Starting phenix.real_space_refine on Tue Jul 23 21:29:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8utp_42545/07_2024/8utp_42545_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8utp_42545/07_2024/8utp_42545.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8utp_42545/07_2024/8utp_42545.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8utp_42545/07_2024/8utp_42545.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8utp_42545/07_2024/8utp_42545_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8utp_42545/07_2024/8utp_42545_neut.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 19 5.49 5 Mg 4 5.21 5 S 153 5.16 5 C 14863 2.51 5 N 4070 2.21 5 O 4683 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "K PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 79": "OE1" <-> "OE2" Residue "K PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 125": "OD1" <-> "OD2" Residue "K PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 152": "OE1" <-> "OE2" Residue "K TYR 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 248": "OD1" <-> "OD2" Residue "K ASP 256": "OD1" <-> "OD2" Residue "N TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 148": "OE1" <-> "OE2" Residue "N TYR 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 33": "OD1" <-> "OD2" Residue "A GLU 254": "OE1" <-> "OE2" Residue "A GLU 290": "OE1" <-> "OE2" Residue "A TYR 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 322": "OD1" <-> "OD2" Residue "A GLU 411": "OE1" <-> "OE2" Residue "A GLU 415": "OE1" <-> "OE2" Residue "A ASP 431": "OD1" <-> "OD2" Residue "A TYR 432": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 26": "OD1" <-> "OD2" Residue "B ASP 31": "OD1" <-> "OD2" Residue "B TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 118": "OD1" <-> "OD2" Residue "B GLU 157": "OE1" <-> "OE2" Residue "B TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 224": "OD1" <-> "OD2" Residue "E ASP 33": "OD1" <-> "OD2" Residue "E TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 155": "OE1" <-> "OE2" Residue "E GLU 434": "OE1" <-> "OE2" Residue "E ASP 438": "OD1" <-> "OD2" Residue "E GLU 447": "OE1" <-> "OE2" Residue "I ASP 41": "OD1" <-> "OD2" Residue "I GLU 69": "OE1" <-> "OE2" Residue "I ASP 88": "OD1" <-> "OD2" Residue "I ASP 197": "OD1" <-> "OD2" Residue "I ASP 327": "OD1" <-> "OD2" Residue "I PHE 385": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 427": "OD1" <-> "OD2" Residue "S ASP 33": "OD1" <-> "OD2" Residue "S PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 77": "OE1" <-> "OE2" Residue "S TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 160": "OD1" <-> "OD2" Residue "S ASP 245": "OD1" <-> "OD2" Residue "S PHE 296": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 297": "OE1" <-> "OE2" Residue "S TYR 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 319": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 392": "OD1" <-> "OD2" Residue "S GLU 411": "OE1" <-> "OE2" Residue "S GLU 415": "OE1" <-> "OE2" Residue "S GLU 423": "OE1" <-> "OE2" Residue "S ASP 431": "OD1" <-> "OD2" 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: 23792 Number of models: 1 Model: "" Number of chains: 16 Chain: "K" Number of atoms: 3038 Number of conformers: 1 Conformer: "" Number of residues, atoms: 386, 3038 Classifications: {'peptide': 386} Link IDs: {'PTRANS': 13, 'TRANS': 372} Chain: "N" Number of atoms: 3055 Number of conformers: 1 Conformer: "" Number of residues, atoms: 389, 3055 Classifications: {'peptide': 389} Link IDs: {'PTRANS': 13, 'TRANS': 375} Chain: "A" Number of atoms: 3437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3437 Classifications: {'peptide': 440} Link IDs: {'PTRANS': 20, 'TRANS': 419} Chain: "B" Number of atoms: 3427 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 432, 3398 Classifications: {'peptide': 432} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 411} Conformer: "B" Number of residues, atoms: 432, 3398 Classifications: {'peptide': 432} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 411} bond proxies already assigned to first conformer: 3444 Chain: "E" Number of atoms: 3524 Number of conformers: 1 Conformer: "" Number of residues, atoms: 451, 3524 Classifications: {'peptide': 451} Link IDs: {'PTRANS': 20, 'TRANS': 430} Chain: "I" Number of atoms: 3445 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 433, 3407 Classifications: {'peptide': 433} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 412} Conformer: "B" Number of residues, atoms: 433, 3407 Classifications: {'peptide': 433} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 412} bond proxies already assigned to first conformer: 3444 Chain: "S" Number of atoms: 3524 Number of conformers: 1 Conformer: "" Number of residues, atoms: 451, 3524 Classifications: {'peptide': 451} Link IDs: {'PTRANS': 20, 'TRANS': 430} Chain: "K" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "N" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 62 Unusual residues: {'TA1': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 62 Unusual residues: {'TA1': 1} Classifications: {'undetermined': 1} Chain: "S" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 9 residue: pdb=" N ATHR B 429 " occ=0.49 ... (12 atoms not shown) pdb=" CG2BTHR B 429 " occ=0.51 residue: pdb=" N AALA B 430 " occ=0.49 ... (8 atoms not shown) pdb=" CB BALA B 430 " occ=0.51 residue: pdb=" N AASP B 431 " occ=0.49 ... (14 atoms not shown) pdb=" OD2BASP B 431 " occ=0.51 residue: pdb=" N AGLU B 432 " occ=0.49 ... (16 atoms not shown) pdb=" OE2BGLU B 432 " occ=0.51 residue: pdb=" N ATHR I 429 " occ=0.54 ... (12 atoms not shown) pdb=" CG2BTHR I 429 " occ=0.46 residue: pdb=" N AALA I 430 " occ=0.54 ... (8 atoms not shown) pdb=" CB BALA I 430 " occ=0.46 residue: pdb=" N AASP I 431 " occ=0.54 ... (14 atoms not shown) pdb=" OD2BASP I 431 " occ=0.46 residue: pdb=" N AGLU I 432 " occ=0.54 ... (16 atoms not shown) pdb=" OE2BGLU I 432 " occ=0.46 residue: pdb=" N AGLN I 433 " occ=0.54 ... (16 atoms not shown) pdb=" NE2BGLN I 433 " occ=0.46 Time building chain proxies: 16.41, per 1000 atoms: 0.69 Number of scatterers: 23792 At special positions: 0 Unit cell: (81.024, 114.784, 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 153 16.00 P 19 15.00 Mg 4 11.99 O 4683 8.00 N 4070 7.00 C 14863 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 9.44 Conformation dependent library (CDL) restraints added in 5.8 seconds 5954 Ramachandran restraints generated. 2977 Oldfield, 0 Emsley, 2977 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5554 Finding SS restraints... Secondary structure from input PDB file: 127 helices and 24 sheets defined 49.4% alpha, 19.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.50 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 88 Processing helix chain 'K' and resid 102 through 108 Processing helix chain 'K' and resid 117 through 134 removed outlier: 3.659A pdb=" N GLN K 121 " --> pdb=" O GLY K 117 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ASP K 132 " --> pdb=" O SER K 128 " (cutoff:3.500A) Processing helix chain 'K' and resid 188 through 203 removed outlier: 3.669A pdb=" N ILE K 192 " --> pdb=" O SER K 188 " (cutoff:3.500A) Processing helix chain 'K' and resid 254 through 259 Processing helix chain 'K' and resid 262 through 295 Proline residue: K 292 - end of helix Processing helix chain 'K' and resid 305 through 308 removed outlier: 3.825A 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 337 through 353 removed outlier: 3.772A pdb=" N GLN K 353 " --> pdb=" O ASP K 349 " (cutoff:3.500A) Processing helix chain 'K' and resid 363 through 386 Processing helix chain 'N' and resid 16 through 22 Processing helix chain 'N' and resid 69 through 77 Processing helix chain 'N' and resid 77 through 87 Processing helix chain 'N' and resid 102 through 108 removed outlier: 3.669A pdb=" N THR N 106 " --> pdb=" O GLY N 102 " (cutoff:3.500A) Processing helix chain 'N' and resid 117 through 133 removed outlier: 3.536A pdb=" N GLN N 121 " --> pdb=" O GLY N 117 " (cutoff:3.500A) Processing helix chain 'N' and resid 188 through 202 removed outlier: 3.614A pdb=" N ALA N 202 " --> pdb=" O SER N 198 " (cutoff:3.500A) 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: 3.806A 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 350 removed outlier: 3.786A pdb=" N ARG N 350 " --> pdb=" O ARG N 346 " (cutoff:3.500A) Processing helix chain 'N' and resid 363 through 386 removed outlier: 3.530A pdb=" N GLN N 386 " --> pdb=" O LEU N 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 10 through 29 Processing helix chain 'A' and resid 36 through 43 removed outlier: 4.119A pdb=" N LYS A 40 " --> pdb=" O MET A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 80 removed outlier: 3.575A 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 128 removed outlier: 4.319A pdb=" N LEU A 117 " --> pdb=" O GLU A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 161 removed outlier: 4.054A pdb=" N THR A 150 " --> pdb=" O GLY A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 190 removed outlier: 3.599A 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: 3.772A 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: 3.671A pdb=" N ASN A 258 " --> pdb=" O GLU A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 282 removed outlier: 3.905A pdb=" N TYR A 282 " --> pdb=" O ALA A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 296 removed outlier: 3.880A 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: 3.549A pdb=" N VAL A 328 " --> pdb=" O VAL A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 400 removed outlier: 3.850A pdb=" N ALA A 387 " --> pdb=" O ALA A 383 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N LEU A 391 " --> pdb=" O ALA A 387 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LYS A 394 " --> pdb=" O ARG A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 410 removed outlier: 3.985A pdb=" N TYR A 408 " --> pdb=" O PHE A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 436 removed outlier: 4.209A pdb=" N SER A 419 " --> pdb=" O GLU A 415 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLY A 436 " --> pdb=" O TYR A 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 29 Processing helix chain 'B' and resid 41 through 46 removed outlier: 3.803A pdb=" N GLU B 45 " --> pdb=" O ASP B 41 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N ARG B 46 " --> pdb=" O LEU B 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 41 through 46' Processing helix chain 'B' and resid 47 through 49 No H-bonds generated for 'chain 'B' and resid 47 through 49' Processing helix chain 'B' and resid 69 through 78 removed outlier: 4.273A 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: 3.762A pdb=" N LEU B 112 " --> pdb=" O GLU B 108 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N ASP B 114 " --> pdb=" O ALA B 110 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N SER B 115 " --> pdb=" O GLU B 111 " (cutoff:3.500A) removed outlier: 3.895A 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 193 removed outlier: 3.604A pdb=" N ASN B 184 " --> pdb=" O VAL B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 214 Processing helix chain 'B' and resid 221 through 237 removed outlier: 3.763A pdb=" N LEU B 225 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 3.788A 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 removed outlier: 3.639A pdb=" N MET B 299 " --> pdb=" O SER B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 308 Processing helix chain 'B' and resid 322 through 337 Processing helix chain 'B' and resid 338 through 341 removed outlier: 3.946A 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: 4.245A