Starting phenix.real_space_refine on Thu Aug 8 17:40:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8utt_42549/08_2024/8utt_42549.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8utt_42549/08_2024/8utt_42549.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8utt_42549/08_2024/8utt_42549.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8utt_42549/08_2024/8utt_42549.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8utt_42549/08_2024/8utt_42549.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8utt_42549/08_2024/8utt_42549.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 14835 2.51 5 N 4060 2.21 5 O 4673 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "K PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 63": "OE1" <-> "OE2" Residue "K TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 76": "OD1" <-> "OD2" Residue "K PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 112": "OE1" <-> "OE2" Residue "K PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 152": "OE1" <-> "OE2" Residue "K ASP 156": "OD1" <-> "OD2" Residue "K GLU 170": "OE1" <-> "OE2" Residue "K GLU 179": "OE1" <-> "OE2" Residue "K TYR 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 63": "OE1" <-> "OE2" Residue "N GLU 80": "OE1" <-> "OE2" Residue "N TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 136": "OD1" <-> "OD2" Residue "N GLU 143": "OE1" <-> "OE2" Residue "N GLU 152": "OE1" <-> "OE2" Residue "N ASP 156": "OD1" <-> "OD2" Residue "N GLU 170": "OE1" <-> "OE2" Residue "N ASP 180": "OD1" <-> "OD2" Residue "N ASP 194": "OD1" <-> "OD2" Residue "N GLU 267": "OE1" <-> "OE2" Residue "N GLU 287": "OE1" <-> "OE2" Residue "N ASP 289": "OD1" <-> "OD2" Residue "N PHE 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 317": "OE1" <-> "OE2" Residue "N TYR 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 363": "OD1" <-> "OD2" Residue "A GLU 22": "OE1" <-> "OE2" Residue "A TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 55": "OE1" <-> "OE2" Residue "A TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 116": "OD1" <-> "OD2" Residue "A ASP 120": "OD1" <-> "OD2" Residue "A ASP 127": "OD1" <-> "OD2" Residue "A ASP 218": "OD1" <-> "OD2" Residue "A GLU 220": "OE1" <-> "OE2" Residue "A PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 254": "OE1" <-> "OE2" Residue "A GLU 417": "OE1" <-> "OE2" Residue "A GLU 423": "OE1" <-> "OE2" Residue "A GLU 433": "OE1" <-> "OE2" Residue "B GLU 3": "OE1" <-> "OE2" Residue "B ASP 41": "OD1" <-> "OD2" Residue "B GLU 53": "OE1" <-> "OE2" Residue "B GLU 111": "OE1" <-> "OE2" Residue "B ASP 114": "OD1" <-> "OD2" Residue "B GLU 123": "OE1" <-> "OE2" Residue "B TYR 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 161": "OD1" <-> "OD2" Residue "B ASP 197": "OD1" <-> "OD2" Residue "B ASP 224": "OD1" <-> "OD2" Residue "B PHE 394": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 401": "OE1" <-> "OE2" Residue "B GLU 407": "OE1" <-> "OE2" Residue "B GLU 421": "OE1" <-> "OE2" Residue "B TYR 425": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 3": "OE1" <-> "OE2" Residue "E TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 116": "OD1" <-> "OD2" Residue "E ASP 127": "OD1" <-> "OD2" Residue "E TYR 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 199": "OD1" <-> "OD2" Residue "E PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 218": "OD1" <-> "OD2" Residue "E GLU 220": "OE1" <-> "OE2" Residue "E GLU 254": "OE1" <-> "OE2" Residue "E GLU 279": "OE1" <-> "OE2" Residue "E TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 290": "OE1" <-> "OE2" Residue "E TYR 319": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 411": "OE1" <-> "OE2" Residue "E PHE 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 420": "OE1" <-> "OE2" Residue "E GLU 423": "OE1" <-> "OE2" Residue "E ASP 424": "OD1" <-> "OD2" Residue "E TYR 432": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 446": "OE1" <-> "OE2" Residue "E GLU 450": "OE1" <-> "OE2" Residue "E TYR 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 22": "OE1" <-> "OE2" Residue "I ASP 26": "OD1" <-> "OD2" Residue "I ASP 31": "OD1" <-> "OD2" Residue "I ASP 41": "OD1" <-> "OD2" Residue "I TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 74": "OD1" <-> "OD2" Residue "I ASP 114": "OD1" <-> "OD2" Residue "I GLU 123": "OE1" <-> "OE2" Residue "I GLU 125": "OE1" <-> "OE2" Residue "I ASP 161": "OD1" <-> "OD2" Residue "I PHE 270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 327": "OD1" <-> "OD2" Residue "I PHE 394": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 404": "OD1" <-> "OD2" Residue "I GLU 412": "OE1" <-> "OE2" Residue "I GLU 421": "OE1" <-> "OE2" Residue "I TYR 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 55": "OE1" <-> "OE2" Residue "S TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 90": "OE1" <-> "OE2" Residue "S GLU 97": "OE1" <-> "OE2" Residue "S TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 120": "OD1" <-> "OD2" Residue "S ASP 160": "OD1" <-> "OD2" Residue "S TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 218": "OD1" <-> "OD2" Residue "S GLU 254": "OE1" <-> "OE2" Residue "S TYR 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 306": "OD1" <-> "OD2" Residue "S TYR 319": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 357": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 367": "OD1" <-> "OD2" Residue "S GLU 386": "OE1" <-> "OE2" Residue "S PHE 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 424": "OD1" <-> "OD2" Residue "S TYR 432": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 433": "OE1" <-> "OE2" Residue "S GLU 443": "OE1" <-> "OE2" Residue "S GLU 447": "OE1" <-> "OE2" Residue "S GLU 450": "OE1" <-> "OE2" Residue "S TYR 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 23744 Number of models: 1 Model: "" Number of chains: 16 Chain: "K" Number of atoms: 3014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 382, 3014 Classifications: {'peptide': 382} Link IDs: {'PTRANS': 12, 'TRANS': 369} Chain: "N" Number of atoms: 3031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 385, 3031 Classifications: {'peptide': 385} Link IDs: {'PTRANS': 12, 'TRANS': 372} 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=0.54 ... (12 atoms not shown) pdb=" CG2BTHR B 429 " occ=0.46 residue: pdb=" N AALA B 430 " occ=0.54 ... (8 atoms not shown) pdb=" CB BALA B 430 " occ=0.46 residue: pdb=" N AASP B 431 " occ=0.54 ... (14 atoms not shown) pdb=" OD2BASP B 431 " occ=0.46 residue: pdb=" N AGLU B 432 " occ=0.54 ... (16 atoms not shown) pdb=" OE2BGLU B 432 " occ=0.46 residue: pdb=" N ATHR I 429 " occ=0.52 ... (12 atoms not shown) pdb=" CG2BTHR I 429 " occ=0.48 residue: pdb=" N AALA I 430 " occ=0.52 ... (8 atoms not shown) pdb=" CB BALA I 430 " occ=0.48 residue: pdb=" N AASP I 431 " occ=0.52 ... (14 atoms not shown) pdb=" OD2BASP I 431 " occ=0.48 residue: pdb=" N AGLU I 432 " occ=0.52 ... (16 atoms not shown) pdb=" OE2BGLU I 432 " occ=0.48 residue: pdb=" N AGLN I 433 " occ=0.52 ... (16 atoms not shown) pdb=" NE2BGLN I 433 " occ=0.48 Time building chain proxies: 12.42, per 1000 atoms: 0.52 Number of scatterers: 23744 At special positions: 0 Unit cell: (106.344, 113.94, 243.072, 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 4673 8.00 N 4060 7.00 C 14835 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: 9.30 Conformation dependent library (CDL) restraints added in 5.9 seconds 5938 Ramachandran restraints generated. 2969 Oldfield, 0 Emsley, 2969 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5546 Finding SS restraints... Secondary structure from input PDB file: 118 helices and 24 sheets defined 48.4% alpha, 18.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.21 Creating SS restraints... Processing helix chain 'K' and resid 16 through 22 removed outlier: 3.522A pdb=" N ARG K 22 " --> pdb=" O ARG K 18 " (cutoff:3.500A) 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 Processing helix chain 'K' and resid 188 through 203 removed outlier: 3.546A pdb=" N ILE K 192 " --> pdb=" O SER K 188 " (cutoff:3.500A) Processing helix chain 'K' and resid 262 through 295 Proline residue: K 292 - end of helix Processing helix chain 'K' and resid 309 through 315 Processing helix chain 'K' and resid 315 through 320 Processing helix chain 'K' and resid 338 through 353 removed outlier: 3.669A pdb=" N GLN K 353 " --> pdb=" O ASP K 349 " (cutoff:3.500A) Processing helix chain 'K' and resid 363 through 385 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 109 removed outlier: 4.020A pdb=" N THR N 106 " --> pdb=" O GLY N 102 " (cutoff:3.500A) Processing helix chain 'N' and resid 117 through 132 removed outlier: 3.682A pdb=" N GLN N 121 " --> pdb=" O GLY N 117 " (cutoff:3.500A) Processing helix chain 'N' and resid 188 through 202 removed outlier: 3.552A pdb=" N ILE N 192 " --> pdb=" O SER N 188 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ALA N 202 " --> pdb=" O SER N 198 " (cutoff:3.500A) Processing helix chain 'N' and resid 262 through 296 removed outlier: 3.515A pdb=" N LYS N 266 " --> pdb=" O GLY N 262 " (cutoff:3.500A) Proline residue: N 292 - end of helix Processing helix chain 'N' and resid 309 through 315 Processing helix chain 'N' and resid 315 through 320 Processing helix chain 'N' and resid 337 through 349 removed outlier: 3.811A pdb=" N THR N 341 " --> pdb=" O ASN N 337 " (cutoff:3.500A) Processing helix chain 'N' and resid 363 through 385 Processing helix chain 'A' and resid 10 through 28 Processing helix chain 'A' and resid 37 through 43 removed outlier: 3.528A pdb=" N THR A 41 " --> pdb=" O PRO A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 80 removed outlier: 3.875A pdb=" N VAL A 78 " --> pdb=" O VAL A 74 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N THR A 80 " --> pdb=" O ASP A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 108 Processing helix chain 'A' and resid 114 through 129 Processing helix chain 'A' and resid 143 through 161 removed outlier: 4.102A pdb=" N THR A 150 " --> pdb=" O GLY A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 197 removed outlier: 3.612A pdb=" N ASN A 186 " --> pdb=" O VAL A 182 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N HIS A 192 " --> pdb=" O ILE A 188 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N THR A 193 " --> pdb=" O LEU A 189 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N THR A 194 " --> pdb=" O THR A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 216 removed outlier: 3.594A pdb=" N ILE A 209 " --> pdb=" O ASP A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 240 removed outlier: 3.806A 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 259 Processing helix chain 'A' and resid 277 through 282 removed outlier: 4.059A pdb=" N TYR A 282 " --> pdb=" O ALA A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 296 removed outlier: 4.245A pdb=" N PHE A 296 " --> pdb=" O THR A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 301 removed outlier: 3.516A pdb=" N GLN A 301 " --> pdb=" O PRO A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 310 Processing helix chain 'A' and resid 324 through 338 Processing helix chain 'A' and resid 383 through 400 removed outlier: 4.216A pdb=" N ALA A 387 " --> pdb=" O ALA A 383 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N TRP A 388 " --> pdb=" O ILE A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 410 removed outlier: 4.038A pdb=" N TYR A 408 " --> pdb=" O PHE A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 435 removed outlier: 4.149A pdb=" N SER A 419 " --> pdb=" O GLU A 415 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ALA A 421 " --> pdb=" O GLU A 417 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLU A 433 " --> pdb=" O GLU A 429 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N VAL A 435 " --> pdb=" O ASP A 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 29 removed outlier: 4.020A pdb=" N ASP B 26 " --> pdb=" O GLU B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 49 Processing helix chain 'B' and resid 69 through 78 removed outlier: 4.333A pdb=" N MET B 73 " --> pdb=" O GLU B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 85 removed outlier: 3.804A pdb=" N PHE B 85 " --> pdb=" O GLY B 82 " (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 127 removed outlier: 3.750A pdb=" N LEU B 112 " --> pdb=" O GLU B 108 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N ASP B 114 " --> pdb=" O ALA B 110 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N SER B 115 " --> pdb=" O GLU B 111 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N SER B 126 " --> pdb=" O LYS B 122 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N CYS B 127 " --> pdb=" O GLU B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 159 Processing helix chain 'B' and resid 180 through 196 removed outlier: 3.664A pdb=" N ASN B 184 " --> pdb=" O VAL B 180 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N GLN B 191 " --> pdb=" O LEU B 187 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N GLU B 194 " --> pdb=" O HIS B 190 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N THR B 196 " --> pdb=" O LEU B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 214 Processing helix chain 'B' and resid 221 through 237 removed outlier: 3.690A pdb=" N LEU B 225 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 3.977A 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 304 through 308 removed outlier: 3.575A pdb=" N HIS B 307 " --> pdb=" O ASP B 304 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLY B 308 " --> pdb=" O PRO B 305 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 304 through 308' Processing