Starting phenix.real_space_refine on Mon Feb 19 08:48:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l1r_23116/02_2024/7l1r_23116_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l1r_23116/02_2024/7l1r_23116.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/7l1r_23116/02_2024/7l1r_23116.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l1r_23116/02_2024/7l1r_23116.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l1r_23116/02_2024/7l1r_23116_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l1r_23116/02_2024/7l1r_23116_updated.pdb" } 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= 0.005 sd= 0.050 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 17 5.49 5 Mg 6 5.21 5 S 78 5.16 5 C 15235 2.51 5 N 4214 2.21 5 O 4649 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 27": "OD1" <-> "OD2" Residue "A ASP 45": "OD1" <-> "OD2" Residue "A GLU 68": "OE1" <-> "OE2" Residue "A GLU 84": "OE1" <-> "OE2" Residue "A ASP 86": "OD1" <-> "OD2" Residue "A GLU 130": "OE1" <-> "OE2" Residue "A ARG 140": "NH1" <-> "NH2" Residue "A ASP 181": "OD1" <-> "OD2" Residue "A ARG 206": "NH1" <-> "NH2" Residue "A TYR 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 271": "NH1" <-> "NH2" Residue "A GLU 272": "OE1" <-> "OE2" Residue "A GLU 284": "OE1" <-> "OE2" Residue "A GLU 299": "OE1" <-> "OE2" Residue "A GLU 320": "OE1" <-> "OE2" Residue "A ASP 325": "OD1" <-> "OD2" Residue "A ASP 339": "OD1" <-> "OD2" Residue "A ASP 347": "OD1" <-> "OD2" Residue "A ARG 365": "NH1" <-> "NH2" Residue "A TYR 389": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 393": "OE1" <-> "OE2" Residue "A PHE 395": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 403": "OD1" <-> "OD2" Residue "A ARG 412": "NH1" <-> "NH2" Residue "A TYR 438": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 442": "NH1" <-> "NH2" Residue "A ASP 447": "OD1" <-> "OD2" Residue "A ASP 452": "OD1" <-> "OD2" Residue "A ARG 454": "NH1" <-> "NH2" Residue "A PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 463": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 484": "OE1" <-> "OE2" Residue "A ASP 485": "OD1" <-> "OD2" Residue "A ASP 486": "OD1" <-> "OD2" Residue "B ASP 27": "OD1" <-> "OD2" Residue "B ASP 45": "OD1" <-> "OD2" Residue "B GLU 68": "OE1" <-> "OE2" Residue "B GLU 84": "OE1" <-> "OE2" Residue "B ASP 86": "OD1" <-> "OD2" Residue "B GLU 87": "OE1" <-> "OE2" Residue "B GLU 130": "OE1" <-> "OE2" Residue "B ARG 140": "NH1" <-> "NH2" Residue "B ASP 181": "OD1" <-> "OD2" Residue "B ARG 206": "NH1" <-> "NH2" Residue "B TYR 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 271": "NH1" <-> "NH2" Residue "B GLU 272": "OE1" <-> "OE2" Residue "B GLU 299": "OE1" <-> "OE2" Residue "B GLU 320": "OE1" <-> "OE2" Residue "B ASP 339": "OD1" <-> "OD2" Residue "B ASP 347": "OD1" <-> "OD2" Residue "B PHE 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 365": "NH1" <-> "NH2" Residue "B GLU 393": "OE1" <-> "OE2" Residue "B ASP 401": "OD1" <-> "OD2" Residue "B ASP 403": "OD1" <-> "OD2" Residue "B ARG 412": "NH1" <-> "NH2" Residue "B TYR 438": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 442": "NH1" <-> "NH2" Residue "B PHE 444": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 447": "OD1" <-> "OD2" Residue "B ASP 452": "OD1" <-> "OD2" Residue "B ARG 454": "NH1" <-> "NH2" Residue "B PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 463": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 484": "OE1" <-> "OE2" Residue "B ASP 485": "OD1" <-> "OD2" Residue "B ASP 486": "OD1" <-> "OD2" Residue "C ASP 27": "OD1" <-> "OD2" Residue "C ASP 45": "OD1" <-> "OD2" Residue "C GLU 68": "OE1" <-> "OE2" Residue "C GLU 84": "OE1" <-> "OE2" Residue "C ASP 86": "OD1" <-> "OD2" Residue "C GLU 130": "OE1" <-> "OE2" Residue "C ARG 140": "NH1" <-> "NH2" Residue "C ASP 181": "OD1" <-> "OD2" Residue "C TYR 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 206": "NH1" <-> "NH2" Residue "C TYR 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 271": "NH1" <-> "NH2" Residue "C GLU 299": "OE1" <-> "OE2" Residue "C GLU 320": "OE1" <-> "OE2" Residue "C ASP 339": "OD1" <-> "OD2" Residue "C ASP 347": "OD1" <-> "OD2" Residue "C ARG 365": "NH1" <-> "NH2" Residue "C GLU 393": "OE1" <-> "OE2" Residue "C PHE 395": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 403": "OD1" <-> "OD2" Residue "C ARG 412": "NH1" <-> "NH2" Residue "C TYR 438": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 442": "NH1" <-> "NH2" Residue "C ASP 447": "OD1" <-> "OD2" Residue "C ASP 452": "OD1" <-> "OD2" Residue "C ARG 454": "NH1" <-> "NH2" Residue "C PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 463": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 484": "OE1" <-> "OE2" Residue "C ASP 485": "OD1" <-> "OD2" Residue "C ASP 486": "OD1" <-> "OD2" Residue "D ARG 5": "NH1" <-> "NH2" Residue "D ASP 15": "OD1" <-> "OD2" Residue "D ARG 37": "NH1" <-> "NH2" Residue "D ASP 43": "OD1" <-> "OD2" Residue "D ASP 68": "OD1" <-> "OD2" Residue "D PHE 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 101": "OE1" <-> "OE2" Residue "D ASP 108": "OD1" <-> "OD2" Residue "D ASP 112": "OD1" <-> "OD2" Residue "D PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 126": "OE1" <-> "OE2" Residue "D GLU 127": "OE1" <-> "OE2" Residue "D GLU 131": "OE1" <-> "OE2" Residue "D PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 178": "OE1" <-> "OE2" Residue "D PHE 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 190": "OD1" <-> "OD2" Residue "D ARG 191": "NH1" <-> "NH2" Residue "D ARG 193": "NH1" <-> "NH2" Residue "D ASP 204": "OD1" <-> "OD2" Residue "D PHE 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 263": "OE1" <-> "OE2" Residue "D GLU 290": "OE1" <-> "OE2" Residue "D TYR 307": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 315": "OD1" <-> "OD2" Residue "D GLU 332": "OE1" <-> "OE2" Residue "D ARG 333": "NH1" <-> "NH2" Residue "D ASP 345": "OD1" <-> "OD2" Residue "D GLU 357": "OE1" <-> "OE2" Residue "D GLU 361": "OE1" <-> "OE2" Residue "D GLU 362": "OE1" <-> "OE2" Residue "D TYR 364": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 382": "OD1" <-> "OD2" Residue "D ASP 390": "OD1" <-> "OD2" Residue "D GLU 391": "OE1" <-> "OE2" Residue "D PHE 408": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 418": "OE1" <-> "OE2" Residue "D TYR 427": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 432": "OE1" <-> "OE2" Residue "D ARG 435": "NH1" <-> "NH2" Residue "D GLU 439": "OE1" <-> "OE2" Residue "D GLU 450": "OE1" <-> "OE2" Residue "D PHE 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 454": "NH1" <-> "NH2" Residue "D GLU 460": "OE1" <-> "OE2" Residue "D GLU 461": "OE1" <-> "OE2" Residue "E ARG 3": "NH1" <-> "NH2" Residue "E ASP 15": "OD1" <-> "OD2" Residue "E PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 43": "OD1" <-> "OD2" Residue "E ARG 72": "NH1" <-> "NH2" Residue "E GLU 89": "OE1" <-> "OE2" Residue "E PHE 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 106": "OE1" <-> "OE2" Residue "E ASP 108": "OD1" <-> "OD2" Residue "E ASP 112": "OD1" <-> "OD2" Residue "E ARG 114": "NH1" <-> "NH2" Residue "E PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 127": "OE1" <-> "OE2" Residue "E GLU 133": "OE1" <-> "OE2" Residue "E PHE 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 190": "OD1" <-> "OD2" Residue "E ASP 197": "OD1" <-> "OD2" Residue "E GLU 220": "OE1" <-> "OE2" Residue "E ARG 240": "NH1" <-> "NH2" Residue "E ASP 252": "OD1" <-> "OD2" Residue "E PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 263": "OE1" <-> "OE2" Residue "E GLU 284": "OE1" <-> "OE2" Residue "E GLU 290": "OE1" <-> "OE2" Residue "E TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 315": "OD1" <-> "OD2" Residue "E ASP 326": "OD1" <-> "OD2" Residue "E GLU 361": "OE1" <-> "OE2" Residue "E ARG 402": "NH1" <-> "NH2" Residue "E ARG 404": "NH1" <-> "NH2" Residue "E GLU 418": "OE1" <-> "OE2" Residue "E TYR 427": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 450": "OE1" <-> "OE2" Residue "E ASP 451": "OD1" <-> "OD2" Residue "E PHE 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 5": "NH1" <-> "NH2" Residue "F PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 37": "NH1" <-> "NH2" Residue "F ASP 57": "OD1" <-> "OD2" Residue "F GLU 89": "OE1" <-> "OE2" Residue "F ARG 120": "NH1" <-> "NH2" Residue "F PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 191": "NH1" <-> "NH2" Residue "F GLU 194": "OE1" <-> "OE2" Residue "F ASP 197": "OD1" <-> "OD2" Residue "F GLU 220": "OE1" <-> "OE2" Residue "F ARG 240": "NH1" <-> "NH2" Residue "F GLU 242": "OE1" <-> "OE2" Residue "F PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 252": "OD1" <-> "OD2" Residue "F GLU 263": "OE1" <-> "OE2" Residue "F ASP 311": "OD1" <-> "OD2" Residue "F TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 315": "OD1" <-> "OD2" Residue "F GLU 332": "OE1" <-> "OE2" Residue "F ARG 352": "NH1" <-> "NH2" Residue "F GLU 362": "OE1" <-> "OE2" Residue "F GLU 379": "OE1" <-> "OE2" Residue "F ASP 382": "OD1" <-> "OD2" Residue "F ASP 390": "OD1" <-> "OD2" Residue "F ASP 394": "OD1" <-> "OD2" Residue "F ARG 402": "NH1" <-> "NH2" Residue "F ARG 404": "NH1" <-> "NH2" Residue "F TYR 427": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 461": "OE1" <-> "OE2" Residue "F GLU 464": "OE1" <-> "OE2" Residue "G ARG 8": "NH1" <-> "NH2" Residue "G ASP 9": "OD1" <-> "OD2" Residue "G ARG 37": "NH1" <-> "NH2" Residue "G GLU 39": "OE1" <-> "OE2" Residue "G TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 50": "OE1" <-> "OE2" Residue "G GLU 54": "OE1" <-> "OE2" Residue "G ASP 87": "OD1" <-> "OD2" Residue "G ARG 88": "NH1" <-> "NH2" Residue "G TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 109": "NH1" <-> "NH2" Residue "G GLU 115": "OE1" <-> "OE2" Residue "G TYR 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 130": "NH1" <-> "NH2" Residue "G ARG 132": "NH1" <-> "NH2" Residue "G ASP 139": "OD1" <-> "OD2" Residue "G PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 154": "OE1" <-> "OE2" Residue "G ASP 169": "OD1" <-> "OD2" Residue "G TYR 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 185": "OE1" <-> "OE2" Residue "G GLU 188": "OE1" <-> "OE2" Residue "G GLU 225": "OE1" <-> "OE2" Residue "G GLU 276": "OE1" <-> "OE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 24199 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 3636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 474, 3636 Classifications: {'peptide': 474} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 451} Chain: "B" Number of atoms: 3643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 475, 3643 Classifications: {'peptide': 475} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 452} Chain: "C" Number of atoms: 3649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 476, 3649 Classifications: {'peptide': 476} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 453} Chain: "D" Number of atoms: 3621 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3621 Classifications: {'peptide': 470} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 446} Chain: "E" Number of atoms: 3622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3622 Classifications: {'peptide': 470} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 446} Chain: "F" Number of atoms: 3629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3629 Classifications: {'peptide': 471} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 447} Chain: "G" Number of atoms: 2211 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 2211 Classifications: {'peptide': 282} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 271} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 13.64, per 1000 atoms: 0.56 Number of scatterers: 24199 At special positions: 0 Unit cell: (152.88, 123.48, 126, 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 78 16.00 P 17 15.00 Mg 6 11.99 O 4649 8.00 N 4214 7.00 C 15235 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: 9.48 Conformation dependent library (CDL) restraints added in 4.7 seconds 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5690 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 114 helices and 22 sheets defined 42.0% alpha, 12.