pdb=" N LEU B 377 " --> pdb=" O ALA B 373 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N PHE B 378 " --> pdb=" O ILE B 374 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 400 removed outlier: 4.205A pdb=" N TYR B 398 " --> pdb=" O PHE B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 427 removed outlier: 3.831A pdb=" N PHE B 408 " --> pdb=" O ASP B 404 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N TYR B 425 " --> pdb=" O GLU B 421 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLN B 426 " --> pdb=" O TYR B 422 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ASP B 427 " --> pdb=" O GLN B 423 " (cutoff:3.500A) Processing helix chain 'E' and resid 10 through 28 Processing helix chain 'E' and resid 36 through 43 removed outlier: 4.026A pdb=" N LYS E 40 " --> pdb=" O MET E 36 " (cutoff:3.500A) Processing helix chain 'E' and resid 72 through 80 removed outlier: 3.734A pdb=" N VAL E 78 " --> pdb=" O VAL E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 102 through 108 Processing helix chain 'E' and resid 114 through 129 removed outlier: 3.508A pdb=" N GLN E 128 " --> pdb=" O LYS E 124 " (cutoff:3.500A) Processing helix chain 'E' and resid 143 through 161 removed outlier: 3.508A pdb=" N SER E 147 " --> pdb=" O GLY E 143 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N THR E 150 " --> pdb=" O GLY E 146 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 190 removed outlier: 3.720A pdb=" N ASN E 186 " --> pdb=" O VAL E 182 " (cutoff:3.500A) Processing helix chain 'E' and resid 190 through 197 Processing helix chain 'E' and resid 205 through 216 Processing helix chain 'E' and resid 223 through 240 removed outlier: 3.785A 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: 3.615A pdb=" N PHE E 255 " --> pdb=" O ASP E 251 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLN E 256 " --> pdb=" O LEU E 252 " (cutoff:3.500A) Processing helix chain 'E' and resid 277 through 282 removed outlier: 4.008A pdb=" N TYR E 282 " --> pdb=" O ALA E 278 " (cutoff:3.500A) Processing helix chain 'E' and resid 287 through 296 removed outlier: 3.715A 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 338 removed outlier: 3.532A pdb=" N THR E 337 " --> pdb=" O ALA E 333 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LYS E 338 " --> pdb=" O THR E 334 " (cutoff:3.500A) Processing helix chain 'E' and resid 383 through 400 removed outlier: 3.852A pdb=" N ALA E 387 " --> pdb=" O ALA E 383 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N LEU E 391 " --> pdb=" O ALA E 387 " (cutoff:3.500A) Processing helix chain 'E' and resid 404 through 410 removed outlier: 4.139A pdb=" N TYR E 408 " --> pdb=" O PHE E 404 " (cutoff:3.500A) Processing helix chain 'E' and resid 415 through 436 removed outlier: 3.814A pdb=" N SER E 419 " --> pdb=" O GLU E 415 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA E 421 " --> pdb=" O GLU E 417 " (cutoff:3.500A) Processing helix chain 'I' and resid 10 through 28 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: 3.715A 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: 3.693A pdb=" N LEU I 112 " --> pdb=" O GLU I 108 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N ASP I 114 " --> pdb=" O ALA I 110 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N SER I 115 " --> pdb=" O GLU I 111 " (cutoff:3.500A) removed outlier: 3.657A 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: 3.597A pdb=" N ASN I 184 " --> pdb=" O VAL I 180 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N GLN I 191 " --> pdb=" O LEU I 187 " (cutoff:3.500A) Processing helix chain 'I' and resid 203 through 214 removed outlier: 3.564A pdb=" N LEU I 207 " --> pdb=" O ASP I 203 " (cutoff:3.500A) Processing helix chain 'I' and resid 221 through 242 removed outlier: 3.612A pdb=" N LEU I 225 " --> pdb=" O THR I 221 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N THR I 237 " --> pdb=" O MET I 233 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N CYS I 239 " --> pdb=" O GLY I 235 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N LEU I 240 " --> pdb=" O VAL I 236 " (cutoff:3.500A) removed outlier: 3.973A 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: 4.277A 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 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: 3.612A 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: 4.262A pdb=" N LEU I 377 " --> pdb=" O ALA I 373 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N PHE I 378 " --> pdb=" O ILE I 374 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ILE I 381 " --> pdb=" O LEU I 377 " (cutoff:3.500A) Processing helix chain 'I' and resid 395 through 400 Processing helix chain 'I' and resid 404 through 424 removed outlier: 4.134A pdb=" N PHE I 408 " --> pdb=" O ASP I 404 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N THR I 409 " --> pdb=" O GLU I 405 " (cutoff:3.500A) Processing helix chain 'S' and resid 10 through 29 Processing helix chain 'S' and resid 36 through 43 removed outlier: 4.128A pdb=" N LYS S 40 " --> pdb=" O MET S 36 " (cutoff:3.500A) Processing helix chain 'S' and resid 71 through 80 removed outlier: 4.343A pdb=" N ILE S 75 " --> pdb=" O GLU S 71 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N VAL S 78 " --> pdb=" O VAL S 74 " (cutoff:3.500A) Processing helix chain 'S' and resid 102 through 108 Processing helix chain 'S' and resid 114 through 129 removed outlier: 3.506A pdb=" N GLN S 128 " --> pdb=" O LYS S 124 " (cutoff:3.500A) Processing helix chain 'S' and resid 143 through 161 removed outlier: 4.170A pdb=" N THR S 150 " --> pdb=" O GLY S 146 " (cutoff:3.500A) Processing helix chain 'S' and resid 182 through 198 removed outlier: 4.482A pdb=" N HIS S 192 " --> pdb=" O ILE S 188 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N THR S 193 " --> pdb=" O LEU S 189 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLU S 196 " --> pdb=" O HIS S 192 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N SER S 198 " --> pdb=" O THR S 194 " (cutoff:3.500A) Processing helix chain 'S' and resid 206 through 216 Processing helix chain 'S' and resid 223 through 240 removed outlier: 3.831A 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: 3.811A pdb=" N GLN S 256 " --> pdb=" O LEU S 252 " (cutoff:3.500A) Processing helix chain 'S' and resid 262 through 266 removed outlier: 4.123A pdb=" N HIS S 266 " --> pdb=" O PRO S 263 " (cutoff:3.500A) Processing helix chain 'S' and resid 277 through 282 removed outlier: 4.092A pdb=" N TYR S 282 " --> pdb=" O ALA S 278 " (cutoff:3.500A) Processing helix chain 'S' and resid 287 through 297 removed outlier: 3.676A pdb=" N PHE S 296 " --> pdb=" O THR S 292 " (cutoff:3.500A) removed outlier: 3.532A 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: 3.703A pdb=" N VAL S 328 " --> pdb=" O VAL S 324 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N THR S 337 " --> pdb=" O ALA S 333 " (cutoff:3.500A) Processing helix chain 'S' and resid 383 through 400 removed outlier: 3.990A pdb=" N ALA S 387 " --> pdb=" O ALA S 383 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N LEU S 391 " --> pdb=" O ALA S 387 " (cutoff:3.500A) Processing helix chain 'S' and resid 404 through 411 removed outlier: 4.412A pdb=" N TYR S 408 " --> pdb=" O PHE S 404 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLU S 411 " --> pdb=" O TRP S 407 " (cutoff:3.500A) Processing helix chain 'S' and resid 414 through 436 removed outlier: 4.284A pdb=" N PHE S 418 " --> pdb=" O GLU S 414 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N SER S 419 " --> pdb=" O GLU S 415 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N GLY S 436 " --> pdb=" O TYR S 432 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'K' and resid 54 through 57 removed outlier: 6.513A pdb=" N LYS K 7 " --> pdb=" O MET K 327 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N ALA K 329 " --> pdb=" O LYS K 7 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ALA K 9 " --> pdb=" O ALA K 329 " (cutoff:3.500A) removed outlier: 7.885A pdb=" N LEU K 331 " --> pdb=" O ALA K 9 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ARG K 11 " --> pdb=" O LEU K 331 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'K' and resid 54 through 57 removed outlier: 6.513A pdb=" N LYS K 7 " --> pdb=" O MET K 327 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N ALA K 329 " --> pdb=" O LYS K 7 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ALA K 9 " --> pdb=" O ALA K 329 " (cutoff:3.500A) removed outlier: 7.885A pdb=" N LEU K 331 " --> pdb=" O ALA K 9 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ARG K 11 " --> pdb=" O LEU K 331 " (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 208 removed outlier: 5.554A pdb=" N ALA K 206 " --> pdb=" O THR K 213 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N THR K 213 " --> pdb=" O ALA K 206 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'N' and resid 54 through 56 removed outlier: 8.245A pdb=" N TYR N 54 " --> pdb=" O VAL N 6 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N VAL N 8 " --> pdb=" O TYR N 54 " (cutoff:3.500A) removed outlier: 8.099A pdb=" N TYR N 56 " --> pdb=" O VAL N 8 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N VAL N 10 " --> pdb=" O TYR N 56 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA N 326 " --> pdb=" O CYS N 92 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N VAL N 91 " --> pdb=" O SER N 245 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N VAL N 247 " --> pdb=" O VAL N 91 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N ILE N 93 " --> pdb=" O VAL N 247 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N THR N 238 " --> pdb=" O ARG N 229 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N ARG N 229 " --> pdb=" O THR N 238 " (cutoff:3.500A) removed outlier: 3.796A 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: 8.245A pdb=" N TYR N 54 " --> pdb=" O VAL N 6 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N VAL N 8 " --> pdb=" O TYR N 54 " (cutoff:3.500A) removed outlier: 8.099A pdb=" N TYR N 56 " --> pdb=" O VAL N 8 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N VAL N 10 " --> pdb=" O TYR N 56 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA N 326 " --> pdb=" O CYS N 92 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N VAL N 91 " --> pdb=" O SER N 245 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N VAL N 247 " --> pdb=" O VAL N 91 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N ILE N 93 " --> pdb=" O VAL N 247 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N THR N 238 " --> pdb=" O ARG N 229 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N ARG N 229 " --> pdb=" O THR N 238 " (cutoff:3.500A) removed outlier: 3.796A 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 removed outlier: 3.574A pdb=" N ALA N 206 " --> pdb=" O SER N 214 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 65 through 68 removed outlier: 7.496A pdb=" N GLU A 3 " --> pdb=" O GLN A 133 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N PHE A 135 " --> pdb=" O GLU A 3 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N ILE A 5 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N VAL A 137 " --> pdb=" O ILE A 5 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ILE A 7 " --> pdb=" O VAL A 137 " (cutoff:3.500A) removed outlier: 5.655A pdb=" N HIS A 139 " --> pdb=" O ILE A 7 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N VAL A 9 " --> pdb=" O HIS A 139 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N GLN A 133 " --> pdb=" O SER A 165 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N LEU A 167 " --> pdb=" O GLN A 133 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N