helix chain 'B' and resid 322 through 337 removed outlier: 3.574A pdb=" N VAL B 326 " --> pdb=" O SER B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 341 removed outlier: 3.796A 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 374 through 390 removed outlier: 3.704A pdb=" N PHE B 378 " --> pdb=" O ILE B 374 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 400 removed outlier: 4.417A pdb=" N TYR B 398 " --> pdb=" O PHE B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 427 removed outlier: 3.884A pdb=" N PHE B 408 " --> pdb=" O ASP B 404 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N TYR B 425 " --> pdb=" O GLU B 421 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLN B 426 " --> pdb=" O TYR B 422 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N ASP B 427 " --> pdb=" O GLN B 423 " (cutoff:3.500A) Processing helix chain 'E' and resid 10 through 29 Processing helix chain 'E' and resid 36 through 43 removed outlier: 3.825A pdb=" N LYS E 40 " --> pdb=" O MET E 36 " (cutoff:3.500A) Processing helix chain 'E' and resid 71 through 80 removed outlier: 4.309A pdb=" N ILE E 75 " --> pdb=" O GLU E 71 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLU E 77 " --> pdb=" O THR E 73 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N VAL E 78 " --> pdb=" O VAL E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 107 Processing helix chain 'E' and resid 114 through 129 Processing helix chain 'E' and resid 143 through 161 removed outlier: 4.253A pdb=" N THR E 150 " --> pdb=" O GLY E 146 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 197 removed outlier: 3.728A pdb=" N ASN E 186 " --> pdb=" O VAL E 182 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N HIS E 192 " --> pdb=" O ILE E 188 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N THR E 193 " --> pdb=" O LEU E 189 " (cutoff:3.500A) Processing helix chain 'E' and resid 205 through 216 Processing helix chain 'E' and resid 223 through 244 removed outlier: 3.789A pdb=" N LEU E 227 " --> pdb=" O THR E 223 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N SER E 241 " --> pdb=" O SER E 237 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N LEU E 242 " --> pdb=" O ILE E 238 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ARG E 243 " --> pdb=" O THR E 239 " (cutoff:3.500A) Processing helix chain 'E' and resid 251 through 260 removed outlier: 3.626A pdb=" N GLN E 256 " --> pdb=" O LEU E 252 " (cutoff:3.500A) Processing helix chain 'E' and resid 277 through 282 removed outlier: 4.224A pdb=" N TYR E 282 " --> pdb=" O ALA E 278 " (cutoff:3.500A) Processing helix chain 'E' and resid 287 through 296 removed outlier: 3.832A pdb=" N PHE E 296 " --> pdb=" O THR E 292 " (cutoff:3.500A) Processing helix chain 'E' and resid 297 through 301 removed outlier: 3.565A pdb=" N GLN E 301 " --> pdb=" O PRO E 298 " (cutoff:3.500A) Processing helix chain 'E' and resid 306 through 310 Processing helix chain 'E' and resid 324 through 338 removed outlier: 3.588A pdb=" N VAL E 328 " --> pdb=" O VAL E 324 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N THR E 337 " --> pdb=" O ALA E 333 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LYS E 338 " --> pdb=" O THR E 334 " (cutoff:3.500A) Processing helix chain 'E' and resid 383 through 400 removed outlier: 4.207A pdb=" N ALA E 387 " --> pdb=" O ALA E 383 " (cutoff:3.500A) Processing helix chain 'E' and resid 404 through 410 removed outlier: 4.317A pdb=" N TYR E 408 " --> pdb=" O PHE E 404 " (cutoff:3.500A) Processing helix chain 'E' and resid 414 through 436 removed outlier: 4.246A pdb=" N PHE E 418 " --> pdb=" O GLU E 414 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N SER E 419 " --> pdb=" O GLU E 415 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ASP E 424 " --> pdb=" O GLU E 420 " (cutoff:3.500A) Processing helix chain 'I' and resid 10 through 29 Processing helix chain 'I' and resid 41 through 45 removed outlier: 3.530A pdb=" N LEU I 44 " --> pdb=" O ASP I 41 " (cutoff:3.500A) Processing helix chain 'I' and resid 46 through 49 Processing helix chain 'I' and resid 69 through 78 removed outlier: 4.707A pdb=" N MET I 73 " --> pdb=" O GLU I 69 " (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: 3.865A pdb=" N LEU I 112 " --> pdb=" O GLU I 108 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N ASP I 114 " --> pdb=" O ALA I 110 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N SER I 115 " --> pdb=" O GLU I 111 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N SER I 126 " --> pdb=" O LYS I 122 " (cutoff:3.500A) Processing helix chain 'I' and resid 141 through 159 removed outlier: 3.579A pdb=" N SER I 145 " --> pdb=" O GLY I 141 " (cutoff:3.500A) Processing helix chain 'I' and resid 180 through 196 removed outlier: 3.757A pdb=" N ASN I 184 " --> pdb=" O VAL I 180 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N GLN I 191 " --> pdb=" O LEU I 187 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N GLU I 194 " --> pdb=" O HIS I 190 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N THR I 196 " --> pdb=" O LEU I 192 " (cutoff:3.500A) Processing helix chain 'I' and resid 203 through 214 Processing helix chain 'I' and resid 221 through 237 removed outlier: 3.586A pdb=" N LEU I 225 " --> pdb=" O THR I 221 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N THR I 237 " --> pdb=" O MET I 233 " (cutoff:3.500A) Processing helix chain 'I' and resid 238 through 241 Processing helix chain 'I' and resid 249 through 258 Processing helix chain 'I' and resid 285 through 294 Processing helix chain 'I' and resid 295 through 299 removed outlier: 3.819A pdb=" N MET I 299 " --> pdb=" O SER I 296 " (cutoff:3.500A) Processing helix chain 'I' and resid 304 through 308 Processing helix chain 'I' and resid 322 through 337 removed outlier: 3.532A pdb=" N VAL I 326 " --> pdb=" O SER I 322 " (cutoff:3.500A) Processing helix chain 'I' and resid 338 through 341 removed outlier: 3.518A 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 374 through 390 removed outlier: 3.819A pdb=" N PHE I 378 " --> pdb=" O ILE I 374 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N ALA I 387 " --> pdb=" O GLU I 383 " (cutoff:3.500A) Processing helix chain 'I' and resid 395 through 400 Processing helix chain 'I' and resid 404 through 425 removed outlier: 4.125A pdb=" N PHE I 408 " --> pdb=" O ASP I 404 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ASN I 414 " --> pdb=" O GLU I 410 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N TYR I 425 " --> pdb=" O GLU I 421 " (cutoff:3.500A) Processing helix chain 'S' and resid 10 through 29 Processing helix chain 'S' and resid 36 through 43 removed outlier: 3.918A pdb=" N LYS S 40 " --> pdb=" O MET S 36 " (cutoff:3.500A) Processing helix chain 'S' and resid 71 through 80 removed outlier: 4.323A pdb=" N ILE S 75 " --> pdb=" O GLU S 71 " (cutoff:3.500A) removed outlier: 4.134A 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 128 removed outlier: 3.586A pdb=" N GLN S 128 " --> pdb=" O LYS S 124 " (cutoff:3.500A) Processing helix chain 'S' and resid 143 through 161 removed outlier: 4.101A pdb=" N THR S 150 " --> pdb=" O GLY S 146 " (cutoff:3.500A) Processing helix chain 'S' and resid 182 through 197 removed outlier: 3.562A pdb=" N ASN S 186 " --> pdb=" O VAL S 182 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N HIS S 192 " --> pdb=" O ILE S 188 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N THR S 193 " --> pdb=" O LEU S 189 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLU S 196 " --> pdb=" O HIS S 192 " (cutoff:3.500A) Processing helix chain 'S' and resid 206 through 216 Processing helix chain 'S' and resid 223 through 240 removed outlier: 3.711A 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: 3.812A pdb=" N GLN S 256 " --> pdb=" O LEU S 252 " (cutoff:3.500A) Processing helix chain 'S' and resid 277 through 282 removed outlier: 4.039A pdb=" N TYR S 282 " --> pdb=" O ALA S 278 " (cutoff:3.500A) Processing helix chain 'S' and resid 287 through 297 removed outlier: 3.808A pdb=" N PHE S 296 " --> pdb=" O THR S 292 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLU S 297 " --> pdb=" O ASN S 293 " (cutoff:3.500A) Processing helix chain 'S' and resid 306 through 310 Processing helix chain 'S' and resid 324 through 337 removed outlier: 3.768A pdb=" N VAL S 328 " --> pdb=" O VAL S 324 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N THR S 337 " --> pdb=" O ALA S 333 " (cutoff:3.500A) Processing helix chain 'S' and resid 383 through 400 removed outlier: 3.939A pdb=" N ALA S 387 " --> pdb=" O ALA S 383 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N LEU S 391 " --> pdb=" O ALA S 387 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LYS S 394 " --> pdb=" O ARG S 390 " (cutoff:3.500A) Processing helix chain 'S' and resid 404 through 411 removed outlier: 4.346A pdb=" N TYR S 408 " --> pdb=" O PHE S 404 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLU S 411 " --> pdb=" O TRP S 407 " (cutoff:3.500A) Processing helix chain 'S' and resid 414 through 436 removed outlier: 4.124A pdb=" N PHE S 418 " --> pdb=" O GLU S 414 " (cutoff:3.500A) removed outlier: 3.662A 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 56 removed outlier: 6.445A pdb=" N LYS K 7 " --> pdb=" O MET K 327 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N ALA K 329 " --> pdb=" O LYS K 7 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N ALA K 9 " --> pdb=" O ALA K 329 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N LEU K 331 " --> pdb=" O ALA K 9 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ARG K 11 " --> pdb=" O LEU K 331 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ASN K 90 " --> pdb=" O ARG K 324 " (cutoff:3.500A) removed outlier: 8.725A pdb=" N ALA K 326 " --> pdb=" O ASN K 90 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N CYS K 92 " --> pdb=" O ALA K 326 " (cutoff:3.500A) removed outlier: 7.996A pdb=" N VAL K 328 " --> pdb=" O CYS K 92 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N PHE K 94 " --> pdb=" O VAL K 328 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N ALA K 330 " --> pdb=" O PHE K 94 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N TYR K 96 " --> pdb=" O ALA K 330 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LYS K 240 " --> pdb=" O GLN K 227 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'K' and resid 54 through 56 removed outlier: 6.445A pdb=" N LYS K 7 " --> pdb=" O MET K 327 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N ALA K 329 " --> pdb=" O LYS K 7 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N ALA K 9 " --> pdb=" O ALA K 329 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N LEU K 331 " --> pdb=" O ALA K 9 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ARG K 11 " --> pdb=" O LEU K 331 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ASN K 90 " --> pdb=" O ARG K 324 " (cutoff:3.500A) removed outlier: 8.725A pdb=" N ALA K 326 " --> pdb=" O ASN K 90 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N CYS K 92 " --> pdb=" O ALA K 326 " (cutoff:3.500A) removed outlier: 7.996A pdb=" N VAL K 328 " --> pdb=" O CYS K 92 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N PHE K 94 " --> pdb=" O VAL K 328 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N ALA K 330 " --> pdb=" O PHE K 94 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N TYR K 96 " --> pdb=" O ALA K 330 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LYS K 240 " --> pdb=" O GLN K 227 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N VAL K 142 " --> pdb=" O VAL K 186 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'K' and resid 28 through 31 Processing sheet with id=AA4, first strand: chain 'K' and resid 168 through 171 Processing sheet with id=AA5, first strand: chain 'K' and resid 205 through 206 Processing sheet with id=AA6, first strand: chain 'N' and resid 54 through 57 removed outlier: 6.266A pdb=" N LYS N 7 " --> pdb=" O MET N 327 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N ALA N 329 " --> pdb=" O LYS N 7 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N ALA N 9 " --> pdb=" O ALA N 329 " (cutoff:3.500A) removed outlier: 8.183A pdb=" N LEU N 331 " --> pdb=" O ALA N 9 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ARG N 11 " --> pdb=" O LEU N 331 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N ASN N 90 " --> pdb=" O ARG N 324 " (cutoff:3.500A) removed outlier: 8.862A pdb=" N ALA N 326 " --> pdb=" O ASN N 90 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N CYS N 92 " --> pdb=" O ALA N 326 " (cutoff:3.500A) removed outlier: 8.405A pdb=" N VAL N 328 " --> pdb=" O CYS N 92 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N PHE N 94 " --> pdb=" O VAL N 328 " (cutoff:3.500A) removed outlier: 8.068A pdb=" N ALA N 330 " --> pdb=" O PHE N 94 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N TYR N 96 " --> pdb=" O ALA N 330 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N THR N 238 " --> pdb=" O ARG N 229 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N ARG N 229 " --> pdb=" O THR N 238 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LYS N 240 " --> pdb=" O GLN N 227 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'N' and resid 54 through 57 removed outlier: 6.266A pdb=" N LYS N 7 " --> pdb=" O MET N 327 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N ALA N 329 " --> pdb=" O LYS N 7 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N ALA N 9 " --> pdb=" O ALA N 329 " (cutoff:3.500A) removed outlier: 8.183A pdb=" N LEU N 331 " --> pdb=" O ALA N 9 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ARG N 11 " --> pdb=" O LEU N 331 