chain N residue 222 ASN Chi-restraints excluded: chain N residue 247 VAL Chi-restraints excluded: chain N residue 258 THR Chi-restraints excluded: chain N residue 261 LYS Chi-restraints excluded: chain N residue 289 ASP Chi-restraints excluded: chain N residue 290 SER Chi-restraints excluded: chain N residue 297 LYS Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 426 GLN Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 98 ASP Chi-restraints excluded: chain E residue 170 SER Chi-restraints excluded: chain E residue 191 THR Chi-restraints excluded: chain E residue 203 MET Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain E residue 245 ASP Chi-restraints excluded: chain E residue 286 LEU Chi-restraints excluded: chain E residue 334 THR Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain E residue 367 ASP Chi-restraints excluded: chain E residue 414 GLU Chi-restraints excluded: chain E residue 417 GLU Chi-restraints excluded: chain E residue 449 GLU Chi-restraints excluded: chain I residue 4 ILE Chi-restraints excluded: chain I residue 26 ASP Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain I residue 176 SER Chi-restraints excluded: chain I residue 313 VAL Chi-restraints excluded: chain I residue 407 GLU Chi-restraints excluded: chain S residue 26 LEU Chi-restraints excluded: chain S residue 80 THR Chi-restraints excluded: chain S residue 125 LEU Chi-restraints excluded: chain S residue 191 THR Chi-restraints excluded: chain S residue 271 THR Chi-restraints excluded: chain S residue 362 VAL Chi-restraints excluded: chain S residue 367 ASP Chi-restraints excluded: chain S residue 371 VAL Chi-restraints excluded: chain S residue 377 MET Chi-restraints excluded: chain S residue 381 THR Chi-restraints excluded: chain S residue 413 MET Chi-restraints excluded: chain S residue 451 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 266 optimal weight: 1.9990 chunk 202 optimal weight: 0.9980 chunk 139 optimal weight: 0.1980 chunk 29 optimal weight: 8.9990 chunk 128 optimal weight: 0.9980 chunk 180 optimal weight: 2.9990 chunk 270 optimal weight: 6.9990 chunk 286 optimal weight: 2.9990 chunk 141 optimal weight: 2.9990 chunk 256 optimal weight: 5.9990 chunk 77 optimal weight: 3.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 318 ASN A 128 GLN A 216 ASN B 165 ASN B 195 ASN B 204 ASN ** B 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 426 GLN E 128 GLN I 195 ASN S 107 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.1731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 24284 Z= 0.281 Angle : 0.562 7.945 32964 Z= 0.283 Chirality : 0.045 0.380 3616 Planarity : 0.004 0.071 4287 Dihedral : 9.625 152.500 3617 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.84 % Favored : 95.99 % Rotamer: Outliers : 4.18 % Allowed : 15.42 % Favored : 80.40 % 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: 0.50 (0.15), residues: 2976 helix: 1.83 (0.15), residues: 1232 sheet: 0.44 (0.22), residues: 530 loop : -1.33 (0.17), residues: 1214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP E 21 HIS 0.007 0.001 HIS E 88 PHE 0.017 0.002 PHE E 255 TYR 0.024 0.001 TYR S 24 ARG 0.006 0.000 ARG B 320 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5952 Ramachandran restraints generated. 2976 Oldfield, 0 Emsley, 2976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5952 Ramachandran restraints generated. 2976 Oldfield, 0 Emsley, 2976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 574 residues out of total 2547 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 473 time to evaluate : 2.667 Fit side-chains REVERT: K 19 GLU cc_start: 0.7870 (mt-10) cc_final: 0.7070 (mp0) REVERT: K 98 GLN cc_start: 0.8586 (pt0) cc_final: 0.8386 (pt0) REVERT: K 340 GLU cc_start: 0.7780 (mp0) cc_final: 0.7215 (mp0) REVERT: N 13 ARG cc_start: 0.7985 (OUTLIER) cc_final: 0.6999 (ppt170) REVERT: N 82 LEU cc_start: 0.6196 (OUTLIER) cc_final: 0.5947 (mt) REVERT: N 107 MET cc_start: 0.7640 (mmm) cc_final: 0.6935 (tpp) REVERT: N 274 SER cc_start: 0.8781 (t) cc_final: 0.8247 (p) REVERT: A 9 VAL cc_start: 0.8765 (t) cc_final: 0.8471 (m) REVERT: A 191 THR cc_start: 0.8312 (m) cc_final: 0.8027 (p) REVERT: A 254 GLU cc_start: 0.4660 (mm-30) cc_final: 0.3676 (tp30) REVERT: B 75 SER cc_start: 0.8648 (t) cc_final: 0.8366 (t) REVERT: B 195 ASN cc_start: 0.8376 (m-40) cc_final: 0.8061 (m-40) REVERT: B 226 ASN cc_start: 0.8133 (m-40) cc_final: 0.7908 (m-40) REVERT: B 237 THR cc_start: 0.8862 (p) cc_final: 0.8523 (t) REVERT: B 426 GLN cc_start: 0.8202 (OUTLIER) cc_final: 0.7984 (tt0) REVERT: E 203 MET cc_start: 0.8557 (OUTLIER) cc_final: 0.8188 (mtt) REVERT: E 449 GLU cc_start: 0.4638 (OUTLIER) cc_final: 0.4361 (pp20) REVERT: I 1 MET cc_start: 0.6180 (mmp) cc_final: 0.5863 (mmp) REVERT: I 213 ARG cc_start: 0.8135 (mtp85) cc_final: 0.7922 (mtp180) REVERT: I 321 MET cc_start: 0.9088 (ptp) cc_final: 0.8869 (ptp) REVERT: S 108 TYR cc_start: 0.8605 (m-80) cc_final: 0.8007 (m-10) REVERT: S 401 LYS cc_start: 0.8974 (mtpp) cc_final: 0.8272 (mtmt) outliers start: 101 outliers final: 79 residues processed: 524 average time/residue: 0.3346 time to fit residues: 277.8423 Evaluate side-chains 548 residues out of total 2547 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 464 time to evaluate : 2.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 28 ILE Chi-restraints excluded: chain K residue 31 SER Chi-restraints excluded: chain K residue 36 THR Chi-restraints excluded: chain K residue 49 SER Chi-restraints excluded: chain K residue 55 SER Chi-restraints excluded: chain K residue 76 ASP Chi-restraints excluded: chain K residue 92 CYS Chi-restraints excluded: chain K residue 118 ILE Chi-restraints excluded: chain K residue 158 LEU Chi-restraints excluded: chain K residue 165 ASN Chi-restraints excluded: chain K residue 210 MET Chi-restraints excluded: chain K residue 234 THR Chi-restraints excluded: chain K residue 236 ILE Chi-restraints excluded: chain K residue 253 GLU Chi-restraints excluded: chain K residue 270 ASN Chi-restraints excluded: chain K residue 312 THR Chi-restraints excluded: chain K residue 318 ASN Chi-restraints excluded: chain K residue 319 LEU Chi-restraints excluded: chain K residue 336 ILE Chi-restraints excluded: chain K residue 361 ASN Chi-restraints excluded: chain N residue 8 VAL