PHE A 135 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N PHE A 169 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N VAL A 137 " --> pdb=" O PHE A 169 " (cutoff:3.500A) removed outlier: 8.072A pdb=" N ILE A 171 " --> pdb=" O VAL A 137 " (cutoff:3.500A) removed outlier: 8.115A pdb=" N HIS A 139 " --> pdb=" O ILE A 171 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N LYS A 166 " --> pdb=" O CYS A 200 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N PHE A 202 " --> pdb=" O LYS A 166 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N GLU A 168 " --> pdb=" O PHE A 202 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N VAL A 204 " --> pdb=" O GLU A 168 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N SER A 170 " --> pdb=" O VAL A 204 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AB4, first strand: chain 'A' and resid 269 through 272 Processing sheet with id=AB5, first strand: chain 'B' and resid 90 through 92 removed outlier: 8.241A pdb=" N VAL B 91 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N LEU B 65 " --> pdb=" O VAL B 91 " (cutoff:3.500A) removed outlier: 5.892A pdb=" N GLU B 3 " --> pdb=" O LEU B 130 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N GLY B 132 " --> pdb=" O GLU B 3 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N SER B 138 " --> pdb=" O ALA B 9 " (cutoff:3.500A) removed outlier: 7.949A pdb=" N TYR B 200 " --> pdb=" O MET B 164 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N THR B 166 " --> pdb=" O TYR B 200 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N ILE B 202 " --> pdb=" O THR B 166 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N SER B 168 " --> pdb=" O ILE B 202 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N THR B 199 " --> pdb=" O PHE B 266 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N CYS B 201 " --> pdb=" O PRO B 268 " (cutoff:3.500A) removed outlier: 10.304A pdb=" N PHE B 270 " --> pdb=" O CYS B 201 " (cutoff:3.500A) removed outlier: 13.716A pdb=" N ASP B 203 " --> pdb=" O PHE B 270 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N PHE B 265 " --> pdb=" O SER B 371 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N SER B 371 " --> pdb=" O PHE B 265 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N THR B 312 " --> pdb=" O ASN B 370 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 51 through 53 Processing sheet with id=AB7, first strand: chain 'E' and resid 65 through 68 removed outlier: 6.120A pdb=" N GLU E 3 " --> pdb=" O LEU E 132 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N GLY E 134 " --> pdb=" O GLU E 3 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N SER E 140 " --> pdb=" O VAL E 9 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N GLN E 133 " --> pdb=" O SER E 165 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N LEU E 167 " --> pdb=" O GLN E 133 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N PHE E 135 " --> pdb=" O LEU E 167 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N PHE E 169 " --> pdb=" O PHE E 135 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N VAL E 137 " --> pdb=" O PHE E 169 " (cutoff:3.500A) removed outlier: 8.052A pdb=" N ILE E 171 " --> pdb=" O VAL E 137 " (cutoff:3.500A) removed outlier: 8.080A pdb=" N HIS E 139 " --> pdb=" O ILE E 171 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N LYS E 166 " --> pdb=" O CYS E 200 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N PHE E 202 " --> pdb=" O LYS E 166 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N GLU E 168 " --> pdb=" O PHE E 202 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N VAL E 204 " --> pdb=" O GLU E 168 " (cutoff:3.500A) removed outlier: 6.514A 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: 6.023A pdb=" N LEU I 65 " --> pdb=" O VAL I 91 " (cutoff:3.500A) removed outlier: 8.640A pdb=" N ILE I 64 " --> pdb=" O ILE I 4 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N HIS I 6 " --> pdb=" O ILE I 64 " (cutoff:3.500A) removed outlier: 8.058A pdb=" N VAL I 66 " --> pdb=" O HIS I 6 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N GLN I 8 " --> pdb=" O VAL I 66 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N GLU I 3 " --> pdb=" O GLN I 131 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N PHE I 133 " --> pdb=" O GLU I 3 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N VAL I 5 " --> pdb=" O PHE I 133 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N LEU I 135 " --> pdb=" O VAL I 5 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N ILE I 7 " --> pdb=" O LEU I 135 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N HIS I 137 " --> pdb=" O ILE I 7 " (cutoff:3.500A) removed outlier: 7.670A 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: 6.023A pdb=" N LEU I 65 " --> pdb=" O VAL I 91 " (cutoff:3.500A) removed outlier: 8.640A pdb=" N ILE I 64 " --> pdb=" O ILE I 4 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N HIS I 6 " --> pdb=" O ILE I 64 " (cutoff:3.500A) removed outlier: 8.058A pdb=" N VAL I 66 " --> pdb=" O HIS I 6 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N GLN I 8 " --> pdb=" O VAL I 66 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N GLU I 3 " --> pdb=" O GLN I 131 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N PHE I 133 " --> pdb=" O GLU I 3 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N VAL I 5 " --> pdb=" O PHE I 133 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N LEU I 135 " --> pdb=" O VAL I 5 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N ILE I 7 " --> pdb=" O LEU I 135 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N HIS I 137 " --> pdb=" O ILE I 7 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N ALA I 9 " --> pdb=" O HIS I 137 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N PHE I 167 " --> pdb=" O PHE I 133 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N LEU I 135 " --> pdb=" O PHE I 167 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N VAL I 169 " --> pdb=" O LEU I 135 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N HIS I 137 " --> pdb=" O VAL I 169 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N THR I 199 " --> pdb=" O PHE I 266 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N CYS I 201 " --> pdb=" O PRO I 268 " (cutoff:3.500A) removed outlier: 10.126A pdb=" N PHE I 270 " --> pdb=" O CYS I 201 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N PHE I 265 " --> pdb=" O SER I 371 " (cutoff:3.500A) removed outlier: 5.061A 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 53 Processing sheet with id=AC4, first strand: chain 'S' and resid 65 through 68 removed outlier: 8.448A pdb=" N VAL S 66 " --> pdb=" O CYS S 4 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N SER S 6 " --> pdb=" O VAL S 66 " (cutoff:3.500A) removed outlier: 8.038A pdb=" N VAL S 68 " --> pdb=" O SER S 6 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N HIS S 8 " --> pdb=" O VAL S 68 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N GLU S 3 " --> pdb=" O LEU S 132 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N GLY S 134 " --> pdb=" O GLU S 3 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N SER S 140 " --> pdb=" O VAL S 9 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N GLN S 133 " --> pdb=" O SER S 165 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N LEU S 167 " --> pdb=" O GLN S 133 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N PHE S 135 " --> pdb=" O LEU S 167 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N PHE S 169 " --> pdb=" O PHE S 135 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N VAL S 137 " --> pdb=" O PHE S 169 " (cutoff:3.500A) removed outlier: 8.167A pdb=" N ILE S 171 " --> pdb=" O VAL S 137 " (cutoff:3.500A) removed outlier: 8.016A pdb=" N HIS S 139 " --> pdb=" O ILE S 171 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N LYS S 166 " --> pdb=" O CYS S 200 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N PHE S 202 " --> pdb=" O LYS S 166 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N GLU S 168 " --> pdb=" O PHE S 202 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N VAL S 204 " --> pdb=" O GLU S 168 " (cutoff:3.500A) removed outlier: 6.574A 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 1185 hydrogen bonds defined for protein. 3390 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: 7.61 Time building geometry restraints manager: 10.36 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: 4079 1.32 - 1.44: 6441 1.44 - 1.57: 13490 1.57 - 1.70: 38 1.70 - 1.82: 244 Bond restraints: 24292 Sorted by residual: bond pdb=" O3A ANP K 502 " pdb=" PB ANP K 502 " ideal model delta sigma weight residual 1.700 1.554 0.146 2.00e-02 2.50e+03 5.33e+01 bond pdb=" O3A ANP N 501 " pdb=" PB ANP N 501 " ideal model delta sigma weight residual 1.700 1.557 0.143 2.00e-02 2.50e+03 5.11e+01 bond pdb=" N3B ANP K 502 " pdb=" PG ANP K 502 " ideal model delta sigma weight residual 1.795 1.687 0.108 2.00e-02 2.50e+03 2.90e+01 bond pdb=" N3B ANP N 501 " pdb=" PG ANP N 501 " ideal model delta sigma weight residual 1.795 1.694 0.101 2.00e-02 2.50e+03 2.55e+01 bond pdb=" CA SER E 277 " pdb=" CB SER E 277 " ideal model delta sigma weight residual 1.529 1.462 0.068 1.64e-02 3.72e+03 1.70e+01 ... (remaining 24287 not shown) Histogram of bond angle deviations from ideal: 85.13 - 95.43: 8 95.43 - 105.74: 531 105.74 - 116.04: 15289 116.04 - 126.35: 16821 126.35 - 136.65: 325 Bond angle restraints: 32974 Sorted by residual: angle pdb=" O ALA B 271 " pdb=" C ALA B 271 " pdb=" N PRO B 272 " ideal model delta sigma weight residual 121.85 116.80 5.05 7.00e-01 2.04e+00 5.20e+01 angle pdb=" O ALA I 271 " pdb=" C ALA I 271 " pdb=" N PRO I 272 " ideal model delta sigma weight residual 121.85 117.47 4.38 7.00e-01 2.04e+00 3.91e+01 angle pdb=" PB ANP K 502 " pdb=" N3B ANP K 502 " pdb=" PG ANP K 502 " ideal model delta sigma weight residual 126.95 108.88 18.07 3.00e+00 1.11e-01 3.63e+01 angle pdb=" PB ANP N 501 " pdb=" N3B ANP N 501 " pdb=" PG ANP N 501 " ideal model delta sigma weight residual 126.95 111.67 15.28 3.00e+00 1.11e-01 2.59e+01 angle pdb=" CA ALA B 271 " pdb=" C ALA B 271 " pdb=" N PRO B 272 " ideal model delta sigma weight residual 118.16 123.49 -5.33 1.08e+00 8.57e-01 2.44e+01 ... (remaining 32969 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.40: 14012 30.40 - 60.80: 634 60.80 - 91.20: 73 91.20 - 121.60: 20 121.60 - 152.00: 25 Dihedral angle restraints: 14764 sinusoidal: 6106 harmonic: 8658 Sorted by residual: dihedral pdb=" C8 GTP A 501 " pdb=" C1' GTP A 501 " pdb=" N9 GTP A 501 " pdb=" O4' GTP A 501 " ideal model delta sinusoidal sigma weight residual 104.59 -47.40 152.00 1 2.00e+01 2.50e-03 4.52e+01 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 -144.61 -146.12 1 2.00e+01 2.50e-03 4.39e+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 260.87 123.02 137.86 1 2.00e+01 2.50e-03 4.18e+01 ... (remaining 14761 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.106: 3422 0.106 - 0.211: 185 0.211 - 0.317: 8 0.317 - 0.423: 0 0.423 - 0.528: 2 Chirality restraints: 3617 Sorted by residual: chirality pdb=" C18 TA1 B 502 " pdb=" C10 TA1 B 502 " pdb=" C17 TA1 B 502 " pdb=" C20 TA1 B 502 " both_signs ideal model delta sigma weight residual False -3.16 -2.63 -0.53 2.00e-01 2.50e+01 6.98e+00 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 -2.63 -0.53 2.00e-01 2.50e+01 6.98e+00 chirality pdb=" C02 TA1 I 502 " pdb=" C01 TA1 I 502 " pdb=" C10 TA1 I 502 " pdb=" O02 TA1 I 502 " both_signs ideal model delta sigma weight residual False 2.56 2.83 -0.27 2.00e-01 2.50e+01 1.85e+00 ... (remaining 3614 not shown) Planarity restraints: 4288 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C29 TA1 I 502 " 0.073 2.00e-02 2.50e+03 6.03e-02 4.54e+01 pdb=" C30 TA1 I 502 " -0.020 2.00e-02 2.50e+03 pdb=" C31 TA1 I 502 " 0.056 2.00e-02 2.50e+03 pdb=" N01 TA1 I 502 " -0.095 2.00e-02 2.50e+03 pdb=" O14 TA1 I 502 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY N 291 " 0.067 5.00e-02 4.00e+02 1.01e-01 1.63e+01 pdb=" N PRO N 292 " -0.174 5.00e-02 4.00e+02 pdb=" CA PRO N 292 " 0.053 5.00e-02 4.00e+02 pdb=" CD PRO N 292 " 0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY K 291 " 0.059 5.00e-02 4.00e+02 8.93e-02 1.28e+01 pdb=" N PRO K 292 " -0.154 5.00e-02 4.00e+02 pdb=" CA PRO K 292 " 0.047 5.00e-02 4.00e+02 pdb=" CD PRO K 292 " 0.048 5.00e-02 4.00e+02 ... (remaining 4285 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.52: 123 2.52 - 3.12: 17570 3.12 - 3.71: 35523 3.71 - 4.31: 49619 4.31 - 4.90: 85633 Nonbonded interactions: 188468 Sorted by model distance: nonbonded pdb=" O1B GTP E 501 " pdb="MG MG E 502 " model vdw 1.930 2.170 nonbonded pdb=" O1B GTP A 501 " pdb="MG MG A 502 " model vdw 1.939 2.170 nonbonded pdb=" O1G GTP A 501 " pdb="MG MG A 502 " model vdw 1.939 2.170 nonbonded pdb=" OE2 GLU E 71 " pdb="MG MG E 502 " model vdw 1.945 2.170 nonbonded pdb=" OE2 GLU A 71 " pdb="MG MG A 502 " model vdw 1.945 2.170 ... (remaining 188463 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=0.46 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: 3.