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N ASN N 90 " --> pdb=" O ARG N 324 " (cutoff:3.500A) removed outlier: 8.862A pdb=" N ALA N 326 " --> pdb=" O ASN N 90 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N CYS N 92 " --> pdb=" O ALA N 326 " (cutoff:3.500A) removed outlier: 8.405A pdb=" N VAL N 328 " --> pdb=" O CYS N 92 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N PHE N 94 " --> pdb=" O VAL N 328 " (cutoff:3.500A) removed outlier: 8.068A pdb=" N ALA N 330 " --> pdb=" O PHE N 94 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N TYR N 96 " --> pdb=" O ALA N 330 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N THR N 238 " --> pdb=" O ARG N 229 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N ARG N 229 " --> pdb=" O THR N 238 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LYS N 240 " --> pdb=" O GLN N 227 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'N' and resid 29 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: 3.516A 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: 7.487A pdb=" N GLU A 3 " --> pdb=" O GLN A 133 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N PHE A 135 " --> pdb=" O GLU A 3 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N ILE A 5 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N VAL A 137 " --> pdb=" O ILE A 5 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N ILE A 7 " --> pdb=" O VAL A 137 " (cutoff:3.500A) removed outlier: 5.698A pdb=" N HIS A 139 " --> pdb=" O ILE A 7 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N VAL A 9 " --> pdb=" O HIS A 139 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N GLN A 133 " --> pdb=" O SER A 165 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N LEU A 167 " --> pdb=" O GLN A 133 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N PHE A 135 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N PHE A 169 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N VAL A 137 " --> pdb=" O PHE A 169 " (cutoff:3.500A) removed outlier: 8.286A pdb=" N ILE A 171 " --> pdb=" O VAL A 137 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N HIS A 139 " --> pdb=" O ILE A 171 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N LYS A 166 " --> pdb=" O CYS A 200 " (cutoff:3.500A) removed outlier: 8.062A pdb=" N PHE A 202 " --> pdb=" O LYS A 166 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N GLU A 168 " --> pdb=" O PHE A 202 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N VAL A 204 " --> pdb=" O GLU A 168 " (cutoff:3.500A) removed outlier: 6.456A 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 91 removed outlier: 8.370A pdb=" N VAL B 91 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N LEU B 65 " --> pdb=" O VAL B 91 " (cutoff:3.500A) removed outlier: 8.611A pdb=" N ILE B 64 " --> pdb=" O ILE B 4 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N HIS B 6 " --> pdb=" O ILE B 64 " (cutoff:3.500A) removed outlier: 8.056A pdb=" N VAL B 66 " --> pdb=" O HIS B 6 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N GLN B 8 " --> pdb=" O VAL B 66 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N GLU B 3 " --> pdb=" O GLN B 131 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N PHE B 133 " --> pdb=" O GLU B 3 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N VAL B 5 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N LEU B 135 " --> pdb=" O VAL B 5 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N ILE B 7 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N HIS B 137 " --> pdb=" O ILE B 7 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N ALA B 9 " --> pdb=" O HIS B 137 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU B 135 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N HIS B 137 " --> pdb=" O PHE B 167 " (cutoff:3.500A) removed outlier: 8.381A pdb=" N TYR B 200 " --> pdb=" O MET B 164 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N THR B 166 " --> pdb=" O TYR B 200 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N ILE B 202 " --> pdb=" O THR B 166 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N SER B 168 " --> pdb=" O ILE B 202 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N PHE B 265 " --> pdb=" O SER B 371 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N SER B 371 " --> pdb=" O PHE B 265 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU B 246 " --> pdb=" O VAL B 353 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 51 through 54 Processing sheet with id=AB7, first strand: chain 'E' and resid 65 through 68 removed outlier: 7.648A pdb=" N GLU E 3 " --> pdb=" O GLN E 133 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N PHE E 135 " --> pdb=" O GLU E 3 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N ILE E 5 " --> pdb=" O PHE E 135 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N VAL E 137 " --> pdb=" O ILE E 5 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ILE E 7 " --> pdb=" O VAL E 137 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N HIS E 139 " --> pdb=" O ILE E 7 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N VAL E 9 " --> pdb=" O HIS E 139 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N SER E 165 " --> pdb=" O GLN E 133 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N HIS E 139 " --> pdb=" O PHE E 169 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ILE E 171 " --> pdb=" O HIS E 139 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N CYS E 200 " --> pdb=" O LYS E 166 " (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 91 removed outlier: 8.340A pdb=" N VAL I 91 " --> pdb=" O ALA I 63 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N LEU I 65 " --> pdb=" O VAL I 91 " (cutoff:3.500A) removed outlier: 8.777A pdb=" N ILE I 64 " --> pdb=" O ILE I 4 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N HIS I 6 " --> pdb=" O ILE I 64 " (cutoff:3.500A) removed outlier: 8.223A pdb=" N VAL I 66 " --> pdb=" O HIS I 6 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N GLN I 8 " --> pdb=" O VAL I 66 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N GLU I 3 " --> pdb=" O GLN I 131 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N PHE I 133 " --> pdb=" O GLU I 3 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N VAL I 5 " --> pdb=" O PHE I 133 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N GLN I 131 " --> pdb=" O ILE I 163 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'I' and resid 51 through 53 Processing sheet with id=AC3, first strand: chain 'I' and resid 136 through 138 removed outlier: 6.345A pdb=" N SER I 168 " --> pdb=" O ILE I 202 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N THR I 199 " --> pdb=" O PHE I 266 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N CYS I 201 " --> pdb=" O PRO I 268 " (cutoff:3.500A) removed outlier: 10.457A pdb=" N PHE I 270 " --> pdb=" O CYS I 201 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N PHE I 265 " --> pdb=" O SER I 371 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N SER I 371 " --> pdb=" O PHE I 265 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'S' and resid 65 through 68 removed outlier: 8.664A pdb=" N VAL S 66 " --> pdb=" O CYS S 4 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N SER S 6 " --> pdb=" O VAL S 66 " (cutoff:3.500A) removed outlier: 7.944A pdb=" N VAL S 68 " --> pdb=" O SER S 6 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N HIS S 8 " --> pdb=" O VAL S 68 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N GLU S 3 " --> pdb=" O GLN S 133 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N PHE S 135 " --> pdb=" O GLU S 3 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N ILE S 5 " --> pdb=" O PHE S 135 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N VAL S 137 " --> pdb=" O ILE S 5 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N ILE S 7 " --> pdb=" O VAL S 137 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N GLN S 133 " --> pdb=" O SER S 165 " (cutoff:3.500A) removed outlier: 7.758A pdb=" N LEU S 167 " --> pdb=" O GLN S 133 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N PHE S 135 " --> pdb=" O LEU S 167 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N PHE S 169 " --> pdb=" O PHE S 135 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N VAL S 137 " --> pdb=" O PHE S 169 " (cutoff:3.500A) removed outlier: 8.262A pdb=" N ILE S 171 " --> pdb=" O VAL S 137 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N LYS S 166 " --> pdb=" O CYS S 200 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N PHE S 202 " --> pdb=" O LYS S 166 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N GLU S 168 " --> pdb=" O PHE S 202 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N VAL S 204 " --> pdb=" O GLU S 168 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N SER S 170 " --> pdb=" O VAL S 204 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'S' and resid 53 through 55 Processing sheet with id=AC6, first strand: chain 'S' and resid 269 through 272 1149 hydrogen bonds defined for protein. 3309 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: 9.24 Time building geometry restraints manager: 10.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 4559 1.33 - 1.45: 6225 1.45 - 1.58: 13180 1.58 - 1.71: 34 1.71 - 1.83: 244 Bond restraints: 24242 Sorted by residual: bond pdb=" C LYS K 299 " pdb=" N LYS K 300 " ideal model delta sigma weight residual 1.331 1.568 -0.238 1.33e-02 5.65e+03 3.19e+02 bond pdb=" N3B ANP N 501 " pdb=" PG ANP N 501 " ideal model delta sigma weight residual 1.795 1.631 0.164 2.00e-02 2.50e+03 6.73e+01 bond pdb=" N3B ANP K 502 " pdb=" PG ANP K 502 " ideal model delta sigma weight residual 1.795 1.632 0.163 2.00e-02 2.50e+03 6.66e+01 bond pdb=" O3A ANP N 501 " pdb=" PB ANP N 501 " ideal model delta sigma weight residual 1.700 1.599 0.101 2.00e-02 2.50e+03 2.53e+01 bond pdb=" O3A ANP K 502 " pdb=" PB ANP K 502 " ideal model delta sigma weight residual 1.700 1.603 0.097 2.00e-02 2.50e+03 2.36e+01 ... (remaining 24237 not shown) Histogram of bond angle deviations from ideal: 84.84 - 95.11: 8 95.11 - 105.38: 473 105.38 - 115.65: 14853 115.65 - 125.92: 17228 125.92 - 136.19: 344 Bond angle restraints: 32906 Sorted by residual: angle pdb=" O LYS K 299 " pdb=" C LYS K 299 " pdb=" N LYS K 300 " ideal model delta sigma weight residual 122.91 130.32 -7.41 1.19e+00 7.06e-01 3.88e+01 angle pdb=" CA LYS K 299 " pdb=" C LYS K 299 " pdb=" N LYS K 300 " ideal model delta sigma weight residual 114.98 106.67 8.31 1.34e+00 5.57e-01 3.85e+01 angle pdb=" CA PRO N 333 " pdb=" N PRO N 333 " pdb=" CD PRO N 333 " ideal model delta sigma weight residual 112.00 104.66 7.34 1.40e+00 5.10e-01 2.75e+01 angle pdb=" C LYS K 299 " pdb=" N LYS K 300 " pdb=" CA LYS K 300 " ideal model delta sigma weight residual 120.71 113.75 6.96 1.42e+00 4.96e-01 2.40e+01 angle pdb=" C LYS K 296 " pdb=" N LYS K 297 " pdb=" CA LYS K 297 " ideal model delta sigma weight residual 121.54 130.62 -9.08 1.91e+00 2.74e-01 2.26e+01 ... (remaining 32901 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.05: 14006 32.05 - 64.09: 606 64.09 - 96.14: 82 96.14 - 128.18: 24 128.18 - 160.23: 18 Dihedral angle restraints: 14736 sinusoidal: 6094 harmonic: 8642 Sorted by residual: dihedral pdb=" C5' GTP E 501 " pdb=" O5' GTP E 501 " pdb=" PA GTP E 501 " pdb=" O3A GTP E 501 " ideal model delta sinusoidal sigma weight residual 69.27 -90.96 160.23 1 2.00e+01 2.50e-03 4.66e+01 dihedral pdb=" C5' GTP S 501 " pdb=" O5' GTP S 501 " pdb=" PA GTP S 501 " pdb=" O3A GTP S 501 " ideal model delta sinusoidal sigma weight residual 69.27 -136.35 -154.38 1 2.00e+01 2.50e-03 4.56e+01 dihedral pdb=" C8 GTP E 501 " pdb=" C1' GTP E 501 " pdb=" N9 GTP E 501 " pdb=" O4' GTP E 501 " ideal model delta sinusoidal sigma weight residual 104.59 -37.70 142.29 1 2.00e+01 2.50e-03 4.30e+01 ... (remaining 14733 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.100: 3302 0.100 - 0.199: 301 0.199 - 0.299: 6 0.299 - 0.398: 2 0.398 - 0.498: 2 Chirality restraints: 3613 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 -2.66 -0.50 2.00e-01 2.50e+01 6.20e+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 -2.68 -0.49 2.00e-01 2.50e+01 5.94e+00 chirality pdb=" C3' ANP K 502 " pdb=" C2' ANP K 502 " pdb=" C4' ANP K 502 " pdb=" O3' ANP K 502 " both_signs ideal model delta sigma weight residual False -2.36 -2.71 0.35 2.00e-01 2.50e+01 3.11e+00 ... (remaining 3610 not shown) Planarity restraints: 4276 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C29 TA1 B 502 " -0.219 2.00e-02 2.50e+03 1.82e-01 4.13e+02 pdb=" C30 TA1 B 502 " 0.062 2.00e-02 2.50e+03 pdb=" C31 TA1 B 502 " -0.157 2.00e-02 2.50e+03 pdb=" N01 TA1 B 502 " 0.298 2.00e-02 2.50e+03 pdb=" O14 TA1 B 502 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY K 291 " 0.062 5.00e-02 4.00e+02 9.35e-02 1.40e+01 pdb=" N PRO K 292 " -0.162 5.00e-02 4.00e+02 pdb=" CA PRO K 292 " 0.049 5.00e-02 4.00e+02 pdb=" CD PRO K 292 " 0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP K 363 " -0.056 5.00e-02 4.00e+02 8.31e-02 1.10e+01 pdb=" N PRO K 364 " 0.144 5.00e-02 4.00e+02 pdb=" CA PRO K 364 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO K 364 " -0.046 5.00e-02 4.00e+02 ... (remaining 4273 not shown) Histogram of nonbonded interaction distances: 1.19 - 1.93: 6 1.93 - 2.67: 542 2.67 - 3.42: 33111 3.42 - 4.16: 53014 4.16 - 4.90: 99389 Nonbonded interactions: 186062 Sorted by model distance: nonbonded pdb="MG MG K 501 " pdb=" O2G ANP K 502 " model vdw 1.190 2.170 nonbonded pdb=" CD2 LEU B 215 " pdb=" NH2 ARG B 276 " model vdw 1.638 3.540 nonbonded pdb="MG MG K 501 " pdb=" PG ANP K 502 " model vdw 1.903 2.530 nonbonded pdb=" O1G GTP S 501 " pdb="MG MG S 502 " model vdw 1.921 2.170 nonbonded pdb=" O1B GTP E 501 " pdb="MG MG E 502 " model vdw 1.929 2.170 ... (remaining 186057 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' 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 385) selection = (chain 'N' and resid 4 through 385) } 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: 30.