Chi-restraints excluded: chain N residue 13 ARG Chi-restraints excluded: chain N residue 28 ILE Chi-restraints excluded: chain N residue 38 VAL Chi-restraints excluded: chain N residue 82 LEU Chi-restraints excluded: chain N residue 182 SER Chi-restraints excluded: chain N residue 222 ASN Chi-restraints excluded: chain N residue 247 VAL Chi-restraints excluded: chain N residue 252 SER Chi-restraints excluded: chain N residue 258 THR Chi-restraints excluded: chain N residue 261 LYS Chi-restraints excluded: chain N residue 289 ASP Chi-restraints excluded: chain N residue 342 LEU Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 426 GLN Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 98 ASP Chi-restraints excluded: chain E residue 170 SER Chi-restraints excluded: chain E residue 191 THR Chi-restraints excluded: chain E residue 203 MET Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain E residue 245 ASP Chi-restraints excluded: chain E residue 286 LEU Chi-restraints excluded: chain E residue 334 THR Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain E residue 367 ASP Chi-restraints excluded: chain E residue 414 GLU Chi-restraints excluded: chain E residue 417 GLU Chi-restraints excluded: chain E residue 449 GLU Chi-restraints excluded: chain I residue 4 ILE Chi-restraints excluded: chain I residue 26 ASP Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain I residue 176 SER Chi-restraints excluded: chain I residue 218 THR Chi-restraints excluded: chain I residue 313 VAL Chi-restraints excluded: chain I residue 404 ASP Chi-restraints excluded: chain I residue 407 GLU Chi-restraints excluded: chain S residue 26 LEU Chi-restraints excluded: chain S residue 68 VAL Chi-restraints excluded: chain S residue 80 THR Chi-restraints excluded: chain S residue 125 LEU Chi-restraints excluded: chain S residue 191 THR Chi-restraints excluded: chain S residue 271 THR Chi-restraints excluded: chain S residue 362 VAL Chi-restraints excluded: chain S residue 367 ASP Chi-restraints excluded: chain S residue 381 THR Chi-restraints excluded: chain S residue 413 MET 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: 2.9990 chunk 4 optimal weight: 3.9990 chunk 213 optimal weight: 0.6980 chunk 118 optimal weight: 2.9990 chunk 244 optimal weight: 1.9990 chunk 197 optimal weight: 0.4980 chunk 0 optimal weight: 8.9990 chunk 146 optimal weight: 0.7980 chunk 256 optimal weight: 1.9990 chunk 72 optimal weight: 0.8980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 322 ASN A 128 GLN B 204 ASN B 335 ASN B 426 GLN I 195 ASN ** I 433 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.1915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 24284 Z= 0.185 Angle : 0.521 7.594 32964 Z= 0.262 Chirality : 0.043 0.316 3616 Planarity : 0.004 0.069 4287 Dihedral : 9.231 154.725 3613 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.71 % Favored : 96.12 % Rotamer: Outliers : 3.87 % Allowed : 16.09 % Favored : 80.05 % 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: 0.65 (0.16), residues: 2976 helix: 1.95 (0.15), residues: 1238 sheet: 0.57 (0.22), residues: 530 loop : -1.29 (0.17), residues: 1208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 21 HIS 0.004 0.001 HIS A 88 PHE 0.013 0.001 PHE K 94 TYR 0.035 0.001 TYR S 24 ARG 0.005 0.000 ARG N 129 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5952 Ramachandran restraints generated. 2976 Oldfield, 0 Emsley, 2976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5952 Ramachandran restraints generated. 2976 Oldfield, 0 Emsley, 2976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 561 residues out of total 2547 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 468 time to evaluate : 2.556 Fit side-chains revert: symmetry clash REVERT: K 19 GLU cc_start: 0.7865 (mt-10) cc_final: 0.7081 (mp0) REVERT: K 146 TYR cc_start: 0.8215 (OUTLIER) cc_final: 0.6934 (t80) REVERT: K 340 GLU cc_start: 0.7770 (mp0) cc_final: 0.7177 (mp0) REVERT: N 82 LEU cc_start: 0.6213 (OUTLIER) cc_final: 0.5932 (mt) REVERT: N 107 MET cc_start: 0.7662 (mmm) cc_final: 0.7010 (tpp) REVERT: N 274 SER cc_start: 0.8764 (t) cc_final: 0.8223 (p) REVERT: A 9 VAL cc_start: 0.8758 (t) cc_final: 0.8453 (m) REVERT: A 105 ARG cc_start: 0.8596 (OUTLIER) cc_final: 0.7742 (ttt-90) REVERT: A 191 THR cc_start: 0.8298 (m) cc_final: 0.8031 (p) REVERT: A 254 GLU cc_start: 0.4704 (mm-30) cc_final: 0.3747 (tp30) REVERT: B 75 SER cc_start: 0.8655 (t) cc_final: 0.8393 (t) REVERT: B 195 ASN cc_start: 0.8319 (m-40) cc_final: 0.8015 (m-40) REVERT: B 219 THR cc_start: 0.8890 (m) cc_final: 0.8565 (p) REVERT: B 226 ASN cc_start: 0.8111 (m-40) cc_final: 0.7823 (m110) REVERT: B 237 THR cc_start: 0.8857 (p) cc_final: 0.8548 (t) REVERT: E 203 MET cc_start: 0.8492 (OUTLIER) cc_final: 0.8110 (mtt) REVERT: I 1 MET cc_start: 0.6161 (mmp) cc_final: 0.5852 (mmp) REVERT: I 306 ARG cc_start: 0.8490 (mtm180) cc_final: 0.8035 (mtm180) REVERT: S 75 ILE cc_start: 0.8843 (mm) cc_final: 0.8482 (mt) REVERT: S 108 TYR cc_start: 0.8603 (m-80) cc_final: 0.7994 (m-10) REVERT: S 177 VAL cc_start: 0.8507 (m) cc_final: 0.8292 (m) REVERT: S 297 GLU cc_start: 0.7911 (mm-30) cc_final: 0.7574 (mm-30) REVERT: S 401 LYS cc_start: 0.8933 (mtpp) cc_final: 0.8220 (mtmt) outliers start: 93 outliers final: 76 residues processed: 510 average time/residue: 0.3337 time to fit residues: 268.9407 Evaluate side-chains 538 residues out of total 2547 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 458 time to evaluate : 2.