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.790 Check model and map are aligned: 0.150 Set scattering table: 0.200 Process input model: 66.360 Find NCS groups from input model: 1.780 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: 0.000 Load rotamer database and sin/cos tables:3.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 76.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.146 24292 Z= 0.340 Angle : 0.849 18.068 32974 Z= 0.459 Chirality : 0.050 0.528 3617 Planarity : 0.006 0.104 4288 Dihedral : 18.534 151.997 9210 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.44 % Allowed : 4.21 % Favored : 95.35 % Rotamer: Outliers : 0.94 % Allowed : 14.36 % Favored : 84.70 % Cbeta Deviations : 0.04 % 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: -0.04 (0.15), residues: 2977 helix: 1.17 (0.15), residues: 1229 sheet: -0.14 (0.22), residues: 542 loop : -1.19 (0.17), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 21 HIS 0.007 0.001 HIS I 137 PHE 0.026 0.002 PHE S 255 TYR 0.040 0.001 TYR S 24 ARG 0.015 0.001 ARG N 346 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5954 Ramachandran restraints generated. 2977 Oldfield, 0 Emsley, 2977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5954 Ramachandran restraints generated. 2977 Oldfield, 0 Emsley, 2977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 547 residues out of total 2548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 529 time to evaluate : 2.720 Fit side-chains revert: symmetry clash REVERT: K 127 PHE cc_start: 0.8179 (OUTLIER) cc_final: 0.7942 (t80) REVERT: K 153 ARG cc_start: 0.8481 (mtp85) cc_final: 0.8196 (mtp85) REVERT: K 367 LYS cc_start: 0.8990 (tptt) cc_final: 0.8575 (tptt) REVERT: N 94 PHE cc_start: 0.8294 (m-80) cc_final: 0.7942 (m-80) REVERT: N 98 GLN cc_start: 0.5933 (mt0) cc_final: 0.5716 (mt0) REVERT: A 24 TYR cc_start: 0.8560 (m-80) cc_final: 0.8137 (m-80) REVERT: A 254 GLU cc_start: 0.5547 (mm-30) cc_final: 0.5191 (mm-30) REVERT: B 1 MET cc_start: 0.6184 (tmm) cc_final: 0.4857 (tmm) REVERT: B 48 ASN cc_start: 0.8508 (m-40) cc_final: 0.8068 (p0) REVERT: B 147 MET cc_start: 0.8346 (mtp) cc_final: 0.8121 (mtp) REVERT: B 168 SER cc_start: 0.8876 (p) cc_final: 0.8538 (m) REVERT: B 282 ARG cc_start: 0.8725 (mtp-110) cc_final: 0.8507 (mtp85) REVERT: S 398 MET cc_start: 0.8378 (mtp) cc_final: 0.8054 (mtp) outliers start: 18 outliers final: 8 residues processed: 536 average time/residue: 0.3641 time to fit residues: 301.2127 Evaluate side-chains 506 residues out of total 2548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 497 time to evaluate : 2.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 125 ASP Chi-restraints excluded: chain K residue 126 LEU Chi-restraints excluded: chain K residue 127 PHE Chi-restraints excluded: chain K residue 131 ASN Chi-restraints excluded: chain N residue 333 PRO Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain E residue 249 ASN Chi-restraints excluded: chain I residue 44 LEU Chi-restraints excluded: chain I residue 424 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 249 optimal weight: 4.9990 chunk 224 optimal weight: 0.9980 chunk 124 optimal weight: 2.9990 chunk 76 optimal weight: 0.6980 chunk 151 optimal weight: 4.9990 chunk 119 optimal weight: 3.9990 chunk 232 optimal weight: 4.9990 chunk 89 optimal weight: 0.7980 chunk 141 optimal weight: 0.6980 chunk 172 optimal weight: 2.9990 chunk 268 optimal weight: 0.0270 overall best weight: 0.6438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 70 GLN N 16 ASN N 42 GLN B 48 ASN E 197 HIS E 358 GLN ** I 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 433 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY** S 18 ASN S 101 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.1041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 24292 Z= 0.160 Angle : 0.556 10.941 32974 Z= 0.274 Chirality : 0.043 0.300 3617 Planarity : 0.004 0.093 4288 Dihedral : 12.314 150.263 3621 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.17 % Favored : 96.63 % Rotamer: Outliers : 1.64 % Allowed : 14.83 % Favored : 83.53 % 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: 0.61 (0.16), residues: 2977 helix: 1.80 (0.15), residues: 1243 sheet: 0.30 (0.22), residues: 527 loop : -1.05 (0.17), residues: 1207 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 21 HIS 0.004 0.001 HIS N 59 PHE 0.016 0.001 PHE K 94 TYR 0.047 0.001 TYR S 24 ARG 0.006 0.000 ARG I 241 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5954 Ramachandran restraints generated. 2977 Oldfield, 0 Emsley, 2977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5954 Ramachandran restraints generated. 2977 Oldfield, 0 Emsley, 2977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 544 residues out of total 2548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 508 time to evaluate : 2.855 Fit side-chains revert: symmetry clash REVERT: K 74 TYR cc_start: 0.8125 (t80) cc_final: 0.7859 (t80) REVERT: K 125 ASP cc_start: 0.7984 (t0) cc_final: 0.7028 (t0) REVERT: K 153 ARG cc_start: 0.8464 (mtp85) cc_final: 0.8049 (mtp85) REVERT: K 319 LEU cc_start: 0.8289 (mm) cc_final: 0.8022 (mm) REVERT: K 367 LYS cc_start: 0.8815 (tptt) cc_final: 0.8462 (tppt) REVERT: N 98 GLN cc_start: 0.6110 (mt0) cc_final: 0.5822 (mt0) REVERT: N 288 MET cc_start: 0.8291 (tmm) cc_final: 0.7916 (tpp) REVERT: N 345 LEU cc_start: 0.9278 (mp) cc_final: 0.9000 (mm) REVERT: A 123 ARG cc_start: 0.8035 (ttp80) cc_final: 0.7697 (ttt180) REVERT: A 408 TYR cc_start: 0.8684 (m-80) cc_final: 0.8180 (m-80) REVERT: B 1 MET cc_start: 0.6179 (tmm) cc_final: 0.5222 (tmm) REVERT: B 3 GLU cc_start: 0.8196 (mp0) cc_final: 0.7707 (mp0) REVERT: B 48 ASN cc_start: 0.8519 (m110) cc_final: 0.8231 (p0) REVERT: B 279 GLN cc_start: 0.8344 (OUTLIER) cc_final: 0.7877 (tp40) REVERT: B 423 GLN cc_start: 0.8020 (mt0) cc_final: 0.7687 (tm-30) REVERT: E 260 VAL cc_start: 0.8861 (t) cc_final: 0.8459 (m) REVERT: I 31 ASP cc_start: 0.8198 (t0) cc_final: 0.7826 (t0) REVERT: I 299 MET cc_start: 0.8648 (mmp) cc_final: 0.8408 (mmt) REVERT: I 342 VAL cc_start: 0.8925 (t) cc_final: 0.8667 (m) REVERT: S 157 LEU cc_start: 0.8734 (mt) cc_final: 0.8338 (mp) REVERT: S 398 MET cc_start: 0.8219 (mtp) cc_final: 0.7905 (mtp) outliers start: 36 outliers final: 24 residues processed: 520 average time/residue: 0.3489 time to fit residues: 283.3862 Evaluate side-chains 494 residues out of total 2548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 469 time to evaluate : 2.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 256 ASP Chi-restraints excluded: chain N residue 6 VAL Chi-restraints excluded: chain N residue 118 ILE Chi-restraints excluded: chain N residue 354 ILE Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 279 GLN Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain I residue 44 LEU Chi-restraints excluded: chain I residue 118 ASP Chi-restraints excluded: chain I residue 274 THR Chi-restraints excluded: chain I residue 415 MET Chi-restraints excluded: chain I residue 424 GLN Chi-restraints excluded: chain S residue 77 GLU Chi-restraints excluded: chain S residue 98 ASP Chi-restraints excluded: chain S residue 227 LEU Chi-restraints excluded: chain S residue 259 LEU 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 397 LEU Chi-restraints excluded: chain S residue 413 MET Chi-restraints excluded: chain S residue 419 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 149 optimal weight: 0.6980 chunk 83 optimal weight: 0.0050 chunk 223 optimal weight: 0.7980 chunk 183 optimal weight: 2.9990 chunk 74 optimal weight: 0.4980 chunk 269 optimal weight: 4.9990 chunk 290 optimal weight: 4.9990 chunk 239 optimal weight: 4.9990 chunk 267 optimal weight: 8.9990 chunk 91 optimal weight: 5.9990 chunk 216 optimal weight: 4.9990 overall best weight: 0.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 83 GLN N 42 GLN A 301 GLN E 107 HIS I 426 GLN ** I 433 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY** S 301 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.1364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 24292 Z= 0.183 Angle : 0.526 8.248 32974 Z= 0.261 Chirality : 0.043 0.476 3617 Planarity : 0.004 0.088 4288 Dihedral : 9.740 147.333 3606 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.64 % Favored : 96.16 % Rotamer: Outliers : 2.19 % Allowed : 15.26 % Favored : 82.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.16), residues: 2977 helix: 2.04 (0.15), residues: 1234 sheet: 0.46 (0.22), residues: 533 loop : -0.97 (0.17), residues: 1210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 21 HIS 0.003 0.001 HIS B 137 PHE 0.031 0.001 PHE K 94 TYR 0.041 0.001 TYR S 24 ARG 0.006 0.000 ARG E 123 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5954 Ramachandran restraints generated. 2977 Oldfield, 0 Emsley, 2977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5954 Ramachandran restraints generated. 2977 Oldfield, 0 Emsley, 2977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 556 residues out of total 2548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 506 time to evaluate : 2.571 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 125 ASP cc_start: 0.7430 (t0) cc_final: 0.6973 (t0) REVERT: K 153 ARG cc_start: 0.8443 (mtp85) cc_final: 0.8039 (mtp85) REVERT: N 98 GLN cc_start: 0.6138 (mt0) cc_final: 0.5762 (mt0) REVERT: N 288 MET cc_start: 0.8204 (tmm) cc_final: 0.7889 (tpp) REVERT: N 319 LEU cc_start: 0.8721 (mm) cc_final: 0.8506 (mt) REVERT: A 123 ARG cc_start: 0.8013 (ttp80) cc_final: 0.7673 (ttt180) REVERT: A 147 SER cc_start: 0.8169 (t) cc_final: 0.7841 (m) REVERT: A 254 GLU cc_start: 0.5579 (mm-30) cc_final: 0.4752 (mm-30) REVERT: B 1 MET cc_start: 0.5951 (tmm) cc_final: 0.4900 (tmm) REVERT: B 3 GLU cc_start: 0.8223 (mp0) cc_final: 0.7667 (mp0) REVERT: B 48 ASN cc_start: 0.8531 (m110) cc_final: 0.8246 (p0) REVERT: B 147 MET cc_start: 0.8409 (mtp) cc_final: 0.8111 (mtp) REVERT: B 279 GLN cc_start: 0.8353 (OUTLIER) cc_final: 0.7874 (tp40) REVERT: B 415 MET cc_start: 0.8623 (tpp) cc_final: 0.8353 (ttt) REVERT: B 423 GLN cc_start: 0.8027 (mt0) cc_final: 0.7704 (tm-30) REVERT: E 260 VAL cc_start: 0.8882 (t) cc_final: 0.8451 (m) REVERT: I 31 ASP cc_start: 0.8234 (t0) cc_final: 0.7855 (t0) REVERT: I 299 MET cc_start: 0.8749 (mmp) cc_final: 0.8483 (mmt) REVERT: I 342 VAL cc_start: 0.8908 (t) cc_final: 0.8639 (m) REVERT: I 359 ARG cc_start: 0.8183 (mtp85) cc_final: 0.7974 (mtp85) REVERT: I 401 GLU cc_start: 0.8454 (mm-30) cc_final: 0.8211 (mm-30) outliers start: 50 outliers final: 34 residues processed: 524 average time/residue: 0.3458 time to fit residues: 282.8058 Evaluate side-chains 513 residues out of total 2548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 478 time to evaluate : 2.