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.91 Creating SS restraints... Processing helix chain 'A' and resid 101 through 103 No H-bonds generated for 'chain 'A' and resid 101 through 103' Processing helix chain 'A' and resid 151 through 156 Processing helix chain 'A' and resid 176 through 186 Processing helix chain 'A' and resid 202 through 214 Processing helix chain 'A' and resid 217 through 220 Processing helix chain 'A' and resid 232 through 252 Proline residue: A 239 - end of helix removed outlier: 3.845A pdb=" N TYR A 248 " --> pdb=" O ALA A 244 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N PHE A 249 " --> pdb=" O MET A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 276 Processing helix chain 'A' and resid 290 through 298 Processing helix chain 'A' and resid 322 through 324 No H-bonds generated for 'chain 'A' and resid 322 through 324' Processing helix chain 'A' and resid 329 through 337 removed outlier: 3.671A pdb=" N SER A 336 " --> pdb=" O THR A 332 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE A 337 " --> pdb=" O ASN A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 351 Processing helix chain 'A' and resid 373 through 396 removed outlier: 3.931A pdb=" N LYS A 377 " --> pdb=" O LYS A 373 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N VAL A 378 " --> pdb=" O ALA A 374 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N THR A 381 " --> pdb=" O LYS A 377 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N LEU A 382 " --> pdb=" O VAL A 378 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LEU A 384 " --> pdb=" O GLY A 380 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LEU A 392 " --> pdb=" O ALA A 388 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N PHE A 395 " --> pdb=" O GLU A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 419 Processing helix chain 'A' and resid 430 through 441 Processing helix chain 'A' and resid 450 through 466 removed outlier: 3.988A pdb=" N ARG A 454 " --> pdb=" O GLU A 451 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N PHE A 456 " --> pdb=" O VAL A 453 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N GLU A 457 " --> pdb=" O ARG A 454 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLU A 459 " --> pdb=" O PHE A 456 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 478 removed outlier: 3.565A pdb=" N HIS A 474 " --> pdb=" O HIS A 470 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ILE A 475 " --> pdb=" O LEU A 471 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ARG A 476 " --> pdb=" O LEU A 472 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N THR A 477 " --> pdb=" O GLU A 473 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 497 Processing helix chain 'B' and resid 101 through 103 No H-bonds generated for 'chain 'B' and resid 101 through 103' Processing helix chain 'B' and resid 151 through 156 Processing helix chain 'B' and resid 175 through 187 removed outlier: 3.516A pdb=" N ALA B 179 " --> pdb=" O LYS B 175 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LYS B 187 " --> pdb=" O ILE B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 214 Processing helix chain 'B' and resid 217 through 220 Processing helix chain 'B' and resid 232 through 252 Proline residue: B 239 - end of helix removed outlier: 3.845A pdb=" N TYR B 248 " --> pdb=" O ALA B 244 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N PHE B 249 " --> pdb=" O MET B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 275 Processing helix chain 'B' and resid 288 through 300 removed outlier: 3.923A pdb=" N PHE B 291 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N TYR B 292 " --> pdb=" O ASP B 289 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N HIS B 294 " --> pdb=" O PHE B 291 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER B 295 " --> pdb=" O TYR B 292 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N GLU B 299 " --> pdb=" O ARG B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 324 No H-bonds generated for 'chain 'B' and resid 322 through 324' Processing helix chain 'B' and resid 329 through 337 removed outlier: 3.510A pdb=" N ILE B 337 " --> pdb=" O ASN B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 351 Processing helix chain 'B' and resid 373 through 379 Processing helix chain 'B' and resid 382 through 398 removed outlier: 3.519A pdb=" N ALA B 387 " --> pdb=" O ARG B 383 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA B 388 " --> pdb=" O LEU B 384 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLU B 391 " --> pdb=" O ALA B 387 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N PHE B 398 " --> pdb=" O ALA B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 419 removed outlier: 3.516A pdb=" N LYS B 409 " --> pdb=" O ALA B 405 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ALA B 414 " --> pdb=" O LEU B 410 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ARG B 415 " --> pdb=" O ALA B 411 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 442 Processing helix chain 'B' and resid 444 through 446 No H-bonds generated for 'chain 'B' and resid 444 through 446' Processing helix chain 'B' and resid 450 through 466 removed outlier: 3.833A pdb=" N ARG B 454 " --> pdb=" O GLU B 451 " (cutoff:3.500A) Processing helix chain 'B' and resid 469 through 478 removed outlier: 3.813A pdb=" N ARG B 476 " --> pdb=" O LEU B 472 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N THR B 477 " --> pdb=" O GLU B 473 " (cutoff:3.500A) Processing helix chain 'B' and resid 484 through 497 removed outlier: 3.607A pdb=" N THR B 497 " --> pdb=" O ALA B 493 " (cutoff:3.500A) Processing helix chain 'C' and resid 101 through 103 No H-bonds generated for 'chain 'C' and resid 101 through 103' Processing helix chain 'C' and resid 151 through 156 Processing helix chain 'C' and resid 175 through 186 Processing helix chain 'C' and resid 202 through 214 Processing helix chain 'C' and resid 217 through 220 Processing helix chain 'C' and resid 232 through 252 Proline residue: C 239 - end of helix removed outlier: 3.845A pdb=" N TYR C 248 " --> pdb=" O ALA C 244 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N PHE C 249 " --> pdb=" O MET C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 276 Processing helix chain 'C' and resid 288 through 300 removed outlier: 3.930A pdb=" N PHE C 291 " --> pdb=" O GLY C 288 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N TYR C 292 " --> pdb=" O ASP C 289 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N HIS C 294 " --> pdb=" O PHE C 291 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N GLU C 299 " --> pdb=" O ARG C 296 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ARG C 300 " --> pdb=" O LEU C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 322 through 324 No H-bonds generated for 'chain 'C' and resid 322 through 324' Processing helix chain 'C' and resid 329 through 337 Processing helix chain 'C' and resid 346 through 351 Processing helix chain 'C' and resid 373 through 378 Processing helix chain 'C' and resid 382 through 398 removed outlier: 4.003A pdb=" N PHE C 398 " --> pdb=" O ALA C 394 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 419 Processing helix chain 'C' and resid 430 through 442 Processing helix chain 'C' and resid 450 through 466 removed outlier: 4.364A pdb=" N ARG C 454 " --> pdb=" O GLU C 451 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLU C 459 " --> pdb=" O PHE C 456 " (cutoff:3.500A) Processing helix chain 'C' and resid 469 through 478 Processing helix chain 'C' and resid 484 through 497 Processing helix chain 'D' and resid 89 through 91 No H-bonds generated for 'chain 'D' and resid 89 through 91' Processing helix chain 'D' and resid 140 through 145 Processing helix chain 'D' and resid 165 through 178 removed outlier: 3.867A pdb=" N GLU D 170 " --> pdb=" O VAL D 166 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N GLN D 177 " --> pdb=" O HIS D 173 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N GLU D 178 " --> pdb=" O ASN D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 192 through 205 removed outlier: 3.801A pdb=" N ASN D 196 " --> pdb=" O THR D 192 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ASP D 197 " --> pdb=" O ARG D 193 " (cutoff:3.500A) Processing helix chain 'D' and resid 207 through 210 Processing helix chain 'D' and resid 222 through 241 removed outlier: 4.662A pdb=" N ALA D 229 " --> pdb=" O ARG D 225 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N LEU D 230 " --> pdb=" O MET D 226 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N THR D 231 " --> pdb=" O ARG D 227 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLY D 232 " --> pdb=" O VAL D 228 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N MET D 235 " --> pdb=" O THR D 231 " (cutoff:3.500A) Processing helix chain 'D' and resid 254 through 268 removed outlier: 3.611A pdb=" N THR D 258 " --> pdb=" O ILE D 254 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLY D 261 " --> pdb=" O PHE D 257 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N SER D 262 " --> pdb=" O THR D 258 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLU D 263 " --> pdb=" O GLN D 259 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ALA D 266 " --> pdb=" O SER D 262 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N LEU D 267 " --> pdb=" O GLU D 263 " (cutoff:3.500A) Processing helix chain 'D' and resid 281 through 291 removed outlier: 3.897A pdb=" N ARG D 291 " --> pdb=" O GLN D 287 " (cutoff:3.500A) Processing helix chain 'D' and resid 316 through 324 removed outlier: 4.003A pdb=" N SER D 323 " --> pdb=" O ALA D 319 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N HIS D 324 " --> pdb=" O THR D 320 " (cutoff:3.500A) Processing helix chain 'D' and resid 333 through 338 Processing helix chain 'D' and resid 356 through 359 No H-bonds generated for 'chain 'D' and resid 356 through 359' Processing helix chain 'D' and resid 361 through 387 removed outlier: 4.149A pdb=" N ASP D 382 " --> pdb=" O LYS D 378 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ILE D 383 " --> pdb=" O GLU D 379 " (cutoff:3.500A) Processing helix chain 'D' and resid 389 through 391 No H-bonds generated for 'chain 'D' and resid 389 through 391' Processing helix chain 'D' and resid 394 through 409 removed outlier: 3.622A pdb=" N ARG D 405 " --> pdb=" O HIS D 401 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 421 removed outlier: 3.838A pdb=" N GLN D 419 " --> pdb=" O VAL D 416 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N THR D 421 " --> pdb=" O GLU D 418 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 442 Processing helix chain 'D' and resid 450 through 453 Processing helix chain 'D' and resid 459 through 469 removed outlier: 3.550A pdb=" N GLU D 464 " --> pdb=" O GLU D 460 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N MET D 469 " --> pdb=" O LYS D 465 " (cutoff:3.500A) Processing helix chain 'E' and resid 89 through 91 No H-bonds generated for 'chain 'E' and resid 89 through 91' Processing helix chain 'E' and resid 140 through 145 Processing helix chain 'E' and resid 164 through 177 Processing helix chain 'E' and resid 192 through 204 removed outlier: 3.797A pdb=" N ASN E 196 " --> pdb=" O THR E 192 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ASP E 197 " --> pdb=" O ARG E 193 " (cutoff:3.500A) Processing helix chain 'E' and resid 207 through 210 Processing helix chain 'E' and resid 222 through 241 removed outlier: 4.960A pdb=" N ALA E 229 " --> pdb=" O ARG E 225 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N LEU E 230 " --> pdb=" O MET E 226 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N TYR E 238 " --> pdb=" O THR E 234 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N PHE E 239 " --> pdb=" O MET E 235 " (cutoff:3.500A) Processing helix chain 'E' and resid 254 through 268 Processing helix chain 'E' and resid 274 through 276 No H-bonds generated for 'chain 'E' and resid 274 through 276' Processing helix chain 'E' and resid 281 through 291 removed outlier: 4.728A pdb=" N ARG E 291 " --> pdb=" O GLN E 287 " (cutoff:3.500A) Processing helix chain 'E' and resid 316 through 324 removed outlier: 3.586A pdb=" N THR E 320 " --> pdb=" O PRO E 316 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N HIS E 324 " --> pdb=" O THR E 320 " (cutoff:3.500A) Processing helix chain 'E' and resid 333 through 338 Processing helix chain 'E' and resid 356 through 359 No H-bonds generated for 'chain 'E' and resid 356 through 359' Processing helix chain 'E' and resid 361 through 386 removed outlier: 4.098A pdb=" N ASP E 382 " --> pdb=" O LYS E 378 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ILE E 383 " --> pdb=" O GLU E 379 " (cutoff:3.500A) Processing helix chain 'E' and resid 389 through 391 No H-bonds generated for 'chain 'E' and resid 389 through 391' Processing helix chain 'E' and resid 394 through 410 removed outlier: 3.962A pdb=" N ARG E 402 " --> pdb=" O LEU E 398 " (cutoff:3.500A) Processing helix chain 'E' and resid 416 through 419 removed outlier: 3.766A pdb=" N GLN E 419 " --> pdb=" O VAL E 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 416 through 419' Processing helix chain 'E' and resid 430 through 442 Processing helix chain 'E' and resid 450 through 453 Processing helix