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 70.610 Find NCS groups from input model: 1.410 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 105.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.238 24242 Z= 0.480 Angle : 0.962 12.071 32906 Z= 0.549 Chirality : 0.055 0.498 3613 Planarity : 0.007 0.182 4276 Dihedral : 19.178 160.227 9190 Min Nonbonded Distance : 1.190 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.44 % Allowed : 5.30 % Favored : 94.26 % Rotamer: Outliers : 1.60 % Allowed : 16.89 % Favored : 81.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.15), residues: 2969 helix: 0.84 (0.15), residues: 1222 sheet: -0.15 (0.22), residues: 533 loop : -1.54 (0.17), residues: 1214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 388 HIS 0.015 0.002 HIS S 107 PHE 0.021 0.002 PHE B 367 TYR 0.026 0.002 TYR N 189 ARG 0.018 0.001 ARG E 221 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5938 Ramachandran restraints generated. 2969 Oldfield, 0 Emsley, 2969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5938 Ramachandran restraints generated. 2969 Oldfield, 0 Emsley, 2969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 561 residues out of total 2544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 524 time to evaluate : 2.647 Fit side-chains REVERT: K 35 THR cc_start: 0.8100 (m) cc_final: 0.7267 (m) REVERT: K 52 PHE cc_start: 0.8339 (m-80) cc_final: 0.7943 (m-80) REVERT: K 57 TRP cc_start: 0.7393 (t-100) cc_final: 0.6403 (t-100) REVERT: K 98 GLN cc_start: 0.7264 (pp30) cc_final: 0.7015 (pp30) REVERT: K 180 ASP cc_start: 0.8419 (t0) cc_final: 0.7811 (t0) REVERT: K 253 GLU cc_start: 0.7808 (OUTLIER) cc_final: 0.7592 (mm-30) REVERT: K 288 MET cc_start: 0.8556 (tmm) cc_final: 0.8171 (tmm) REVERT: N 13 ARG cc_start: 0.6561 (OUTLIER) cc_final: 0.6342 (ttp-170) REVERT: N 159 ASN cc_start: 0.8875 (t0) cc_final: 0.8671 (t0) REVERT: N 254 ARG cc_start: 0.6126 (mtp-110) cc_final: 0.5475 (mtp-110) REVERT: E 221 ARG cc_start: 0.8912 (mtt-85) cc_final: 0.8420 (mtt-85) REVERT: E 414 GLU cc_start: 0.7852 (pt0) cc_final: 0.7336 (pt0) REVERT: I 162 ARG cc_start: 0.8588 (OUTLIER) cc_final: 0.7341 (mmp80) REVERT: I 163 ILE cc_start: 0.8733 (mm) cc_final: 0.8501 (mt) REVERT: I 213 ARG cc_start: 0.8073 (ttm110) cc_final: 0.7769 (ttm-80) REVERT: S 6 SER cc_start: 0.8853 (m) cc_final: 0.8559 (t) REVERT: S 24 TYR cc_start: 0.8023 (m-80) cc_final: 0.7666 (m-80) REVERT: S 50 ASN cc_start: 0.7419 (t0) cc_final: 0.6900 (t0) REVERT: S 217 LEU cc_start: 0.8988 (mt) cc_final: 0.8755 (tt) REVERT: S 420 GLU cc_start: 0.8567 (mt-10) cc_final: 0.8169 (mt-10) REVERT: S 450 GLU cc_start: 0.3357 (OUTLIER) cc_final: 0.1504 (mm-30) outliers start: 37 outliers final: 10 residues processed: 542 average time/residue: 0.3678 time to fit residues: 306.2108 Evaluate side-chains 494 residues out of total 2544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 480 time to evaluate : 2.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 103 LYS Chi-restraints excluded: chain K residue 215 SER Chi-restraints excluded: chain K residue 253 GLU Chi-restraints excluded: chain K residue 281 VAL Chi-restraints excluded: chain N residue 13 ARG Chi-restraints excluded: chain N residue 303 PHE Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain E residue 109 THR Chi-restraints excluded: chain E residue 295 CYS Chi-restraints excluded: chain I residue 162 ARG Chi-restraints excluded: chain I residue 196 THR Chi-restraints excluded: chain I residue 322 SER Chi-restraints excluded: chain S residue 424 ASP Chi-restraints excluded: chain S residue 450 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 249 optimal weight: 3.9990 chunk 224 optimal weight: 3.9990 chunk 124 optimal weight: 0.6980 chunk 76 optimal weight: 4.9990 chunk 151 optimal weight: 0.8980 chunk 119 optimal weight: 2.9990 chunk 232 optimal weight: 2.9990 chunk 89 optimal weight: 0.9990 chunk 141 optimal weight: 1.9990 chunk 172 optimal weight: 4.9990 chunk 268 optimal weight: 9.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 59 HIS N 171 HIS A 15 GLN A 18 ASN A 107 HIS ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 266 HIS B 279 GLN B 292 GLN E 28 HIS E 107 HIS I 105 HIS I 204 ASN I 279 GLN I 332 ASN S 358 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.1490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 24242 Z= 0.265 Angle : 0.632 10.814 32906 Z= 0.315 Chirality : 0.045 0.181 3613 Planarity : 0.005 0.084 4276 Dihedral : 13.543 155.523 3622 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.55 % Favored : 96.25 % Rotamer: Outliers : 3.32 % Allowed : 15.52 % Favored : 81.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % 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: 0.28 (0.16), residues: 2969 helix: 1.54 (0.15), residues: 1235 sheet: 0.18 (0.22), residues: 536 loop : -1.26 (0.17), residues: 1198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 388 HIS 0.008 0.001 HIS E 107 PHE 0.020 0.002 PHE B 367 TYR 0.027 0.001 TYR N 189 ARG 0.007 0.001 ARG I 391 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5938 Ramachandran restraints generated. 2969 Oldfield, 0 Emsley, 2969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5938 Ramachandran restraints generated. 2969 Oldfield, 0 Emsley, 2969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 589 residues out of total 2544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 507 time to evaluate : 2.657 Fit side-chains REVERT: K 27 ILE cc_start: 0.8717 (mm) cc_final: 0.8438 (mm) REVERT: K 98 GLN cc_start: 0.7507 (pp30) cc_final: 0.7233 (pp30) REVERT: K 179 GLU cc_start: 0.8387 (tt0) cc_final: 0.8144 (tm-30) REVERT: K 180 ASP cc_start: 0.8542 (t0) cc_final: 0.8116 (t0) REVERT: K 253 GLU cc_start: 0.7899 (tp30) cc_final: 0.7690 (mm-30) REVERT: K 288 MET cc_start: 0.8527 (tmm) cc_final: 0.8165 (tmm) REVERT: N 159 ASN cc_start: 0.8888 (t0) cc_final: 0.8674 (t0) REVERT: N 171 HIS cc_start: 0.8802 (t-90) cc_final: 0.8526 (t-90) REVERT: N 254 ARG cc_start: 0.6293 (mtp-110) cc_final: 0.5573 (mtp-110) REVERT: N 347 TYR cc_start: 0.8436 (t80) cc_final: 0.7452 (t80) REVERT: A 24 TYR cc_start: 0.8581 (m-80) cc_final: 0.8253 (m-80) REVERT: A 254 GLU cc_start: 0.7790 (mm-30) cc_final: 0.7588 (mm-30) REVERT: A 279 GLU cc_start: 0.8406 (mm-30) cc_final: 0.8160 (mp0) REVERT: B 188 SER cc_start: 0.9077 (t) cc_final: 0.8827 (p) REVERT: B 212 PHE cc_start: 0.8197 (OUTLIER) cc_final: 0.7369 (m-80) REVERT: B 279 GLN cc_start: 0.8331 (mt0) cc_final: 0.8108 (mt0) REVERT: E 92 LEU cc_start: 0.8870 (mt) cc_final: 0.8621 (mm) REVERT: E 379 SER cc_start: 0.9039 (t) cc_final: 0.8447 (p) REVERT: E 414 GLU cc_start: 0.7664 (pt0) cc_final: 0.7158 (pt0) REVERT: E 445 GLU cc_start: 0.2786 (OUTLIER) cc_final: 0.2488 (tm-30) REVERT: I 136 THR cc_start: 0.8888 (m) cc_final: 0.8623 (p) REVERT: I 164 MET cc_start: 0.8574 (tpp) cc_final: 0.8091 (tpp) REVERT: I 213 ARG cc_start: 0.8159 (ttm110) cc_final: 0.7866 (ttm-80) REVERT: I 388 MET cc_start: 0.8864 (mtp) cc_final: 0.8603 (ttm) REVERT: I 406 MET cc_start: 0.7799 (ttp) cc_final: 0.7505 (ttp) REVERT: I 417 ASP cc_start: 0.8609 (m-30) cc_final: 0.8339 (m-30) REVERT: S 1 MET cc_start: 0.6081 (tpp) cc_final: 0.5585 (tpp) REVERT: S 3 GLU cc_start: 0.6958 (mp0) cc_final: 0.6757 (mp0) REVERT: S 6 SER cc_start: 0.8902 (m) cc_final: 0.8587 (t) REVERT: S 15 GLN cc_start: 0.7739 (OUTLIER) cc_final: 0.7452 (mm-40) REVERT: S 24 TYR cc_start: 0.8140 (m-80) cc_final: 0.7757 (m-80) REVERT: S 50 ASN cc_start: 0.7739 (t0) cc_final: 0.6730 (t0) REVERT: S 136 LEU cc_start: 0.8033 (mt) cc_final: 0.7742 (mp) REVERT: S 217 LEU cc_start: 0.9098 (mt) cc_final: 0.8771 (mt) REVERT: S 242 LEU cc_start: 0.8383 (OUTLIER) cc_final: 0.7999 (pp) REVERT: S 297 GLU cc_start: 0.8102 (mm-30) cc_final: 0.7627 (mm-30) REVERT: S 377 MET cc_start: 0.8636 (OUTLIER) cc_final: 0.8322 (ttm) REVERT: S 450 GLU cc_start: 0.3297 (OUTLIER) cc_final: 0.1277 (mm-30) outliers start: 82 outliers final: 47 residues processed: 543 average time/residue: 0.3564 time to fit residues: 304.0928 Evaluate side-chains 521 residues out of total 2544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 468 time to evaluate : 2.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 51 SER Chi-restraints excluded: chain K residue 99 THR Chi-restraints excluded: chain K residue 118 ILE Chi-restraints excluded: chain K residue 127 PHE Chi-restraints excluded: chain K residue 157 LEU Chi-restraints excluded: chain K residue 342 LEU Chi-restraints excluded: chain N residue 13 ARG Chi-restraints excluded: chain N residue 28 ILE Chi-restraints excluded: chain N residue 265 LEU Chi-restraints excluded: chain N residue 308 ASP Chi-restraints excluded: chain N residue 319 LEU Chi-restraints excluded: chain N residue 382 LEU Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 128 GLN Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 266 HIS Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 174 LYS Chi-restraints excluded: chain B residue 212 PHE Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 109 THR Chi-restraints excluded: chain E residue 198 SER Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 295 CYS Chi-restraints excluded: chain E residue 334 THR Chi-restraints excluded: chain E residue 335 ILE Chi-restraints excluded: chain E residue 445 GLU Chi-restraints excluded: chain I residue 166 THR Chi-restraints excluded: chain I residue 176 SER Chi-restraints excluded: chain S residue 2 ARG Chi-restraints excluded: chain S residue 15 GLN Chi-restraints excluded: chain S residue 129 CYS Chi-restraints excluded: chain S residue 130 THR Chi-restraints excluded: chain S residue 204 VAL Chi-restraints excluded: chain S residue 242 LEU Chi-restraints excluded: chain S residue 248 LEU Chi-restraints excluded: chain S residue 259 LEU Chi-restraints excluded: chain S residue 347 CYS Chi-restraints excluded: chain S residue 362 VAL Chi-restraints excluded: chain S residue 377 MET Chi-restraints excluded: chain S residue 450 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 149 optimal weight: 1.9990 chunk 83 optimal weight: 3.9990 chunk 223 optimal weight: 0.9980 chunk 183 optimal weight: 2.9990 chunk 74 optimal weight: 4.9990 chunk 269 optimal weight: 9.9990 chunk 290 optimal weight: 0.9990 chunk 239 optimal weight: 2.9990 chunk 267 optimal weight: 7.9990 chunk 91 optimal weight: 4.9990 chunk 216 optimal weight: 4.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 235 ASN N 66 ASN N 270 ASN ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 298 ASN E 139 HIS I 332 ASN I 433 GLN A Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.2115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 24242 Z= 0.313 Angle : 0.612 9.735 32906 Z= 0.306 Chirality : 0.046 0.472 3613 Planarity : 0.005 0.082 4276 Dihedral : 10.691 155.246 3602 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.95 % Favored : 95.84 % Rotamer: Outliers : 3.36 % Allowed : 16.97 % Favored : 79.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % 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: 0.44 (0.16), residues: 2969 helix: 1.67 (0.15), residues: 1251 sheet: 0.29 (0.22), residues: 532 loop : -1.22 (0.17), residues: 1186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 344 HIS 0.037 0.002 HIS A 266 PHE 0.020 0.002 PHE B 367 TYR 0.020 0.002 TYR K 74 ARG 0.005 0.001 ARG I 391 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5938 Ramachandran restraints generated. 2969 Oldfield, 0 Emsley, 2969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5938 Ramachandran restraints generated. 2969 Oldfield, 0 Emsley, 2969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 572 residues out of total 2544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 489 time to evaluate : 2.724 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 15 PHE cc_start: 0.8461 (m-80) cc_final: 0.8134 (m-10) REVERT: K 27 ILE cc_start: 0.8488 (mm) cc_final: 0.8258 (mm) REVERT: K 98 GLN cc_start: 0.7525 (pp30) cc_final: 0.7305 (pp30) REVERT: K 179 GLU cc_start: 0.8455 (tt0) cc_final: 0.8169 (tm-30) REVERT: K 180 ASP cc_start: 0.8669 (t0) cc_final: 0.7900 (t0) REVERT: K 288 MET cc_start: 0.8556 (tmm) cc_final: 0.8148 (tmm) REVERT: K 293 ASN cc_start: 0.6602 (OUTLIER) cc_final: 0.6185 (m110) REVERT: N 319 LEU cc_start: 0.8870 (OUTLIER) cc_final: 0.8600 (mp) REVERT: N 347 TYR cc_start: 0.8498 (t80) cc_final: 0.7861 (t80) REVERT: A 24 TYR cc_start: 0.8659 (m-80) cc_final: 0.8291 (m-80) REVERT: A 123 ARG cc_start: 0.8351 (ttp80) cc_final: 0.8102 (ttm170) REVERT: A 279 GLU cc_start: 0.8472 (mm-30) cc_final: 0.8211 (mp0) REVERT: A 334 THR cc_start: 0.8986 (m) cc_final: 0.8710 (t) REVERT: A 379 SER cc_start: 0.8822 (OUTLIER) cc_final: 0.8575 (p) REVERT: B 31 ASP cc_start: 0.8151 (OUTLIER) cc_final: 0.7834 (t70) REVERT: B 188 SER cc_start: 0.9098 (t) cc_final: 0.8872 (p) REVERT: B 197 ASP cc_start: 0.8152 (m-30) cc_final: 0.7906 (m-30) REVERT: B 212 PHE cc_start: 0.8310 (OUTLIER) cc_final: 0.7516 (m-80) REVERT: B 218 THR cc_start: 0.9023 (p) cc_final: 0.8822 (p) REVERT: B 407 GLU cc_start: 0.8035 (OUTLIER) cc_final: 0.7762 (mm-30) REVERT: E 92 LEU cc_start: 0.8784 (mt) cc_final: 0.8570 (mm) REVERT: E 379 SER cc_start: 0.9034 (t) cc_final: 0.8412 (p) REVERT: E 414 GLU cc_start: 0.7699 (pt0) cc_final: 0.7299 (pt0) REVERT: E 445 GLU cc_start: 0.2996 (OUTLIER) cc_final: 0.2713 (tm-30) REVERT: I 136 THR cc_start: 0.8898 (m) cc_final: 0.8683 (p) REVERT: I 164 MET cc_start: 0.8604 (tpp) cc_final: 0.8144 (tpp) REVERT: I 209 ASP cc_start: 0.8321 (t70) cc_final: 0.8092 (t0) REVERT: I 213 ARG cc_start: 0.8198 (ttm110) cc_final: 0.7963 (ttm-80) REVERT: I 406 MET cc_start: 0.7773 (ttp) cc_final: 0.6994 (ttp) REVERT: I 410 GLU cc_start: 0.8097 (mt-10) cc_final: 0.7824 (mt-10) REVERT: S 6 SER cc_start: 0.8970 (m) cc_final: 0.8638 (t) REVERT: S 50 ASN cc_start: 0.7837 (t0) cc_final: 0.6677 (t0) REVERT: S 136 LEU cc_start: 0.8143 (mt) cc_final: 0.7811 (mp) REVERT: S 182 VAL cc_start: 0.8055 (m) cc_final: 0.7725 (m) REVERT: S 297 GLU cc_start: 0.8155 (mm-30) cc_final: 0.7652 (mm-30) REVERT: S 377 MET cc_start: 0.8649 (OUTLIER) cc_final: 0.8373 (ttm) REVERT: S 391 LEU cc_start: 0.9004 (tp) cc_final: 0.8714 (tp) REVERT: S 422 ARG cc_start: 0.8184 (tpt90) cc_final: 0.7969 (tpt90) REVERT: S 450 GLU cc_start: 0.3312 (OUTLIER) cc_final: 0.1208 (mm-30) outliers start: 83 outliers final: 53 residues processed: 533 average time/residue: 0.3367 time to fit residues: 280.8545 Evaluate side-chains 521 residues out of total 2544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 459 time to evaluate : 2.