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 70 GLN Chi-restraints excluded: chain K residue 108 MET Chi-restraints excluded: chain K residue 188 SER Chi-restraints excluded: chain K residue 226 THR Chi-restraints excluded: chain K residue 256 ASP Chi-restraints excluded: chain N residue 6 VAL Chi-restraints excluded: chain N residue 118 ILE Chi-restraints excluded: chain N residue 195 LEU Chi-restraints excluded: chain N residue 208 THR Chi-restraints excluded: chain N residue 354 ILE Chi-restraints excluded: chain A residue 98 ASP Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain A residue 258 ASN Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain B residue 114 ASP Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 279 GLN Chi-restraints excluded: chain E residue 190 THR Chi-restraints excluded: chain I residue 44 LEU Chi-restraints excluded: chain I residue 118 ASP Chi-restraints excluded: chain I residue 313 VAL Chi-restraints excluded: chain I residue 415 MET Chi-restraints excluded: chain I residue 424 GLN Chi-restraints excluded: chain S residue 50 ASN Chi-restraints excluded: chain S residue 77 GLU Chi-restraints excluded: chain S residue 98 ASP Chi-restraints excluded: chain S residue 227 LEU Chi-restraints excluded: chain S residue 259 LEU 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 Chi-restraints excluded: chain S residue 419 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 266 optimal weight: 10.0000 chunk 202 optimal weight: 3.9990 chunk 139 optimal weight: 6.9990 chunk 29 optimal weight: 20.0000 chunk 128 optimal weight: 0.8980 chunk 180 optimal weight: 0.9990 chunk 270 optimal weight: 0.0010 chunk 286 optimal weight: 4.9990 chunk 141 optimal weight: 4.9990 chunk 256 optimal weight: 1.9990 chunk 77 optimal weight: 5.9990 overall best weight: 1.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 42 GLN N 83 GLN B 204 ASN ** B 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 249 ASN I 195 ASN I 426 GLN ** I 433 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY** S 8 HIS S 35 GLN S 300 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.1583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 24292 Z= 0.250 Angle : 0.541 9.242 32974 Z= 0.269 Chirality : 0.044 0.367 3617 Planarity : 0.004 0.085 4288 Dihedral : 9.379 145.366 3606 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.87 % Favored : 95.92 % Rotamer: Outliers : 2.93 % Allowed : 16.04 % Favored : 81.03 % 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: 0.88 (0.16), residues: 2977 helix: 2.09 (0.15), residues: 1232 sheet: 0.52 (0.22), residues: 533 loop : -1.00 (0.17), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 21 HIS 0.007 0.001 HIS B 137 PHE 0.026 0.001 PHE K 94 TYR 0.026 0.001 TYR S 24 ARG 0.005 0.000 ARG N 346 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5954 Ramachandran restraints generated. 2977 Oldfield, 0 Emsley, 2977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5954 Ramachandran restraints generated. 2977 Oldfield, 0 Emsley, 2977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 582 residues out of total 2548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 513 time to evaluate : 2.698 Fit side-chains REVERT: K 125 ASP cc_start: 0.7417 (t0) cc_final: 0.6916 (t0) REVERT: K 129 ARG cc_start: 0.7616 (ttm170) cc_final: 0.7256 (ttm170) REVERT: K 153 ARG cc_start: 0.8443 (mtp85) cc_final: 0.8039 (mtp85) REVERT: K 201 LYS cc_start: 0.8941 (OUTLIER) cc_final: 0.8397 (tptp) REVERT: K 244 ILE cc_start: 0.8270 (mt) cc_final: 0.7988 (tt) REVERT: N 76 ASP cc_start: 0.8545 (OUTLIER) cc_final: 0.8333 (t0) REVERT: N 98 GLN cc_start: 0.6139 (mt0) cc_final: 0.5801 (mt0) REVERT: N 243 LYS cc_start: 0.8535 (mtpp) cc_final: 0.7851 (mtpp) REVERT: N 288 MET cc_start: 0.8166 (tmm) cc_final: 0.7868 (tpp) REVERT: N 310 VAL cc_start: 0.9074 (m) cc_final: 0.8816 (p) REVERT: A 123 ARG cc_start: 0.8058 (ttp80) cc_final: 0.7721 (ttt180) REVERT: A 147 SER cc_start: 0.8310 (t) cc_final: 0.7921 (m) REVERT: A 254 GLU cc_start: 0.5648 (mm-30) cc_final: 0.4781 (mm-30) REVERT: A 275 VAL cc_start: 0.8863 (t) cc_final: 0.8647 (p) REVERT: A 305 CYS cc_start: 0.8392 (OUTLIER) cc_final: 0.8170 (p) REVERT: B 1 MET cc_start: 0.5894 (OUTLIER) cc_final: 0.4827 (tmm) REVERT: B 3 GLU cc_start: 0.8233 (mp0) cc_final: 0.7660 (mp0) REVERT: B 48 ASN cc_start: 0.8549 (m110) cc_final: 0.8265 (p0) REVERT: B 219 THR cc_start: 0.9275 (m) cc_final: 0.8920 (p) REVERT: B 257 MET cc_start: 0.8458 (mmm) cc_final: 0.7969 (mmm) REVERT: B 279 GLN cc_start: 0.8347 (OUTLIER) cc_final: 0.7855 (tp40) REVERT: B 415 MET cc_start: 0.8684 (tpp) cc_final: 0.8368 (ttm) REVERT: B 423 GLN cc_start: 0.8019 (mt0) cc_final: 0.7689 (tm-30) REVERT: E 84 ARG cc_start: 0.8311 (ptt-90) cc_final: 0.7939 (ptp90) REVERT: I 31 ASP cc_start: 0.8313 (t0) cc_final: 0.7940 (t0) REVERT: I 209 ASP cc_start: 0.8086 (OUTLIER) cc_final: 0.7841 (t0) REVERT: I 246 LEU cc_start: 0.8599 (tp) cc_final: 0.8179 (tt) REVERT: I 279 GLN cc_start: 0.7924 (tp40) cc_final: 0.7705 (tp40) REVERT: I 342 VAL cc_start: 0.8933 (t) cc_final: 0.8691 (m) REVERT: I 401 GLU cc_start: 0.8442 (mm-30) cc_final: 0.8158 (mm-30) outliers start: 69 outliers final: 45 residues processed: 538 average time/residue: 0.3509 time to fit residues: 292.1673 Evaluate side-chains 545 residues out of total 2548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 494 time to evaluate : 2.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 108 MET Chi-restraints excluded: chain K residue 188 SER Chi-restraints excluded: chain K residue 194 ASP Chi-restraints excluded: chain K residue 201 LYS Chi-restraints excluded: chain K residue 226 THR Chi-restraints excluded: chain K residue 256 ASP Chi-restraints excluded: chain N residue 53 ASP Chi-restraints excluded: chain N residue 76 ASP Chi-restraints excluded: chain N residue 118 ILE Chi-restraints excluded: chain N residue 192 ILE Chi-restraints excluded: chain N residue 195 LEU Chi-restraints excluded: chain N residue 208 THR Chi-restraints excluded: chain N residue 245 SER Chi-restraints excluded: chain N residue 354 ILE Chi-restraints excluded: chain A residue 98 ASP Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain A residue 258 ASN Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain A residue 434 GLU Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 279 GLN Chi-restraints excluded: chain E residue 190 THR Chi-restraints excluded: chain E residue 245 ASP Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain I residue 44 LEU Chi-restraints excluded: chain I residue 118 ASP Chi-restraints excluded: chain I residue 209 ASP Chi-restraints excluded: chain I residue 313 VAL Chi-restraints excluded: chain I residue 415 MET Chi-restraints excluded: chain I residue 424 GLN Chi-restraints excluded: chain S residue 26 LEU Chi-restraints excluded: chain S residue 50 ASN Chi-restraints excluded: chain S residue 77 GLU Chi-restraints excluded: chain S residue 98 ASP Chi-restraints excluded: chain S residue 178 SER Chi-restraints excluded: chain S residue 227 LEU Chi-restraints excluded: chain S residue 239 THR Chi-restraints excluded: chain S residue 259 LEU 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 Chi-restraints excluded: chain S residue 419 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 238 optimal weight: 3.9990 chunk 162 optimal weight: 1.9990 chunk 4 optimal weight: 7.9990 chunk 213 optimal weight: 2.9990 chunk 118 optimal weight: 4.9990 chunk 244 optimal weight: 3.9990 chunk 197 optimal weight: 0.0060 chunk 0 optimal weight: 8.9990 chunk 146 optimal weight: 0.9990 chunk 256 optimal weight: 5.9990 chunk 72 optimal weight: 3.9990 overall best weight: 2.0004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 42 GLN N 83 GLN B 165 ASN ** B 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 101 ASN I 426 GLN ** I 433 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY** S 300 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.1744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 24292 Z= 0.301 Angle : 0.552 8.162 32974 Z= 0.277 Chirality : 0.044 0.305 3617 Planarity : 0.004 0.083 4288 Dihedral : 9.294 146.913 3606 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.77 % Favored : 96.06 % Rotamer: Outliers : 3.36 % Allowed : 16.51 % Favored : 80.13 % 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: 2977 helix: 2.04 (0.15), residues: 1233 sheet: 0.45 (0.22), residues: 533 loop : -1.02 (0.17), residues: 1211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 21 HIS 0.009 0.001 HIS B 137 PHE 0.026 0.002 PHE K 94 TYR 0.014 0.001 TYR S 24 ARG 0.006 0.000 ARG N 346 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5954 Ramachandran restraints generated. 2977 Oldfield, 0 Emsley, 2977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5954 Ramachandran restraints generated. 2977 Oldfield, 0 Emsley, 2977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 582 residues out of total 2548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 502 time to evaluate : 2.430 Fit side-chains revert: symmetry clash REVERT: K 76 ASP cc_start: 0.7897 (OUTLIER) cc_final: 0.7680 (t0) REVERT: K 82 LEU cc_start: 0.8803 (tp) cc_final: 0.8590 (tp) REVERT: K 125 ASP cc_start: 0.7499 (t0) cc_final: 0.7041 (t0) REVERT: K 126 LEU cc_start: 0.8352 (OUTLIER) cc_final: 0.8088 (tp) REVERT: K 153 ARG cc_start: 0.8442 (mtp85) cc_final: 0.8048 (mtp85) REVERT: K 201 LYS cc_start: 0.8943 (OUTLIER) cc_final: 0.8399 (tptp) REVERT: K 244 ILE cc_start: 0.8305 (mt) cc_final: 0.8013 (tt) REVERT: N 76 ASP cc_start: 0.8535 (OUTLIER) cc_final: 0.8265 (t0) REVERT: N 98 GLN cc_start: 0.6204 (mt0) cc_final: 0.5888 (mt0) REVERT: N 243 LYS cc_start: 0.8524 (mtpp) cc_final: 0.7847 (mtpp) REVERT: N 288 MET cc_start: 0.8182 (tmm) cc_final: 0.7886 (tpp) REVERT: A 147 SER cc_start: 0.8361 (t) cc_final: 0.7933 (m) REVERT: A 254 GLU cc_start: 0.5744 (mm-30) cc_final: 0.5437 (mm-30) REVERT: A 305 CYS cc_start: 0.8411 (OUTLIER) cc_final: 0.8206 (p) REVERT: B 1 MET cc_start: 0.5865 (OUTLIER) cc_final: 0.4727 (tmm) REVERT: B 3 GLU cc_start: 0.8199 (mp0) cc_final: 0.7547 (mp0) REVERT: B 48 ASN cc_start: 0.8557 (m110) cc_final: 0.8254 (p0) REVERT: B 219 THR cc_start: 0.9258 (m) cc_final: 0.8966 (p) REVERT: B 257 MET cc_start: 0.8476 (mmm) cc_final: 0.7965 (mmm) REVERT: B 279 GLN cc_start: 0.8343 (OUTLIER) cc_final: 0.7839 (tp40) REVERT: B 423 GLN cc_start: 0.8026 (mt0) cc_final: 0.7727 (tm-30) REVERT: E 84 ARG cc_start: 0.8361 (ptt-90) cc_final: 0.7922 (ptp90) REVERT: E 260 VAL cc_start: 0.8903 (t) cc_final: 0.8502 (m) REVERT: E 265 ILE cc_start: 0.8805 (pt) cc_final: 0.8432 (mt) REVERT: E 392 ASP cc_start: 0.8203 (m-30) cc_final: 0.7820 (m-30) REVERT: E 414 GLU cc_start: 0.8042 (pm20) cc_final: 0.7813 (pm20) REVERT: I 31 ASP cc_start: 0.8367 (t0) cc_final: 0.7954 (t0) REVERT: I 209 ASP cc_start: 0.8100 (OUTLIER) cc_final: 0.7846 (t0) REVERT: I 342 VAL cc_start: 0.8950 (t) cc_final: 0.8736 (m) REVERT: S 242 LEU cc_start: 0.9043 (OUTLIER) cc_final: 0.8825 (pp) REVERT: S 297 GLU cc_start: 0.8166 (mm-30) cc_final: 0.7946 (mm-30) outliers start: 80 outliers final: 53 residues processed: 537 average time/residue: 0.3427 time to fit residues: 286.8605 Evaluate side-chains 545 residues out of total 2548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 483 time to evaluate : 2.