chain 'E' and resid 459 through 469 removed outlier: 3.632A pdb=" N VAL E 463 " --> pdb=" O ILE E 459 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N MET E 469 " --> pdb=" O LYS E 465 " (cutoff:3.500A) Processing helix chain 'F' and resid 89 through 91 No H-bonds generated for 'chain 'F' and resid 89 through 91' Processing helix chain 'F' and resid 140 through 145 Processing helix chain 'F' and resid 164 through 178 removed outlier: 3.816A pdb=" N GLN F 177 " --> pdb=" O HIS F 173 " (cutoff:3.500A) Processing helix chain 'F' and resid 194 through 205 Processing helix chain 'F' and resid 207 through 210 Processing helix chain 'F' and resid 222 through 241 removed outlier: 3.531A pdb=" N MET F 226 " --> pdb=" O PRO F 222 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ARG F 227 " --> pdb=" O GLY F 223 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ALA F 229 " --> pdb=" O ARG F 225 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N LEU F 230 " --> pdb=" O MET F 226 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N MET F 235 " --> pdb=" O THR F 231 " (cutoff:3.500A) Processing helix chain 'F' and resid 255 through 268 removed outlier: 3.788A pdb=" N ALA F 266 " --> pdb=" O SER F 262 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N LEU F 267 " --> pdb=" O GLU F 263 " (cutoff:3.500A) Processing helix chain 'F' and resid 281 through 291 removed outlier: 3.614A pdb=" N LEU F 288 " --> pdb=" O GLU F 284 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ARG F 291 " --> pdb=" O GLN F 287 " (cutoff:3.500A) Processing helix chain 'F' and resid 316 through 324 removed outlier: 3.549A pdb=" N THR F 320 " --> pdb=" O PRO F 316 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N SER F 323 " --> pdb=" O ALA F 319 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N HIS F 324 " --> pdb=" O THR F 320 " (cutoff:3.500A) Processing helix chain 'F' and resid 333 through 338 Processing helix chain 'F' and resid 356 through 359 No H-bonds generated for 'chain 'F' and resid 356 through 359' Processing helix chain 'F' and resid 361 through 384 removed outlier: 4.986A pdb=" N ASP F 382 " --> pdb=" O LYS F 378 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N ILE F 383 " --> pdb=" O GLU F 379 " (cutoff:3.500A) Processing helix chain 'F' and resid 394 through 409 removed outlier: 3.530A pdb=" N VAL F 399 " --> pdb=" O ASP F 396 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N PHE F 408 " --> pdb=" O ARG F 405 " (cutoff:3.500A) Processing helix chain 'F' and resid 415 through 417 No H-bonds generated for 'chain 'F' and resid 415 through 417' Processing helix chain 'F' and resid 430 through 442 Processing helix chain 'F' and resid 450 through 453 Processing helix chain 'F' and resid 459 through 469 removed outlier: 3.550A pdb=" N MET F 469 " --> pdb=" O LYS F 465 " (cutoff:3.500A) Processing helix chain 'G' and resid 7 through 61 Proline residue: G 47 - end of helix Processing helix chain 'G' and resid 94 through 109 removed outlier: 3.569A pdb=" N VAL G 98 " --> pdb=" O TYR G 94 " (cutoff:3.500A) Processing helix chain 'G' and resid 113 through 115 No H-bonds generated for 'chain 'G' and resid 113 through 115' Processing helix chain 'G' and resid 123 through 130 Processing helix chain 'G' and resid 149 through 164 removed outlier: 3.930A pdb=" N GLU G 154 " --> pdb=" O ALA G 150 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ILE G 155 " --> pdb=" O ASP G 151 " (cutoff:3.500A) Processing helix chain 'G' and resid 212 through 286 removed outlier: 3.596A pdb=" N VAL G 218 " --> pdb=" O GLU G 214 " (cutoff:3.500A) Proline residue: G 221 - end of helix removed outlier: 3.523A pdb=" N SER G 264 " --> pdb=" O THR G 260 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ILE G 277 " --> pdb=" O ILE G 273 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 28 through 30 removed outlier: 6.853A pdb=" N GLY A 72 " --> pdb=" O LEU A 64 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N LEU A 66 " --> pdb=" O ASN A 70 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N ASN A 70 " --> pdb=" O LEU A 66 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLN A 33 " --> pdb=" O ARG A 40 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N HIS A 42 " --> pdb=" O VAL A 31 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N VAL A 31 " --> pdb=" O HIS A 42 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 96 through 99 Processing sheet with id= C, first strand: chain 'A' and resid 341 through 344 removed outlier: 6.656A pdb=" N LEU A 166 " --> pdb=" O ILE A 342 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N LEU A 344 " --> pdb=" O LEU A 166 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N ILE A 168 " --> pdb=" O LEU A 344 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 221 through 226 removed outlier: 7.020A pdb=" N SER A 193 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 8.297A pdb=" N VAL A 224 " --> pdb=" O SER A 193 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N TYR A 195 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N ALA A 226 " --> pdb=" O TYR A 195 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ALA A 197 " --> pdb=" O ALA A 226 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N SER A 312 " --> pdb=" O VAL A 256 " (cutoff:3.500A) removed outlier: 7.784A pdb=" N VAL A 258 " --> pdb=" O SER A 312 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N THR A 314 " --> pdb=" O VAL A 258 " (cutoff:3.500A) removed outlier: 8.125A pdb=" N TYR A 260 " --> pdb=" O THR A 314 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N LEU A 316 " --> pdb=" O TYR A 260 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 38 through 41 removed outlier: 3.604A pdb=" N ILE B 73 " --> pdb=" O ALA B 39 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N VAL B 74 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N ALA B 63 " --> pdb=" O VAL B 74 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 96 through 99 Processing sheet with id= G, first strand: chain 'B' and resid 341 through 343 removed outlier: 6.573A pdb=" N LEU B 166 " --> pdb=" O ILE B 342 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 221 through 226 removed outlier: 6.939A pdb=" N SER B 193 " --> pdb=" O ILE B 222 " (cutoff:3.500A) removed outlier: 8.200A pdb=" N VAL B 224 " --> pdb=" O SER B 193 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N TYR B 195 " --> pdb=" O VAL B 224 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N ALA B 226 " --> pdb=" O TYR B 195 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ALA B 197 " --> pdb=" O ALA B 226 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N TYR B 260 " --> pdb=" O LEU B 316 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 28 through 30 removed outlier: 6.873A pdb=" N GLY C 72 " --> pdb=" O LEU C 64 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N LEU C 66 " --> pdb=" O ASN C 70 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N ASN C 70 " --> pdb=" O LEU C 66 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLN C 33 " --> pdb=" O ARG C 40 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N HIS C 42 " --> pdb=" O VAL C 31 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N VAL C 31 " --> pdb=" O HIS C 42 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 96 through 99 Processing sheet with id= K, first strand: chain 'C' and resid 107 through 109 removed outlier: 8.827A pdb=" N VAL C 108 " --> pdb=" O THR C 221 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N VAL C 223 " --> pdb=" O VAL C 108 " (cutoff:3.500A) removed outlier: 8.646A pdb=" N ILE C 222 " --> pdb=" O MET C 191 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N SER C 193 " --> pdb=" O ILE C 222 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N VAL C 224 " --> pdb=" O SER C 193 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N TYR C 195 " --> pdb=" O VAL C 224 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N ALA C 226 " --> pdb=" O TYR C 195 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N ALA C 197 " --> pdb=" O ALA C 226 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N HIS C 255 " --> pdb=" O ILE C 192 " (cutoff:3.500A) removed outlier: 8.479A pdb=" N ILE C 194 " --> pdb=" O HIS C 255 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N LEU C 257 " --> pdb=" O ILE C 194 " (cutoff:3.500A) removed outlier: 7.899A pdb=" N VAL C 196 " --> pdb=" O LEU C 257 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N VAL C 259 " --> pdb=" O VAL C 196 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N ILE C 198 " --> pdb=" O VAL C 259 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 318 through 320 removed outlier: 6.578A pdb=" N ILE C 167 " --> pdb=" O VAL C 319 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N ILE C 342 " --> pdb=" O ILE C 168 " (cutoff:3.500A) No H-bonds generated for sheet with id= L Processing sheet with id= M, first strand: chain 'D' and resid 5 through 10 removed outlier: 6.728A pdb=" N ASP D 15 " --> pdb=" O ILE D 7 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N VAL D 9 " --> pdb=" O VAL D 13 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N VAL D 13 " --> pdb=" O VAL D 9 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU D 52 " --> pdb=" O ARG D 60 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ILE D 62 " --> pdb=" O VAL D 50 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N VAL D 50 " --> pdb=" O ILE D 62 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 84 through 86 Processing sheet with id= O, first strand: chain 'D' and resid 327 through 331 removed outlier: 7.687A pdb=" N ILE D 154 " --> pdb=" O ILE D 300 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N SER D 302 " --> pdb=" O ILE D 154 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N LEU D 156 " --> pdb=" O SER D 302 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N GLN D 304 " --> pdb=" O LEU D 156 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N GLY D 158 " --> pdb=" O GLN D 304 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N ILE D 306 " --> pdb=" O GLY D 158 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N VAL D 247 " --> pdb=" O THR D 301 " (cutoff:3.500A) removed outlier: 8.117A pdb=" N ILE D 303 " --> pdb=" O VAL D 247 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N LEU D 249 " --> pdb=" O ILE D 303 " (cutoff:3.500A) removed outlier: 8.095A pdb=" N ALA D 305 " --> pdb=" O LEU D 249 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N ILE D 251 " --> pdb=" O ALA D 305 " (cutoff:3.500A) removed outlier: 8.552A pdb=" N TYR D 307 " --> pdb=" O ILE D 251 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'E' and resid 5 through 10 removed outlier: 6.426A pdb=" N ASP E 15 " --> pdb=" O ILE E 7 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N VAL E 9 " --> pdb=" O VAL E 13 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N VAL E 13 " --> pdb=" O VAL E 9 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N ILE E 62 " --> pdb=" O VAL E 50 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N VAL E 50 " --> pdb=" O ILE E 62 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'E' and resid 84 through 86 Processing sheet with id= R, first strand: chain 'E' and resid 327 through 331 removed outlier: 3.524A pdb=" N ALA E 327 " --> pdb=" O LYS E 153 " (cutoff:3.500A) removed outlier: 8.516A pdb=" N ILE E 154 " --> pdb=" O ILE E 300 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N SER E 302 " --> pdb=" O ILE E 154 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N LEU E 156 " --> pdb=" O SER E 302 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N GLN E 304 " --> pdb=" O LEU E 156 " (cutoff:3.500A) removed outlier: 8.342A pdb=" N GLY E 158 " --> pdb=" O GLN E 304 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N VAL E 247 " --> pdb=" O THR E 301 " (cutoff:3.500A) removed outlier: 8.082A pdb=" N ILE E 303 " --> pdb=" O VAL E 247 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N LEU E 249 " --> pdb=" O ILE E 303 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N ALA E 305 " --> pdb=" O LEU E 249 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N ILE E 251 " --> pdb=" O ALA E 305 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'F' and resid 5 through 10 removed outlier: 6.621A pdb=" N ASP F 15 " --> pdb=" O ILE F 7 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N VAL F 9 " --> pdb=" O VAL F 13 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N VAL F 13 " --> pdb=" O VAL F 9 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N ILE F 62 " --> pdb=" O VAL F 50 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N VAL F 50 " --> pdb=" O ILE F 62 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'F' and resid 84 through 86 Processing sheet with id= U, first strand: chain 'F' and resid 327 through 330 removed outlier: 8.098A pdb=" N ILE F 154 " --> pdb=" O ILE F 300 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N SER F 302 " --> pdb=" O ILE F 154 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N LEU F 156 " --> pdb=" O SER F 302 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N GLN F 304 " --> pdb=" O LEU F 156 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N GLY F 158 " --> pdb=" O GLN F 304 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N ILE F 306 " --> pdb=" O GLY F 158 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N VAL F 247 " --> pdb=" O THR F 301 " (cutoff:3.500A) removed outlier: 8.038A pdb=" N ILE F 303 " --> pdb=" O VAL F 247 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N LEU F 249 " --> pdb=" O ILE F 303 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N ALA F 305 " --> pdb=" O LEU F 249 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N ILE F 251 " --> pdb=" O ALA F 305 " (cutoff:3.500A) removed outlier: 8.547A pdb=" N TYR F 307 " --> pdb=" O ILE F 251 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N ILE F 182 " --> pdb=" O LEU F 248 " (cutoff:3.500A) removed outlier: 8.460A pdb=" N PHE F 250 " --> pdb=" O ILE F 182 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N VAL F 184 " --> pdb=" O PHE F 250 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'G' and resid 184 through 192 removed outlier: 7.301A pdb=" N LEU G 171 " --> pdb=" O LEU G 191 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N ASN G 176 " --> pdb=" O ILE G 84 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N LEU G 138 " --> pdb=" O VAL G 120 " (cutoff:3.500A) 927 hydrogen bonds defined for protein. 