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 51 SER Chi-restraints excluded: chain K residue 99 THR Chi-restraints excluded: chain K residue 118 ILE Chi-restraints excluded: chain K residue 154 VAL Chi-restraints excluded: chain K residue 178 VAL Chi-restraints excluded: chain K residue 270 ASN Chi-restraints excluded: chain K residue 293 ASN Chi-restraints excluded: chain K residue 342 LEU Chi-restraints excluded: chain N residue 28 ILE Chi-restraints excluded: chain N residue 31 SER Chi-restraints excluded: chain N residue 196 MET Chi-restraints excluded: chain N residue 303 PHE Chi-restraints excluded: chain N residue 305 LEU Chi-restraints excluded: chain N residue 308 ASP Chi-restraints excluded: chain N residue 319 LEU Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 128 GLN Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 340 SER Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 212 PHE Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 407 GLU Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 109 THR Chi-restraints excluded: chain E residue 198 SER Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 295 CYS Chi-restraints excluded: chain E residue 334 THR Chi-restraints excluded: chain E residue 335 ILE Chi-restraints excluded: chain E residue 435 VAL Chi-restraints excluded: chain E residue 445 GLU Chi-restraints excluded: chain I residue 166 THR Chi-restraints excluded: chain I residue 342 VAL Chi-restraints excluded: chain S residue 93 ILE Chi-restraints excluded: chain S residue 129 CYS Chi-restraints excluded: chain S residue 130 THR Chi-restraints excluded: chain S residue 194 THR Chi-restraints excluded: chain S residue 204 VAL Chi-restraints excluded: chain S residue 248 LEU Chi-restraints excluded: chain S residue 259 LEU Chi-restraints excluded: chain S residue 288 VAL Chi-restraints excluded: chain S residue 295 CYS Chi-restraints excluded: chain S residue 316 CYS Chi-restraints excluded: chain S residue 362 VAL Chi-restraints excluded: chain S residue 377 MET Chi-restraints excluded: chain S residue 450 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 266 optimal weight: 1.9990 chunk 202 optimal weight: 1.9990 chunk 139 optimal weight: 3.9990 chunk 29 optimal weight: 5.9990 chunk 128 optimal weight: 0.9980 chunk 180 optimal weight: 0.7980 chunk 270 optimal weight: 2.9990 chunk 286 optimal weight: 3.9990 chunk 141 optimal weight: 5.9990 chunk 256 optimal weight: 0.6980 chunk 77 optimal weight: 3.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 293 ASN N 171 HIS ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 279 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.2475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 24242 Z= 0.224 Angle : 0.564 7.104 32906 Z= 0.282 Chirality : 0.044 0.402 3613 Planarity : 0.004 0.081 4276 Dihedral : 9.719 155.316 3598 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.78 % Favored : 96.08 % Rotamer: Outliers : 3.13 % Allowed : 17.75 % Favored : 79.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % 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: 0.59 (0.16), residues: 2969 helix: 1.82 (0.15), residues: 1250 sheet: 0.31 (0.22), residues: 546 loop : -1.16 (0.17), residues: 1173 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 344 HIS 0.008 0.001 HIS N 171 PHE 0.022 0.001 PHE B 367 TYR 0.016 0.001 TYR N 189 ARG 0.004 0.000 ARG E 221 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5938 Ramachandran restraints generated. 2969 Oldfield, 0 Emsley, 2969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5938 Ramachandran restraints generated. 2969 Oldfield, 0 Emsley, 2969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 559 residues out of total 2544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 483 time to evaluate : 2.578 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 15 PHE cc_start: 0.8516 (m-80) cc_final: 0.8154 (m-10) REVERT: K 27 ILE cc_start: 0.8278 (mm) cc_final: 0.8064 (mm) REVERT: K 98 GLN cc_start: 0.7640 (pp30) cc_final: 0.7408 (pp30) REVERT: K 179 GLU cc_start: 0.8461 (tt0) cc_final: 0.8175 (tm-30) REVERT: K 180 ASP cc_start: 0.8632 (t0) cc_final: 0.7995 (t0) REVERT: K 288 MET cc_start: 0.8483 (tmm) cc_final: 0.8101 (tmm) REVERT: N 110 LYS cc_start: 0.8249 (tptt) cc_final: 0.7742 (tptt) REVERT: N 319 LEU cc_start: 0.8907 (OUTLIER) cc_final: 0.8696 (mp) REVERT: N 347 TYR cc_start: 0.8497 (t80) cc_final: 0.7961 (t80) REVERT: A 24 TYR cc_start: 0.8639 (m-80) cc_final: 0.8359 (m-80) REVERT: A 123 ARG cc_start: 0.8384 (ttp80) cc_final: 0.8169 (ttp80) REVERT: A 230 LEU cc_start: 0.8724 (mt) cc_final: 0.8459 (mp) REVERT: A 279 GLU cc_start: 0.8485 (mm-30) cc_final: 0.8212 (mp0) REVERT: A 334 THR cc_start: 0.8974 (m) cc_final: 0.8700 (t) REVERT: A 379 SER cc_start: 0.8826 (OUTLIER) cc_final: 0.8561 (p) REVERT: B 31 ASP cc_start: 0.8122 (OUTLIER) cc_final: 0.7877 (t70) REVERT: B 174 LYS cc_start: 0.8846 (OUTLIER) cc_final: 0.8632 (ptpt) REVERT: B 188 SER cc_start: 0.9041 (t) cc_final: 0.8813 (p) REVERT: B 197 ASP cc_start: 0.8186 (m-30) cc_final: 0.7943 (m-30) REVERT: B 212 PHE cc_start: 0.8290 (OUTLIER) cc_final: 0.7484 (m-80) REVERT: B 282 ARG cc_start: 0.8180 (mtp85) cc_final: 0.7647 (mmt-90) REVERT: B 407 GLU cc_start: 0.7924 (OUTLIER) cc_final: 0.7473 (mm-30) REVERT: E 275 VAL cc_start: 0.8924 (OUTLIER) cc_final: 0.8698 (m) REVERT: E 379 SER cc_start: 0.9012 (t) cc_final: 0.8422 (p) REVERT: E 392 ASP cc_start: 0.8609 (m-30) cc_final: 0.8395 (m-30) REVERT: E 445 GLU cc_start: 0.3239 (OUTLIER) cc_final: 0.2854 (tm-30) REVERT: I 161 ASP cc_start: 0.8370 (t0) cc_final: 0.8003 (t0) REVERT: I 209 ASP cc_start: 0.8350 (t70) cc_final: 0.8092 (t0) REVERT: I 213 ARG cc_start: 0.8263 (ttm110) cc_final: 0.8037 (ttm-80) REVERT: I 406 MET cc_start: 0.7622 (ttp) cc_final: 0.6970 (ttp) REVERT: I 410 GLU cc_start: 0.8112 (mt-10) cc_final: 0.7907 (mt-10) REVERT: I 417 ASP cc_start: 0.8562 (m-30) cc_final: 0.8318 (m-30) REVERT: I 426 GLN cc_start: 0.8290 (tm-30) cc_final: 0.8072 (tm-30) REVERT: S 6 SER cc_start: 0.8966 (m) cc_final: 0.8631 (t) REVERT: S 27 GLU cc_start: 0.8624 (mm-30) cc_final: 0.8338 (mm-30) REVERT: S 50 ASN cc_start: 0.7750 (t0) cc_final: 0.7448 (t0) REVERT: S 182 VAL cc_start: 0.8078 (m) cc_final: 0.7758 (m) REVERT: S 377 MET cc_start: 0.8610 (OUTLIER) cc_final: 0.8285 (ttm) REVERT: S 391 LEU cc_start: 0.9008 (tp) cc_final: 0.8706 (tp) REVERT: S 450 GLU cc_start: 0.3166 (OUTLIER) cc_final: 0.1178 (mm-30) outliers start: 76 outliers final: 50 residues processed: 518 average time/residue: 0.3415 time to fit residues: 277.3288 Evaluate side-chains 516 residues out of total 2544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 456 time to evaluate : 2.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 51 SER Chi-restraints excluded: chain K residue 99 THR Chi-restraints excluded: chain K residue 118 ILE Chi-restraints excluded: chain K residue 178 VAL Chi-restraints excluded: chain K residue 305 LEU Chi-restraints excluded: chain K residue 342 LEU Chi-restraints excluded: chain K residue 366 ASN Chi-restraints excluded: chain N residue 8 VAL Chi-restraints excluded: chain N residue 28 ILE Chi-restraints excluded: chain N residue 305 LEU Chi-restraints excluded: chain N residue 308 ASP Chi-restraints excluded: chain N residue 319 LEU Chi-restraints excluded: chain A residue 128 GLN Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 340 SER Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 174 LYS Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 212 PHE Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 407 GLU Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 109 THR Chi-restraints excluded: chain E residue 191 THR Chi-restraints excluded: chain E residue 198 SER Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 295 CYS Chi-restraints excluded: chain E residue 334 THR Chi-restraints excluded: chain E residue 335 ILE Chi-restraints excluded: chain E residue 435 VAL Chi-restraints excluded: chain E residue 438 ASP Chi-restraints excluded: chain E residue 445 GLU Chi-restraints excluded: chain I residue 75 SER Chi-restraints excluded: chain I residue 166 THR Chi-restraints excluded: chain I residue 175 VAL Chi-restraints excluded: chain S residue 2 ARG Chi-restraints excluded: chain S residue 77 GLU Chi-restraints excluded: chain S residue 93 ILE Chi-restraints excluded: chain S residue 130 THR Chi-restraints excluded: chain S residue 194 THR Chi-restraints excluded: chain S residue 204 VAL Chi-restraints excluded: chain S residue 217 LEU Chi-restraints excluded: chain S residue 248 LEU Chi-restraints excluded: chain S residue 259 LEU Chi-restraints excluded: chain S residue 295 CYS Chi-restraints excluded: chain S residue 316 CYS Chi-restraints excluded: chain S residue 362 VAL Chi-restraints excluded: chain S residue 377 MET Chi-restraints excluded: chain S residue 424 ASP Chi-restraints excluded: chain S residue 450 GLU 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: 4.9990 chunk 4 optimal weight: 5.9990 chunk 213 optimal weight: 0.0970 chunk 118 optimal weight: 3.9990 chunk 244 optimal weight: 0.9990 chunk 197 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 146 optimal weight: 0.8980 chunk 256 optimal weight: 0.4980 chunk 72 optimal weight: 0.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 171 HIS A 216 ASN A 226 ASN A 309 HIS ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.2736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 24242 Z= 0.165 Angle : 0.542 7.118 32906 Z= 0.268 Chirality : 0.043 0.342 3613 Planarity : 0.004 0.081 4276 Dihedral : 9.304 154.927 3598 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.75 % Favored : 96.11 % Rotamer: Outliers : 2.85 % Allowed : 18.26 % Favored : 78.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % 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: 0.82 (0.16), residues: 2969 helix: 2.01 (0.15), residues: 1248 sheet: 0.48 (0.22), residues: 544 loop : -1.06 (0.18), residues: 1177 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP I 344 HIS 0.007 0.001 HIS S 406 PHE 0.023 0.001 PHE K 303 TYR 0.015 0.001 TYR K 105 ARG 0.004 0.000 ARG E 221 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5938 Ramachandran restraints generated. 2969 Oldfield, 0 Emsley, 2969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5938 Ramachandran restraints generated. 2969 Oldfield, 0 Emsley, 2969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 550 residues out of total 2544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 481 time to evaluate : 3.011 Fit side-chains revert: symmetry clash REVERT: K 15 PHE cc_start: 0.8522 (m-80) cc_final: 0.8164 (m-10) REVERT: K 44 LYS cc_start: 0.8909 (tptm) cc_final: 0.8390 (pptt) REVERT: K 74 TYR cc_start: 0.8241 (t80) cc_final: 0.7768 (t80) REVERT: K 98 GLN cc_start: 0.7656 (pp30) cc_final: 0.7405 (pp30) REVERT: K 105 TYR cc_start: 0.8443 (t80) cc_final: 0.8053 (t80) REVERT: K 108 MET cc_start: 0.8135 (OUTLIER) cc_final: 0.7822 (tpp) REVERT: K 142 VAL cc_start: 0.8457 (t) cc_final: 0.8241 (m) REVERT: K 179 GLU cc_start: 0.8460 (tt0) cc_final: 0.8227 (tm-30) REVERT: K 212 GLU cc_start: 0.8386 (mp0) cc_final: 0.8141 (mp0) REVERT: K 288 MET cc_start: 0.8192 (tmm) cc_final: 0.7961 (tmm) REVERT: N 91 VAL cc_start: 0.7965 (OUTLIER) cc_final: 0.7744 (t) REVERT: N 110 LYS cc_start: 0.8203 (tptt) cc_final: 0.7720 (tptt) REVERT: N 178 VAL cc_start: 0.8858 (t) cc_final: 0.8580 (p) REVERT: N 197 ASP cc_start: 0.8486 (t0) cc_final: 0.8150 (t0) REVERT: N 201 LYS cc_start: 0.8652 (tppt) cc_final: 0.8335 (mtmt) REVERT: N 347 TYR cc_start: 0.8454 (t80) cc_final: 0.7811 (t80) REVERT: A 24 TYR cc_start: 0.8651 (m-80) cc_final: 0.8352 (m-80) REVERT: A 49 PHE cc_start: 0.7896 (m-80) cc_final: 0.7613 (m-10) REVERT: A 230 LEU cc_start: 0.8724 (mt) cc_final: 0.8451 (mp) REVERT: A 239 THR cc_start: 0.8658 (OUTLIER) cc_final: 0.8443 (t) REVERT: A 279 GLU cc_start: 0.8485 (mm-30) cc_final: 0.8206 (mp0) REVERT: A 379 SER cc_start: 0.8816 (t) cc_final: 0.8550 (p) REVERT: B 31 ASP cc_start: 0.8098 (OUTLIER) cc_final: 0.7854 (t70) REVERT: B 136 THR cc_start: 0.8962 (m) cc_final: 0.8714 (p) REVERT: B 174 LYS cc_start: 0.8886 (OUTLIER) cc_final: 0.8672 (ptpt) REVERT: B 188 SER cc_start: 0.9005 (t) cc_final: 0.8791 (p) REVERT: B 197 ASP cc_start: 0.8093 (m-30) cc_final: 0.7869 (m-30) REVERT: B 212 PHE cc_start: 0.8260 (OUTLIER) cc_final: 0.7433 (m-80) REVERT: B 282 ARG cc_start: 0.8161 (mtp85) cc_final: 0.7638 (mmt-90) REVERT: B 407 GLU cc_start: 0.7800 (OUTLIER) cc_final: 0.7415 (mm-30) REVERT: E 3 GLU cc_start: 0.8243 (mp0) cc_final: 0.7951 (mp0) REVERT: E 195 LEU cc_start: 0.7825 (tt) cc_final: 0.7575 (tp) REVERT: E 275 VAL cc_start: 0.8909 (OUTLIER) cc_final: 0.8688 (m) REVERT: E 379 SER cc_start: 0.9012 (t) cc_final: 0.8393 (p) REVERT: E 392 ASP cc_start: 0.8498 (m-30) cc_final: 0.8271 (m-30) REVERT: E 445 GLU cc_start: 0.3290 (OUTLIER) cc_final: 0.2919 (tm-30) REVERT: I 164 MET cc_start: 0.8613 (tpp) cc_final: 0.8093 (tpp) REVERT: I 209 ASP cc_start: 0.8363 (t70) cc_final: 0.8077 (t0) REVERT: I 213 ARG cc_start: 0.8257 (ttm110) cc_final: 0.7930 (ttm-80) REVERT: I 406 MET cc_start: 0.7495 (ttp) cc_final: 0.7269 (ttp) REVERT: I 417 ASP cc_start: 0.8547 (m-30) cc_final: 0.8288 (m-30) REVERT: I 426 GLN cc_start: 0.8233 (tm-30) cc_final: 0.8007 (tm-30) REVERT: S 6 SER cc_start: 0.9032 (m) cc_final: 0.8693 (t) REVERT: S 50 ASN cc_start: 0.8033 (t0) cc_final: 0.7452 (t0) REVERT: S 55 GLU cc_start: 0.7746 (tt0) cc_final: 0.7312 (mt-10) REVERT: S 85 GLN cc_start: 0.8492 (mm110) cc_final: 0.8270 (mm-40) REVERT: S 154 MET cc_start: 0.7989 (mmm) cc_final: 0.7707 (mmm) REVERT: S 179 THR cc_start: 0.8887 (p) cc_final: 0.8668 (t) REVERT: S 297 GLU cc_start: 0.8211 (mm-30) cc_final: 0.7704 (mm-30) REVERT: S 377 MET cc_start: 0.8607 (OUTLIER) cc_final: 0.8245 (ttm) REVERT: S 391 LEU cc_start: 0.9013 (tp) cc_final: 0.8696 (tp) REVERT: S 422 ARG cc_start: 0.8155 (tpt90) cc_final: 0.7913 (tpt90) REVERT: S 450 GLU cc_start: 0.3139 (OUTLIER) cc_final: 0.1226 (mm-30) outliers start: 69 outliers final: 44 residues processed: 516 average time/residue: 0.3502 time to fit residues: 283.7027 Evaluate side-chains 514 residues out of total 2544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 459 time to evaluate : 2.