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 28 ILE Chi-restraints excluded: chain K residue 36 THR Chi-restraints excluded: chain K residue 49 SER Chi-restraints excluded: chain K residue 76 ASP Chi-restraints excluded: chain K residue 92 CYS Chi-restraints excluded: chain K residue 118 ILE Chi-restraints excluded: chain K residue 146 TYR Chi-restraints excluded: chain K residue 158 LEU Chi-restraints excluded: chain K residue 165 ASN Chi-restraints excluded: chain K residue 210 MET Chi-restraints excluded: chain K residue 234 THR Chi-restraints excluded: chain K residue 236 ILE Chi-restraints excluded: chain K residue 270 ASN Chi-restraints excluded: chain K residue 319 LEU Chi-restraints excluded: chain K residue 336 ILE Chi-restraints excluded: chain N residue 8 VAL Chi-restraints excluded: chain N residue 28 ILE Chi-restraints excluded: chain N residue 38 VAL Chi-restraints excluded: chain N residue 82 LEU Chi-restraints excluded: chain N residue 182 SER Chi-restraints excluded: chain N residue 222 ASN Chi-restraints excluded: chain N residue 247 VAL Chi-restraints excluded: chain N residue 252 SER Chi-restraints excluded: chain N residue 258 THR Chi-restraints excluded: chain N residue 261 LYS Chi-restraints excluded: chain N residue 283 SER Chi-restraints excluded: chain N residue 331 LEU Chi-restraints excluded: chain N residue 342 LEU Chi-restraints excluded: chain A residue 3 GLU Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 105 ARG Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 404 ASP Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 98 ASP Chi-restraints excluded: chain E residue 170 SER Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 191 THR Chi-restraints excluded: chain E residue 203 MET Chi-restraints excluded: chain E residue 245 ASP Chi-restraints excluded: chain E residue 286 LEU Chi-restraints excluded: chain E residue 334 THR Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain E residue 414 GLU Chi-restraints excluded: chain E residue 417 GLU Chi-restraints excluded: chain E residue 449 GLU Chi-restraints excluded: chain I residue 4 ILE Chi-restraints excluded: chain I residue 24 ILE Chi-restraints excluded: chain I residue 26 ASP Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain I residue 176 SER Chi-restraints excluded: chain I residue 218 THR Chi-restraints excluded: chain I residue 230 SER Chi-restraints excluded: chain I residue 407 GLU Chi-restraints excluded: chain S residue 26 LEU Chi-restraints excluded: chain S residue 68 VAL Chi-restraints excluded: chain S residue 80 THR Chi-restraints excluded: chain S residue 125 LEU Chi-restraints excluded: chain S residue 191 THR Chi-restraints excluded: chain S residue 362 VAL Chi-restraints excluded: chain S residue 367 ASP Chi-restraints excluded: chain S residue 371 VAL Chi-restraints excluded: chain S residue 377 MET Chi-restraints excluded: chain S residue 381 THR Chi-restraints excluded: chain S residue 413 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 96 optimal weight: 0.8980 chunk 257 optimal weight: 9.9990 chunk 56 optimal weight: 9.9990 chunk 167 optimal weight: 3.9990 chunk 70 optimal weight: 10.0000 chunk 286 optimal weight: 4.9990 chunk 237 optimal weight: 2.9990 chunk 132 optimal weight: 0.9980 chunk 23 optimal weight: 10.0000 chunk 94 optimal weight: 0.6980 chunk 150 optimal weight: 0.5980 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 256 GLN B 165 ASN B 204 ASN B 335 ASN ** I 433 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.2018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 24284 Z= 0.250 Angle : 0.539 7.826 32964 Z= 0.271 Chirality : 0.044 0.285 3616 Planarity : 0.004 0.068 4287 Dihedral : 9.161 155.052 3611 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.77 % Favored : 96.09 % Rotamer: Outliers : 4.45 % Allowed : 16.05 % Favored : 79.50 % 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: 0.67 (0.16), residues: 2976 helix: 1.97 (0.15), residues: 1234 sheet: 0.59 (0.22), residues: 527 loop : -1.28 (0.17), residues: 1215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 21 HIS 0.006 0.001 HIS A 88 PHE 0.015 0.002 PHE E 255 TYR 0.029 0.001 TYR S 24 ARG 0.006 0.000 ARG N 129 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5952 Ramachandran restraints generated. 2976 Oldfield, 0 Emsley, 2976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5952 Ramachandran restraints generated. 2976 Oldfield, 0 Emsley, 2976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 577 residues out of total 2547 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 469 time to evaluate : 2.625 Fit side-chains revert: symmetry clash REVERT: K 98 GLN cc_start: 0.8463 (pt0) cc_final: 0.8261 (pt0) REVERT: K 146 TYR cc_start: 0.8252 (OUTLIER) cc_final: 0.6981 (t80) REVERT: K 340 GLU cc_start: 0.7837 (mp0) cc_final: 0.7118 (mp0) REVERT: N 82 LEU cc_start: 0.6222 (OUTLIER) cc_final: 0.5944 (mt) REVERT: N 107 MET cc_start: 0.7664 (mmm) cc_final: 0.7017 (tpp) REVERT: N 274 SER cc_start: 0.8774 (t) cc_final: 0.8231 (p) REVERT: N 345 LEU cc_start: 0.8495 (OUTLIER) cc_final: 0.8255 (mp) REVERT: A 9 VAL cc_start: 0.8787 (t) cc_final: 0.8501 (m) REVERT: A 105 ARG cc_start: 0.8610 (OUTLIER) cc_final: 0.7932 (ttt-90) REVERT: A 191 THR cc_start: 0.8296 (m) cc_final: 0.8044 (p) REVERT: A 254 GLU cc_start: 0.4764 (mm-30) cc_final: 0.3894 (tp30) REVERT: B 75 SER cc_start: 0.8603 (t) cc_final: 0.8345 (t) REVERT: B 195 ASN cc_start: 0.8359 (m-40) cc_final: 0.8062 (m-40) REVERT: B 219 THR cc_start: 0.8894 (m) cc_final: 0.8612 (p) REVERT: B 226 ASN cc_start: 0.8133 (m-40) cc_final: 0.7776 (m110) REVERT: B 237 THR cc_start: 0.8872 (p) cc_final: 0.8543 (t) REVERT: E 203 MET cc_start: 0.8544 (OUTLIER) cc_final: 0.8179 (mtt) REVERT: I 1 MET cc_start: 0.6083 (mmp) cc_final: 0.5762 (mmp) REVERT: I 213 ARG cc_start: 0.8057 (mtp180) cc_final: 0.7823 (mtm180) REVERT: S 108 TYR cc_start: 0.8605 (m-80) cc_final: 0.7874 (m-10) REVERT: S 177 VAL cc_start: 0.8522 (m) cc_final: 0.8314 (m) REVERT: S 297 GLU cc_start: 0.7899 (mm-30) cc_final: 0.7696 (mm-30) REVERT: S 401 LYS cc_start: 0.8929 (mtpp) cc_final: 0.8215 (mtmt) REVERT: S 434 GLU cc_start: 0.7841 (mt-10) cc_final: 0.7572 (mt-10) outliers start: 108 outliers final: 91 residues processed: 522 average time/residue: 0.3311 time to fit residues: 273.6785 Evaluate side-chains 555 residues out of total 2547 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 459 time to evaluate : 2.