2538 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.71 Time building geometry restraints manager: 10.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 4272 1.31 - 1.44: 5802 1.44 - 1.57: 14343 1.57 - 1.69: 33 1.69 - 1.82: 154 Bond restraints: 24604 Sorted by residual: bond pdb=" C PRO B 280 " pdb=" O PRO B 280 " ideal model delta sigma weight residual 1.246 1.196 0.049 8.50e-03 1.38e+04 3.34e+01 bond pdb=" C4 ADP E 501 " pdb=" C5 ADP E 501 " ideal model delta sigma weight residual 1.490 1.379 0.111 2.00e-02 2.50e+03 3.10e+01 bond pdb=" CA SER A 295 " pdb=" CB SER A 295 " ideal model delta sigma weight residual 1.528 1.463 0.066 1.56e-02 4.11e+03 1.76e+01 bond pdb=" C5 ADP E 501 " pdb=" C6 ADP E 501 " ideal model delta sigma weight residual 1.490 1.407 0.083 2.00e-02 2.50e+03 1.72e+01 bond pdb=" C ARG B 40 " pdb=" O ARG B 40 " ideal model delta sigma weight residual 1.234 1.184 0.050 1.22e-02 6.72e+03 1.71e+01 ... (remaining 24599 not shown) Histogram of bond angle deviations from ideal: 98.12 - 105.06: 612 105.06 - 111.99: 9833 111.99 - 118.93: 10046 118.93 - 125.86: 12521 125.86 - 132.80: 352 Bond angle restraints: 33364 Sorted by residual: angle pdb=" PB ATP D 500 " pdb=" O3B ATP D 500 " pdb=" PG ATP D 500 " ideal model delta sigma weight residual 139.87 123.33 16.54 1.00e+00 1.00e+00 2.74e+02 angle pdb=" PB ATP C 600 " pdb=" O3B ATP C 600 " pdb=" PG ATP C 600 " ideal model delta sigma weight residual 139.87 125.52 14.35 1.00e+00 1.00e+00 2.06e+02 angle pdb=" PB ATP F 500 " pdb=" O3B ATP F 500 " pdb=" PG ATP F 500 " ideal model delta sigma weight residual 139.87 126.51 13.36 1.00e+00 1.00e+00 1.78e+02 angle pdb=" PA ATP D 500 " pdb=" O3A ATP D 500 " pdb=" PB ATP D 500 " ideal model delta sigma weight residual 136.83 123.69 13.14 1.00e+00 1.00e+00 1.73e+02 angle pdb=" PB ATP A 600 " pdb=" O3B ATP A 600 " pdb=" PG ATP A 600 " ideal model delta sigma weight residual 139.87 127.16 12.71 1.00e+00 1.00e+00 1.62e+02 ... (remaining 33359 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.03: 14488 30.03 - 60.07: 486 60.07 - 90.10: 68 90.10 - 120.13: 0 120.13 - 150.16: 2 Dihedral angle restraints: 15044 sinusoidal: 6152 harmonic: 8892 Sorted by residual: dihedral pdb=" C ARG A 283 " pdb=" N ARG A 283 " pdb=" CA ARG A 283 " pdb=" CB ARG A 283 " ideal model delta harmonic sigma weight residual -122.60 -140.28 17.68 0 2.50e+00 1.60e-01 5.00e+01 dihedral pdb=" C ASP C 261 " pdb=" N ASP C 261 " pdb=" CA ASP C 261 " pdb=" CB ASP C 261 " ideal model delta harmonic sigma weight residual -122.60 -139.55 16.95 0 2.50e+00 1.60e-01 4.60e+01 dihedral pdb=" O1B ADP E 501 " pdb=" O3A ADP E 501 " pdb=" PB ADP E 501 " pdb=" PA ADP E 501 " ideal model delta sinusoidal sigma weight residual 300.00 149.83 150.16 1 2.00e+01 2.50e-03 4.48e+01 ... (remaining 15041 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.133: 3061 0.133 - 0.266: 685 0.266 - 0.399: 76 0.399 - 0.531: 15 0.531 - 0.664: 3 Chirality restraints: 3840 Sorted by residual: chirality pdb=" CA ASP C 261 " pdb=" N ASP C 261 " pdb=" C ASP C 261 " pdb=" CB ASP C 261 " both_signs ideal model delta sigma weight residual False 2.51 1.85 0.66 2.00e-01 2.50e+01 1.10e+01 chirality pdb=" CA ARG A 283 " pdb=" N ARG A 283 " pdb=" C ARG A 283 " pdb=" CB ARG A 283 " both_signs ideal model delta sigma weight residual False 2.51 1.85 0.66 2.00e-01 2.50e+01 1.08e+01 chirality pdb=" CA TYR D 27 " pdb=" N TYR D 27 " pdb=" C TYR D 27 " pdb=" CB TYR D 27 " both_signs ideal model delta sigma weight residual False 2.51 1.96 0.55 2.00e-01 2.50e+01 7.58e+00 ... (remaining 3837 not shown) Planarity restraints: 4349 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 220 " -0.101 2.00e-02 2.50e+03 6.26e-02 7.84e+01 pdb=" CG TYR A 220 " 0.001 2.00e-02 2.50e+03 pdb=" CD1 TYR A 220 " 0.040 2.00e-02 2.50e+03 pdb=" CD2 TYR A 220 " 0.072 2.00e-02 2.50e+03 pdb=" CE1 TYR A 220 " 0.052 2.00e-02 2.50e+03 pdb=" CE2 TYR A 220 " 0.030 2.00e-02 2.50e+03 pdb=" CZ TYR A 220 " 0.008 2.00e-02 2.50e+03 pdb=" OH TYR A 220 " -0.103 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 199 " 0.110 2.00e-02 2.50e+03 6.02e-02 7.25e+01 pdb=" CG TYR D 199 " -0.040 2.00e-02 2.50e+03 pdb=" CD1 TYR D 199 " -0.044 2.00e-02 2.50e+03 pdb=" CD2 TYR D 199 " -0.042 2.00e-02 2.50e+03 pdb=" CE1 TYR D 199 " -0.034 2.00e-02 2.50e+03 pdb=" CE2 TYR D 199 " -0.039 2.00e-02 2.50e+03 pdb=" CZ TYR D 199 " -0.005 2.00e-02 2.50e+03 pdb=" OH TYR D 199 " 0.095 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 313 " 0.081 2.00e-02 2.50e+03 5.47e-02 5.97e+01 pdb=" CG TYR D 313 " -0.003 2.00e-02 2.50e+03 pdb=" CD1 TYR D 313 " -0.041 2.00e-02 2.50e+03 pdb=" CD2 TYR D 313 " -0.028 2.00e-02 2.50e+03 pdb=" CE1 TYR D 313 " -0.034 2.00e-02 2.50e+03 pdb=" CE2 TYR D 313 " -0.050 2.00e-02 2.50e+03 pdb=" CZ TYR D 313 " -0.026 2.00e-02 2.50e+03 pdb=" OH TYR D 313 " 0.102 2.00e-02 2.50e+03 ... (remaining 4346 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 99 2.55 - 3.14: 18833 3.14 - 3.73: 34567 3.73 - 4.31: 51288 4.31 - 4.90: 84644 Nonbonded interactions: 189431 Sorted by model distance: nonbonded pdb=" O2G ATP C 600 " pdb="MG MG C 601 " model vdw 1.965 2.170 nonbonded pdb=" O THR F 192 " pdb=" OG1 THR F 192 " model vdw 2.043 2.440 nonbonded pdb=" O1G ATP D 500 " pdb="MG MG D 501 " model vdw 2.098 2.170 nonbonded pdb=" O1G ATP F 500 " pdb="MG MG F 501 " model vdw 2.107 2.170 nonbonded pdb=" OG1 THR B 176 " pdb="MG MG B 601 " model vdw 2.201 2.170 ... (remaining 189426 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 499 or resid 600 through 601)) selection = (chain 'B' and (resid 27 through 499 or resid 600 through 601)) selection = (chain 'C' and (resid 27 through 499 or resid 600 through 601)) } ncs_group { reference = (chain 'D' and (resid 2 through 470 or resid 501)) selection = (chain 'E' and (resid 2 through 470 or resid 502)) selection = (chain 'F' and (resid 2 through 470 or resid 501)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.760 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: 0.030 Extract box with map and model: 4.860 Check model and map are aligned: 0.370 Set scattering table: 0.220 Process input model: 66.610 Find NCS groups from input model: 1.640 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:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 77.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6843 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 : 0.011 0.111 24604 Z= 0.749 Angle : 1.763 16.538 33364 Z= 1.202 Chirality : 0.111 0.664 3840 Planarity : 0.010 0.089 4349 Dihedral : 14.952 150.162 9354 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.25 % Favored : 96.71 % Rotamer: Outliers : 3.32 % Allowed : 9.73 % Favored : 86.94 % Cbeta Deviations : 0.98 % Peptide Plane: Cis-proline : 4.83 % 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 (0.14), residues: 3104 helix: -0.08 (0.14), residues: 1225 sheet: 0.26 (0.24), residues: 461 loop : -0.79 (0.16), residues: 1418 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.024 0.004 HIS F 173 PHE 0.093 0.009 PHE A 395 TYR 0.110 0.012 TYR D 199 ARG 0.105 0.005 ARG F 270 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1295 residues out of total 2558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 1210 time to evaluate : 2.725 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 ASP cc_start: 0.6611 (m-30) cc_final: 0.6241 (m-30) REVERT: A 38 ILE cc_start: 0.7211 (mm) cc_final: 0.6931 (mm) REVERT: A 48 MET cc_start: 0.7287 (mtm) cc_final: 0.6872 (mtm) REVERT: A 60 MET cc_start: 0.6973 (mmt) cc_final: 0.6750 (mmm) REVERT: A 93 ARG cc_start: 0.6450 (ptt180) cc_final: 0.6067 (ptt180) REVERT: A 127 ARG cc_start: 0.6613 (mtp85) cc_final: 0.6051 (mtp85) REVERT: A 144 GLU cc_start: 0.7080 (pt0) cc_final: 0.6673 (pt0) REVERT: A 163 GLN cc_start: 0.7617 (tt0) cc_final: 0.7397 (tt0) REVERT: A 181 ASP cc_start: 0.7614 (m-30) cc_final: 0.7384 (m-30) REVERT: A 185 ASN cc_start: 0.7455 (t0) cc_final: 0.7087 (t0) REVERT: A 272 GLU cc_start: 0.6724 (tt0) cc_final: 0.6331 (tt0) REVERT: A 296 ARG cc_start: 0.7316 (mtm180) cc_final: 0.7040 (mtm-85) REVERT: A 299 GLU cc_start: 0.7829 (mm-30) cc_final: 0.7346 (mm-30) REVERT: A 313 LEU cc_start: 0.6879 (tp) cc_final: 0.6671 (tp) REVERT: A 341 GLN cc_start: 0.6849 (pm20) cc_final: 0.6520 (pm20) REVERT: A 358 ASN cc_start: 0.7107 (t0) cc_final: 0.6808 (t0) REVERT: A 375 MET cc_start: 0.7748 (OUTLIER) cc_final: 0.6951 (tpp) REVERT: A 391 GLU cc_start: 0.6866 (tp30) cc_final: 0.6651 (tp30) REVERT: A 426 GLN cc_start: 0.6986 (mm-40) cc_final: 0.6629 (mm-40) REVERT: A 427 PRO cc_start: 0.8032 (Cg_endo) cc_final: 0.7770 (Cg_exo) REVERT: A 431 GLU cc_start: 0.7501 (pm20) cc_final: 0.7144 (pm20) REVERT: A 474 HIS cc_start: 0.6589 (t-90) cc_final: 0.5753 (t-170) REVERT: A 478 THR cc_start: 0.7293 (m) cc_final: 0.7059 (t) REVERT: B 49 SER cc_start: 0.7711 (t) cc_final: 0.7133 (m) REVERT: B 51 GLU cc_start: 0.7006 (tt0) cc_final: 0.6248 (mt-10) REVERT: B 53 VAL cc_start: 0.6475 (OUTLIER) cc_final: 0.6218 (m) REVERT: B 67 GLU cc_start: 0.6538 (mm-30) cc_final: 0.6061 (mm-30) REVERT: B 127 ARG cc_start: 0.7119 (mtp85) cc_final: 0.6855 (mtp85) REVERT: B 159 ILE cc_start: 0.7544 (mt) cc_final: 0.7192 (mt) REVERT: B 163 GLN cc_start: 0.8093 (tt0) cc_final: 0.7829 (tt0) REVERT: B 177 SER cc_start: 0.6777 (p) cc_final: 0.6462 (m) REVERT: B 181 ASP cc_start: 0.7620 (m-30) cc_final: 0.7311 (m-30) REVERT: B 185 ASN cc_start: 0.8070 (t0) cc_final: 0.7623 (t0) REVERT: B 202 GLU cc_start: 0.6651 (tp30) cc_final: 0.6283 (tp30) REVERT: B 222 ILE cc_start: 0.7288 (mt) cc_final: 0.7087 (mt) REVERT: B 227 SER cc_start: 0.7298 (p) cc_final: 0.6609 (p) REVERT: B 229 SER cc_start: 0.7132 (t) cc_final: 0.6748 (p) REVERT: B 230 GLN cc_start: 0.6805 (mm-40) cc_final: 0.6442 (mm-40) REVERT: B 272 GLU cc_start: 0.6834 (tt0) cc_final: 0.6361 (tt0) REVERT: B 312 SER cc_start: 0.8155 (t) cc_final: 0.7701 (p) REVERT: B 320 GLU cc_start: 0.7190 (tt0) cc_final: 0.6925 (tt0) REVERT: B 385 ASP cc_start: 0.7003 (m-30) cc_final: 0.6574 (m-30) REVERT: B 428 ILE cc_start: 0.7848 (mt) cc_final: 0.7594 (mm) REVERT: B 449 PRO cc_start: 0.6591 (Cg_exo) cc_final: 0.6251 (Cg_endo) REVERT: B 467 ASN cc_start: 0.8260 (t0) cc_final: 0.7934 (t0) REVERT: B 478 THR cc_start: 0.7397 (OUTLIER) cc_final: 0.7163 (t) REVERT: C 34 VAL cc_start: 0.7563 (OUTLIER) cc_final: 0.7239 (p) REVERT: C 53 VAL cc_start: 0.6816 (p) cc_final: 0.6570 (m) REVERT: C 60 MET cc_start: 0.6349 (mmt) cc_final: 0.5976 (mmt) REVERT: C 62 MET cc_start: 0.6627 (ttt) cc_final: 0.6258 (ptm) REVERT: C 90 ARG cc_start: 0.7552 (ttp80) cc_final: 0.7155 (mtp-110) REVERT: C 109 ASN cc_start: 0.6996 (t0) cc_final: 0.6669 (t0) REVERT: C 122 GLU cc_start: 0.7579 (tp30) cc_final: 0.6938 (tp30) REVERT: C 127 ARG cc_start: 0.7311 (mtp85) cc_final: 0.6888 (mtp-110) REVERT: C 137 MET cc_start: 0.8068 (mmm) cc_final: 0.7788 (mmm) REVERT: C 139 ARG cc_start: 0.7775 (mtt-85) cc_final: 0.7353 (mtt180) REVERT: C 144 GLU cc_start: 0.6740 (pt0) cc_final: 