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 51 SER Chi-restraints excluded: chain K residue 99 THR Chi-restraints excluded: chain K residue 108 MET Chi-restraints excluded: chain K residue 154 VAL Chi-restraints excluded: chain K residue 178 VAL Chi-restraints excluded: chain K residue 342 LEU Chi-restraints excluded: chain K residue 354 ILE Chi-restraints excluded: chain N residue 8 VAL Chi-restraints excluded: chain N residue 28 ILE Chi-restraints excluded: chain N residue 91 VAL Chi-restraints excluded: chain N residue 196 MET Chi-restraints excluded: chain N residue 305 LEU Chi-restraints excluded: chain A residue 128 GLN Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 266 HIS Chi-restraints excluded: chain A residue 295 CYS Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 174 LYS Chi-restraints excluded: chain B residue 212 PHE Chi-restraints excluded: chain B residue 330 MET Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 407 GLU Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 109 THR Chi-restraints excluded: chain E residue 191 THR Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 295 CYS Chi-restraints excluded: chain E residue 435 VAL Chi-restraints excluded: chain E residue 445 GLU Chi-restraints excluded: chain I residue 44 LEU Chi-restraints excluded: chain I residue 175 VAL Chi-restraints excluded: chain I residue 342 VAL Chi-restraints excluded: chain I residue 422 TYR Chi-restraints excluded: chain S residue 62 VAL Chi-restraints excluded: chain S residue 77 GLU Chi-restraints excluded: chain S residue 130 THR Chi-restraints excluded: chain S residue 194 THR Chi-restraints excluded: chain S residue 204 VAL Chi-restraints excluded: chain S residue 217 LEU Chi-restraints excluded: chain S residue 242 LEU Chi-restraints excluded: chain S residue 288 VAL Chi-restraints excluded: chain S residue 295 CYS Chi-restraints excluded: chain S residue 347 CYS Chi-restraints excluded: chain S residue 362 VAL Chi-restraints excluded: chain S residue 377 MET Chi-restraints excluded: chain S residue 450 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 96 optimal weight: 4.9990 chunk 257 optimal weight: 4.9990 chunk 56 optimal weight: 9.9990 chunk 167 optimal weight: 3.9990 chunk 70 optimal weight: 0.9990 chunk 286 optimal weight: 6.9990 chunk 237 optimal weight: 4.9990 chunk 132 optimal weight: 2.9990 chunk 23 optimal weight: 6.9990 chunk 94 optimal weight: 0.5980 chunk 150 optimal weight: 1.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 318 ASN N 171 HIS ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.2915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 24242 Z= 0.326 Angle : 0.593 8.274 32906 Z= 0.297 Chirality : 0.045 0.290 3613 Planarity : 0.005 0.079 4276 Dihedral : 9.327 154.715 3598 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.89 % Favored : 95.98 % Rotamer: Outliers : 3.60 % Allowed : 17.90 % Favored : 78.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % 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: 0.72 (0.16), residues: 2969 helix: 1.96 (0.15), residues: 1247 sheet: 0.36 (0.22), residues: 550 loop : -1.12 (0.17), residues: 1172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 344 HIS 0.007 0.001 HIS N 171 PHE 0.024 0.002 PHE I 270 TYR 0.014 0.001 TYR N 338 ARG 0.004 0.000 ARG E 221 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5938 Ramachandran restraints generated. 2969 Oldfield, 0 Emsley, 2969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5938 Ramachandran restraints generated. 2969 Oldfield, 0 Emsley, 2969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 553 residues out of total 2544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 465 time to evaluate : 2.829 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 44 LYS cc_start: 0.8931 (tptm) cc_final: 0.8444 (pptt) REVERT: K 74 TYR cc_start: 0.8401 (t80) cc_final: 0.8062 (t80) REVERT: K 98 GLN cc_start: 0.7642 (pp30) cc_final: 0.7351 (pp30) REVERT: K 105 TYR cc_start: 0.8473 (t80) cc_final: 0.8072 (t80) REVERT: K 142 VAL cc_start: 0.8446 (t) cc_final: 0.8228 (m) REVERT: K 179 GLU cc_start: 0.8488 (tt0) cc_final: 0.8272 (tm-30) REVERT: K 275 LEU cc_start: 0.9029 (mm) cc_final: 0.8699 (mp) REVERT: K 288 MET cc_start: 0.8255 (tmm) cc_final: 0.8035 (tmm) REVERT: N 91 VAL cc_start: 0.7978 (OUTLIER) cc_final: 0.7753 (t) REVERT: N 107 MET cc_start: 0.7454 (mmm) cc_final: 0.7247 (tpp) REVERT: N 110 LYS cc_start: 0.8202 (tptt) cc_final: 0.7708 (tptt) REVERT: N 178 VAL cc_start: 0.8886 (t) cc_final: 0.8589 (p) REVERT: N 197 ASP cc_start: 0.8490 (t0) cc_final: 0.8174 (t0) REVERT: N 201 LYS cc_start: 0.8695 (tppt) cc_final: 0.8383 (mtmt) REVERT: A 24 TYR cc_start: 0.8698 (m-80) cc_final: 0.8335 (m-80) REVERT: A 230 LEU cc_start: 0.8749 (mt) cc_final: 0.8493 (mp) REVERT: A 279 GLU cc_start: 0.8486 (mm-30) cc_final: 0.8236 (mp0) REVERT: A 334 THR cc_start: 0.8968 (m) cc_final: 0.8715 (t) REVERT: A 377 MET cc_start: 0.8739 (ttt) cc_final: 0.8538 (ttm) REVERT: A 379 SER cc_start: 0.8816 (OUTLIER) cc_final: 0.8568 (p) REVERT: B 31 ASP cc_start: 0.8130 (OUTLIER) cc_final: 0.7881 (t70) REVERT: B 174 LYS cc_start: 0.8882 (OUTLIER) cc_final: 0.8659 (ptpt) REVERT: B 212 PHE cc_start: 0.8381 (OUTLIER) cc_final: 0.7597 (m-80) REVERT: B 282 ARG cc_start: 0.8207 (mtp85) cc_final: 0.7663 (mmt-90) REVERT: B 407 GLU cc_start: 0.8028 (OUTLIER) cc_final: 0.7731 (mm-30) REVERT: E 24 TYR cc_start: 0.8810 (m-10) cc_final: 0.8593 (m-10) REVERT: E 195 LEU cc_start: 0.7945 (tt) cc_final: 0.7697 (tp) REVERT: E 265 ILE cc_start: 0.8702 (pt) cc_final: 0.8358 (mt) REVERT: E 379 SER cc_start: 0.9026 (t) cc_final: 0.8417 (p) REVERT: E 392 ASP cc_start: 0.8535 (m-30) cc_final: 0.8333 (m-30) REVERT: E 445 GLU cc_start: 0.3349 (OUTLIER) cc_final: 0.2982 (tm-30) REVERT: I 164 MET cc_start: 0.8618 (tpp) cc_final: 0.8033 (tpp) REVERT: I 209 ASP cc_start: 0.8401 (t70) cc_final: 0.8150 (t0) REVERT: I 213 ARG cc_start: 0.8316 (ttm110) cc_final: 0.7945 (ttm-80) REVERT: I 406 MET cc_start: 0.7696 (ttp) cc_final: 0.7481 (ttp) REVERT: I 417 ASP cc_start: 0.8601 (m-30) cc_final: 0.8385 (m-30) REVERT: S 6 SER cc_start: 0.9054 (m) cc_final: 0.8610 (t) REVERT: S 16 ILE cc_start: 0.8519 (mt) cc_final: 0.7838 (mp) REVERT: S 20 CYS cc_start: 0.7934 (m) cc_final: 0.7416 (m) REVERT: S 24 TYR cc_start: 0.8425 (m-80) cc_final: 0.8160 (m-80) REVERT: S 50 ASN cc_start: 0.7991 (t0) cc_final: 0.7416 (t0) REVERT: S 55 GLU cc_start: 0.7811 (tt0) cc_final: 0.7313 (mt-10) REVERT: S 136 LEU cc_start: 0.8232 (mt) cc_final: 0.7962 (mp) REVERT: S 179 THR cc_start: 0.8860 (p) cc_final: 0.8624 (t) REVERT: S 297 GLU cc_start: 0.8293 (mm-30) cc_final: 0.7727 (mm-30) REVERT: S 377 MET cc_start: 0.8641 (OUTLIER) cc_final: 0.8292 (ttm) REVERT: S 420 GLU cc_start: 0.8592 (mt-10) cc_final: 0.8296 (mt-10) REVERT: S 450 GLU cc_start: 0.3001 (OUTLIER) cc_final: 0.1216 (mm-30) outliers start: 88 outliers final: 60 residues processed: 512 average time/residue: 0.3505 time to fit residues: 281.1219 Evaluate side-chains 519 residues out of total 2544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 450 time to evaluate : 2.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 37 ILE Chi-restraints excluded: chain K residue 51 SER Chi-restraints excluded: chain K residue 99 THR Chi-restraints excluded: chain K residue 118 ILE Chi-restraints excluded: chain K residue 154 VAL Chi-restraints excluded: chain K residue 178 VAL Chi-restraints excluded: chain K residue 305 LEU Chi-restraints excluded: chain K residue 342 LEU Chi-restraints excluded: chain K residue 366 ASN Chi-restraints excluded: chain N residue 8 VAL Chi-restraints excluded: chain N residue 28 ILE Chi-restraints excluded: chain N residue 91 VAL Chi-restraints excluded: chain N residue 196 MET Chi-restraints excluded: chain N residue 214 SER Chi-restraints excluded: chain N residue 305 LEU Chi-restraints excluded: chain A residue 2 ARG Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 266 HIS Chi-restraints excluded: chain A residue 295 CYS Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 340 SER Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 379 SER 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 31 ASP Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 174 LYS Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 212 PHE Chi-restraints excluded: chain B residue 330 MET Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 407 GLU Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 109 THR Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 191 THR Chi-restraints excluded: chain E residue 295 CYS Chi-restraints excluded: chain E residue 435 VAL Chi-restraints excluded: chain E residue 437 VAL Chi-restraints excluded: chain E residue 445 GLU Chi-restraints excluded: chain I residue 75 SER Chi-restraints excluded: chain I residue 162 ARG Chi-restraints excluded: chain I residue 166 THR Chi-restraints excluded: chain I residue 175 VAL Chi-restraints excluded: chain I residue 342 VAL Chi-restraints excluded: chain S residue 62 VAL Chi-restraints excluded: chain S residue 74 VAL Chi-restraints excluded: chain S residue 77 GLU Chi-restraints excluded: chain S residue 92 LEU Chi-restraints excluded: chain S residue 129 CYS Chi-restraints excluded: chain S residue 130 THR Chi-restraints excluded: chain S residue 194 THR Chi-restraints excluded: chain S residue 204 VAL Chi-restraints excluded: chain S residue 217 LEU Chi-restraints excluded: chain S residue 248 LEU Chi-restraints excluded: chain S residue 259 LEU Chi-restraints excluded: chain S residue 288 VAL Chi-restraints excluded: chain S residue 295 CYS Chi-restraints excluded: chain S residue 347 CYS Chi-restraints excluded: chain S residue 362 VAL Chi-restraints excluded: chain S residue 377 MET Chi-restraints excluded: chain S residue 450 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 276 optimal weight: 0.6980 chunk 32 optimal weight: 5.9990 chunk 163 optimal weight: 1.9990 chunk 209 optimal weight: 4.9990 chunk 162 optimal weight: 0.8980 chunk 241 optimal weight: 4.9990 chunk 159 optimal weight: 2.9990 chunk 285 optimal weight: 0.8980 chunk 178 optimal weight: 0.8980 chunk 173 optimal weight: 2.9990 chunk 131 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 171 HIS N 318 ASN A 61 HIS ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.3097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 24242 Z= 0.177 Angle : 0.549 8.487 32906 Z= 0.272 Chirality : 0.043 0.243 3613 Planarity : 0.004 0.078 4276 Dihedral : 9.050 156.022 3598 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.65 % Favored : 96.25 % Rotamer: Outliers : 3.17 % Allowed : 18.53 % Favored : 78.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % 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: 2969 helix: 2.10 (0.15), residues: 1243 sheet: 0.46 (0.22), residues: 557 loop : -1.06 (0.18), residues: 1169 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP I 344 HIS 0.007 0.001 HIS S 406 PHE 0.026 0.001 PHE K 303 TYR 0.013 0.001 TYR K 105 ARG 0.005 0.000 ARG E 221 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5938 Ramachandran restraints generated. 2969 Oldfield, 0 Emsley, 2969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5938 Ramachandran restraints generated. 