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 28 ILE Chi-restraints excluded: chain K residue 36 THR Chi-restraints excluded: chain K residue 49 SER Chi-restraints excluded: chain K residue 76 ASP Chi-restraints excluded: chain K residue 92 CYS Chi-restraints excluded: chain K residue 118 ILE Chi-restraints excluded: chain K residue 146 TYR Chi-restraints excluded: chain K residue 158 LEU Chi-restraints excluded: chain K residue 165 ASN Chi-restraints excluded: chain K residue 186 VAL Chi-restraints excluded: chain K residue 204 THR Chi-restraints excluded: chain K residue 210 MET Chi-restraints excluded: chain K residue 234 THR Chi-restraints excluded: chain K residue 236 ILE Chi-restraints excluded: chain K residue 253 GLU Chi-restraints excluded: chain K residue 270 ASN Chi-restraints excluded: chain K residue 312 THR Chi-restraints excluded: chain K residue 318 ASN Chi-restraints excluded: chain K residue 336 ILE Chi-restraints excluded: chain N residue 8 VAL Chi-restraints excluded: chain N residue 28 ILE Chi-restraints excluded: chain N residue 38 VAL Chi-restraints excluded: chain N residue 82 LEU Chi-restraints excluded: chain N residue 182 SER Chi-restraints excluded: chain N residue 247 VAL Chi-restraints excluded: chain N residue 252 SER Chi-restraints excluded: chain N residue 258 THR Chi-restraints excluded: chain N residue 261 LYS Chi-restraints excluded: chain N residue 283 SER Chi-restraints excluded: chain N residue 290 SER Chi-restraints excluded: chain N residue 342 LEU Chi-restraints excluded: chain N residue 345 LEU Chi-restraints excluded: chain A residue 3 GLU 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 105 ARG Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 356 ILE Chi-restraints excluded: chain B residue 404 ASP Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 98 ASP Chi-restraints excluded: chain E residue 170 SER Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 191 THR Chi-restraints excluded: chain E residue 203 MET Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain E residue 245 ASP Chi-restraints excluded: chain E residue 286 LEU Chi-restraints excluded: chain E residue 334 THR Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain E residue 367 ASP Chi-restraints excluded: chain E residue 414 GLU Chi-restraints excluded: chain E residue 417 GLU Chi-restraints excluded: chain I residue 4 ILE Chi-restraints excluded: chain I residue 24 ILE Chi-restraints excluded: chain I residue 26 ASP Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain I residue 176 SER Chi-restraints excluded: chain I residue 196 THR Chi-restraints excluded: chain I residue 218 THR Chi-restraints excluded: chain I residue 219 THR Chi-restraints excluded: chain I residue 230 SER Chi-restraints excluded: chain I residue 313 VAL Chi-restraints excluded: chain I residue 404 ASP Chi-restraints excluded: chain I residue 407 GLU Chi-restraints excluded: chain S residue 26 LEU Chi-restraints excluded: chain S residue 68 VAL Chi-restraints excluded: chain S residue 80 THR Chi-restraints excluded: chain S residue 122 ILE Chi-restraints excluded: chain S residue 125 LEU Chi-restraints excluded: chain S residue 191 THR Chi-restraints excluded: chain S residue 259 LEU Chi-restraints excluded: chain S residue 271 THR Chi-restraints excluded: chain S residue 303 VAL Chi-restraints excluded: chain S residue 362 VAL Chi-restraints excluded: chain S residue 367 ASP Chi-restraints excluded: chain S residue 377 MET Chi-restraints excluded: chain S residue 381 THR Chi-restraints excluded: chain S residue 413 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 276 optimal weight: 1.9990 chunk 32 optimal weight: 10.0000 chunk 163 optimal weight: 4.9990 chunk 209 optimal weight: 3.9990 chunk 162 optimal weight: 0.9990 chunk 241 optimal weight: 4.9990 chunk 159 optimal weight: 2.9990 chunk 285 optimal weight: 3.9990 chunk 178 optimal weight: 0.9980 chunk 173 optimal weight: 0.9990 chunk 131 optimal weight: 0.8980 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 200 ASN B 204 ASN B 335 ASN ** I 433 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.2135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 24284 Z= 0.240 Angle : 0.538 9.139 32964 Z= 0.270 Chirality : 0.044 0.254 3616 Planarity : 0.004 0.063 4287 Dihedral : 9.014 155.296 3608 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.94 % Favored : 95.92 % Rotamer: Outliers : 4.65 % Allowed : 15.89 % Favored : 79.46 % 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: 2976 helix: 1.99 (0.15), residues: 1233 sheet: 0.63 (0.22), residues: 526 loop : -1.29 (0.17), residues: 1217 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 21 HIS 0.005 0.001 HIS A 88 PHE 0.014 0.002 PHE S 296 TYR 0.028 0.001 TYR S 24 ARG 0.005 0.000 ARG S 215 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5952 Ramachandran restraints generated. 2976 Oldfield, 0 Emsley, 2976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5952 Ramachandran restraints generated. 2976 Oldfield, 0 Emsley, 2976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 591 residues out of total 2547 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 478 time to evaluate : 2.892 Fit side-chains revert: symmetry clash REVERT: K 146 TYR cc_start: 0.8254 (OUTLIER) cc_final: 0.7005 (t80) REVERT: K 317 GLU cc_start: 0.7592 (mm-30) cc_final: 0.7227 (mm-30) REVERT: K 340 GLU cc_start: 0.7847 (mp0) cc_final: 0.7054 (mp0) REVERT: N 82 LEU cc_start: 0.6217 (OUTLIER) cc_final: 0.5925 (mt) REVERT: N 98 GLN cc_start: 0.7144 (mp10) cc_final: 0.6905 (mp10) REVERT: N 107 MET cc_start: 0.7713 (mmm) cc_final: 0.7028 (tpp) REVERT: N 157 LEU cc_start: 0.7741 (mt) cc_final: 0.7517 (mt) REVERT: N 274 SER cc_start: 0.8770 (t) cc_final: 0.8234 (p) REVERT: A 9 VAL cc_start: 0.8791 (t) cc_final: 0.8510 (m) REVERT: A 105 ARG cc_start: 0.8613 (OUTLIER) cc_final: 0.7671 (ttt-90) REVERT: A 191 THR cc_start: 0.8280 (m) cc_final: 0.8071 (p) REVERT: A 254 GLU cc_start: 0.4735 (mm-30) cc_final: 0.3898 (tp30) REVERT: B 75 SER cc_start: 0.8602 (t) cc_final: 0.8345 (t) REVERT: B 219 THR cc_start: 0.8909 (m) cc_final: 0.8642 (p) REVERT: B 226 ASN cc_start: 0.8118 (m-40) cc_final: 0.7837 (m110) REVERT: B 237 THR cc_start: 0.8872 (p) cc_final: 0.8543 (t) REVERT: B 426 GLN cc_start: 0.8437 (tm-30) cc_final: 0.8032 (tm-30) REVERT: E 203 MET cc_start: 0.8546 (OUTLIER) cc_final: 0.8179 (mtt) REVERT: I 1 MET cc_start: 0.6123 (mmp) cc_final: 0.5808 (mmp) REVERT: I 26 ASP cc_start: 0.8321 (OUTLIER) cc_final: 0.7995 (t0) REVERT: I 213 ARG cc_start: 0.8090 (mtp180) cc_final: 0.7872 (mtm180) REVERT: S 108 TYR cc_start: 0.8611 (m-80) cc_final: 0.7926 (m-10) REVERT: S 177 VAL cc_start: 0.8508 (m) cc_final: 0.8295 (m) REVERT: S 401 LYS cc_start: 0.8885 (mtpp) cc_final: 0.8163 (mtmt) REVERT: S 434 GLU cc_start: 0.7861 (mt-10) cc_final: 0.7572 (mt-10) outliers start: 113 outliers final: 94 residues processed: 536 average time/residue: 0.3364 time to fit residues: 286.4467 Evaluate side-chains 565 residues out of total 2547 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 466 time to evaluate : 2.