0.6374 (pt0) REVERT: C 147 GLN cc_start: 0.7571 (mm-40) cc_final: 0.7320 (mm110) REVERT: C 163 GLN cc_start: 0.7828 (tt0) cc_final: 0.7577 (tt0) REVERT: C 181 ASP cc_start: 0.7816 (m-30) cc_final: 0.7487 (m-30) REVERT: C 185 ASN cc_start: 0.7869 (t0) cc_final: 0.7569 (t0) REVERT: C 196 VAL cc_start: 0.7816 (t) cc_final: 0.7445 (m) REVERT: C 206 ARG cc_start: 0.7232 (ttt180) cc_final: 0.7019 (ttm-80) REVERT: C 210 GLU cc_start: 0.6737 (mm-30) cc_final: 0.6525 (mm-30) REVERT: C 222 ILE cc_start: 0.7332 (mt) cc_final: 0.7108 (mt) REVERT: C 254 LYS cc_start: 0.7538 (mmtm) cc_final: 0.7273 (mtmm) REVERT: C 260 TYR cc_start: 0.7308 (m-80) cc_final: 0.7029 (m-80) REVERT: C 272 GLU cc_start: 0.7030 (mt-10) cc_final: 0.6701 (mt-10) REVERT: C 279 ARG cc_start: 0.7262 (mtt180) cc_final: 0.6568 (mtt-85) REVERT: C 361 LEU cc_start: 0.7587 (mp) cc_final: 0.7294 (mp) REVERT: C 385 ASP cc_start: 0.6920 (m-30) cc_final: 0.6661 (m-30) REVERT: C 409 LYS cc_start: 0.7461 (tptt) cc_final: 0.6883 (tptt) REVERT: C 418 GLU cc_start: 0.7135 (mm-30) cc_final: 0.6847 (mm-30) REVERT: C 419 VAL cc_start: 0.7328 (t) cc_final: 0.7045 (p) REVERT: C 452 ASP cc_start: 0.7317 (m-30) cc_final: 0.7026 (m-30) REVERT: C 486 ASP cc_start: 0.7732 (m-30) cc_final: 0.7513 (m-30) REVERT: C 496 LYS cc_start: 0.8668 (mttt) cc_final: 0.8364 (mttt) REVERT: D 3 ARG cc_start: 0.6321 (mtm-85) cc_final: 0.5888 (mtm-85) REVERT: D 5 ARG cc_start: 0.6400 (mtm-85) cc_final: 0.6046 (mtm-85) REVERT: D 10 MET cc_start: 0.6669 (mtm) cc_final: 0.6230 (mtm) REVERT: D 26 ILE cc_start: 0.8149 (mt) cc_final: 0.7900 (mp) REVERT: D 37 ARG cc_start: 0.6856 (mtm180) cc_final: 0.6504 (mtm180) REVERT: D 64 MET cc_start: 0.6719 (mmt) cc_final: 0.6429 (mmt) REVERT: D 74 MET cc_start: 0.7380 (mtt) cc_final: 0.6905 (mtt) REVERT: D 75 GLU cc_start: 0.7476 (tt0) cc_final: 0.7178 (tt0) REVERT: D 84 SER cc_start: 0.7837 (m) cc_final: 0.7399 (p) REVERT: D 101 GLU cc_start: 0.6946 (mt-10) cc_final: 0.6499 (mt-10) REVERT: D 114 ARG cc_start: 0.7071 (ttt180) cc_final: 0.6572 (ttt180) REVERT: D 115 ARG cc_start: 0.7495 (mtt-85) cc_final: 0.7123 (mtt-85) REVERT: D 116 ASP cc_start: 0.6914 (m-30) cc_final: 0.6344 (m-30) REVERT: D 125 PHE cc_start: 0.7641 (t80) cc_final: 0.7319 (t80) REVERT: D 133 GLU cc_start: 0.7261 (mt-10) cc_final: 0.6618 (mt-10) REVERT: D 190 ASP cc_start: 0.6741 (m-30) cc_final: 0.5862 (m-30) REVERT: D 197 ASP cc_start: 0.6863 (t0) cc_final: 0.6571 (t0) REVERT: D 214 VAL cc_start: 0.7615 (t) cc_final: 0.7055 (p) REVERT: D 227 ARG cc_start: 0.7107 (mmt180) cc_final: 0.6590 (mmt90) REVERT: D 228 VAL cc_start: 0.7594 (OUTLIER) cc_final: 0.7306 (p) REVERT: D 237 GLU cc_start: 0.7143 (mt-10) cc_final: 0.6760 (mt-10) REVERT: D 241 ASP cc_start: 0.7116 (m-30) cc_final: 0.6899 (m-30) REVERT: D 252 ASP cc_start: 0.6631 (t0) cc_final: 0.6335 (t0) REVERT: D 270 ARG cc_start: 0.7165 (mtt180) cc_final: 0.6722 (mtt-85) REVERT: D 271 MET cc_start: 0.7818 (mtt) cc_final: 0.7561 (ttm) REVERT: D 284 GLU cc_start: 0.6253 (mt-10) cc_final: 0.5672 (mt-10) REVERT: D 285 MET cc_start: 0.6711 (ttm) cc_final: 0.6310 (ttm) REVERT: D 307 TYR cc_start: 0.7769 (t80) cc_final: 0.7472 (t80) REVERT: D 326 ASP cc_start: 0.6757 (m-30) cc_final: 0.6162 (m-30) REVERT: D 352 ARG cc_start: 0.7040 (mtp180) cc_final: 0.6810 (mtp180) REVERT: D 356 PRO cc_start: 0.7859 (Cg_endo) cc_final: 0.7489 (Cg_exo) REVERT: D 364 TYR cc_start: 0.7658 (t80) cc_final: 0.7426 (t80) REVERT: D 375 GLN cc_start: 0.7210 (tp40) cc_final: 0.6911 (tp40) REVERT: D 378 LYS cc_start: 0.6824 (tttt) cc_final: 0.6589 (ttmm) REVERT: D 386 ILE cc_start: 0.7625 (mt) cc_final: 0.7346 (mp) REVERT: D 389 MET cc_start: 0.7814 (ttt) cc_final: 0.7376 (ttt) REVERT: D 404 ARG cc_start: 0.6966 (mmm160) cc_final: 0.6667 (mmm-85) REVERT: D 427 TYR cc_start: 0.7611 (t80) cc_final: 0.7154 (t80) REVERT: D 428 VAL cc_start: 0.8536 (t) cc_final: 0.8242 (m) REVERT: D 431 LYS cc_start: 0.7856 (mtpt) cc_final: 0.7562 (mtpt) REVERT: D 450 GLU cc_start: 0.7079 (pt0) cc_final: 0.6642 (pt0) REVERT: E 1 MET cc_start: 0.3442 (mmt) cc_final: 0.3033 (mmt) REVERT: E 3 ARG cc_start: 0.6700 (mtm-85) cc_final: 0.6413 (mtm-85) REVERT: E 5 ARG cc_start: 0.6445 (ptp-110) cc_final: 0.6168 (ptp-110) REVERT: E 17 LYS cc_start: 0.7530 (tttt) cc_final: 0.7326 (tttt) REVERT: E 43 ASP cc_start: 0.7123 (m-30) cc_final: 0.6844 (m-30) REVERT: E 71 ILE cc_start: 0.7720 (mt) cc_final: 0.7437 (mt) REVERT: E 74 MET cc_start: 0.7241 (ttm) cc_final: 0.7031 (ttm) REVERT: E 89 GLU cc_start: 0.7460 (mm-30) cc_final: 0.7164 (mm-30) REVERT: E 120 ARG cc_start: 0.6820 (mtp85) cc_final: 0.6562 (mtp85) REVERT: E 127 GLU cc_start: 0.6579 (mt-10) cc_final: 0.6267 (mt-10) REVERT: E 134 ILE cc_start: 0.8200 (mt) cc_final: 0.7970 (tt) REVERT: E 143 ASP cc_start: 0.5987 (m-30) cc_final: 0.5711 (m-30) REVERT: E 178 GLU cc_start: 0.7280 (mm-30) cc_final: 0.7019 (mm-30) REVERT: E 202 MET cc_start: 0.7675 (mmt) cc_final: 0.7416 (mmt) REVERT: E 227 ARG cc_start: 0.6623 (mmt180) cc_final: 0.6158 (mmt90) REVERT: E 234 THR cc_start: 0.7331 (OUTLIER) cc_final: 0.7020 (m) REVERT: E 240 ARG cc_start: 0.7214 (OUTLIER) cc_final: 0.6187 (ttp80) REVERT: E 247 VAL cc_start: 0.7787 (t) cc_final: 0.7294 (m) REVERT: E 256 ARG cc_start: 0.6877 (mtm-85) cc_final: 0.6674 (mtm-85) REVERT: E 284 GLU cc_start: 0.6247 (mt-10) cc_final: 0.5658 (mt-10) REVERT: E 290 GLU cc_start: 0.7438 (mm-30) cc_final: 0.7169 (mm-30) REVERT: E 304 GLN cc_start: 0.7289 (mt0) cc_final: 0.7071 (mt0) REVERT: E 307 TYR cc_start: 0.7993 (t80) cc_final: 0.7045 (t80) REVERT: E 312 ASP cc_start: 0.6943 (t0) cc_final: 0.6665 (t0) REVERT: E 359 VAL cc_start: 0.7648 (m) cc_final: 0.7400 (m) REVERT: E 365 GLN cc_start: 0.7711 (mt0) cc_final: 0.7317 (mt0) REVERT: E 375 GLN cc_start: 0.7521 (tp-100) cc_final: 0.7273 (tp-100) REVERT: E 376 ARG cc_start: 0.7601 (tpt170) cc_final: 0.6961 (tpt170) REVERT: E 379 GLU cc_start: 0.7629 (mt-10) cc_final: 0.7274 (mt-10) REVERT: E 387 LEU cc_start: 0.7482 (mt) cc_final: 0.7098 (mt) REVERT: E 391 GLU cc_start: 0.7816 (mt-10) cc_final: 0.7457 (mt-10) REVERT: E 405 ARG cc_start: 0.7578 (mpt180) cc_final: 0.7297 (mpt180) REVERT: E 406 ILE cc_start: 0.7679 (mt) cc_final: 0.7476 (mt) REVERT: E 418 GLU cc_start: 0.7468 (tt0) cc_final: 0.7033 (tt0) REVERT: E 423 GLN cc_start: 0.7538 (mm-40) cc_final: 0.7278 (mm-40) REVERT: E 430 VAL cc_start: 0.7233 (p) cc_final: 0.6985 (m) REVERT: E 431 LYS cc_start: 0.7715 (ptmm) cc_final: 0.7419 (ptmm) REVERT: E 435 ARG cc_start: 0.7333 (ttp80) cc_final: 0.6912 (ttp80) REVERT: E 438 LYS cc_start: 0.7792 (ttpt) cc_final: 0.6907 (ttpt) REVERT: E 439 GLU cc_start: 0.7549 (mm-30) cc_final: 0.6933 (mm-30) REVERT: E 442 GLU cc_start: 0.7792 (mt-10) cc_final: 0.6984 (mt-10) REVERT: E 450 GLU cc_start: 0.7830 (pm20) cc_final: 0.7253 (pm20) REVERT: E 464 GLU cc_start: 0.7690 (mt-10) cc_final: 0.7405 (mt-10) REVERT: F 5 ARG cc_start: 0.5986 (mmt180) cc_final: 0.5393 (mmt180) REVERT: F 10 MET cc_start: 0.6740 (mtm) cc_final: 0.6524 (mtm) REVERT: F 15 ASP cc_start: 0.7059 (OUTLIER) cc_final: 0.6458 (m-30) REVERT: F 23 LEU cc_start: 0.8247 (mp) cc_final: 0.8020 (mt) REVERT: F 33 GLN cc_start: 0.7626 (mt0) cc_final: 0.7400 (mt0) REVERT: F 62 ILE cc_start: 0.7232 (mt) cc_final: 0.6995 (mt) REVERT: F 74 MET cc_start: 0.6824 (mtt) cc_final: 0.6353 (mtt) REVERT: F 89 GLU cc_start: 0.7493 (tp30) cc_final: 0.7264 (tp30) REVERT: F 114 ARG cc_start: 0.7199 (ttp-170) cc_final: 0.6845 (ttp80) REVERT: F 120 ARG cc_start: 0.7261 (ptm-80) cc_final: 0.6828 (ptt90) REVERT: F 124 LYS cc_start: 0.6851 (mttm) cc_final: 0.6459 (mttm) REVERT: F 127 GLU cc_start: 0.7384 (mt-10) cc_final: 0.6858 (mt-10) REVERT: F 170 GLU cc_start: 0.6940 (tp30) cc_final: 0.6731 (tp30) REVERT: F 201 GLU cc_start: 0.6761 (tp30) cc_final: 0.6496 (tp30) REVERT: F 202 MET cc_start: 0.6807 (mmp) cc_final: 0.6600 (mmp) REVERT: F 213 MET cc_start: 0.7479 (mtp) cc_final: 0.7179 (mtm) REVERT: F 215 PHE cc_start: 0.7665 (m-80) cc_final: 0.7352 (m-10) REVERT: F 237 GLU cc_start: 0.7072 (tt0) cc_final: 0.6618 (tt0) REVERT: F 242 GLU cc_start: 0.7076 (mm-30) cc_final: 0.6747 (mm-30) REVERT: F 262 SER cc_start: 0.7086 (t) cc_final: 0.6871 (t) REVERT: F 271 MET cc_start: 0.8202 (mtp) cc_final: 0.7984 (mtm) REVERT: F 290 GLU cc_start: 0.7170 (mm-30) cc_final: 0.6956 (mm-30) REVERT: F 292 ILE cc_start: 0.7601 (mt) cc_final: 0.7354 (mt) REVERT: F 303 ILE cc_start: 0.7677 (mt) cc_final: 0.7354 (mp) REVERT: F 364 TYR cc_start: 0.7314 (t80) cc_final: 0.6445 (t80) REVERT: F 378 LYS cc_start: 0.7453 (OUTLIER) cc_final: 0.7218 (ttmm) REVERT: F 381 GLN cc_start: 0.6986 (tt0) cc_final: 0.6728 (tt0) REVERT: F 389 MET cc_start: 0.7450 (mtm) cc_final: 0.6913 (mtm) REVERT: F 397 LYS cc_start: 0.7388 (tttm) cc_final: 0.7174 (tttm) REVERT: F 432 GLU cc_start: 0.7294 (mm-30) cc_final: 0.6883 (mm-30) REVERT: F 435 ARG cc_start: 0.7965 (ttp80) cc_final: 0.7371 (ttp80) REVERT: F 438 LYS cc_start: 0.7533 (tttt) cc_final: 0.7158 (tttt) REVERT: F 439 GLU cc_start: 0.7694 (mt-10) cc_final: 0.6801 (mt-10) REVERT: F 442 GLU cc_start: 0.7314 (mt-10) cc_final: 0.6600 (mt-10) REVERT: F 444 LYS cc_start: 0.7986 (tttt) cc_final: 0.7378 (tttt) REVERT: F 445 TYR cc_start: 0.8263 (m-80) cc_final: 0.7550 (m-80) REVERT: F 451 ASP cc_start: 0.7794 (m-30) cc_final: 0.7591 (m-30) REVERT: F 454 ARG cc_start: 0.7676 (mtp180) cc_final: 0.7412 (mtp85) REVERT: F 460 GLU cc_start: 0.8025 (mp0) cc_final: 0.7726 (mp0) REVERT: G 17 THR cc_start: 0.6796 (p) cc_final: 0.6580 (t) REVERT: G 18 LYS cc_start: 0.7552 (mttm) cc_final: 0.7323 (mttm) REVERT: G 25 LYS cc_start: 0.7149 (tptt) cc_final: 0.6907 (tptt) REVERT: G 27 MET cc_start: 0.7973 (mtp) cc_final: 0.7679 (mtp) REVERT: G 28 GLU cc_start: 0.7559 (tt0) cc_final: 0.7204 (tt0) REVERT: G 29 MET cc_start: 0.7112 (mmm) cc_final: 0.6615 (mmm) REVERT: G 31 SER cc_start: 0.8140 (t) cc_final: 0.7819 (p) REVERT: G 33 SER cc_start: 0.7994 (t) cc_final: 0.7663 (p) REVERT: G 39 GLU cc_start: 0.8506 (tt0) cc_final: 0.8198 (tt0) REVERT: G 70 MET cc_start: 0.7754 (mmm) cc_final: 0.7161 (mmm) REVERT: G 88 ARG cc_start: 0.7077 (ptt180) cc_final: 0.6690 (ptt180) REVERT: G 99 LEU cc_start: 0.8077 (mt) cc_final: 0.7866 (mt) REVERT: G 105 THR cc_start: 0.7059 (m) cc_final: 0.6609 (m) REVERT: G 109 ARG cc_start: 0.6789 (ptt90) cc_final: 0.6327 (ptt90) REVERT: G 116 TYR cc_start: 0.7674 (p90) cc_final: 0.7126 (p90) REVERT: G 134 MET cc_start: 0.6476 (mtm) cc_final: 0.5772 (mtm) REVERT: G 173 MET cc_start: 0.7328 (mtm) cc_final: 0.7058 (mtm) REVERT: G 174 TYR cc_start: 0.7327 (m-80) cc_final: 0.5851 (m-80) REVERT: G 188 GLU cc_start: 0.6291 (OUTLIER) cc_final: 0.6000 (tt0) REVERT: G 220 LEU cc_start: 0.8563 (mm) cc_final: 0.8342 (mm) REVERT: G 256 GLU cc_start: 0.6806 (tp30) cc_final: 0.6517 (tp30) REVERT: G 269 ARG cc_start: 0.7127 (ttp80) cc_final: 0.6879 (ttp-110) outliers start: 85 outliers final: 23 residues processed: 1252 average time/residue: 0.4417 time to fit residues: 793.6299 Evaluate side-chains 1136 residues out of total 2558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 1103 time to evaluate : 2.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ASN Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 375 MET Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain B residue 452 ASP Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 177 SER Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 375 MET Chi-restraints excluded: chain C residue 390 ARG Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 191 ARG Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain E residue 234 THR Chi-restraints excluded: chain E residue 240 ARG Chi-restraints excluded: chain E residue 254 ILE Chi-restraints excluded: chain E residue 315 ASP Chi-restraints excluded: chain E residue 328 THR Chi-restraints excluded: chain E residue 421 THR Chi-restraints excluded: chain F residue 15 ASP Chi-restraints excluded: chain F residue 98 VAL Chi-restraints excluded: chain F residue 378 LYS Chi-restraints excluded: chain F residue 447 HIS Chi-restraints excluded: chain G residue 90 LEU Chi-restraints excluded: chain G residue 188 GLU Chi-restraints excluded: chain G residue 192 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 261 optimal weight: 1.9990 chunk 234 optimal weight: 6.9990 chunk 130 optimal weight: 2.9990 chunk 80 optimal weight: 0.8980 chunk 158 optimal weight: 1.9990 chunk 125 optimal weight: 0.2980 chunk 242 optimal weight: 2.9990 chunk 94 optimal weight: 5.9990 chunk 147 optimal weight: 1.9990 chunk 180 optimal weight: 6.9990 chunk 281 optimal weight: 1.