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 76 ASP Chi-restraints excluded: chain K residue 108 MET Chi-restraints excluded: chain K residue 126 LEU Chi-restraints excluded: chain K residue 188 SER Chi-restraints excluded: chain K residue 194 ASP Chi-restraints excluded: chain K residue 201 LYS Chi-restraints excluded: chain K residue 252 SER Chi-restraints excluded: chain K residue 256 ASP Chi-restraints excluded: chain N residue 53 ASP Chi-restraints excluded: chain N residue 76 ASP Chi-restraints excluded: chain N residue 91 VAL Chi-restraints excluded: chain N residue 118 ILE Chi-restraints excluded: chain N residue 195 LEU Chi-restraints excluded: chain N residue 208 THR Chi-restraints excluded: chain N residue 245 SER Chi-restraints excluded: chain N residue 258 THR Chi-restraints excluded: chain N residue 354 ILE Chi-restraints excluded: chain A residue 2 ARG Chi-restraints excluded: chain A residue 98 ASP Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain A residue 258 ASN Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain A residue 434 GLU Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 114 ASP Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 279 GLN Chi-restraints excluded: chain B residue 336 LYS Chi-restraints excluded: chain B residue 417 ASP Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 245 ASP Chi-restraints excluded: chain E residue 295 CYS Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain I residue 118 ASP Chi-restraints excluded: chain I residue 209 ASP Chi-restraints excluded: chain I residue 313 VAL Chi-restraints excluded: chain I residue 415 MET Chi-restraints excluded: chain I residue 424 GLN Chi-restraints excluded: chain S residue 26 LEU Chi-restraints excluded: chain S residue 50 ASN Chi-restraints excluded: chain S residue 98 ASP Chi-restraints excluded: chain S residue 178 SER Chi-restraints excluded: chain S residue 227 LEU Chi-restraints excluded: chain S residue 239 THR Chi-restraints excluded: chain S residue 242 LEU Chi-restraints excluded: chain S residue 259 LEU 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 Chi-restraints excluded: chain S residue 419 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 96 optimal weight: 2.9990 chunk 257 optimal weight: 7.9990 chunk 56 optimal weight: 9.9990 chunk 167 optimal weight: 10.0000 chunk 70 optimal weight: 9.9990 chunk 286 optimal weight: 3.9990 chunk 237 optimal weight: 3.9990 chunk 132 optimal weight: 0.8980 chunk 23 optimal weight: 9.9990 chunk 94 optimal weight: 0.7980 chunk 150 optimal weight: 0.0970 overall best weight: 1.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 42 GLN B 165 ASN ** B 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 249 ASN ** I 433 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY** S 18 ASN S 35 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.1883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 24292 Z= 0.272 Angle : 0.548 10.165 32974 Z= 0.275 Chirality : 0.044 0.274 3617 Planarity : 0.004 0.081 4288 Dihedral : 9.146 148.300 3604 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.04 % Favored : 95.79 % Rotamer: Outliers : 3.43 % Allowed : 16.71 % Favored : 79.86 % 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: 0.78 (0.16), residues: 2977 helix: 2.01 (0.15), residues: 1233 sheet: 0.43 (0.22), residues: 533 loop : -1.04 (0.17), residues: 1211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 21 HIS 0.008 0.001 HIS B 137 PHE 0.025 0.002 PHE K 94 TYR 0.018 0.001 TYR S 24 ARG 0.006 0.000 ARG N 346 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5954 Ramachandran restraints generated. 2977 Oldfield, 0 Emsley, 2977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5954 Ramachandran restraints generated. 2977 Oldfield, 0 Emsley, 2977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 579 residues out of total 2548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 497 time to evaluate : 2.481 Fit side-chains REVERT: K 125 ASP cc_start: 0.7456 (t0) cc_final: 0.7113 (t0) REVERT: K 126 LEU cc_start: 0.8351 (OUTLIER) cc_final: 0.8107 (tp) REVERT: K 153 ARG cc_start: 0.8438 (mtp85) cc_final: 0.8037 (mtp85) REVERT: K 201 LYS cc_start: 0.8918 (OUTLIER) cc_final: 0.8367 (tptp) REVERT: K 244 ILE cc_start: 0.8334 (mt) cc_final: 0.8051 (tt) REVERT: N 76 ASP cc_start: 0.8494 (OUTLIER) cc_final: 0.8221 (t0) REVERT: N 81 MET cc_start: 0.7972 (ttm) cc_final: 0.7757 (ttm) REVERT: N 98 GLN cc_start: 0.6236 (mt0) cc_final: 0.5910 (mt0) REVERT: N 243 LYS cc_start: 0.8513 (mtpp) cc_final: 0.7838 (mtpp) REVERT: N 288 MET cc_start: 0.8172 (tmm) cc_final: 0.7881 (tpp) REVERT: A 147 SER cc_start: 0.8352 (t) cc_final: 0.7952 (m) REVERT: A 254 GLU cc_start: 0.5707 (mm-30) cc_final: 0.5092 (mm-30) REVERT: A 408 TYR cc_start: 0.8666 (m-80) cc_final: 0.8291 (m-80) REVERT: B 1 MET cc_start: 0.5883 (OUTLIER) cc_final: 0.4727 (tmm) REVERT: B 3 GLU cc_start: 0.8181 (mp0) cc_final: 0.7502 (mp0) REVERT: B 48 ASN cc_start: 0.8545 (m110) cc_final: 0.8239 (p0) REVERT: B 170 MET cc_start: 0.8434 (mtt) cc_final: 0.8088 (mtt) REVERT: B 219 THR cc_start: 0.9288 (m) cc_final: 0.8976 (p) REVERT: B 257 MET cc_start: 0.8468 (mmm) cc_final: 0.7948 (mmm) REVERT: B 423 GLN cc_start: 0.8034 (mt0) cc_final: 0.7752 (tm-30) REVERT: E 84 ARG cc_start: 0.8366 (ptt-90) cc_final: 0.7905 (ptp90) REVERT: E 242 LEU cc_start: 0.9066 (OUTLIER) cc_final: 0.8800 (pp) REVERT: E 265 ILE cc_start: 0.8794 (pt) cc_final: 0.8391 (mt) REVERT: E 392 ASP cc_start: 0.8186 (m-30) cc_final: 0.7820 (m-30) REVERT: E 414 GLU cc_start: 0.8037 (pm20) cc_final: 0.7790 (pm20) REVERT: I 31 ASP cc_start: 0.8375 (t0) cc_final: 0.7983 (t0) REVERT: I 209 ASP cc_start: 0.8098 (OUTLIER) cc_final: 0.7848 (t0) REVERT: I 342 VAL cc_start: 0.8938 (t) cc_final: 0.8726 (m) REVERT: I 401 GLU cc_start: 0.8412 (mm-30) cc_final: 0.8152 (mm-30) REVERT: S 242 LEU cc_start: 0.9039 (OUTLIER) cc_final: 0.8825 (pp) outliers start: 82 outliers final: 61 residues processed: 532 average time/residue: 0.3386 time to fit residues: 281.7506 Evaluate side-chains 549 residues out of total 2548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 481 time to evaluate : 2.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 106 THR Chi-restraints excluded: chain K residue 108 MET Chi-restraints excluded: chain K residue 126 LEU Chi-restraints excluded: chain K residue 188 SER Chi-restraints excluded: chain K residue 194 ASP Chi-restraints excluded: chain K residue 201 LYS Chi-restraints excluded: chain K residue 252 SER Chi-restraints excluded: chain K residue 256 ASP Chi-restraints excluded: chain K residue 331 LEU Chi-restraints excluded: chain N residue 53 ASP Chi-restraints excluded: chain N residue 76 ASP Chi-restraints excluded: chain N residue 91 VAL Chi-restraints excluded: chain N residue 118 ILE Chi-restraints excluded: chain N residue 192 ILE Chi-restraints excluded: chain N residue 195 LEU Chi-restraints excluded: chain N residue 208 THR Chi-restraints excluded: chain N residue 258 THR Chi-restraints excluded: chain N residue 354 ILE Chi-restraints excluded: chain A residue 2 ARG Chi-restraints excluded: chain A residue 98 ASP Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain A residue 258 ASN 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 349 THR Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 336 LYS Chi-restraints excluded: chain B residue 417 ASP Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 178 SER Chi-restraints excluded: chain E residue 242 LEU Chi-restraints excluded: chain E residue 245 ASP Chi-restraints excluded: chain E residue 249 ASN Chi-restraints excluded: chain E residue 295 CYS Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain I residue 118 ASP Chi-restraints excluded: chain I residue 209 ASP Chi-restraints excluded: chain I residue 293 MET Chi-restraints excluded: chain I residue 313 VAL Chi-restraints excluded: chain I residue 415 MET Chi-restraints excluded: chain I residue 424 GLN Chi-restraints excluded: chain S residue 26 LEU Chi-restraints excluded: chain S residue 50 ASN Chi-restraints excluded: chain S residue 77 GLU Chi-restraints excluded: chain S residue 98 ASP Chi-restraints excluded: chain S residue 119 LEU Chi-restraints excluded: chain S residue 227 LEU Chi-restraints excluded: chain S residue 239 THR Chi-restraints excluded: chain S residue 242 LEU Chi-restraints excluded: chain S residue 259 LEU 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 Chi-restraints excluded: chain S residue 419 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 276 optimal weight: 0.9980 chunk 32 optimal weight: 5.9990 chunk 163 optimal weight: 5.9990 chunk 209 optimal weight: 4.9990 chunk 162 optimal weight: 3.9990 chunk 241 optimal weight: 1.9990 chunk 159 optimal weight: 2.9990 chunk 285 optimal weight: 0.9990 chunk 178 optimal weight: 1.9990 chunk 173 optimal weight: 4.9990 chunk 131 optimal weight: 3.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 83 GLN N 42 GLN B 165 ASN E 249 ASN S 18 ASN ** S 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.1951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 24292 Z= 0.276 Angle : 0.563 12.820 32974 Z= 0.280 Chirality : 0.044 0.254 3617 Planarity : 0.004 0.080 4288 Dihedral : 9.080 149.029 3604 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.01 % Favored : 95.82 % Rotamer: Outliers : 3.24 % Allowed : 17.68 % Favored : 79.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.16), residues: 2977 helix: 2.03 (0.15), residues: 1233 sheet: 0.43 (0.22), residues: 533 loop : -1.06 (0.17), residues: 1211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 21 HIS 0.008 0.001 HIS B 137 PHE 0.025 0.002 PHE K 94 TYR 0.018 0.001 TYR S 24 ARG 0.006 0.000 ARG E 123 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5954 Ramachandran restraints generated. 2977 Oldfield, 0 Emsley, 2977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5954 Ramachandran restraints generated. 2977 Oldfield, 0 Emsley, 2977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 566 residues out of total 2548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 489 time to evaluate : 2.642 Fit side-chains REVERT: K 125 ASP cc_start: 0.7477 (t0) cc_final: 0.6947 (t0) REVERT: K 126 LEU cc_start: 0.8311 (tt) cc_final: 0.8010 (tp) REVERT: K 153 ARG cc_start: 0.8437 (mtp85) cc_final: 0.8043 (mtp85) REVERT: K 201 LYS cc_start: 0.8920 (OUTLIER) cc_final: 0.8363 (tptp) REVERT: K 244 ILE cc_start: 0.8345 (mt) cc_final: 0.8049 (tt) REVERT: N 76 ASP cc_start: 0.8470 (OUTLIER) cc_final: 0.8200 (t0) REVERT: N 81 MET cc_start: 0.7908 (ttm) cc_final: 0.7673 (ttm) REVERT: N 98 GLN cc_start: 0.6213 (mt0) cc_final: 0.5871 (mt0) REVERT: N 243 LYS cc_start: 0.8497 (mtpp) cc_final: 0.7859 (mtpp) REVERT: N 288 MET cc_start: 0.8163 (tmm) cc_final: 0.7868 (tpp) REVERT: N 310 VAL cc_start: 0.9070 (m) cc_final: 0.8800 (p) REVERT: A 3 GLU cc_start: 0.7805 (pm20) cc_final: 0.7434 (pm20) REVERT: A 147 SER cc_start: 0.8361 (t) cc_final: 0.7945 (m) REVERT: A 254 GLU cc_start: 0.5708 (mm-30) cc_final: 0.5057 (mm-30) REVERT: B 1 MET cc_start: 0.5887 (OUTLIER) cc_final: 0.4793 (tmm) REVERT: B 3 GLU cc_start: 0.8193 (mp0) cc_final: 0.7488 (mp0) REVERT: B 48 ASN cc_start: 0.8548 (m110) cc_final: 0.8266 (p0) REVERT: B 170 MET cc_start: 0.8434 (mtt) cc_final: 0.8091 (mtt) REVERT: B 219 THR cc_start: 0.9287 (m) cc_final: 0.8989 (p) REVERT: B 257 MET cc_start: 0.8450 (mmm) cc_final: 0.7919 (mmm) REVERT: B 415 MET cc_start: 0.8641 (tpp) cc_final: 0.8129 (ttp) REVERT: B 423 GLN cc_start: 0.8080 (mt0) cc_final: 0.7765 (tm-30) REVERT: E 84 ARG cc_start: 0.8370 (ptt-90) cc_final: 0.7896 (ptp90) REVERT: E 242 LEU cc_start: 0.9069 (OUTLIER) cc_final: 0.8822 (pp) REVERT: E 260 VAL cc_start: 0.8887 (t) cc_final: 0.8515 (m) REVERT: E 392 ASP cc_start: 0.8214 (m-30) cc_final: 0.7861 (m-30) REVERT: E 414 GLU cc_start: 0.8075 (pm20) cc_final: 0.7833 (pm20) REVERT: I 31 ASP cc_start: 0.8384 (t0) cc_final: 0.7995 (t0) REVERT: I 209 ASP cc_start: 0.8095 (OUTLIER) cc_final: 0.7847 (t0) REVERT: I 342 VAL cc_start: 0.8931 (t) cc_final: 0.8727 (m) REVERT: I 401 GLU cc_start: 0.8397 (mm-30) cc_final: 0.8128 (mm-30) REVERT: S 242 LEU cc_start: 0.9039 (OUTLIER) cc_final: 0.8824 (pp) outliers start: 77 outliers final: 60 residues processed: 525 average time/residue: 0.3436 time to fit residues: 282.0694 Evaluate side-chains 549 residues out of total 2548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 483 time to evaluate : 2.