2969 Oldfield, 0 Emsley, 2969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 536 residues out of total 2544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 459 time to evaluate : 2.857 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 74 TYR cc_start: 0.8308 (t80) cc_final: 0.7966 (t80) REVERT: K 98 GLN cc_start: 0.7658 (pp30) cc_final: 0.7406 (pp30) REVERT: K 105 TYR cc_start: 0.8452 (t80) cc_final: 0.8103 (t80) REVERT: K 108 MET cc_start: 0.8176 (OUTLIER) cc_final: 0.7857 (tpp) REVERT: K 179 GLU cc_start: 0.8485 (tt0) cc_final: 0.8201 (tm-30) REVERT: K 275 LEU cc_start: 0.8971 (mm) cc_final: 0.8647 (mp) REVERT: N 110 LYS cc_start: 0.8193 (tptt) cc_final: 0.7694 (tptt) REVERT: N 178 VAL cc_start: 0.8883 (t) cc_final: 0.8601 (p) REVERT: N 197 ASP cc_start: 0.8495 (t0) cc_final: 0.8187 (t0) REVERT: N 201 LYS cc_start: 0.8639 (tppt) cc_final: 0.8243 (mtmm) REVERT: N 261 LYS cc_start: 0.8130 (mptt) cc_final: 0.7916 (mmtm) REVERT: A 24 TYR cc_start: 0.8651 (m-80) cc_final: 0.8346 (m-80) REVERT: A 230 LEU cc_start: 0.8700 (mt) cc_final: 0.8425 (mp) REVERT: A 254 GLU cc_start: 0.7627 (mm-30) cc_final: 0.7099 (mt-10) REVERT: A 279 GLU cc_start: 0.8491 (mm-30) cc_final: 0.8233 (mp0) REVERT: A 379 SER cc_start: 0.8778 (OUTLIER) cc_final: 0.8534 (p) REVERT: B 31 ASP cc_start: 0.8095 (OUTLIER) cc_final: 0.7843 (t70) REVERT: B 136 THR cc_start: 0.8980 (OUTLIER) cc_final: 0.8734 (p) REVERT: B 188 SER cc_start: 0.9064 (t) cc_final: 0.8730 (p) REVERT: B 212 PHE cc_start: 0.8303 (OUTLIER) cc_final: 0.7494 (m-80) REVERT: B 213 ARG cc_start: 0.8195 (ttp-110) cc_final: 0.7507 (mtm-85) REVERT: B 282 ARG cc_start: 0.8208 (mtp85) cc_final: 0.7648 (mmt-90) REVERT: B 363 MET cc_start: 0.8613 (mtt) cc_final: 0.8308 (mtm) REVERT: B 407 GLU cc_start: 0.7844 (OUTLIER) cc_final: 0.7446 (mm-30) REVERT: E 1 MET cc_start: 0.7437 (mmm) cc_final: 0.7083 (mmm) REVERT: E 265 ILE cc_start: 0.8531 (pt) cc_final: 0.8150 (mt) REVERT: E 322 ASP cc_start: 0.8540 (t0) cc_final: 0.8223 (t70) REVERT: E 379 SER cc_start: 0.9000 (t) cc_final: 0.8424 (p) REVERT: E 392 ASP cc_start: 0.8475 (m-30) cc_final: 0.8244 (m-30) REVERT: I 209 ASP cc_start: 0.8383 (t70) cc_final: 0.8175 (t0) REVERT: I 213 ARG cc_start: 0.8300 (ttm110) cc_final: 0.8074 (ttm-80) REVERT: I 417 ASP cc_start: 0.8583 (m-30) cc_final: 0.8297 (m-30) REVERT: S 6 SER cc_start: 0.9069 (m) cc_final: 0.8631 (t) REVERT: S 16 ILE cc_start: 0.8485 (mt) cc_final: 0.7825 (mp) REVERT: S 20 CYS cc_start: 0.7901 (m) cc_final: 0.7411 (m) REVERT: S 24 TYR cc_start: 0.8442 (m-80) cc_final: 0.8194 (m-80) REVERT: S 50 ASN cc_start: 0.7878 (t0) cc_final: 0.7281 (t0) REVERT: S 55 GLU cc_start: 0.7827 (tt0) cc_final: 0.7323 (mt-10) REVERT: S 85 GLN cc_start: 0.8560 (mm110) cc_final: 0.8345 (mm-40) REVERT: S 136 LEU cc_start: 0.8253 (mt) cc_final: 0.7991 (mp) REVERT: S 297 GLU cc_start: 0.8305 (mm-30) cc_final: 0.7711 (mm-30) REVERT: S 377 MET cc_start: 0.8590 (OUTLIER) cc_final: 0.8211 (ttm) REVERT: S 420 GLU cc_start: 0.8588 (mt-10) cc_final: 0.8267 (mt-10) REVERT: S 422 ARG cc_start: 0.8297 (OUTLIER) cc_final: 0.7900 (tpt90) REVERT: S 434 GLU cc_start: 0.8363 (tm-30) cc_final: 0.8123 (tm-30) REVERT: S 450 GLU cc_start: 0.2996 (OUTLIER) cc_final: 0.1336 (mm-30) outliers start: 77 outliers final: 55 residues processed: 502 average time/residue: 0.3412 time to fit residues: 270.2412 Evaluate side-chains 512 residues out of total 2544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 448 time to evaluate : 2.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 37 ILE Chi-restraints excluded: chain K residue 51 SER Chi-restraints excluded: chain K residue 99 THR Chi-restraints excluded: chain K residue 108 MET Chi-restraints excluded: chain K residue 154 VAL Chi-restraints excluded: chain K residue 178 VAL Chi-restraints excluded: chain K residue 258 THR Chi-restraints excluded: chain K residue 305 LEU Chi-restraints excluded: chain K residue 342 LEU Chi-restraints excluded: chain K residue 366 ASN Chi-restraints excluded: chain N residue 8 VAL Chi-restraints excluded: chain N residue 28 ILE Chi-restraints excluded: chain N residue 108 MET Chi-restraints excluded: chain N residue 196 MET Chi-restraints excluded: chain N residue 214 SER Chi-restraints excluded: chain N residue 305 LEU Chi-restraints excluded: chain N residue 342 LEU Chi-restraints excluded: chain A residue 2 ARG Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 295 CYS Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 212 PHE Chi-restraints excluded: chain B residue 330 MET Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 407 GLU Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 109 THR Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 191 THR Chi-restraints excluded: chain E residue 295 CYS Chi-restraints excluded: chain E residue 435 VAL Chi-restraints excluded: chain E residue 445 GLU Chi-restraints excluded: chain I residue 44 LEU Chi-restraints excluded: chain I residue 166 THR Chi-restraints excluded: chain I residue 175 VAL Chi-restraints excluded: chain I residue 342 VAL Chi-restraints excluded: chain S residue 2 ARG Chi-restraints excluded: chain S residue 4 CYS Chi-restraints excluded: chain S residue 62 VAL Chi-restraints excluded: chain S residue 74 VAL Chi-restraints excluded: chain S residue 77 GLU Chi-restraints excluded: chain S residue 130 THR Chi-restraints excluded: chain S residue 194 THR Chi-restraints excluded: chain S residue 204 VAL Chi-restraints excluded: chain S residue 217 LEU 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 347 CYS Chi-restraints excluded: chain S residue 362 VAL Chi-restraints excluded: chain S residue 377 MET Chi-restraints excluded: chain S residue 396 ASP Chi-restraints excluded: chain S residue 422 ARG Chi-restraints excluded: chain S residue 450 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 176 optimal weight: 0.8980 chunk 113 optimal weight: 5.9990 chunk 170 optimal weight: 2.9990 chunk 85 optimal weight: 5.9990 chunk 56 optimal weight: 20.0000 chunk 55 optimal weight: 1.9990 chunk 181 optimal weight: 0.9980 chunk 194 optimal weight: 1.9990 chunk 141 optimal weight: 3.9990 chunk 26 optimal weight: 6.9990 chunk 224 optimal weight: 0.8980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 272 ASN N 171 HIS A 216 ASN ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 31 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.3233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 24242 Z= 0.231 Angle : 0.575 10.860 32906 Z= 0.283 Chirality : 0.043 0.223 3613 Planarity : 0.004 0.076 4276 Dihedral : 9.015 156.336 3598 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.89 % Favored : 95.95 % Rotamer: Outliers : 2.97 % Allowed : 18.73 % Favored : 78.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % 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: 2969 helix: 2.13 (0.15), residues: 1246 sheet: 0.48 (0.22), residues: 553 loop : -1.04 (0.18), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP I 344 HIS 0.007 0.001 HIS S 406 PHE 0.029 0.001 PHE K 303 TYR 0.014 0.001 TYR N 189 ARG 0.007 0.000 ARG I 162 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5938 Ramachandran restraints generated. 2969 Oldfield, 0 Emsley, 2969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5938 Ramachandran restraints generated. 2969 Oldfield, 0 Emsley, 2969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 534 residues out of total 2544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 462 time to evaluate : 2.644 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 46 THR cc_start: 0.5873 (OUTLIER) cc_final: 0.5657 (p) REVERT: K 74 TYR cc_start: 0.8387 (t80) cc_final: 0.8102 (t80) REVERT: K 98 GLN cc_start: 0.7659 (pp30) cc_final: 0.7380 (pp30) REVERT: K 105 TYR cc_start: 0.8484 (t80) cc_final: 0.8117 (t80) REVERT: K 275 LEU cc_start: 0.8972 (mm) cc_final: 0.8639 (mp) REVERT: N 178 VAL cc_start: 0.8852 (t) cc_final: 0.8603 (p) REVERT: N 197 ASP cc_start: 0.8492 (t0) cc_final: 0.8178 (t0) REVERT: N 201 LYS cc_start: 0.8669 (tppt) cc_final: 0.8265 (mtmm) REVERT: A 24 TYR cc_start: 0.8672 (m-80) cc_final: 0.8333 (m-80) REVERT: A 49 PHE cc_start: 0.7781 (m-80) cc_final: 0.7415 (m-10) REVERT: A 230 LEU cc_start: 0.8731 (mt) cc_final: 0.8458 (mp) REVERT: A 254 GLU cc_start: 0.7661 (mm-30) cc_final: 0.7135 (mt-10) REVERT: A 279 GLU cc_start: 0.8502 (mm-30) cc_final: 0.8250 (mp0) REVERT: A 379 SER cc_start: 0.8809 (OUTLIER) cc_final: 0.8560 (p) REVERT: B 31 ASP cc_start: 0.8101 (OUTLIER) cc_final: 0.7845 (t70) REVERT: B 188 SER cc_start: 0.9090 (t) cc_final: 0.8747 (p) REVERT: B 212 PHE cc_start: 0.8336 (OUTLIER) cc_final: 0.7528 (m-80) REVERT: B 213 ARG cc_start: 0.8181 (ttp-110) cc_final: 0.7809 (mtm-85) REVERT: B 282 ARG cc_start: 0.8218 (mtp85) cc_final: 0.7687 (mmt-90) REVERT: B 407 GLU cc_start: 0.7945 (OUTLIER) cc_final: 0.7612 (mm-30) REVERT: E 24 TYR cc_start: 0.8785 (m-10) cc_final: 0.8565 (m-10) REVERT: E 195 LEU cc_start: 0.7857 (tt) cc_final: 0.7595 (tp) REVERT: E 265 ILE cc_start: 0.8670 (pt) cc_final: 0.8338 (mt) REVERT: E 379 SER cc_start: 0.9005 (t) cc_final: 0.8417 (p) REVERT: E 392 ASP cc_start: 0.8487 (m-30) cc_final: 0.8250 (m-30) REVERT: I 209 ASP cc_start: 0.8397 (t70) cc_final: 0.8149 (t0) REVERT: I 213 ARG cc_start: 0.8342 (ttm110) cc_final: 0.7990 (ttm-80) REVERT: I 406 MET cc_start: 0.7434 (ttp) cc_final: 0.7185 (ttp) REVERT: I 417 ASP cc_start: 0.8581 (m-30) cc_final: 0.8319 (m-30) REVERT: S 6 SER cc_start: 0.9075 (m) cc_final: 0.8619 (t) REVERT: S 20 CYS cc_start: 0.8020 (m) cc_final: 0.7585 (m) REVERT: S 24 TYR cc_start: 0.8474 (m-80) cc_final: 0.8251 (m-80) REVERT: S 50 ASN cc_start: 0.7810 (t0) cc_final: 0.7221 (t0) REVERT: S 55 GLU cc_start: 0.7816 (tt0) cc_final: 0.7301 (mt-10) REVERT: S 85 GLN cc_start: 0.8582 (mm110) cc_final: 0.8374 (mm-40) REVERT: S 136 LEU cc_start: 0.8257 (mt) cc_final: 0.8013 (mp) REVERT: S 245 ASP cc_start: 0.8127 (t0) cc_final: 0.7919 (t70) REVERT: S 297 GLU cc_start: 0.8311 (mm-30) cc_final: 0.7771 (mm-30) REVERT: S 377 MET cc_start: 0.8594 (OUTLIER) cc_final: 0.8229 (ttm) REVERT: S 420 GLU cc_start: 0.8620 (mt-10) cc_final: 0.8273 (mt-10) REVERT: S 422 ARG cc_start: 0.8300 (tpt90) cc_final: 0.7657 (tpt90) REVERT: S 434 GLU cc_start: 0.8406 (tm-30) cc_final: 0.8172 (tm-30) REVERT: S 450 GLU cc_start: 0.3018 (OUTLIER) cc_final: 0.1436 (mm-30) outliers start: 72 outliers final: 57 residues processed: 503 average time/residue: 0.3458 time to fit residues: 274.5073 Evaluate side-chains 520 residues out of total 2544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 456 time to evaluate : 2.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 37 ILE Chi-restraints excluded: chain K residue 46 THR Chi-restraints excluded: chain K residue 51 SER Chi-restraints excluded: chain K residue 99 THR Chi-restraints excluded: chain K residue 127 PHE Chi-restraints excluded: chain K residue 154 VAL Chi-restraints excluded: chain K residue 178 VAL Chi-restraints excluded: chain K residue 305 LEU Chi-restraints excluded: chain K residue 342 LEU Chi-restraints excluded: chain K residue 366 ASN Chi-restraints excluded: chain N residue 8 VAL Chi-restraints excluded: chain N residue 196 MET Chi-restraints excluded: chain N residue 214 SER Chi-restraints excluded: chain N residue 305 LEU Chi-restraints excluded: chain A residue 2 ARG Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 266 HIS Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 212 PHE Chi-restraints excluded: chain B residue 330 MET Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 407 GLU Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 109 THR Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 191 THR Chi-restraints excluded: chain E residue 295 CYS Chi-restraints excluded: chain E residue 435 VAL Chi-restraints excluded: chain E residue 437 VAL Chi-restraints excluded: chain E residue 445 GLU Chi-restraints excluded: chain I residue 75 SER Chi-restraints excluded: chain I residue 175 VAL Chi-restraints excluded: chain I residue 342 VAL Chi-restraints excluded: chain S residue 2 ARG Chi-restraints excluded: chain S residue 4 CYS Chi-restraints excluded: chain S residue 62 VAL Chi-restraints excluded: chain S residue 77 GLU Chi-restraints excluded: chain S residue 130 THR Chi-restraints excluded: chain S residue 194 THR Chi-restraints excluded: chain S residue 204 VAL Chi-restraints excluded: chain S residue 217 LEU Chi-restraints excluded: chain S residue 242 LEU Chi-restraints excluded: chain S residue 259 LEU Chi-restraints excluded: chain S residue 288 VAL Chi-restraints excluded: chain S residue 295 CYS Chi-restraints excluded: chain S residue 347 CYS Chi-restraints excluded: chain S residue 362 VAL Chi-restraints excluded: chain S residue 377 MET Chi-restraints excluded: chain S residue 428 LEU Chi-restraints excluded: chain S residue 432 TYR Chi-restraints excluded: chain S residue 450 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 259 optimal weight: 5.9990 chunk 273 optimal weight: 2.9990 chunk 249 optimal weight: 3.9990 chunk 265 optimal weight: 1.9990 chunk 160 optimal weight: 4.9990 chunk 115 optimal weight: 3.9990 chunk 208 optimal weight: 5.9990 chunk 81 optimal weight: 1.9990 chunk 240 optimal weight: 0.8980 chunk 251 optimal weight: 10.0000 chunk 264 optimal weight: 1.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 171 HIS A 216 ASN ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 292 GLN I 195 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.3346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 24242 Z= 0.306 Angle : 0.611 10.384 32906 Z= 0.302 Chirality : 0.044 0.195 3613 Planarity : 0.005 0.076 4276 Dihedral : 9.123 156.631 3598 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.12 % Favored : 95.71 % Rotamer: Outliers : 3.05 % Allowed : 18.73 % Favored : 78.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % 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: 0.76 (0.16), residues: 2969 helix: 2.01 (0.15), residues: 1246 sheet: 0.33 (0.22), residues: 559 loop : -1.09 (0.17), residues: 1164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 344 HIS 0.007 0.001 HIS S 406 PHE 0.030 0.002 PHE K 303 TYR 0.013 0.001 TYR N 338 ARG 0.006 0.000 ARG I 162 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5938 Ramachandran restraints generated. 