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 186 GLN A 200 GLN A 266 GLN A 345 GLN A 371 GLN A 425 HIS A 466 GLN A 488 ASN B 33 GLN B 185 ASN B 186 GLN B 371 GLN B 397 GLN B 488 ASN C 46 ASN C 345 GLN C 397 GLN C 407 GLN C 422 GLN C 425 HIS C 466 GLN C 488 ASN D 8 GLN D 33 GLN D 169 GLN D 253 ASN D 304 GLN D 365 GLN E 33 GLN E 119 HIS E 169 GLN E 363 HIS E 412 GLN F 8 GLN F 173 HIS F 217 GLN F 324 HIS F 371 GLN F 372 GLN F 423 GLN G 41 ASN G 110 HIS G 183 GLN G 184 GLN G 240 HIS G 249 ASN G 253 ASN G 285 ASN Total number of N/Q/H flips: 48 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6852 moved from start: 0.2535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 24604 Z= 0.230 Angle : 0.649 10.113 33364 Z= 0.349 Chirality : 0.046 0.156 3840 Planarity : 0.005 0.060 4349 Dihedral : 10.044 139.372 3632 Min Nonbonded Distance : 1.734 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 3.91 % Allowed : 17.28 % Favored : 78.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.83 % 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: 0.11 (0.15), residues: 3104 helix: 0.87 (0.14), residues: 1236 sheet: 0.26 (0.23), residues: 499 loop : -0.67 (0.16), residues: 1369 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS F 447 PHE 0.017 0.002 PHE C 236 TYR 0.027 0.002 TYR C 248 ARG 0.012 0.001 ARG F 405 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1204 residues out of total 2558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 1104 time to evaluate : 2.712 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 MET cc_start: 0.7365 (mtm) cc_final: 0.6936 (ptp) REVERT: A 96 GLU cc_start: 0.5564 (mt-10) cc_final: 0.5330 (tt0) REVERT: A 127 ARG cc_start: 0.6720 (mtp85) cc_final: 0.6187 (mtp85) REVERT: A 140 ARG cc_start: 0.7273 (ttt-90) cc_final: 0.6879 (ttt90) REVERT: A 144 GLU cc_start: 0.7226 (pt0) cc_final: 0.6825 (pt0) REVERT: A 146 LEU cc_start: 0.7424 (OUTLIER) cc_final: 0.7222 (tp) REVERT: A 211 THR cc_start: 0.6088 (m) cc_final: 0.5881 (p) REVERT: A 272 GLU cc_start: 0.6750 (tt0) cc_final: 0.6334 (tt0) REVERT: A 299 GLU cc_start: 0.7733 (mm-30) cc_final: 0.7305 (mm-30) REVERT: A 303 LYS cc_start: 0.7545 (tptp) cc_final: 0.7264 (tttp) REVERT: A 341 GLN cc_start: 0.6823 (pm20) cc_final: 0.6595 (pm20) REVERT: A 358 ASN cc_start: 0.7179 (t0) cc_final: 0.6924 (t0) REVERT: A 375 MET cc_start: 0.7223 (tpp) cc_final: 0.6619 (tpp) REVERT: A 376 LYS cc_start: 0.6862 (ttmm) cc_final: 0.6325 (ttmm) REVERT: A 404 LYS cc_start: 0.7677 (mttt) cc_final: 0.7394 (mttt) REVERT: A 407 GLN cc_start: 0.7335 (OUTLIER) cc_final: 0.7096 (mt0) REVERT: A 426 GLN cc_start: 0.6995 (mm-40) cc_final: 0.6714 (mm-40) REVERT: A 458 LYS cc_start: 0.7142 (OUTLIER) cc_final: 0.6934 (tmmt) REVERT: A 489 LYS cc_start: 0.7248 (tttt) cc_final: 0.6996 (tttt) REVERT: B 33 GLN cc_start: 0.6990 (mt0) cc_final: 0.6665 (mt0) REVERT: B 49 SER cc_start: 0.7682 (t) cc_final: 0.7176 (m) REVERT: B 51 GLU cc_start: 0.7085 (tt0) cc_final: 0.6315 (mt-10) REVERT: B 53 VAL cc_start: 0.6618 (OUTLIER) cc_final: 0.6383 (m) REVERT: B 67 GLU cc_start: 0.6847 (mm-30) cc_final: 0.6407 (mm-30) REVERT: B 95 MET cc_start: 0.6955 (tpt) cc_final: 0.6479 (tpt) REVERT: B 159 ILE cc_start: 0.7507 (mt) cc_final: 0.7289 (mt) REVERT: B 164 ARG cc_start: 0.6861 (mtm180) cc_final: 0.6547 (mtm-85) REVERT: B 177 SER cc_start: 0.6409 (p) cc_final: 0.5735 (m) REVERT: B 181 ASP cc_start: 0.7332 (m-30) cc_final: 0.7114 (m-30) REVERT: B 185 ASN cc_start: 0.7644 (t0) cc_final: 0.7327 (t0) REVERT: B 200 GLN cc_start: 0.7984 (mm-40) cc_final: 0.7014 (mp10) REVERT: B 202 GLU cc_start: 0.5974 (tp30) cc_final: 0.5546 (tp30) REVERT: B 211 THR cc_start: 0.4982 (m) cc_final: 0.4734 (p) REVERT: B 227 SER cc_start: 0.6802 (p) cc_final: 0.6278 (p) REVERT: B 229 SER cc_start: 0.7250 (t) cc_final: 0.6854 (p) REVERT: B 272 GLU cc_start: 0.6742 (tt0) cc_final: 0.6368 (tt0) REVERT: B 312 SER cc_start: 0.8355 (t) cc_final: 0.7863 (p) REVERT: B 345 GLN cc_start: 0.6502 (OUTLIER) cc_final: 0.6163 (tt0) REVERT: B 428 ILE cc_start: 0.7793 (mt) cc_final: 0.7550 (mm) REVERT: B 442 ARG cc_start: 0.7803 (OUTLIER) cc_final: 0.7323 (mmt-90) REVERT: B 467 ASN cc_start: 0.8321 (t0) cc_final: 0.8057 (t0) REVERT: B 478 THR cc_start: 0.7136 (OUTLIER) cc_final: 0.6921 (t) REVERT: B 480 ASP cc_start: 0.6427 (t0) cc_final: 0.5830 (t0) REVERT: B 481 LEU cc_start: 0.8154 (tp) cc_final: 0.7867 (tp) REVERT: C 34 VAL cc_start: 0.7827 (t) cc_final: 0.7609 (p) REVERT: C 40 ARG cc_start: 0.6883 (mmt90) cc_final: 0.6639 (mmt90) REVERT: C 51 GLU cc_start: 0.7417 (tt0) cc_final: 0.7026 (tt0) REVERT: C 62 MET cc_start: 0.6580 (ttt) cc_final: 0.6204 (ttp) REVERT: C 90 ARG cc_start: 0.7749 (ttp80) cc_final: 0.7391 (ttp-110) REVERT: C 122 GLU cc_start: 0.7498 (tp30) cc_final: 0.6941 (tp30) REVERT: C 127 ARG cc_start: 0.7383 (mtp85) cc_final: 0.6968 (mtp85) REVERT: C 137 MET cc_start: 0.8018 (mmm) cc_final: 0.7779 (mmm) REVERT: C 144 GLU cc_start: 0.6810 (pt0) cc_final: 0.6196 (pt0) REVERT: C 147 GLN cc_start: 0.7404 (mm-40) cc_final: 0.7167 (mm110) REVERT: C 181 ASP cc_start: 0.7560 (m-30) cc_final: 0.7195 (m-30) REVERT: C 185 ASN cc_start: 0.7718 (t0) cc_final: 0.7470 (t0) REVERT: C 222 ILE cc_start: 0.7258 (mt) cc_final: 0.6999 (mt) REVERT: C 229 SER cc_start: 0.7343 (t) cc_final: 0.7060 (p) REVERT: C 254 LYS cc_start: 0.7306 (mmtm) cc_final: 0.6953 (mtmm) REVERT: C 260 TYR cc_start: 0.6748 (m-80) cc_final: 0.6493 (m-80) REVERT: C 272 GLU cc_start: 0.6928 (mt-10) cc_final: 0.6581 (mt-10) REVERT: C 279 ARG cc_start: 0.7245 (mtt180) cc_final: 0.6626 (mtt-85) REVERT: C 361 LEU cc_start: 0.7542 (mp) cc_final: 0.7341 (mp) REVERT: C 442 ARG cc_start: 0.7394 (mmt-90) cc_final: 0.7111 (mmt90) REVERT: C 451 GLU cc_start: 0.7596 (mp0) cc_final: 0.7129 (mp0) REVERT: C 496 LYS cc_start: 0.8576 (mttt) cc_final: 0.8050 (mttt) REVERT: D 3 ARG cc_start: 0.6422 (mtm-85) cc_final: 0.5992 (mtm-85) REVERT: D 5 ARG cc_start: 0.6149 (mtm-85) cc_final: 0.5921 (mtm-85) REVERT: D 10 MET cc_start: 0.6179 (mtm) cc_final: 0.5661 (mtm) REVERT: D 17 LYS cc_start: 0.7024 (tttt) cc_final: 0.6788 (tttm) REVERT: D 26 ILE cc_start: 0.7973 (mt) cc_final: 0.7738 (mp) REVERT: D 37 ARG cc_start: 0.6729 (mtm180) cc_final: 0.6515 (mtm180) REVERT: D 64 MET cc_start: 0.6749 (mmt) cc_final: 0.6384 (mmt) REVERT: D 74 MET cc_start: 0.7388 (mtt) cc_final: 0.6954 (mtt) REVERT: D 75 GLU cc_start: 0.7428 (tt0) cc_final: 0.7131 (tt0) REVERT: D 84 SER cc_start: 0.7798 (m) cc_final: 0.7406 (p) REVERT: D 101 GLU cc_start: 0.7000 (mt-10) cc_final: 0.6582 (mt-10) REVERT: D 114 ARG cc_start: 0.7229 (ttt180) cc_final: 0.6758 (ttp80) REVERT: D 116 ASP cc_start: 0.7063 (m-30) cc_final: 0.6499 (m-30) REVERT: D 133 GLU cc_start: 0.7253 (mt-10) cc_final: 0.6627 (mt-10) REVERT: D 190 ASP cc_start: 0.6466 (m-30) cc_final: 0.5530 (m-30) REVERT: D 197 ASP cc_start: 0.6833 (t0) cc_final: 0.6598 (t70) REVERT: D 214 VAL cc_start: 0.7287 (t) cc_final: 0.7019 (m) REVERT: D 227 ARG cc_start: 0.6589 (mmt180) cc_final: 0.6101 (mmt90) REVERT: D 228 VAL cc_start: 0.6936 (OUTLIER) cc_final: 0.6736 (p) REVERT: D 237 GLU cc_start: 0.7041 (mt-10) cc_final: 0.6580 (mt-10) REVERT: D 241 ASP cc_start: 0.7185 (m-30) cc_final: 0.6870 (m-30) REVERT: D 252 ASP cc_start: 0.6452 (t0) cc_final: 0.6037 (t0) REVERT: D 270 ARG cc_start: 0.7248 (mtt180) cc_final: 0.6831 (mtt-85) REVERT: D 271 MET cc_start: 0.7849 (mtt) cc_final: 0.7591 (ttm) REVERT: D 284 GLU cc_start: 0.6137 (mt-10) cc_final: 0.5653 (mt-10) REVERT: D 285 MET cc_start: 0.6520 (ttm) cc_final: 0.6179 (ttm) REVERT: D 337 GLU cc_start: 0.7073 (mt-10) cc_final: 0.6585 (mt-10) REVERT: D 387 LEU cc_start: 0.7824 (mt) cc_final: 0.7543 (mp) REVERT: D 389 MET cc_start: 0.7795 (ttt) cc_final: 0.7572 (ttt) REVERT: D 428 VAL cc_start: 0.8501 (t) cc_final: 0.8089 (m) REVERT: D 439 GLU cc_start: 0.7283 (mm-30) cc_final: 0.6829 (mm-30) REVERT: D 455 LEU cc_start: 0.7706 (OUTLIER) cc_final: 0.7471 (mm) REVERT: E 1 MET cc_start: 0.3446 (mmt) cc_final: 0.3073 (mmt) REVERT: E 3 ARG cc_start: 0.6668 (mtm-85) cc_final: 0.6369 (mtm-85) REVERT: E 5 ARG cc_start: 0.6458 (ptp-110) cc_final: 0.6052 (ptp-110) REVERT: E 10 MET cc_start: 0.6088 (ptp) cc_final: 0.5593 (ptp) REVERT: E 31 LYS cc_start: 0.7488 (mmtt) cc_final: 0.7000 (mmtt) REVERT: E 43 ASP cc_start: 0.6801 (m-30) cc_final: 0.6300 (m-30) REVERT: E 71 ILE cc_start: 0.7684 (mt) cc_final: 0.7316 (mt) REVERT: E 74 MET cc_start: 0.7045 (ttm) cc_final: 0.6839 (ttm) REVERT: E 89 GLU cc_start: 0.7503 (mm-30) cc_final: 0.7187 (mm-30) REVERT: E 127 GLU cc_start: 0.6788 (mt-10) cc_final: 0.6322 (mt-10) REVERT: E 134 ILE cc_start: 0.8229 (mt) cc_final: 0.7907 (tt) REVERT: E 170 GLU cc_start: 0.6982 (tp30) cc_final: 0.6724 (tt0) REVERT: E 210 LYS cc_start: 0.7447 (mttt) cc_final: 0.7061 (mttt) REVERT: E 227 ARG cc_start: 0.6349 (mmt180) cc_final: 0.6062 (mmt90) REVERT: E 237 GLU cc_start: 0.6981 (tt0) cc_final: 0.6774 (mt-10) REVERT: E 284 GLU cc_start: 0.6164 (mt-10) cc_final: 0.5818 (mt-10) REVERT: E 304 GLN cc_start: 0.7356 (mt0) cc_final: 0.7151 (mt0) REVERT: E 359 VAL cc_start: 0.7654 (m) cc_final: 0.7448 (m) REVERT: E 362 GLU cc_start: 0.7674 (pm20) cc_final: 0.7357 (pm20) REVERT: E 365 GLN cc_start: 0.7555 (mt0) cc_final: 0.7176 (mt0) REVERT: E 376 ARG cc_start: 0.7655 (tpt170) cc_final: 0.7238 (tpt170) REVERT: E 387 LEU cc_start: 0.7296 (mt) cc_final: 0.7023 (mt) REVERT: E 391 GLU cc_start: 0.7770 (mt-10) cc_final: 0.7449 (mt-10) REVERT: E 402 ARG cc_start: 0.7610 (mmm-85) cc_final: 0.6986 (mtt-85) REVERT: E 405 ARG cc_start: 0.7476 (mpt180) cc_final: 0.7184 (mmt90) REVERT: E 407 GLN cc_start: 0.7560 (tt0) cc_final: 0.7050 (tp40) REVERT: E 418 GLU cc_start: 0.7519 (tt0) cc_final: 0.7069 (tt0) REVERT: E 420 PHE cc_start: 0.7575 (m-10) cc_final: 0.7369 (m-10) REVERT: E 423 GLN cc_start: 0.7308 (mm-40) cc_final: 0.7053 (mm-40) REVERT: E 431 LYS cc_start: 0.7650 (ptmm) cc_final: 0.7394 (ptmm) REVERT: E 435 ARG cc_start: 0.7290 (ttp80) cc_final: 0.7029 (ttp80) REVERT: E 438 LYS cc_start: 0.7837 (ttpt) cc_final: 0.6913 (ttpt) REVERT: E 439 GLU cc_start: 0.7552 (mm-30) cc_final: 0.6774 (mm-30) REVERT: E 441 LEU cc_start: 0.8294 (mt) cc_final: 0.8074 (mt) REVERT: E 442 GLU cc_start: 0.7850 (mt-10) cc_final: 0.7160 (mt-10) REVERT: E 450 GLU cc_start: 0.7794 (pm20) cc_final: 0.7241 (pm20) REVERT: F 3 ARG cc_start: 0.6631 (mtt180) cc_final: 0.6358 (mtt180) REVERT: F 5 ARG cc_start: 0.5978 (mmt180) cc_final: 0.5439 (mmt180) REVERT: F 10 MET cc_start: 0.6926 (mtm) cc_final: 0.6700 (mtm) REVERT: F 15 ASP cc_start: 0.6943 (m-30) cc_final: 0.6445 (m-30) REVERT: F 23 LEU cc_start: 0.8230 (mp) cc_final: 0.8026 (mt) REVERT: F 33 GLN cc_start: 0.7475 (mt0) cc_final: 0.7135 (mt0) REVERT: F 39 GLU cc_start: 0.7471 (mp0) cc_final: 0.6960 (mp0) REVERT: F 74 MET cc_start: 0.6868 (mtt) cc_final: 0.6419 (mtt) REVERT: F 89 GLU cc_start: 0.7519 (tp30) cc_final: 0.7216 (tp30) REVERT: F 114 ARG cc_start: 0.7222 (ttp-170) cc_final: 0.6838 (ttp80) REVERT: F 120 ARG cc_start: 0.7054 (ptm-80) cc_final: 0.6717 (ptt90) REVERT: F 124 LYS cc_start: 0.7090 (mttm) cc_final: 0.6747 (mttm) REVERT: F 127 GLU cc_start: 0.7308 (mt-10) cc_final: 0.6868 (mt-10) REVERT: F 213 MET cc_start: 0.7392 (mtp) cc_final: 0.7135 (mtm) REVERT: F 220 GLU cc_start: 0.6762 (mm-30) cc_final: 0.6543 (mm-30) REVERT: F 277 TYR cc_start: 0.6798 (m-80) cc_final: 0.6493 (m-80) REVERT: F 285 MET cc_start: 0.6889 (ttm) cc_final: 0.6658 (ttm) REVERT: F 290 GLU cc_start: 0.7179 (mm-30) cc_final: 0.6957 (mm-30) REVERT: F 303 ILE cc_start: 0.7588 (mt) cc_final: 0.7353 (mm) REVERT: F 352 ARG cc_start: 0.7246 (ttm-80) cc_final: 0.7029 (ttm-80) REVERT: F 389 MET cc_start: 0.7180 (mtm) cc_final: 0.6689 (mtm) REVERT: F 397 LYS cc_start: 0.7279 (tttm) cc_final: 0.7004 (tttm) REVERT: F 423 GLN cc_start: 0.7435 (pt0) cc_final: 0.7197 (pt0) REVERT: F 438 LYS cc_start: 0.7634 (tttt) cc_final: 0.7246 (tttt) REVERT: F 439 GLU cc_start: 0.7599 (mt-10) cc_final: 0.6843 (mt-10) REVERT: F 442 GLU cc_start: 0.7159 (mt-10) cc_final: 0.6462 (mt-10) REVERT: F 444 LYS cc_start: 0.8006 (tttt) cc_final: 0.7308 (tttt) REVERT: F 445 TYR cc_start: 0.8297 (m-80) cc_final: 0.7605 (m-80) REVERT: F 451 ASP cc_start: 0.7836 (m-30) cc_final: 0.7610 (m-30) REVERT: G 17 THR cc_start: 0.6469 (p) cc_final: 0.6269 (t) REVERT: G 33 SER cc_start: 0.7753 (t) cc_final: 0.7424 (p) REVERT: G 54 GLU cc_start: 0.8770 (mt-10) cc_final: 0.8437 (mt-10) REVERT: G 70 MET cc_start: 0.7774 (mmm) cc_final: 0.7276 (mmm) REVERT: G 88 ARG cc_start: 0.6948 (ptt180) cc_final: 0.6682 (ptt180) REVERT: G 95 ASN cc_start: 0.7826 (m-40) cc_final: 0.7583 (m-40) REVERT: G 115 GLU cc_start: 0.8117 (mm-30) cc_final: 0.7676 (mm-30) REVERT: G 116 TYR cc_start: 0.7745 (p90) cc_final: 0.7044 (p90) REVERT: G 134 MET cc_start: 0.6435 (mtm) cc_final: 0.5977 (mtm) REVERT: G 173 MET cc_start: 0.7151 (mtm) cc_final: 0.6782 (mtm) REVERT: G 185 GLU cc_start: 0.6487 (mm-30) cc_final: 0.6232 (mm-30) REVERT: G 188 GLU cc_start: 0.6182 (OUTLIER) cc_final: 0.5597 (tt0) REVERT: G 225 GLU cc_start: 0.8598 (mt-10) cc_final: 0.8243 (mt-10) REVERT: G 227 LEU cc_start: 0.8089 (mm) cc_final: 0.7825 (mm) REVERT: G 256 GLU cc_start: 0.6679 (tp30) cc_final: 0.6403 (tp30) REVERT: G 261 LEU cc_start: 0.7214 (mt) cc_final: 0.6952 (mt) outliers start: 100 outliers final: 53 residues processed: 1144 average time/residue: 0.4207 time to fit residues: 700.2189 Evaluate side-chains 1131 residues out of total 2558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 1068 time to evaluate : 2.