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 28 ILE Chi-restraints excluded: chain K residue 31 SER Chi-restraints excluded: chain K residue 36 THR Chi-restraints excluded: chain K residue 55 SER Chi-restraints excluded: chain K residue 76 ASP Chi-restraints excluded: chain K residue 92 CYS Chi-restraints excluded: chain K residue 118 ILE Chi-restraints excluded: chain K residue 128 SER Chi-restraints excluded: chain K residue 146 TYR Chi-restraints excluded: chain K residue 158 LEU Chi-restraints excluded: chain K residue 165 ASN Chi-restraints excluded: chain K residue 204 THR Chi-restraints excluded: chain K residue 210 MET Chi-restraints excluded: chain K residue 234 THR Chi-restraints excluded: chain K residue 236 ILE Chi-restraints excluded: chain K residue 253 GLU Chi-restraints excluded: chain K residue 270 ASN Chi-restraints excluded: chain K residue 336 ILE Chi-restraints excluded: chain K residue 361 ASN Chi-restraints excluded: chain N residue 8 VAL Chi-restraints excluded: chain N residue 28 ILE Chi-restraints excluded: chain N residue 38 VAL Chi-restraints excluded: chain N residue 82 LEU Chi-restraints excluded: chain N residue 182 SER Chi-restraints excluded: chain N residue 247 VAL Chi-restraints excluded: chain N residue 252 SER Chi-restraints excluded: chain N residue 258 THR Chi-restraints excluded: chain N residue 261 LYS Chi-restraints excluded: chain N residue 283 SER Chi-restraints excluded: chain N residue 290 SER Chi-restraints excluded: chain N residue 342 LEU Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 98 ASP Chi-restraints excluded: chain A residue 105 ARG Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 404 ASP Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 98 ASP Chi-restraints excluded: chain E residue 170 SER Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 191 THR Chi-restraints excluded: chain E residue 203 MET Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain E residue 245 ASP Chi-restraints excluded: chain E residue 286 LEU Chi-restraints excluded: chain E residue 334 THR Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain E residue 367 ASP Chi-restraints excluded: chain E residue 414 GLU Chi-restraints excluded: chain E residue 417 GLU Chi-restraints excluded: chain I residue 4 ILE Chi-restraints excluded: chain I residue 24 ILE Chi-restraints excluded: chain I residue 26 ASP Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain I residue 176 SER Chi-restraints excluded: chain I residue 196 THR Chi-restraints excluded: chain I residue 218 THR Chi-restraints excluded: chain I residue 219 THR Chi-restraints excluded: chain I residue 313 VAL Chi-restraints excluded: chain I residue 404 ASP Chi-restraints excluded: chain I residue 407 GLU Chi-restraints excluded: chain S residue 26 LEU Chi-restraints excluded: chain S residue 68 VAL Chi-restraints excluded: chain S residue 80 THR Chi-restraints excluded: chain S residue 98 ASP Chi-restraints excluded: chain S residue 122 ILE Chi-restraints excluded: chain S residue 191 THR Chi-restraints excluded: chain S residue 242 LEU Chi-restraints excluded: chain S residue 259 LEU Chi-restraints excluded: chain S residue 271 THR Chi-restraints excluded: chain S residue 295 CYS Chi-restraints excluded: chain S residue 303 VAL Chi-restraints excluded: chain S residue 362 VAL Chi-restraints excluded: chain S residue 367 ASP Chi-restraints excluded: chain S residue 381 THR Chi-restraints excluded: chain S residue 413 MET 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: 0.8980 chunk 170 optimal weight: 0.9990 chunk 85 optimal weight: 4.9990 chunk 56 optimal weight: 10.0000 chunk 55 optimal weight: 0.0970 chunk 181 optimal weight: 0.5980 chunk 194 optimal weight: 0.8980 chunk 141 optimal weight: 2.9990 chunk 26 optimal weight: 0.8980 chunk 224 optimal weight: 2.9990 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 98 GLN B 204 ASN B 335 ASN E 301 GLN I 396 HIS S 101 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.2293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 24284 Z= 0.171 Angle : 0.512 7.343 32964 Z= 0.256 Chirality : 0.042 0.236 3616 Planarity : 0.004 0.060 4287 Dihedral : 8.796 157.494 3608 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.88 % Favored : 95.99 % Rotamer: Outliers : 3.98 % Allowed : 16.95 % Favored : 79.07 % 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: 0.81 (0.16), residues: 2976 helix: 2.10 (0.15), residues: 1233 sheet: 0.64 (0.22), residues: 529 loop : -1.21 (0.17), residues: 1214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 388 HIS 0.003 0.001 HIS A 88 PHE 0.015 0.001 PHE E 255 TYR 0.032 0.001 TYR S 24 ARG 0.005 0.000 ARG S 215 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5952 Ramachandran restraints generated. 2976 Oldfield, 0 Emsley, 2976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5952 Ramachandran restraints generated. 2976 Oldfield, 0 Emsley, 2976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 581 residues out of total 2547 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 485 time to evaluate : 2.674 Fit side-chains revert: symmetry clash REVERT: K 146 TYR cc_start: 0.8185 (OUTLIER) cc_final: 0.7010 (t80) REVERT: K 317 GLU cc_start: 0.7587 (mm-30) cc_final: 0.7234 (mm-30) REVERT: K 340 GLU cc_start: 0.7716 (mp0) cc_final: 0.7322 (mp0) REVERT: N 82 LEU cc_start: 0.6255 (OUTLIER) cc_final: 0.5945 (mt) REVERT: N 107 MET cc_start: 0.7725 (mmm) cc_final: 0.7045 (tpp) REVERT: N 138 MET cc_start: 0.7537 (tpp) cc_final: 0.7257 (mmm) REVERT: N 270 ASN cc_start: 0.8259 (m-40) cc_final: 0.8032 (m-40) REVERT: N 274 SER cc_start: 0.8751 (t) cc_final: 0.8220 (p) REVERT: N 276 THR cc_start: 0.8152 (m) cc_final: 0.7138 (p) REVERT: A 9 VAL cc_start: 0.8749 (t) cc_final: 0.8448 (m) REVERT: A 254 GLU cc_start: 0.4652 (mm-30) cc_final: 0.3867 (tp30) REVERT: B 75 SER cc_start: 0.8579 (t) cc_final: 0.8315 (t) REVERT: B 195 ASN cc_start: 0.8266 (m-40) cc_final: 0.8007 (m-40) REVERT: B 218 THR cc_start: 0.8724 (OUTLIER) cc_final: 0.8382 (m) REVERT: B 219 THR cc_start: 0.8911 (m) cc_final: 0.8679 (p) REVERT: B 226 ASN cc_start: 0.8092 (m-40) cc_final: 0.7805 (m110) REVERT: B 237 THR cc_start: 0.8838 (p) cc_final: 0.8574 (t) REVERT: B 426 GLN cc_start: 0.8400 (tm-30) cc_final: 0.8049 (tm-30) REVERT: E 1 MET cc_start: 0.6939 (mpp) cc_final: 0.6626 (mpp) REVERT: I 1 MET cc_start: 0.6164 (mmp) cc_final: 0.5849 (mmp) REVERT: I 297 LYS cc_start: 0.8769 (pttt) cc_final: 0.8401 (pttm) REVERT: I 306 ARG cc_start: 0.8472 (mtm180) cc_final: 0.8008 (mtm180) REVERT: S 52 PHE cc_start: 0.7643 (m-10) cc_final: 0.7403 (m-10) REVERT: S 108 TYR cc_start: 0.8611 (m-80) cc_final: 0.7931 (m-10) REVERT: S 177 VAL cc_start: 0.8509 (m) cc_final: 0.8292 (m) REVERT: S 340 SER cc_start: 0.8797 (p) cc_final: 0.8434 (t) REVERT: S 401 LYS cc_start: 0.8859 (mtpp) cc_final: 0.8135 (mtmt) REVERT: S 434 GLU cc_start: 0.7835 (mt-10) cc_final: 0.7543 (mt-10) outliers start: 96 outliers final: 81 residues processed: 534 average time/residue: 0.3389 time to fit residues: 287.5133 Evaluate side-chains 552 residues out of total 2547 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 468 time to evaluate : 2.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 28 ILE Chi-restraints excluded: chain K residue 31 SER Chi-restraints excluded: chain K residue 36 THR Chi-restraints excluded: chain K residue 92 CYS Chi-restraints excluded: chain K residue 98 GLN Chi-restraints excluded: chain K residue 128 SER Chi-restraints excluded: chain K residue 146 TYR Chi-restraints excluded: chain K residue 158 LEU Chi-restraints excluded: chain K residue 165 ASN Chi-restraints excluded: chain K residue 204 THR Chi-restraints excluded: chain K residue 210 MET Chi-restraints excluded: chain K residue 234 THR Chi-restraints excluded: chain K residue 236 ILE Chi-restraints excluded: chain K residue 253 GLU Chi-restraints excluded: chain K residue 270 ASN Chi-restraints excluded: chain K residue 312 THR Chi-restraints excluded: chain K residue 336 ILE Chi-restraints excluded: chain K residue 361 ASN Chi-restraints excluded: chain N residue 8 VAL Chi-restraints excluded: chain N residue 28 ILE Chi-restraints excluded: chain N residue 38 VAL Chi-restraints excluded: chain N residue 82 LEU Chi-restraints excluded: chain N residue 182 SER Chi-restraints excluded: chain N residue 247 VAL Chi-restraints excluded: chain N residue 252 SER Chi-restraints excluded: chain N residue 258 THR Chi-restraints excluded: chain N residue 261 LYS Chi-restraints excluded: chain N residue 283 SER Chi-restraints excluded: chain N residue 290 SER Chi-restraints excluded: chain N residue 342 LEU Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 404 ASP Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 93 ILE Chi-restraints excluded: chain E residue 98 ASP Chi-restraints excluded: chain E residue 170 SER Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 191 THR Chi-restraints excluded: chain E residue 245 ASP Chi-restraints excluded: chain E residue 286 LEU Chi-restraints excluded: chain E residue 334 THR Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain E residue 367 ASP Chi-restraints excluded: chain E residue 414 GLU Chi-restraints excluded: chain E residue 417 GLU Chi-restraints excluded: chain I residue 4 ILE Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain I residue 170 MET Chi-restraints excluded: chain I residue 176 SER Chi-restraints excluded: chain I residue 196 THR Chi-restraints excluded: chain I residue 218 THR Chi-restraints excluded: chain I residue 313 VAL Chi-restraints excluded: chain I residue 404 ASP Chi-restraints excluded: chain I residue 407 GLU Chi-restraints excluded: chain S residue 68 VAL Chi-restraints excluded: chain S residue 80 THR Chi-restraints excluded: chain S residue 122 ILE Chi-restraints excluded: chain S residue 191 THR Chi-restraints excluded: chain S residue 230 LEU Chi-restraints excluded: chain S residue 242 LEU Chi-restraints excluded: chain S residue 271 THR Chi-restraints excluded: chain S residue 295 CYS Chi-restraints excluded: chain S residue 362 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 413 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 259 optimal weight: 6.9990 chunk 273 optimal weight: 8.9990 chunk 249 optimal weight: 3.9990 chunk 265 optimal weight: 1.9990 chunk 160 optimal weight: 2.9990 chunk 115 optimal weight: 0.9980 chunk 208 optimal weight: 4.9990 chunk 81 optimal weight: 2.9990 chunk 240 optimal weight: 0.7980 chunk 251 optimal weight: 7.9990 chunk 264 optimal weight: 0.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 98 GLN A 128 GLN A 216 ASN A 256 GLN B 335 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.2314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 24284 Z= 0.302 Angle : 0.573 9.718 32964 Z= 0.288 Chirality : 0.045 0.242 3616 Planarity : 0.004 0.058 4287 Dihedral : 8.913 155.751 3606 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.98 % Favored : 95.92 % Rotamer: Outliers : 4.30 % Allowed : 16.91 % Favored : 78.80 % 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: 0.67 (0.16), residues: 2976 helix: 1.99 (0.15), residues: 1229 sheet: 0.61 (0.22), residues: 529 loop : -1.31 (0.17), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 21 HIS 0.008 0.001 HIS A 88 PHE 0.017 0.002 PHE A 141 TYR 0.038 0.001 TYR S 24 ARG 0.008 0.000 ARG B 320 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5952 Ramachandran restraints generated. 2976 Oldfield, 0 Emsley, 2976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5952 Ramachandran restraints generated. 