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 108 MET Chi-restraints excluded: chain K residue 194 ASP Chi-restraints excluded: chain K residue 201 LYS Chi-restraints excluded: chain K residue 252 SER Chi-restraints excluded: chain K residue 256 ASP Chi-restraints excluded: chain N residue 53 ASP Chi-restraints excluded: chain N residue 76 ASP Chi-restraints excluded: chain N residue 91 VAL Chi-restraints excluded: chain N residue 118 ILE Chi-restraints excluded: chain N residue 195 LEU Chi-restraints excluded: chain N residue 208 THR Chi-restraints excluded: chain N residue 245 SER Chi-restraints excluded: chain N residue 258 THR Chi-restraints excluded: chain N residue 354 ILE Chi-restraints excluded: chain A residue 2 ARG Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 98 ASP Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain A residue 258 ASN Chi-restraints excluded: chain A residue 334 THR 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 391 LEU Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 279 GLN Chi-restraints excluded: chain B residue 336 LYS Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 178 SER Chi-restraints excluded: chain E residue 242 LEU Chi-restraints excluded: chain E residue 295 CYS Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain I residue 118 ASP Chi-restraints excluded: chain I residue 209 ASP Chi-restraints excluded: chain I residue 293 MET Chi-restraints excluded: chain I residue 313 VAL Chi-restraints excluded: chain I residue 415 MET Chi-restraints excluded: chain I residue 424 GLN Chi-restraints excluded: chain S residue 26 LEU Chi-restraints excluded: chain S residue 50 ASN Chi-restraints excluded: chain S residue 77 GLU Chi-restraints excluded: chain S residue 98 ASP Chi-restraints excluded: chain S residue 119 LEU Chi-restraints excluded: chain S residue 226 ASN Chi-restraints excluded: chain S residue 227 LEU Chi-restraints excluded: chain S residue 239 THR Chi-restraints excluded: chain S residue 242 LEU Chi-restraints excluded: chain S residue 259 LEU 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 381 THR Chi-restraints excluded: chain S residue 398 MET Chi-restraints excluded: chain S residue 413 MET Chi-restraints excluded: chain S residue 419 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 176 optimal weight: 4.9990 chunk 113 optimal weight: 0.3980 chunk 170 optimal weight: 0.7980 chunk 85 optimal weight: 0.2980 chunk 56 optimal weight: 2.9990 chunk 55 optimal weight: 0.9990 chunk 181 optimal weight: 0.0020 chunk 194 optimal weight: 2.9990 chunk 141 optimal weight: 0.9980 chunk 26 optimal weight: 6.9990 chunk 224 optimal weight: 2.9990 overall best weight: 0.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 42 GLN A 256 GLN ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 131 GLN B 165 ASN E 15 GLN E 101 ASN E 249 ASN I 99 ASN I 375 GLN S 18 ASN S 197 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.2114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 24292 Z= 0.138 Angle : 0.515 11.716 32974 Z= 0.254 Chirality : 0.041 0.215 3617 Planarity : 0.004 0.078 4288 Dihedral : 8.827 151.637 3604 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.37 % Favored : 96.46 % Rotamer: Outliers : 2.42 % Allowed : 18.38 % Favored : 79.20 % 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: 0.95 (0.16), residues: 2977 helix: 2.16 (0.15), residues: 1244 sheet: 0.51 (0.22), residues: 531 loop : -0.98 (0.17), residues: 1202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 21 HIS 0.005 0.001 HIS B 137 PHE 0.022 0.001 PHE K 94 TYR 0.016 0.001 TYR S 24 ARG 0.007 0.000 ARG N 346 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5954 Ramachandran restraints generated. 2977 Oldfield, 0 Emsley, 2977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5954 Ramachandran restraints generated. 2977 Oldfield, 0 Emsley, 2977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 568 residues out of total 2548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 512 time to evaluate : 2.909 Fit side-chains REVERT: K 80 GLU cc_start: 0.8042 (tm-30) cc_final: 0.7627 (tm-30) REVERT: K 125 ASP cc_start: 0.7472 (t0) cc_final: 0.7013 (t0) REVERT: K 126 LEU cc_start: 0.8316 (tt) cc_final: 0.8035 (tp) REVERT: K 153 ARG cc_start: 0.8413 (mtp85) cc_final: 0.8016 (mtp85) REVERT: K 201 LYS cc_start: 0.8884 (ttmm) cc_final: 0.8303 (tptp) REVERT: K 244 ILE cc_start: 0.8316 (mt) cc_final: 0.8072 (tt) REVERT: K 319 LEU cc_start: 0.8331 (mt) cc_final: 0.8053 (mm) REVERT: N 76 ASP cc_start: 0.8463 (OUTLIER) cc_final: 0.8227 (t0) REVERT: N 98 GLN cc_start: 0.5998 (mt0) cc_final: 0.5597 (mt0) REVERT: N 243 LYS cc_start: 0.8427 (mtpp) cc_final: 0.7803 (mtpp) REVERT: N 288 MET cc_start: 0.8082 (tmm) cc_final: 0.7786 (tpp) REVERT: A 123 ARG cc_start: 0.8065 (ttp80) cc_final: 0.7727 (ttt180) REVERT: A 147 SER cc_start: 0.8253 (t) cc_final: 0.7862 (m) REVERT: A 150 THR cc_start: 0.8242 (m) cc_final: 0.8006 (m) REVERT: A 254 GLU cc_start: 0.5554 (mm-30) cc_final: 0.4641 (mm-30) REVERT: A 432 TYR cc_start: 0.8838 (OUTLIER) cc_final: 0.7631 (t80) REVERT: B 1 MET cc_start: 0.5927 (OUTLIER) cc_final: 0.4854 (tmm) REVERT: B 3 GLU cc_start: 0.8150 (mp0) cc_final: 0.7773 (mp0) REVERT: B 48 ASN cc_start: 0.8514 (m110) cc_final: 0.8253 (p0) REVERT: B 170 MET cc_start: 0.8363 (mtt) cc_final: 0.8052 (mtt) REVERT: B 219 THR cc_start: 0.9265 (m) cc_final: 0.8973 (p) REVERT: B 257 MET cc_start: 0.8388 (mmm) cc_final: 0.7883 (mmm) REVERT: B 299 MET cc_start: 0.9109 (mmm) cc_final: 0.8879 (mmt) REVERT: B 415 MET cc_start: 0.8608 (tpp) cc_final: 0.8051 (ttp) REVERT: B 423 GLN cc_start: 0.7990 (mt0) cc_final: 0.7737 (tm-30) REVERT: E 3 GLU cc_start: 0.7605 (mt-10) cc_final: 0.7086 (pt0) REVERT: E 242 LEU cc_start: 0.9044 (OUTLIER) cc_final: 0.8811 (pp) REVERT: E 265 ILE cc_start: 0.8667 (pt) cc_final: 0.8249 (mt) REVERT: E 392 ASP cc_start: 0.8242 (m-30) cc_final: 0.7848 (m-30) REVERT: E 414 GLU cc_start: 0.7948 (pm20) cc_final: 0.7732 (pm20) REVERT: I 31 ASP cc_start: 0.8359 (t0) cc_final: 0.7946 (t0) REVERT: I 257 MET cc_start: 0.8649 (mtp) cc_final: 0.8239 (mtp) REVERT: I 299 MET cc_start: 0.8807 (mmp) cc_final: 0.8550 (mmt) REVERT: I 342 VAL cc_start: 0.8848 (t) cc_final: 0.8583 (m) REVERT: I 401 GLU cc_start: 0.8402 (mm-30) cc_final: 0.8134 (mm-30) REVERT: S 2 ARG cc_start: 0.7289 (mpp80) cc_final: 0.7027 (mpp-170) REVERT: S 242 LEU cc_start: 0.9030 (OUTLIER) cc_final: 0.8763 (pp) REVERT: S 322 ASP cc_start: 0.8544 (t0) cc_final: 0.8326 (t0) outliers start: 56 outliers final: 40 residues processed: 539 average time/residue: 0.3491 time to fit residues: 297.3438 Evaluate side-chains 533 residues out of total 2548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 488 time to evaluate : 2.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 108 MET Chi-restraints excluded: chain K residue 119 ILE Chi-restraints excluded: chain K residue 194 ASP Chi-restraints excluded: chain K residue 252 SER Chi-restraints excluded: chain K residue 256 ASP Chi-restraints excluded: chain N residue 76 ASP Chi-restraints excluded: chain N residue 91 VAL Chi-restraints excluded: chain N residue 208 THR Chi-restraints excluded: chain N residue 245 SER Chi-restraints excluded: chain N residue 247 VAL Chi-restraints excluded: chain N residue 354 ILE Chi-restraints excluded: chain A residue 2 ARG Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 98 ASP Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain A residue 434 GLU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 336 LYS Chi-restraints excluded: chain E residue 242 LEU Chi-restraints excluded: chain E residue 245 ASP Chi-restraints excluded: chain E residue 249 ASN Chi-restraints excluded: chain E residue 295 CYS Chi-restraints excluded: chain I residue 218 THR Chi-restraints excluded: chain I residue 313 VAL Chi-restraints excluded: chain I residue 424 GLN Chi-restraints excluded: chain S residue 77 GLU Chi-restraints excluded: chain S residue 98 ASP Chi-restraints excluded: chain S residue 119 LEU Chi-restraints excluded: chain S residue 227 LEU Chi-restraints excluded: chain S residue 239 THR Chi-restraints excluded: chain S residue 242 LEU Chi-restraints excluded: chain S residue 259 LEU Chi-restraints excluded: chain S residue 362 VAL Chi-restraints excluded: chain S residue 381 THR Chi-restraints excluded: chain S residue 398 MET 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: 3.9990 chunk 273 optimal weight: 0.5980 chunk 249 optimal weight: 5.9990 chunk 265 optimal weight: 9.9990 chunk 160 optimal weight: 3.9990 chunk 115 optimal weight: 0.7980 chunk 208 optimal weight: 5.9990 chunk 81 optimal weight: 3.9990 chunk 240 optimal weight: 4.9990 chunk 251 optimal weight: 5.9990 chunk 264 optimal weight: 0.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 29 GLN N 42 GLN A 256 GLN E 101 ASN I 99 ASN I 375 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.2131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 24292 Z= 0.321 Angle : 0.583 10.919 32974 Z= 0.291 Chirality : 0.044 0.230 3617 Planarity : 0.004 0.077 4288 Dihedral : 8.923 151.343 3604 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.18 % Favored : 95.65 % Rotamer: Outliers : 2.62 % Allowed : 18.31 % Favored : 79.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.16), residues: 2977 helix: 2.09 (0.15), residues: 1237 sheet: 0.43 (0.22), residues: 530 loop : -1.02 (0.17), residues: 1210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 21 HIS 0.008 0.001 HIS B 137 PHE 0.036 0.002 PHE K 94 TYR 0.022 0.001 TYR S 24 ARG 0.007 0.001 ARG E 123 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5954 Ramachandran restraints generated. 2977 Oldfield, 0 Emsley, 2977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5954 Ramachandran restraints generated. 