2969 Oldfield, 0 Emsley, 2969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5938 Ramachandran restraints generated. 2969 Oldfield, 0 Emsley, 2969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 538 residues out of total 2544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 464 time to evaluate : 2.588 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 46 THR cc_start: 0.5891 (OUTLIER) cc_final: 0.5672 (p) REVERT: K 74 TYR cc_start: 0.8454 (t80) cc_final: 0.8197 (t80) REVERT: K 98 GLN cc_start: 0.7694 (pp30) cc_final: 0.7432 (pp30) REVERT: K 105 TYR cc_start: 0.8505 (t80) cc_final: 0.8155 (t80) REVERT: K 180 ASP cc_start: 0.8732 (t0) cc_final: 0.8133 (t0) REVERT: K 275 LEU cc_start: 0.8996 (mm) cc_final: 0.8658 (mp) REVERT: K 331 LEU cc_start: 0.8629 (mt) cc_final: 0.8389 (mp) REVERT: N 178 VAL cc_start: 0.8880 (t) cc_final: 0.8609 (p) REVERT: N 197 ASP cc_start: 0.8467 (t0) cc_final: 0.8159 (t0) REVERT: N 201 LYS cc_start: 0.8702 (tppt) cc_final: 0.8287 (mtmm) REVERT: A 24 TYR cc_start: 0.8670 (m-80) cc_final: 0.8373 (m-80) REVERT: A 230 LEU cc_start: 0.8740 (mt) cc_final: 0.8476 (mp) REVERT: A 379 SER cc_start: 0.8804 (OUTLIER) cc_final: 0.8555 (p) REVERT: B 31 ASP cc_start: 0.8119 (OUTLIER) cc_final: 0.7852 (t70) REVERT: B 212 PHE cc_start: 0.8397 (OUTLIER) cc_final: 0.7614 (m-80) REVERT: B 213 ARG cc_start: 0.8191 (ttp-110) cc_final: 0.7829 (mtm-85) REVERT: B 407 GLU cc_start: 0.8033 (OUTLIER) cc_final: 0.7690 (mm-30) REVERT: E 24 TYR cc_start: 0.8793 (m-10) cc_final: 0.8574 (m-10) REVERT: E 265 ILE cc_start: 0.8640 (pt) cc_final: 0.8302 (mt) REVERT: E 379 SER cc_start: 0.9015 (t) cc_final: 0.8423 (p) REVERT: E 392 ASP cc_start: 0.8513 (m-30) cc_final: 0.8189 (m-30) REVERT: E 429 GLU cc_start: 0.8679 (mt-10) cc_final: 0.8315 (mt-10) REVERT: I 209 ASP cc_start: 0.8423 (t70) cc_final: 0.8164 (t0) REVERT: I 213 ARG cc_start: 0.8371 (ttm110) cc_final: 0.7990 (ttm-80) REVERT: I 406 MET cc_start: 0.7620 (ttp) cc_final: 0.7364 (ttp) REVERT: I 417 ASP cc_start: 0.8614 (m-30) cc_final: 0.8342 (m-30) REVERT: S 6 SER cc_start: 0.9101 (m) cc_final: 0.8583 (t) REVERT: S 16 ILE cc_start: 0.8575 (mp) cc_final: 0.7952 (mp) REVERT: S 20 CYS cc_start: 0.8094 (m) cc_final: 0.7738 (m) REVERT: S 50 ASN cc_start: 0.7751 (t0) cc_final: 0.7097 (t0) REVERT: S 55 GLU cc_start: 0.7777 (tt0) cc_final: 0.7261 (mt-10) REVERT: S 136 LEU cc_start: 0.8255 (mt) cc_final: 0.8010 (mp) REVERT: S 245 ASP cc_start: 0.8152 (t0) cc_final: 0.7948 (t0) REVERT: S 297 GLU cc_start: 0.8345 (mm-30) cc_final: 0.7811 (mm-30) REVERT: S 377 MET cc_start: 0.8605 (OUTLIER) cc_final: 0.8255 (ttm) REVERT: S 411 GLU cc_start: 0.7751 (mm-30) cc_final: 0.7201 (mm-30) REVERT: S 420 GLU cc_start: 0.8590 (mt-10) cc_final: 0.8231 (mt-10) REVERT: S 422 ARG cc_start: 0.8316 (tpt90) cc_final: 0.7674 (tpt90) REVERT: S 434 GLU cc_start: 0.8420 (tm-30) cc_final: 0.8179 (tm-30) REVERT: S 450 GLU cc_start: 0.2939 (OUTLIER) cc_final: 0.1448 (mm-30) outliers start: 74 outliers final: 57 residues processed: 506 average time/residue: 0.3474 time to fit residues: 275.6179 Evaluate side-chains 514 residues out of total 2544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 450 time to evaluate : 2.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 37 ILE Chi-restraints excluded: chain K residue 46 THR Chi-restraints excluded: chain K residue 51 SER Chi-restraints excluded: chain K residue 99 THR Chi-restraints excluded: chain K residue 154 VAL Chi-restraints excluded: chain K residue 178 VAL Chi-restraints excluded: chain K residue 305 LEU Chi-restraints excluded: chain K residue 342 LEU Chi-restraints excluded: chain K residue 366 ASN Chi-restraints excluded: chain N residue 8 VAL Chi-restraints excluded: chain N residue 196 MET Chi-restraints excluded: chain N residue 305 LEU Chi-restraints excluded: chain A residue 2 ARG Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 266 HIS Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 212 PHE Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 330 MET Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 407 GLU Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain E residue 6 SER Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 109 THR Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 191 THR Chi-restraints excluded: chain E residue 295 CYS Chi-restraints excluded: chain E residue 435 VAL Chi-restraints excluded: chain E residue 437 VAL Chi-restraints excluded: chain E residue 445 GLU Chi-restraints excluded: chain I residue 75 SER Chi-restraints excluded: chain I residue 166 THR Chi-restraints excluded: chain I residue 175 VAL Chi-restraints excluded: chain I residue 342 VAL Chi-restraints excluded: chain S residue 2 ARG Chi-restraints excluded: chain S residue 4 CYS Chi-restraints excluded: chain S residue 62 VAL Chi-restraints excluded: chain S residue 74 VAL Chi-restraints excluded: chain S residue 77 GLU Chi-restraints excluded: chain S residue 130 THR Chi-restraints excluded: chain S residue 194 THR Chi-restraints excluded: chain S residue 204 VAL Chi-restraints excluded: chain S residue 217 LEU 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 377 MET Chi-restraints excluded: chain S residue 450 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 174 optimal weight: 4.9990 chunk 281 optimal weight: 0.6980 chunk 171 optimal weight: 0.0000 chunk 133 optimal weight: 1.9990 chunk 195 optimal weight: 2.9990 chunk 294 optimal weight: 0.6980 chunk 271 optimal weight: 3.9990 chunk 234 optimal weight: 2.9990 chunk 24 optimal weight: 8.9990 chunk 181 optimal weight: 0.6980 chunk 143 optimal weight: 0.8980 overall best weight: 0.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 171 HIS A 216 ASN ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.3510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 24242 Z= 0.163 Angle : 0.572 11.882 32906 Z= 0.281 Chirality : 0.042 0.191 3613 Planarity : 0.004 0.076 4276 Dihedral : 8.877 155.841 3598 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.99 % Favored : 95.88 % Rotamer: Outliers : 2.27 % Allowed : 19.70 % Favored : 78.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % 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: 0.98 (0.16), residues: 2969 helix: 2.16 (0.15), residues: 1236 sheet: 0.59 (0.22), residues: 551 loop : -0.99 (0.18), residues: 1182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP I 344 HIS 0.007 0.001 HIS S 406 PHE 0.034 0.001 PHE K 303 TYR 0.033 0.001 TYR S 24 ARG 0.005 0.000 ARG E 221 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5938 Ramachandran restraints generated. 2969 Oldfield, 0 Emsley, 2969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5938 Ramachandran restraints generated. 2969 Oldfield, 0 Emsley, 2969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 508 residues out of total 2544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 454 time to evaluate : 2.590 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 46 THR cc_start: 0.5880 (OUTLIER) cc_final: 0.5661 (p) REVERT: K 74 TYR cc_start: 0.8391 (t80) cc_final: 0.8118 (t80) REVERT: K 98 GLN cc_start: 0.7631 (pp30) cc_final: 0.7402 (pp30) REVERT: K 105 TYR cc_start: 0.8517 (t80) cc_final: 0.8201 (t80) REVERT: K 180 ASP cc_start: 0.8737 (t0) cc_final: 0.8197 (t0) REVERT: K 275 LEU cc_start: 0.8948 (mm) cc_final: 0.8624 (mp) REVERT: N 178 VAL cc_start: 0.8812 (t) cc_final: 0.8591 (p) REVERT: N 197 ASP cc_start: 0.8449 (t0) cc_final: 0.8024 (t0) REVERT: N 201 LYS cc_start: 0.8667 (tppt) cc_final: 0.8391 (mtpt) REVERT: A 24 TYR cc_start: 0.8593 (m-80) cc_final: 0.8299 (m-80) REVERT: A 49 PHE cc_start: 0.7678 (m-10) cc_final: 0.7336 (m-10) REVERT: A 230 LEU cc_start: 0.8714 (mt) cc_final: 0.8445 (mp) REVERT: A 254 GLU cc_start: 0.7668 (mm-30) cc_final: 0.7181 (mt-10) REVERT: A 279 GLU cc_start: 0.8466 (mm-30) cc_final: 0.8237 (mp0) REVERT: A 379 SER cc_start: 0.8777 (OUTLIER) cc_final: 0.8521 (p) REVERT: B 31 ASP cc_start: 0.8082 (OUTLIER) cc_final: 0.7828 (t70) REVERT: B 136 THR cc_start: 0.8953 (OUTLIER) cc_final: 0.8748 (p) REVERT: B 188 SER cc_start: 0.9043 (t) cc_final: 0.8706 (p) REVERT: B 212 PHE cc_start: 0.8306 (OUTLIER) cc_final: 0.7483 (m-80) REVERT: B 213 ARG cc_start: 0.8190 (ttp-110) cc_final: 0.7531 (mtm-85) REVERT: B 407 GLU cc_start: 0.7801 (OUTLIER) cc_final: 0.7414 (mm-30) REVERT: E 265 ILE cc_start: 0.8575 (pt) cc_final: 0.8211 (mt) REVERT: E 379 SER cc_start: 0.9008 (t) cc_final: 0.8440 (p) REVERT: E 392 ASP cc_start: 0.8429 (m-30) cc_final: 0.8204 (m-30) REVERT: I 27 GLU cc_start: 0.8646 (tp30) cc_final: 0.8331 (tt0) REVERT: I 209 ASP cc_start: 0.8392 (t70) cc_final: 0.8153 (t0) REVERT: I 213 ARG cc_start: 0.8376 (ttm110) cc_final: 0.8049 (ttm-80) REVERT: I 406 MET cc_start: 0.7326 (ttp) cc_final: 0.7055 (ttp) REVERT: I 417 ASP cc_start: 0.8582 (m-30) cc_final: 0.8279 (m-30) REVERT: S 3 GLU cc_start: 0.7752 (mp0) cc_final: 0.7369 (mp0) REVERT: S 6 SER cc_start: 0.9087 (m) cc_final: 0.8613 (t) REVERT: S 16 ILE cc_start: 0.8622 (mp) cc_final: 0.7953 (mp) REVERT: S 20 CYS cc_start: 0.7971 (m) cc_final: 0.7594 (m) REVERT: S 24 TYR cc_start: 0.8547 (m-80) cc_final: 0.8301 (m-80) REVERT: S 50 ASN cc_start: 0.7654 (t0) cc_final: 0.7173 (t0) REVERT: S 55 GLU cc_start: 0.7789 (tt0) cc_final: 0.7309 (mt-10) REVERT: S 136 LEU cc_start: 0.8245 (mt) cc_final: 0.8011 (mp) REVERT: S 377 MET cc_start: 0.8571 (OUTLIER) cc_final: 0.8193 (ttm) REVERT: S 411 GLU cc_start: 0.7796 (mm-30) cc_final: 0.7292 (mm-30) REVERT: S 420 GLU cc_start: 0.8596 (mt-10) cc_final: 0.8258 (mt-10) REVERT: S 422 ARG cc_start: 0.8304 (tpt90) cc_final: 0.7743 (tpt90) REVERT: S 434 GLU cc_start: 0.8398 (tm-30) cc_final: 0.8170 (tm-30) outliers start: 54 outliers final: 39 residues processed: 481 average time/residue: 0.3491 time to fit residues: 263.0112 Evaluate side-chains 490 residues out of total 2544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 444 time to evaluate : 2.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 37 ILE Chi-restraints excluded: chain K residue 46 THR Chi-restraints excluded: chain K residue 99 THR Chi-restraints excluded: chain K residue 178 VAL Chi-restraints excluded: chain K residue 342 LEU Chi-restraints excluded: chain K residue 366 ASN Chi-restraints excluded: chain N residue 305 LEU Chi-restraints excluded: chain A residue 2 ARG Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 266 HIS Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 212 PHE Chi-restraints excluded: chain B residue 330 MET Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 407 GLU Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 109 THR Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 191 THR Chi-restraints excluded: chain E residue 295 CYS Chi-restraints excluded: chain E residue 437 VAL Chi-restraints excluded: chain E residue 445 GLU Chi-restraints excluded: chain I residue 166 THR Chi-restraints excluded: chain I residue 175 VAL Chi-restraints excluded: chain I residue 342 VAL Chi-restraints excluded: chain S residue 2 ARG Chi-restraints excluded: chain S residue 4 CYS Chi-restraints excluded: chain S residue 62 VAL Chi-restraints excluded: chain S residue 74 VAL Chi-restraints excluded: chain S residue 130 THR Chi-restraints excluded: chain S residue 194 THR Chi-restraints excluded: chain S residue 204 VAL Chi-restraints excluded: chain S residue 242 LEU Chi-restraints excluded: chain S residue 295 CYS Chi-restraints excluded: chain S residue 362 VAL Chi-restraints excluded: chain S residue 377 MET Chi-restraints excluded: chain S residue 432 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 186 optimal weight: 4.9990 chunk 250 optimal weight: 0.9980 chunk 71 optimal weight: 20.0000 chunk 216 optimal weight: 0.9980 chunk 34 optimal weight: 0.8980 chunk 65 optimal weight: 6.9990 chunk 235 optimal weight: 0.4980 chunk 98 optimal weight: 4.9990 chunk 241 optimal weight: 0.9980 chunk 29 optimal weight: 0.9980 chunk 43 optimal weight: 10.0000 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 171 HIS N 318 ASN A 216 ASN ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.128611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.092315 restraints weight = 34674.519| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 2.32 r_work: 0.3301 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3148 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3137 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3137 r_free = 0.3137 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3137 r_free = 0.3137 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3137 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.3559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 24242 Z= 0.187 Angle : 0.586 11.571 32906 Z= 0.285 Chirality : 0.043 0.231 3613 Planarity : 0.004 0.076 4276 Dihedral : 8.737 153.519 3595 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.12 % Favored : 95.74 % Rotamer: Outliers : 2.07 % Allowed : 20.05 % Favored : 77.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.16), residues: 2969 helix: 2.16 (0.15), residues: 1247 sheet: 0.67 (0.22), residues: 541 loop : -0.94 (0.18), residues: 1181 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP I 344 HIS 0.007 0.001 HIS S 406 PHE 0.034 0.001 PHE K 303 TYR 0.025 0.001 TYR S 24 ARG 0.006 0.000 ARG E 221 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6452.72 seconds wall clock time: 115 minutes 36.84 seconds (6936.84 seconds total)