2976 Oldfield, 0 Emsley, 2976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 599 residues out of total 2547 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 495 time to evaluate : 2.709 Fit side-chains revert: symmetry clash REVERT: K 146 TYR cc_start: 0.8295 (OUTLIER) cc_final: 0.7080 (t80) REVERT: K 340 GLU cc_start: 0.7787 (mp0) cc_final: 0.7387 (mp0) REVERT: N 49 SER cc_start: 0.7644 (p) cc_final: 0.7111 (t) REVERT: N 107 MET cc_start: 0.7719 (mmm) cc_final: 0.7031 (tpp) REVERT: N 138 MET cc_start: 0.7604 (tpp) cc_final: 0.7324 (mmm) REVERT: N 274 SER cc_start: 0.8782 (t) cc_final: 0.8245 (p) REVERT: A 9 VAL cc_start: 0.8805 (t) cc_final: 0.8536 (m) REVERT: A 254 GLU cc_start: 0.4696 (mm-30) cc_final: 0.3873 (tp30) REVERT: A 433 GLU cc_start: 0.7770 (tt0) cc_final: 0.7448 (tt0) REVERT: B 75 SER cc_start: 0.8584 (t) cc_final: 0.8325 (t) REVERT: B 218 THR cc_start: 0.8737 (OUTLIER) cc_final: 0.8412 (m) REVERT: B 219 THR cc_start: 0.8911 (m) cc_final: 0.8696 (p) REVERT: B 226 ASN cc_start: 0.8162 (m-40) cc_final: 0.7835 (m110) REVERT: B 237 THR cc_start: 0.8872 (p) cc_final: 0.8533 (t) REVERT: B 426 GLN cc_start: 0.8476 (tm-30) cc_final: 0.8198 (tm-30) REVERT: E 1 MET cc_start: 0.7034 (mpp) cc_final: 0.6749 (mpp) REVERT: E 203 MET cc_start: 0.8580 (OUTLIER) cc_final: 0.8238 (mtt) REVERT: I 297 LYS cc_start: 0.8791 (pttt) cc_final: 0.8436 (pttm) REVERT: S 108 TYR cc_start: 0.8629 (m-80) cc_final: 0.7985 (m-10) REVERT: S 306 ASP cc_start: 0.8231 (t0) cc_final: 0.8025 (t0) REVERT: S 340 SER cc_start: 0.8805 (p) cc_final: 0.8424 (t) REVERT: S 401 LYS cc_start: 0.8875 (mtpp) cc_final: 0.8147 (mtmt) REVERT: S 434 GLU cc_start: 0.7903 (mt-10) cc_final: 0.7607 (mt-10) outliers start: 104 outliers final: 94 residues processed: 547 average time/residue: 0.3461 time to fit residues: 302.0543 Evaluate side-chains 576 residues out of total 2547 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 479 time to evaluate : 2.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 28 ILE Chi-restraints excluded: chain K residue 31 SER Chi-restraints excluded: chain K residue 36 THR Chi-restraints excluded: chain K residue 55 SER Chi-restraints excluded: chain K residue 76 ASP Chi-restraints excluded: chain K residue 98 GLN Chi-restraints excluded: chain K residue 118 ILE Chi-restraints excluded: chain K residue 128 SER Chi-restraints excluded: chain K residue 146 TYR Chi-restraints excluded: chain K residue 158 LEU Chi-restraints excluded: chain K residue 165 ASN Chi-restraints excluded: chain K residue 204 THR Chi-restraints excluded: chain K residue 210 MET Chi-restraints excluded: chain K residue 234 THR Chi-restraints excluded: chain K residue 236 ILE Chi-restraints excluded: chain K residue 253 GLU Chi-restraints excluded: chain K residue 270 ASN Chi-restraints excluded: chain K residue 312 THR Chi-restraints excluded: chain K residue 318 ASN Chi-restraints excluded: chain K residue 336 ILE Chi-restraints excluded: chain K residue 361 ASN Chi-restraints excluded: chain N residue 8 VAL Chi-restraints excluded: chain N residue 28 ILE Chi-restraints excluded: chain N residue 82 LEU Chi-restraints excluded: chain N residue 182 SER Chi-restraints excluded: chain N residue 247 VAL Chi-restraints excluded: chain N residue 252 SER Chi-restraints excluded: chain N residue 258 THR Chi-restraints excluded: chain N residue 261 LYS Chi-restraints excluded: chain N residue 283 SER Chi-restraints excluded: chain N residue 342 LEU Chi-restraints excluded: chain N residue 345 LEU Chi-restraints excluded: chain A residue 1 MET 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 93 ILE Chi-restraints excluded: chain A residue 98 ASP Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 404 ASP Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 93 ILE Chi-restraints excluded: chain E residue 98 ASP Chi-restraints excluded: chain E residue 170 SER Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 191 THR Chi-restraints excluded: chain E residue 203 MET Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain E residue 245 ASP 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 414 GLU Chi-restraints excluded: chain E residue 417 GLU Chi-restraints excluded: chain I residue 4 ILE Chi-restraints excluded: chain I residue 24 ILE Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain I residue 170 MET Chi-restraints excluded: chain I residue 176 SER Chi-restraints excluded: chain I residue 196 THR Chi-restraints excluded: chain I residue 218 THR Chi-restraints excluded: chain I residue 219 THR Chi-restraints excluded: chain I residue 230 SER Chi-restraints excluded: chain I residue 313 VAL Chi-restraints excluded: chain I residue 404 ASP Chi-restraints excluded: chain I residue 407 GLU Chi-restraints excluded: chain S residue 68 VAL Chi-restraints excluded: chain S residue 80 THR Chi-restraints excluded: chain S residue 98 ASP Chi-restraints excluded: chain S residue 122 ILE Chi-restraints excluded: chain S residue 130 THR Chi-restraints excluded: chain S residue 191 THR Chi-restraints excluded: chain S residue 230 LEU Chi-restraints excluded: chain S residue 259 LEU Chi-restraints excluded: chain S residue 271 THR Chi-restraints excluded: chain S residue 295 CYS Chi-restraints excluded: chain S residue 303 VAL Chi-restraints excluded: chain S residue 362 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 413 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 174 optimal weight: 0.8980 chunk 281 optimal weight: 0.7980 chunk 171 optimal weight: 0.5980 chunk 133 optimal weight: 0.9980 chunk 195 optimal weight: 0.8980 chunk 294 optimal weight: 0.9990 chunk 271 optimal weight: 2.9990 chunk 234 optimal weight: 0.7980 chunk 24 optimal weight: 9.9990 chunk 181 optimal weight: 0.5980 chunk 143 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 98 GLN B 195 ASN B 204 ASN ** B 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 335 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.2423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 24284 Z= 0.178 Angle : 0.527 8.781 32964 Z= 0.264 Chirality : 0.043 0.246 3616 Planarity : 0.004 0.057 4287 Dihedral : 8.759 156.639 3606 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.98 % Favored : 95.92 % Rotamer: Outliers : 3.51 % Allowed : 17.88 % Favored : 78.60 % 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: 2976 helix: 2.06 (0.15), residues: 1234 sheet: 0.66 (0.22), residues: 529 loop : -1.25 (0.17), residues: 1213 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP S 388 HIS 0.003 0.001 HIS I 137 PHE 0.024 0.001 PHE S 52 TYR 0.042 0.001 TYR S 24 ARG 0.007 0.000 ARG B 320 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5952 Ramachandran restraints generated. 2976 Oldfield, 0 Emsley, 2976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5952 Ramachandran restraints generated. 