2977 Oldfield, 0 Emsley, 2977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 564 residues out of total 2548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 503 time to evaluate : 2.636 Fit side-chains REVERT: K 42 GLN cc_start: 0.8248 (mm-40) cc_final: 0.8043 (mp10) REVERT: K 80 GLU cc_start: 0.8051 (tm-30) cc_final: 0.7656 (tm-30) REVERT: K 113 LYS cc_start: 0.8266 (mmtt) cc_final: 0.7988 (tppt) REVERT: K 125 ASP cc_start: 0.7522 (t0) cc_final: 0.7047 (t0) REVERT: K 126 LEU cc_start: 0.8295 (tt) cc_final: 0.8093 (tt) REVERT: K 127 PHE cc_start: 0.8246 (OUTLIER) cc_final: 0.7846 (t80) REVERT: K 153 ARG cc_start: 0.8444 (mtp85) cc_final: 0.8047 (mtp85) REVERT: K 244 ILE cc_start: 0.8334 (mt) cc_final: 0.8058 (tt) REVERT: N 76 ASP cc_start: 0.8458 (OUTLIER) cc_final: 0.8208 (t0) REVERT: N 98 GLN cc_start: 0.6165 (mt0) cc_final: 0.5789 (mt0) REVERT: N 243 LYS cc_start: 0.8451 (mtpp) cc_final: 0.7827 (mtpp) REVERT: N 288 MET cc_start: 0.8142 (tmm) cc_final: 0.7864 (tpp) REVERT: N 310 VAL cc_start: 0.9081 (m) cc_final: 0.8803 (p) REVERT: A 147 SER cc_start: 0.8381 (t) cc_final: 0.7913 (m) REVERT: A 150 THR cc_start: 0.8323 (m) cc_final: 0.8083 (m) REVERT: A 254 GLU cc_start: 0.5735 (mm-30) cc_final: 0.5105 (mm-30) REVERT: B 1 MET cc_start: 0.5905 (OUTLIER) cc_final: 0.4769 (tmm) REVERT: B 3 GLU cc_start: 0.8157 (mp0) cc_final: 0.7749 (mp0) REVERT: B 48 ASN cc_start: 0.8548 (m110) cc_final: 0.8260 (p0) REVERT: B 170 MET cc_start: 0.8454 (mtt) cc_final: 0.8086 (mtt) REVERT: B 219 THR cc_start: 0.9289 (m) cc_final: 0.8993 (p) REVERT: B 257 MET cc_start: 0.8452 (mmm) cc_final: 0.7913 (mmm) REVERT: B 415 MET cc_start: 0.8653 (tpp) cc_final: 0.8361 (ttm) REVERT: B 423 GLN cc_start: 0.8088 (mt0) cc_final: 0.7783 (tm-30) REVERT: E 242 LEU cc_start: 0.9093 (OUTLIER) cc_final: 0.8852 (pp) REVERT: E 260 VAL cc_start: 0.8927 (t) cc_final: 0.8538 (m) REVERT: E 265 ILE cc_start: 0.8810 (pt) cc_final: 0.8510 (mt) REVERT: E 392 ASP cc_start: 0.8234 (m-30) cc_final: 0.7869 (m-30) REVERT: E 414 GLU cc_start: 0.8058 (pm20) cc_final: 0.7782 (pm20) REVERT: I 31 ASP cc_start: 0.8397 (t0) cc_final: 0.8004 (t0) REVERT: I 342 VAL cc_start: 0.8903 (t) cc_final: 0.8700 (m) REVERT: I 401 GLU cc_start: 0.8395 (mm-30) cc_final: 0.8115 (mm-30) REVERT: S 35 GLN cc_start: 0.7952 (mp10) cc_final: 0.7547 (mp10) REVERT: S 203 MET cc_start: 0.8226 (mmt) cc_final: 0.7828 (mmm) REVERT: S 242 LEU cc_start: 0.9048 (OUTLIER) cc_final: 0.8846 (pp) REVERT: S 322 ASP cc_start: 0.8604 (t0) cc_final: 0.8384 (t0) REVERT: S 392 ASP cc_start: 0.8759 (m-30) cc_final: 0.8344 (t0) outliers start: 61 outliers final: 48 residues processed: 530 average time/residue: 0.3639 time to fit residues: 302.9313 Evaluate side-chains 547 residues out of total 2548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 494 time to evaluate : 2.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 108 MET Chi-restraints excluded: chain K residue 127 PHE Chi-restraints excluded: chain K residue 194 ASP Chi-restraints excluded: chain K residue 252 SER Chi-restraints excluded: chain K residue 256 ASP Chi-restraints excluded: chain N residue 76 ASP Chi-restraints excluded: chain N residue 91 VAL Chi-restraints excluded: chain N residue 118 ILE Chi-restraints excluded: chain N residue 208 THR Chi-restraints excluded: chain N residue 245 SER Chi-restraints excluded: chain N residue 354 ILE Chi-restraints excluded: chain A residue 2 ARG Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 98 ASP Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain A residue 434 GLU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 336 LYS Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 178 SER Chi-restraints excluded: chain E residue 218 ASP Chi-restraints excluded: chain E residue 242 LEU Chi-restraints excluded: chain E residue 245 ASP Chi-restraints excluded: chain E residue 295 CYS Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain I residue 118 ASP Chi-restraints excluded: chain I residue 170 MET Chi-restraints excluded: chain I residue 218 THR Chi-restraints excluded: chain I residue 313 VAL Chi-restraints excluded: chain I residue 415 MET Chi-restraints excluded: chain I residue 424 GLN Chi-restraints excluded: chain S residue 26 LEU Chi-restraints excluded: chain S residue 77 GLU Chi-restraints excluded: chain S residue 98 ASP Chi-restraints excluded: chain S residue 119 LEU Chi-restraints excluded: chain S residue 226 ASN Chi-restraints excluded: chain S residue 242 LEU Chi-restraints excluded: chain S residue 259 LEU 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 381 THR Chi-restraints excluded: chain S residue 398 MET 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: 3.9990 chunk 281 optimal weight: 8.9990 chunk 171 optimal weight: 2.9990 chunk 133 optimal weight: 1.9990 chunk 195 optimal weight: 0.6980 chunk 294 optimal weight: 4.9990 chunk 271 optimal weight: 1.9990 chunk 234 optimal weight: 0.2980 chunk 24 optimal weight: 9.9990 chunk 181 optimal weight: 0.0980 chunk 143 optimal weight: 3.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 42 GLN A 256 GLN E 101 ASN I 99 ASN S 15 GLN S 18 ASN S 300 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.2197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 24292 Z= 0.187 Angle : 0.541 10.629 32974 Z= 0.267 Chirality : 0.042 0.210 3617 Planarity : 0.004 0.077 4288 Dihedral : 8.804 153.329 3604 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.57 % Favored : 96.29 % Rotamer: Outliers : 2.26 % Allowed : 19.13 % Favored : 78.61 % 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: 0.91 (0.16), residues: 2977 helix: 2.14 (0.15), residues: 1234 sheet: 0.49 (0.22), residues: 528 loop : -0.98 (0.17), residues: 1215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 21 HIS 0.007 0.001 HIS B 137 PHE 0.033 0.001 PHE K 94 TYR 0.027 0.001 TYR K 56 ARG 0.007 0.000 ARG E 123 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5954 Ramachandran restraints generated. 2977 Oldfield, 0 Emsley, 2977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5954 Ramachandran restraints generated. 2977 Oldfield, 0 Emsley, 2977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 545 residues out of total 2548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 493 time to evaluate : 2.775 Fit side-chains revert: symmetry clash REVERT: K 42 GLN cc_start: 0.8240 (mm-40) cc_final: 0.7998 (mm110) REVERT: K 80 GLU cc_start: 0.8057 (tm-30) cc_final: 0.7667 (tm-30) REVERT: K 113 LYS cc_start: 0.8335 (mmtt) cc_final: 0.7946 (tppt) REVERT: K 125 ASP cc_start: 0.7529 (t0) cc_final: 0.7062 (t0) REVERT: K 153 ARG cc_start: 0.8427 (mtp85) cc_final: 0.8037 (mtp85) REVERT: K 244 ILE cc_start: 0.8337 (mt) cc_final: 0.8091 (tt) REVERT: N 42 GLN cc_start: 0.7370 (mp-120) cc_final: 0.7084 (mm-40) REVERT: N 76 ASP cc_start: 0.8438 (OUTLIER) cc_final: 0.8209 (t0) REVERT: N 98 GLN cc_start: 0.6082 (mt0) cc_final: 0.5823 (mt0) REVERT: N 243 LYS cc_start: 0.8416 (mtpp) cc_final: 0.7830 (mtpp) REVERT: N 253 GLU cc_start: 0.8193 (mp0) cc_final: 0.7953 (mp0) REVERT: N 288 MET cc_start: 0.8126 (tmm) cc_final: 0.7855 (tpp) REVERT: N 310 VAL cc_start: 0.9061 (m) cc_final: 0.8788 (p) REVERT: A 2 ARG cc_start: 0.8055 (OUTLIER) cc_final: 0.6595 (mtm-85) REVERT: A 123 ARG cc_start: 0.8078 (ttp80) cc_final: 0.7736 (ttt180) REVERT: A 147 SER cc_start: 0.8307 (t) cc_final: 0.7890 (m) REVERT: A 150 THR cc_start: 0.8288 (m) cc_final: 0.8048 (m) REVERT: A 254 GLU cc_start: 0.5609 (mm-30) cc_final: 0.5015 (mm-30) REVERT: A 432 TYR cc_start: 0.8810 (OUTLIER) cc_final: 0.7621 (t80) REVERT: B 1 MET cc_start: 0.5918 (OUTLIER) cc_final: 0.4839 (tmm) REVERT: B 3 GLU cc_start: 0.8140 (mp0) cc_final: 0.7762 (mp0) REVERT: B 48 ASN cc_start: 0.8525 (m110) cc_final: 0.8251 (p0) REVERT: B 170 MET cc_start: 0.8405 (mtt) cc_final: 0.8071 (mtt) REVERT: B 212 PHE cc_start: 0.8542 (m-80) cc_final: 0.8295 (m-80) REVERT: B 219 THR cc_start: 0.9267 (m) cc_final: 0.8970 (p) REVERT: B 233 MET cc_start: 0.8887 (mtp) cc_final: 0.8653 (mtp) REVERT: B 257 MET cc_start: 0.8402 (mmm) cc_final: 0.7862 (mmm) REVERT: B 415 MET cc_start: 0.8626 (tpp) cc_final: 0.8323 (ttm) REVERT: B 423 GLN cc_start: 0.8031 (mt0) cc_final: 0.7765 (tm-30) REVERT: E 170 SER cc_start: 0.8748 (p) cc_final: 0.8547 (m) REVERT: E 242 LEU cc_start: 0.9077 (OUTLIER) cc_final: 0.8848 (pp) REVERT: E 265 ILE cc_start: 0.8703 (pt) cc_final: 0.8296 (mt) REVERT: E 392 ASP cc_start: 0.8248 (m-30) cc_final: 0.7874 (m-30) REVERT: I 31 ASP cc_start: 0.8374 (t0) cc_final: 0.7982 (t0) REVERT: I 342 VAL cc_start: 0.8855 (t) cc_final: 0.8606 (m) REVERT: S 35 GLN cc_start: 0.7949 (mp10) cc_final: 0.7541 (mp10) REVERT: S 242 LEU cc_start: 0.9046 (OUTLIER) cc_final: 0.8838 (pp) REVERT: S 322 ASP cc_start: 0.8585 (t0) cc_final: 0.8366 (t0) REVERT: S 392 ASP cc_start: 0.8733 (m-30) cc_final: 0.8307 (t0) outliers start: 52 outliers final: 41 residues processed: 521 average time/residue: 0.3404 time to fit residues: 277.6097 Evaluate side-chains 531 residues out of total 2548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 484 time to evaluate : 2.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 108 MET Chi-restraints excluded: chain K residue 119 ILE Chi-restraints excluded: chain K residue 194 ASP Chi-restraints excluded: chain K residue 241 VAL Chi-restraints excluded: chain K residue 256 ASP Chi-restraints excluded: chain N residue 60 THR Chi-restraints excluded: chain N residue 76 ASP Chi-restraints excluded: chain N residue 91 VAL Chi-restraints excluded: chain N residue 208 THR Chi-restraints excluded: chain N residue 245 SER Chi-restraints excluded: chain N residue 354 ILE Chi-restraints excluded: chain A residue 2 ARG Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 98 ASP Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain A residue 434 GLU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 336 LYS Chi-restraints excluded: chain E residue 178 SER Chi-restraints excluded: chain E residue 242 LEU Chi-restraints excluded: chain E residue 295 CYS Chi-restraints excluded: chain I residue 170 MET Chi-restraints excluded: chain I residue 218 THR Chi-restraints excluded: chain I residue 313 VAL Chi-restraints excluded: chain I residue 424 GLN Chi-restraints excluded: chain S residue 26 LEU Chi-restraints excluded: chain S residue 50 ASN Chi-restraints excluded: chain S residue 77 GLU Chi-restraints excluded: chain S residue 98 ASP Chi-restraints excluded: chain S residue 119 LEU Chi-restraints excluded: chain S residue 226 ASN Chi-restraints excluded: chain S residue 239 THR Chi-restraints excluded: chain S residue 242 LEU Chi-restraints excluded: chain S residue 259 LEU 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 381 THR Chi-restraints excluded: chain S residue 398 MET 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: 3.9990 chunk 250 optimal weight: 3.9990 chunk 71 optimal weight: 0.9980 chunk 216 optimal weight: 2.9990 chunk 34 optimal weight: 0.8980 chunk 65 optimal weight: 0.8980 chunk 235 optimal weight: 2.9990 chunk 98 optimal weight: 0.9990 chunk 241 optimal weight: 0.4980 chunk 29 optimal weight: 10.0000 chunk 43 optimal weight: 2.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 59 HIS N 322 ASN I 99 ASN S 18 ASN S 300 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.120628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.094058 restraints weight = 37473.488| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 2.58 r_work: 0.3204 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3209 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3209 r_free = 0.3209 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3209 r_free = 0.3209 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3209 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.2288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 24292 Z= 0.173 Angle : 0.533 10.533 32974 Z= 0.264 Chirality : 0.042 0.205 3617 Planarity : 0.004 0.076 4288 Dihedral : 8.697 155.105 3604 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.81 % Favored : 96.06 % Rotamer: Outliers : 2.22 % Allowed : 19.28 % Favored : 78.49 % 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: 0.96 (0.16), residues: 2977 helix: 2.17 (0.15), residues: 1237 sheet: 0.52 (0.22), residues: 521 loop : -0.96 (0.17), residues: 1219 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 21 HIS 0.007 0.001 HIS B 137 PHE 0.033 0.001 PHE K 94 TYR 0.028 0.001 TYR K 56 ARG 0.007 0.000 ARG E 123 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6129.43 seconds wall clock time: 109 minutes 15.97 seconds (6555.97 seconds total)