2976 Oldfield, 0 Emsley, 2976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 570 residues out of total 2547 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 486 time to evaluate : 2.945 Fit side-chains revert: symmetry clash REVERT: K 146 TYR cc_start: 0.8213 (OUTLIER) cc_final: 0.6916 (t80) REVERT: K 340 GLU cc_start: 0.7773 (mp0) cc_final: 0.7495 (mp0) REVERT: N 49 SER cc_start: 0.7572 (p) cc_final: 0.7056 (t) REVERT: N 107 MET cc_start: 0.7732 (mmm) cc_final: 0.7054 (tpp) REVERT: N 138 MET cc_start: 0.7603 (tpp) cc_final: 0.7279 (mmm) REVERT: N 274 SER cc_start: 0.8760 (t) cc_final: 0.8234 (p) REVERT: N 276 THR cc_start: 0.8168 (m) cc_final: 0.7165 (p) REVERT: A 254 GLU cc_start: 0.4592 (mm-30) cc_final: 0.3697 (tp30) REVERT: B 75 SER cc_start: 0.8564 (t) cc_final: 0.8300 (t) REVERT: B 195 ASN cc_start: 0.8260 (m-40) cc_final: 0.8009 (m-40) REVERT: B 218 THR cc_start: 0.8708 (OUTLIER) cc_final: 0.8396 (m) REVERT: B 226 ASN cc_start: 0.8090 (m-40) cc_final: 0.7735 (m110) REVERT: B 237 THR cc_start: 0.8839 (p) cc_final: 0.8558 (t) REVERT: B 426 GLN cc_start: 0.8394 (tm-30) cc_final: 0.8164 (tm-30) REVERT: E 1 MET cc_start: 0.6999 (mpp) cc_final: 0.6735 (mpp) REVERT: E 203 MET cc_start: 0.8503 (OUTLIER) cc_final: 0.8118 (mtt) REVERT: I 297 LYS cc_start: 0.8786 (pttt) cc_final: 0.8425 (pttm) REVERT: S 108 TYR cc_start: 0.8634 (m-80) cc_final: 0.7972 (m-10) REVERT: S 238 ILE cc_start: 0.8136 (mt) cc_final: 0.7672 (tt) REVERT: S 340 SER cc_start: 0.8813 (p) cc_final: 0.8455 (t) REVERT: S 401 LYS cc_start: 0.8870 (mtpp) cc_final: 0.8150 (mtmt) REVERT: S 434 GLU cc_start: 0.7885 (mt-10) cc_final: 0.7591 (mt-10) outliers start: 84 outliers final: 76 residues processed: 531 average time/residue: 0.3315 time to fit residues: 278.2851 Evaluate side-chains 552 residues out of total 2547 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 473 time to evaluate : 2.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 31 SER Chi-restraints excluded: chain K residue 36 THR Chi-restraints excluded: chain K residue 98 GLN Chi-restraints excluded: chain K residue 118 ILE Chi-restraints excluded: chain K residue 128 SER Chi-restraints excluded: chain K residue 146 TYR Chi-restraints excluded: chain K residue 158 LEU Chi-restraints excluded: chain K residue 165 ASN Chi-restraints excluded: chain K residue 210 MET Chi-restraints excluded: chain K residue 234 THR Chi-restraints excluded: chain K residue 236 ILE Chi-restraints excluded: chain K residue 253 GLU Chi-restraints excluded: chain K residue 270 ASN Chi-restraints excluded: chain K residue 312 THR Chi-restraints excluded: chain K residue 336 ILE Chi-restraints excluded: chain K residue 361 ASN Chi-restraints excluded: chain N residue 8 VAL Chi-restraints excluded: chain N residue 28 ILE Chi-restraints excluded: chain N residue 82 LEU Chi-restraints excluded: chain N residue 182 SER Chi-restraints excluded: chain N residue 247 VAL Chi-restraints excluded: chain N residue 252 SER Chi-restraints excluded: chain N residue 258 THR Chi-restraints excluded: chain N residue 261 LYS Chi-restraints excluded: chain N residue 283 SER Chi-restraints excluded: chain N residue 345 LEU Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 404 ASP Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 93 ILE Chi-restraints excluded: chain E residue 98 ASP Chi-restraints excluded: chain E residue 170 SER Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 191 THR Chi-restraints excluded: chain E residue 203 MET Chi-restraints excluded: chain E residue 245 ASP Chi-restraints excluded: chain E residue 334 THR Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain E residue 367 ASP Chi-restraints excluded: chain E residue 414 GLU Chi-restraints excluded: chain E residue 417 GLU Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain I residue 170 MET Chi-restraints excluded: chain I residue 176 SER Chi-restraints excluded: chain I residue 196 THR Chi-restraints excluded: chain I residue 218 THR Chi-restraints excluded: chain I residue 313 VAL Chi-restraints excluded: chain I residue 404 ASP Chi-restraints excluded: chain I residue 407 GLU Chi-restraints excluded: chain S residue 68 VAL Chi-restraints excluded: chain S residue 80 THR Chi-restraints excluded: chain S residue 122 ILE Chi-restraints excluded: chain S residue 130 THR Chi-restraints excluded: chain S residue 191 THR Chi-restraints excluded: chain S residue 230 LEU Chi-restraints excluded: chain S residue 271 THR Chi-restraints excluded: chain S residue 295 CYS Chi-restraints excluded: chain S residue 362 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 413 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 186 optimal weight: 2.9990 chunk 250 optimal weight: 0.9980 chunk 71 optimal weight: 0.9990 chunk 216 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 65 optimal weight: 5.9990 chunk 235 optimal weight: 0.9990 chunk 98 optimal weight: 2.9990 chunk 241 optimal weight: 0.9990 chunk 29 optimal weight: 0.0770 chunk 43 optimal weight: 0.6980 overall best weight: 0.7542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 98 GLN N 200 ASN A 128 GLN A 256 GLN B 204 ASN ** B 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 335 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.135758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.104111 restraints weight = 33465.860| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 2.18 r_work: 0.3353 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3194 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3198 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3198 r_free = 0.3198 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3198 r_free = 0.3198 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3198 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.2503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 24284 Z= 0.185 Angle : 0.534 8.492 32964 Z= 0.266 Chirality : 0.043 0.243 3616 Planarity : 0.004 0.056 4287 Dihedral : 8.696 157.910 3606 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.01 % Favored : 95.92 % Rotamer: Outliers : 3.59 % Allowed : 18.00 % Favored : 78.41 % 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: 0.83 (0.16), residues: 2976 helix: 2.11 (0.15), residues: 1234 sheet: 0.65 (0.22), residues: 534 loop : -1.21 (0.17), residues: 1208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP S 388 HIS 0.003 0.001 HIS E 88 PHE 0.018 0.001 PHE S 52 TYR 0.044 0.001 TYR S 24 ARG 0.007 0.000 ARG B 320 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6374.11 seconds wall clock time: 113 minutes 16.24 seconds (6796.24 seconds total)