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 407 GLN Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 90 ARG Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 137 MET Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 299 GLU Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 345 GLN Chi-restraints excluded: chain B residue 366 VAL Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 442 ARG Chi-restraints excluded: chain B residue 452 ASP Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 177 SER Chi-restraints excluded: chain C residue 470 HIS Chi-restraints excluded: chain C residue 491 ILE Chi-restraints excluded: chain D residue 57 ASP Chi-restraints excluded: chain D residue 103 ILE Chi-restraints excluded: chain D residue 112 ASP Chi-restraints excluded: chain D residue 191 ARG Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 350 THR Chi-restraints excluded: chain D residue 382 ASP Chi-restraints excluded: chain D residue 455 LEU Chi-restraints excluded: chain D residue 459 ILE Chi-restraints excluded: chain E residue 57 ASP Chi-restraints excluded: chain E residue 67 THR Chi-restraints excluded: chain E residue 211 THR Chi-restraints excluded: chain E residue 226 MET Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 293 THR Chi-restraints excluded: chain E residue 380 LEU Chi-restraints excluded: chain E residue 381 GLN Chi-restraints excluded: chain E residue 399 VAL Chi-restraints excluded: chain F residue 84 SER Chi-restraints excluded: chain F residue 205 SER Chi-restraints excluded: chain F residue 233 LEU Chi-restraints excluded: chain F residue 278 GLN Chi-restraints excluded: chain F residue 338 MET Chi-restraints excluded: chain F residue 455 LEU Chi-restraints excluded: chain F residue 464 GLU Chi-restraints excluded: chain G residue 22 GLN Chi-restraints excluded: chain G residue 23 ILE Chi-restraints excluded: chain G residue 83 VAL Chi-restraints excluded: chain G residue 101 LEU Chi-restraints excluded: chain G residue 148 SER Chi-restraints excluded: chain G residue 184 GLN Chi-restraints excluded: chain G residue 188 GLU Chi-restraints excluded: chain G residue 232 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 156 optimal weight: 8.9990 chunk 87 optimal weight: 3.9990 chunk 234 optimal weight: 3.9990 chunk 191 optimal weight: 6.9990 chunk 77 optimal weight: 0.0570 chunk 282 optimal weight: 0.8980 chunk 304 optimal weight: 10.0000 chunk 251 optimal weight: 3.9990 chunk 279 optimal weight: 1.9990 chunk 96 optimal weight: 4.9990 chunk 226 optimal weight: 7.9990 overall best weight: 2.1904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 GLN A 294 HIS A 345 GLN A 469 GLN B 46 ASN B 185 ASN C 371 GLN C 474 HIS D 119 HIS D 304 GLN E 412 GLN G 110 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6915 moved from start: 0.3288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 24604 Z= 0.281 Angle : 0.614 6.988 33364 Z= 0.328 Chirality : 0.046 0.157 3840 Planarity : 0.005 0.053 4349 Dihedral : 9.326 129.294 3588 Min Nonbonded Distance : 1.745 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 5.20 % Allowed : 20.68 % Favored : 74.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.83 % 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: 0.10 (0.15), residues: 3104 helix: 0.95 (0.15), residues: 1228 sheet: 0.16 (0.22), residues: 535 loop : -0.74 (0.16), residues: 1341 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS B 294 PHE 0.020 0.002 PHE A 236 TYR 0.022 0.002 TYR C 248 ARG 0.009 0.001 ARG C 415 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1234 residues out of total 2558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 1101 time to evaluate : 2.907 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 ASP cc_start: 0.5796 (m-30) cc_final: 0.5398 (m-30) REVERT: A 96 GLU cc_start: 0.5970 (mt-10) cc_final: 0.5646 (tt0) REVERT: A 140 ARG cc_start: 0.7279 (ttt-90) cc_final: 0.6821 (ttt90) REVERT: A 144 GLU cc_start: 0.7183 (pt0) cc_final: 0.6646 (pt0) REVERT: A 248 TYR cc_start: 0.7338 (t80) cc_final: 0.7099 (t80) REVERT: A 251 TYR cc_start: 0.7005 (m-80) cc_final: 0.6707 (m-80) REVERT: A 272 GLU cc_start: 0.6719 (tt0) cc_final: 0.6244 (tt0) REVERT: A 299 GLU cc_start: 0.7802 (mm-30) cc_final: 0.7328 (mm-30) REVERT: A 314 THR cc_start: 0.7245 (OUTLIER) cc_final: 0.6691 (p) REVERT: A 375 MET cc_start: 0.7246 (tpp) cc_final: 0.6596 (tpp) REVERT: A 376 LYS cc_start: 0.6838 (ttmm) cc_final: 0.6439 (ttmm) REVERT: A 421 LYS cc_start: 0.7537 (mttp) cc_final: 0.7089 (mtpp) REVERT: A 426 GLN cc_start: 0.7135 (mm-40) cc_final: 0.6695 (mm-40) REVERT: A 427 PRO cc_start: 0.8103 (Cg_endo) cc_final: 0.7869 (Cg_exo) REVERT: A 438 TYR cc_start: 0.7718 (t80) cc_final: 0.7352 (t80) REVERT: A 458 LYS cc_start: 0.7225 (ttmt) cc_final: 0.6981 (tmmt) REVERT: A 476 ARG cc_start: 0.8073 (ttm-80) cc_final: 0.7870 (ttm-80) REVERT: A 486 ASP cc_start: 0.8157 (m-30) cc_final: 0.7953 (t0) REVERT: A 489 LYS cc_start: 0.7368 (tttt) cc_final: 0.7111 (tttt) REVERT: B 33 GLN cc_start: 0.7053 (mt0) cc_final: 0.6726 (mt0) REVERT: B 67 GLU cc_start: 0.7055 (mm-30) cc_final: 0.6689 (mm-30) REVERT: B 95 MET cc_start: 0.6918 (tpt) cc_final: 0.6510 (mmm) REVERT: B 171 ARG cc_start: 0.7086 (mtm110) cc_final: 0.6860 (mtm110) REVERT: B 177 SER cc_start: 0.6426 (p) cc_final: 0.5853 (m) REVERT: B 181 ASP cc_start: 0.7375 (m-30) cc_final: 0.7149 (m-30) REVERT: B 185 ASN cc_start: 0.7685 (t0) cc_final: 0.7384 (t0) REVERT: B 202 GLU cc_start: 0.6027 (tp30) cc_final: 0.5694 (tp30) REVERT: B 229 SER cc_start: 0.7392 (t) cc_final: 0.7190 (p) REVERT: B 272 GLU cc_start: 0.6742 (tt0) cc_final: 0.6364 (tt0) REVERT: B 345 GLN cc_start: 0.6640 (OUTLIER) cc_final: 0.6376 (tt0) REVERT: B 378 VAL cc_start: 0.7821 (t) cc_final: 0.7574 (p) REVERT: B 418 GLU cc_start: 0.7486 (mm-30) cc_final: 0.7212 (mm-30) REVERT: B 442 ARG cc_start: 0.7758 (OUTLIER) cc_final: 0.7228 (mmt-90) REVERT: B 467 ASN cc_start: 0.8326 (t0) cc_final: 0.8022 (t0) REVERT: B 479 LYS cc_start: 0.7251 (mptt) cc_final: 0.6727 (mptt) REVERT: B 480 ASP cc_start: 0.6570 (t0) cc_final: 0.6041 (t0) REVERT: B 481 LEU cc_start: 0.8157 (tp) cc_final: 0.7766 (tp) REVERT: C 34 VAL cc_start: 0.7774 (t) cc_final: 0.7547 (p) REVERT: C 51 GLU cc_start: 0.7502 (tt0) cc_final: 0.7275 (tt0) REVERT: C 62 MET cc_start: 0.6591 (ttt) cc_final: 0.6339 (ttp) REVERT: C 80 THR cc_start: 0.7938 (p) cc_final: 0.7680 (m) REVERT: C 127 ARG cc_start: 0.7364 (mtp85) cc_final: 0.6983 (mtp85) REVERT: C 137 MET cc_start: 0.8017 (mmm) cc_final: 0.7751 (mmm) REVERT: C 144 GLU cc_start: 0.6894 (pt0) cc_final: 0.6277 (pt0) REVERT: C 147 GLN cc_start: 0.7434 (mm-40) cc_final: 0.6718 (mm-40) REVERT: C 181 ASP cc_start: 0.7566 (m-30) cc_final: 0.7216 (m-30) REVERT: C 185 ASN cc_start: 0.7829 (t0) cc_final: 0.7551 (t0) REVERT: C 196 VAL cc_start: 0.7806 (t) cc_final: 0.7474 (m) REVERT: C 222 ILE cc_start: 0.7278 (mt) cc_final: 0.7028 (mt) REVERT: C 254 LYS cc_start: 0.7354 (mmtm) cc_final: 0.6950 (mtmm) REVERT: C 260 TYR cc_start: 0.6760 (m-80) cc_final: 0.6441 (m-80) REVERT: C 272 GLU cc_start: 0.6934 (mt-10) cc_final: 0.6524 (mt-10) REVERT: C 274 SER cc_start: 0.7036 (p) cc_final: 0.6831 (m) REVERT: C 314 THR cc_start: 0.7540 (OUTLIER) cc_final: 0.7013 (p) REVERT: C 343 PHE cc_start: 0.8099 (t80) cc_final: 0.7775 (t80) REVERT: C 361 LEU cc_start: 0.7669 (mp) cc_final: 0.7390 (mp) REVERT: C 372 ILE cc_start: 0.7553 (mp) cc_final: 0.7329 (mm) REVERT: C 376 LYS cc_start: 0.7436 (mtpt) cc_final: 0.7141 (ttpt) REVERT: C 390 ARG cc_start: 0.6872 (mmt180) cc_final: 0.6566 (mmm160) REVERT: C 442 ARG cc_start: 0.7395 (mmt-90) cc_final: 0.7121 (mmt90) REVERT: C 451 GLU cc_start: 0.7631 (mp0) cc_final: 0.7161 (mp0) REVERT: C 473 GLU cc_start: 0.8060 (mm-30) cc_final: 0.7825 (mm-30) REVERT: C 496 LYS cc_start: 0.8574 (mttt) cc_final: 0.8057 (mttt) REVERT: D 5 ARG cc_start: 0.6158 (mtm-85) cc_final: 0.5892 (mtm-85) REVERT: D 7 ILE cc_start: 0.7611 (OUTLIER) cc_final: 0.7302 (mm) REVERT: D 10 MET cc_start: 0.6354 (mtm) cc_final: 0.5747 (mtm) REVERT: D 15 ASP cc_start: 0.6921 (m-30) cc_final: 0.6643 (m-30) REVERT: D 17 LYS cc_start: 0.7067 (tttt) cc_final: 0.6828 (tttm) REVERT: D 26 ILE cc_start: 0.8034 (mt) cc_final: 0.7762 (mp) REVERT: D 37 ARG cc_start: 0.6871 (mtm180) cc_final: 0.6445 (mtm180) REVERT: D 41 GLU cc_start: 0.6902 (mt-10) cc_final: 0.6661 (mt-10) REVERT: D 64 MET cc_start: 0.6762 (mmt) cc_final: 0.6429 (mmt) REVERT: D 74 MET cc_start: 0.7509 (mtt) cc_final: 0.7050 (mtt) REVERT: D 75 GLU cc_start: 0.7377 (tt0) cc_final: 0.6911 (tt0) REVERT: D 84 SER cc_start: 0.7843 (m) cc_final: 0.7411 (p) REVERT: D 96 PHE cc_start: 0.7462 (m-80) cc_final: 0.6986 (m-80) REVERT: D 101 GLU cc_start: 0.7133 (mt-10) cc_final: 0.6725 (mt-10) REVERT: D 114 ARG cc_start: 0.7258 (ttt180) cc_final: 0.6797 (ttp80) REVERT: D 116 ASP cc_start: 0.7068 (m-30) cc_final: 0.6441 (m-30) REVERT: D 120 ARG cc_start: 0.7162 (ttt90) cc_final: 0.6608 (ptm160) REVERT: D 133 GLU cc_start: 0.7234 (mt-10) cc_final: 0.6662 (mt-10) REVERT: D 173 HIS cc_start: 0.8251 (t70) cc_final: 0.8039 (t-90) REVERT: D 190 ASP cc_start: 0.6849 (m-30) cc_final: 0.5566 (m-30) REVERT: D 197 ASP cc_start: 0.6874 (t0) cc_final: 0.6621 (t0) REVERT: D 214 VAL cc_start: 0.7463 (t) cc_final: 0.6947 (p) REVERT: D 227 ARG cc_start: 0.6703 (mmt180) cc_final: 0.6156 (mmt90) REVERT: D 237 GLU cc_start: 0.7060 (mt-10) cc_final: 0.6588 (mt-10) REVERT: D 241 ASP cc_start: 0.7136 (m-30) cc_final: 0.6777 (m-30) REVERT: D 252 ASP cc_start: 0.6498 (t0) cc_final: 0.5999 (t0) REVERT: D 270 ARG cc_start: 0.7519 (mtt180) cc_final: 0.7036 (mtt-85) REVERT: D 271 MET cc_start: 0.7870 (mtt) cc_final: 0.7567 (ttm) REVERT: D 284 GLU cc_start: 0.6102 (mt-10) cc_final: 0.5576 (mt-10) REVERT: D 285 MET cc_start: 0.6479 (ttm) cc_final: 0.6178 (ttm) REVERT: D 326 ASP cc_start: 0.7051 (m-30) cc_final: 0.6305 (m-30) REVERT: D 337 GLU cc_start: 0.7027 (mt-10) cc_final: 0.6762 (mt-10) REVERT: D 352 ARG cc_start: 0.7161 (mtp180) cc_final: 0.6887 (mtp180) REVERT: D 387 LEU cc_start: 0.7835 (mt) cc_final: 0.7579 (mp) REVERT: D 389 MET cc_start: 0.7779 (ttt) cc_final: 0.7539 (ttt) REVERT: D 428 VAL cc_start: 0.8401 (OUTLIER) cc_final: 0.8061 (m) REVERT: D 439 GLU cc_start: 0.7337 (mm-30) cc_final: 0.6818 (mm-30) REVERT: D 455 LEU cc_start: 0.7828 (OUTLIER) cc_final: 0.7606 (mm) REVERT: E 1 MET cc_start: 0.3474 (mmt) cc_final: 0.3093 (mmt) REVERT: E 3 ARG cc_start: 0.6693 (mtm-85) cc_final: 0.6420 (mtm-85) REVERT: E 5 ARG cc_start: 0.6477 (ptp-110) cc_final: 0.6144 (ptp-110) REVERT: E 10 MET cc_start: 0.6244 (ptp) cc_final: 0.5763 (ptp) REVERT: E 17 LYS cc_start: 0.7341 (tttt) cc_final: 0.6872 (ttmm) REVERT: E 43 ASP cc_start: 0.6862 (OUTLIER) cc_final: 0.6395 (m-30) REVERT: E 71 ILE cc_start: 0.7720 (mt) cc_final: 0.7439 (mt) REVERT: E 89 GLU cc_start: 0.7382 (mm-30) cc_final: 0.7042 (mm-30) REVERT: E 127 GLU cc_start: 0.6888 (mt-10) cc_final: 0.6508 (mt-10) REVERT: E 133 GLU cc_start: 0.7790 (mt-10) cc_final: 0.7583 (mt-10) REVERT: E 134 ILE cc_start: 0.8276 (mt) cc_final: 0.7952 (tt) REVERT: E 149 ILE cc_start: 0.7756 (mt) cc_final: 0.7412 (mm) REVERT: E 170 GLU cc_start: 0.7030 (tp30) cc_final: 0.6719 (tt0) REVERT: E 178 GLU cc_start: 0.6983 (mm-30) cc_final: 0.6782 (mm-30) REVERT: E 210 LYS cc_start: 0.7483 (mttt) cc_final: 0.7144 (mttt) REVERT: E 238 TYR cc_start: 0.7305 (t80) cc_final: 0.7101 (t80) REVERT: E 256 ARG cc_start: 0.6605 (mtt90) cc_final: 0.6285 (mtt90) REVERT: E 284 GLU cc_start: 0.6060 (mt-10) cc_final: 0.5701 (mt-10) REVERT: E 334 LYS cc_start: 0.7294 (mmmm) cc_final: 0.7072 (mmmm) REVERT: E 362 GLU cc_start: 0.7683 (pm20) cc_final: 0.7404 (pm20) REVERT: E 365 GLN cc_start: 0.7593 (mt0) cc_final: 0.7153 (mt0) REVERT: E 375 GLN cc_start: 0.7675 (tp-100) cc_final: 0.7336 (tp40) REVERT: E 376 ARG cc_start: 0.7756 (tpt170) cc_final: 0.7319 (tpt170) REVERT: E 387 LEU cc_start: 0.7258 (mt) cc_final: 0.6929 (mt) REVERT: E 391 GLU cc_start: 0.7605 (mt-10) cc_final: 0.7198 (mt-10) REVERT: E 402 ARG cc_start: 0.7694 (mmm-85) cc_final: 0.7130 (mtt-85) REVERT: E 405 ARG cc_start: 0.7491 (mpt180) cc_final: 0.7275 (mpt180) REVERT: E 407 GLN cc_start: 0.7554 (tt0) cc_final: 0.7109 (tp40) REVERT: E 408 PHE cc_start: 0.6978 (m-80) cc_final: 0.6776 (m-80) REVERT: E 418 GLU cc_start: 0.7430 (tt0) cc_final: 0.6957 (tt0) REVERT: E 421 THR cc_start: 0.7536 (t) cc_final: 0.7258 (p) REVERT: E 423 GLN cc_start: 0.7243 (mm-40) cc_final: 0.6977 (mm-40) REVERT: E 431 LYS cc_start: 0.7669 (ptmm) cc_final: 0.7419 (ptmm) REVERT: E 435 ARG cc_start: 0.7375 (ttp80) cc_final: 0.7043 (ttp80) REVERT: E 438 LYS cc_start: 0.7777 (ttpt) cc_final: 0.6814 (ttpt) REVERT: E 439 GLU cc_start: 0.7624 (mm-30) cc_final: 0.6634 (mm-30) REVERT: E 441 LEU cc_start: 0.8341 (mt) cc_final: 0.8068 (mt) REVERT: E 442 GLU cc_start: 0.7822 (mt-10) cc_final: 0.7234 (mt-10) REVERT: E 445 TYR cc_start: 0.7482 (m-80) cc_final: 0.6631 (m-80) REVERT: E 446 ASP cc_start: 0.7436 (m-30) cc_final: 0.7213 (m-30) REVERT: E 450 GLU cc_start: 0.7778 (pm20) cc_final: 0.7235 (pm20) REVERT: E 461 GLU cc_start: 0.7437 (mt-10) cc_final: 0.7216 (mt-10) REVERT: F 3 ARG cc_start: 0.6734 (mtt180) cc_final: 0.6355 (mtt180) REVERT: F 5 ARG cc_start: 0.6039 (mmt180) cc_final: 0.5525 (mmt180) REVERT: F 8 GLN cc_start: 0.7285 (mt0) cc_final: 0.6900 (mt0) REVERT: F 10 MET cc_start: 0.6992 (mtm) cc_final: 0.6691 (mtm) REVERT: F 15 ASP cc_start: 0.6963 (m-30) cc_final: 0.6448 (m-30) REVERT: F 23 LEU cc_start: 0.8307 (mp) cc_final: 0.8100 (mt) REVERT: F 33 GLN cc_start: 0.7401 (mt0) cc_final: 0.7079 (mt0) REVERT: F 37 ARG cc_start: 0.7344 (ttm170) cc_final: 0.7106 (ttm170) REVERT: F 39 GLU cc_start: 0.7482 (mp0) cc_final: 0.6994 (mp0) REVERT: F 74 MET cc_start: 0.6772 (mtt) cc_final: 0.6295 (mtt) REVERT: F 89 GLU cc_start: 0.7553 (tp30) cc_final: 0.7247 (tp30) REVERT: F 114 ARG cc_start: 0.7421 (ttp-170) cc_final: 0.7049 (ttp80) REVERT: F 115 ARG cc_start: 0.7375 (mtt90) cc_final: 0.7023 (mtt90) REVERT: F 116 ASP cc_start: 0.7364 (m-30) cc_final: 0.6969 (m-30) REVERT: F 124 LYS cc_start: 0.7132 (mttm) cc_final: 0.6743 (mttm) REVERT: F 127 GLU cc_start: 0.7323 (mt-10) cc_final: 0.6882 (mt-10) REVERT: F 213 MET cc_start: 0.7375 (mtp) cc_final: 0.6843 (mtp) REVERT: F 220 GLU cc_start: 0.6792 (mm-30) cc_final: 0.6525 (mm-30) REVERT: F 237 GLU cc_start: 0.6489 (tt0) cc_final: 0.6044 (mt-10) REVERT: F 285 MET cc_start: 0.6896 (ttm) cc_final: 0.6635 (ttm) REVERT: F 290 GLU cc_start: 0.7252 (mm-30) cc_final: 0.7018 (mm-30) REVERT: F 300 ILE cc_start: 0.7716 (mt) cc_final: 0.7423 (tt) REVERT: F 303 ILE cc_start: 0.7595 (mt) cc_final: 0.7304 (mp) REVERT: F 389 MET cc_start: 0.7319 (mtm) cc_final: 0.6673 (mtm) REVERT: F 395 GLU cc_start: 0.6708 (pm20) cc_final: 0.6413 (pm20) REVERT: F 397 LYS cc_start: 0.7219 (tttm) cc_final: 0.6917 (tttm) REVERT: F 423 GLN cc_start: 0.7510 (pt0) cc_final: 0.7286 (pt0) REVERT: F 438 LYS cc_start: 0.7668 (tttt) cc_final: 0.7149 (tttt) REVERT: F 439 GLU cc_start: 0.7591 (mt-10) cc_final: 0.6829 (mt-10) REVERT: F 442 GLU cc_start: 0.7238 (mt-10) cc_final: 0.6544 (mt-10) REVERT: F 444 LYS cc_start: 0.7982 (tttt) cc_final: 0.7435 (tttt) REVERT: F 445 TYR cc_start: 0.8293 (m-80) cc_final: 0.7641 (m-80) REVERT: F 451 ASP cc_start: 0.7769 (m-30) cc_final: 0.7541 (m-30) REVERT: G 11 LYS cc_start: 0.7284 (tptt) cc_final: 0.6913 (tptt) REVERT: G 32 THR cc_start: 0.7783 (m) cc_final: 0.7343 (p) REVERT: G 33 SER cc_start: 0.7775 (t) cc_final: 0.7301 (p) REVERT: G 39 GLU cc_start: 0.8431 (tt0) cc_final: 0.8204 (tp30) REVERT: G 54 GLU cc_start: 0.8744 (mt-10) cc_final: 0.8425 (mt-10) REVERT: G 70 MET cc_start: 0.7862 (mmm) cc_final: 0.7274 (mmm) REVERT: G 85 THR cc_start: 0.7662 (OUTLIER) cc_final: 0.7116 (t) REVERT: G 88 ARG cc_start: 0.7016 (ptt180) cc_final: 0.6619 (ptt180) REVERT: G 115 GLU cc_start: 0.8093 (mm-30) cc_final: 0.7651 (mm-30) REVERT: G 116 TYR cc_start: 0.7536 (p90) cc_final: 0.7051 (p90) REVERT: G 134 MET cc_start: 0.6529 (mtm) cc_final: 0.5547 (mtm) REVERT: G 170 GLU cc_start: 0.6779 (tt0) cc_final: 0.6376 (tt0) REVERT: G 173 MET cc_start: 0.7101 (mtm) cc_final: 0.6876 (mtm) REVERT: G 185 GLU cc_start: 0.6546 (mm-30) cc_final: 0.6219 (mm-30) REVERT: G 188 GLU cc_start: 0.5958 (tt0) cc_final: 0.5608 (tt0) REVERT: G 225 GLU cc_start: 0.8596 (mt-10) cc_final: 0.8260 (mt-10) REVERT: G 227 LEU cc_start: 0.8034 (mm) cc_final: 0.7756 (mm) REVERT: G 229 TYR cc_start: 0.7793 (t80) cc_final: 0.7479 (t80) outliers start: 133 outliers final: 80 residues processed: 1141 average time/residue: 0.4223 time to fit residues: 698.6785 Evaluate side-chains 1160 residues out of total 2558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 1071 time to evaluate : 2.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 46 ASN Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 90 ARG Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 144 GLU Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 306 ASP Chi-restraints excluded: chain B residue 345 GLN Chi-restraints excluded: chain B residue 366 VAL Chi-restraints excluded: chain B residue 375 MET Chi-restraints excluded: chain B residue 377 LYS Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 442 ARG Chi-restraints excluded: chain B residue 452 ASP Chi-restraints excluded: chain C residue 28 VAL Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 262 ASP Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 332 THR Chi-restraints excluded: chain C residue 366 VAL Chi-restraints excluded: chain C residue 375 MET Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 450 VAL Chi-restraints excluded: chain C residue 459 GLU Chi-restraints excluded: chain C residue 470 HIS Chi-restraints excluded: chain C residue 486 ASP Chi-restraints excluded: chain D residue 2 THR Chi-restraints excluded: chain D residue 7 ILE Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 57 ASP Chi-restraints excluded: chain D residue 112 ASP Chi-restraints excluded: chain D residue 131 GLU Chi-restraints excluded: chain D residue 207 VAL Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 295 THR Chi-restraints excluded: chain D residue 299 SER Chi-restraints excluded: chain D residue 351 SER Chi-restraints excluded: chain D residue 382 ASP Chi-restraints excluded: chain D residue 428 VAL Chi-restraints excluded: chain D residue 455 LEU Chi-restraints excluded: chain D residue 456 VAL Chi-restraints excluded: chain E residue 43 ASP Chi-restraints excluded: chain E residue 67 THR Chi-restraints excluded: chain E residue 103 ILE Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 265 SER Chi-restraints excluded: chain E residue 293 THR Chi-restraints excluded: chain E residue 357 GLU Chi-restraints excluded: chain E residue 380 LEU Chi-restraints excluded: chain E residue 400 VAL Chi-restraints excluded: chain E residue 456 VAL Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 46 LEU Chi-restraints excluded: chain F residue 84 SER Chi-restraints excluded: chain F residue 106 GLU Chi-restraints excluded: chain F residue 183 SER Chi-restraints excluded: chain F residue 233 LEU Chi-restraints excluded: chain F residue 265 SER Chi-restraints excluded: chain F residue 292 ILE Chi-restraints excluded: chain F residue 329 THR Chi-restraints excluded: chain F residue 330 ASN Chi-restraints excluded: chain F residue 378 LYS Chi-restraints excluded: chain F residue 462 VAL Chi-restraints excluded: chain F residue 464 GLU Chi-restraints excluded: chain G residue 22 GLN Chi-restraints excluded: chain G residue 23 ILE Chi-restraints excluded: chain G residue 83 VAL Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain G residue 101 LEU Chi-restraints excluded: chain G residue 105 THR Chi-restraints excluded: chain G residue 148 SER Chi-restraints excluded: chain G residue 186 VAL Chi-restraints excluded: chain G residue 232 LEU Chi-restraints excluded: chain G residue 274 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 278 optimal weight: 0.7980 chunk 212 optimal weight: 9.9990 chunk 146 optimal weight: 5.9990 chunk 31 optimal weight: 6.9990 chunk 134 optimal weight: 1.9990 chunk 189 optimal weight: 5.9990 chunk 283 optimal weight: 3.9990 chunk 299 optimal weight: 5.9990 chunk 147 optimal weight: 2.9990 chunk 268 optimal weight: 8.9990 chunk 80 optimal weight: 0.5980 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 GLN A 172 GLN ** A 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 474 HIS C 172 GLN C 474 HIS D 174 ASN D 219 ASN D 304 GLN E 169 GLN E 412 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6929 moved from start: 0.3712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 24604 Z= 0.260 Angle : 0.575 7.096 33364 Z= 0.306 Chirality : 0.045 0.147 3840 Planarity : 0.005 0.053 4349 Dihedral : 8.653 121.037 3575 Min Nonbonded Distance : 1.766 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 4.69 % Allowed : 22.99 % Favored : 72.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.83 % 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: 0.17 (0.15), residues: 3104 helix: 1.05 (0.15), residues: 1229 sheet: 0.12 (0.22), residues: 538 loop : -0.71 (0.17), residues: 1337 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS A 474 PHE 0.015 0.002 PHE A 236 TYR 0.023 0.002 TYR E 427 ARG 0.009 0.001 ARG C 140 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1223 residues out of total 2558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 1103 time to evaluate : 3.019 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 LEU cc_start: 0.7208 (tp) cc_final: 0.6919 (mp) REVERT: A 96 GLU cc_start: 0.6105 (mt-10) cc_final: 0.5831 (tt0) REVERT: A 125 GLU cc_start: 0.6521 (OUTLIER) cc_final: 0.6283 (pt0) REVERT: A 140 ARG cc_start: 0.7293 (ttt-90) cc_final: 0.6900 (ttt90) REVERT: A 144 GLU cc_start: 0.7242 (pt0) cc_final: 0.6696 (pt0) REVERT: A 248 TYR cc_start: 0.7283 (t80) cc_final: 0.7030 (t80) REVERT: A 251 TYR cc_start: 0.7096 (m-80) cc_final: 0.6810 (m-80) REVERT: A 272 GLU cc_start: 0.6709 (tt0) cc_final: 0.6219 (tt0) REVERT: A 299 GLU cc_start: 0.7760 (mm-30) cc_final: 0.7303 (mm-30) REVERT: A 303 LYS cc_start: 0.7506 (tptp) cc_final: 0.7198 (tptp) REVERT: A 375 MET cc_start: 0.7250 (tpp) cc_final: 0.6579 (tpp) REVERT: A 376 LYS cc_start: 0.6812 (ttmm) cc_final: 0.6535 (ttmm) REVERT: A 426 GLN cc_start: 0.7135 (mm-40) cc_final: 0.6737 (mm-40) REVERT: A 458 LYS cc_start: 0.7252 (ttmt) cc_final: 0.7014 (tmmt) REVERT: A 476 ARG cc_start: 0.8016 (ttm-80) cc_final: 0.7789 (ttm-80) REVERT: A 486 ASP cc_start: 0.8229 (m-30) cc_final: 0.7979 (t0) REVERT: A 489 LYS cc_start: 0.7499 (tttt) cc_final: 0.7227 (tttt) REVERT: B 46 ASN cc_start: 0.7126 (m110) cc_final: 0.6891 (m110) REVERT: B 67 GLU cc_start: 0.7052 (mm-30) cc_final: 0.6642 (mm-30) REVERT: B 95 MET cc_start: 0.6877 (tpt) cc_final: 0.6212 (tpt) REVERT: B 144 GLU cc_start: 0.6871 (OUTLIER) cc_final: 0.5913 (pt0) REVERT: B 177 SER cc_start: 0.6400 (p) cc_final: 0.5840 (m) REVERT: B 181 ASP cc_start: 0.7353 (m-30) cc_final: 0.7142 (m-30) REVERT: B 202 GLU cc_start: 0.5869 (tp30) cc_final: 0.5663 (tp30) REVERT: B 272 GLU cc_start: 0.6731 (tt0) cc_final: 0.6378 (tt0) REVERT: B 343 PHE cc_start: 0.7509 (t80) cc_final: 0.7269 (t80) REVERT: B 378 VAL cc_start: 0.7934 (t) cc_final: 0.7720 (p) REVERT: B 418 GLU cc_start: 0.7493 (mm-30) cc_final: 0.7198 (mm-30) REVERT: B 442 ARG cc_start: 0.7683 (OUTLIER) cc_final: 0.7130 (mmt-90) REVERT: B 467 ASN cc_start: 0.8280 (t0) cc_final: 0.7964 (t0) REVERT: B 479 LYS cc_start: 0.7131 (mptt) cc_final: 0.6626 (mptt) REVERT: B 481 LEU cc_start: 0.8175 (tp) cc_final: 0.7847 (tp) REVERT: C 34 VAL cc_start: 0.7841 (t) cc_final: 0.7607 (p) REVERT: C 62 MET cc_start: 0.6606 (ttt) cc_final: 0.6239 (ttp) REVERT: C 80 THR cc_start: 0.7938 (p) cc_final: 0.7683 (m) REVERT: C 90 ARG cc_start: 0.7632 (ttt-90) cc_final: 0.7381 (ttp-110) REVERT: C 127 ARG cc_start: 0.7367 (mtp85) cc_final: 0.6953 (mtp85) REVERT: C 137 MET cc_start: 0.7980 (mmm) cc_final: 0.7753 (mmm) REVERT: C 140 ARG cc_start: 0.7699 (ttt90) cc_final: 0.7431 (ttt-90) REVERT: C 144 GLU cc_start: 0.6971 (pt0) cc_final: 0.6287 (pt0) REVERT: C 147 GLN cc_start: 0.7426 (mm-40) cc_final: 0.6839 (mm110) REVERT: C 181 ASP cc_start: 0.7564 (m-30) cc_final: 0.7231 (m-30) REVERT: C 185 ASN cc_start: 0.7871 (t0) cc_final: 0.7581 (t0) REVERT: C 196 VAL cc_start: 0.7772 (t) cc_final: 0.7443 (m) REVERT: C 222 ILE cc_start: 0.7294 (mt) cc_final: 0.7039 (mt) REVERT: C 254 LYS cc_start: 0.7321 (mmtm) cc_final: 0.6924 (mtmm) REVERT: C 262 ASP cc_start: 0.7040 (OUTLIER) cc_final: 0.6812 (t0) REVERT: C 272 GLU cc_start: 0.6918 (mt-10) cc_final: 0.6512 (mt-10) REVERT: C 314 THR cc_start: 0.7510 (OUTLIER) cc_final: 0.6995 (p) REVERT: C 343 PHE cc_start: 0.8079 (t80) cc_final: 0.7737 (t80) REVERT: C 354 ARG cc_start: 0.7118 (mtt90) cc_final: 0.6618 (mtt90) REVERT: C 361 LEU cc_start: 0.7685 (mp) cc_final: 0.7388 (mp) REVERT: C 372 ILE cc_start: 0.7604 (mp) cc_final: 0.7365 (mm) REVERT: C 376 LYS cc_start: 0.7464 (mtpt) cc_final: 0.7168 (ttpt) REVERT: C 390 ARG cc_start: 0.6871 (mmt180) cc_final: 0.6644 (mmm160) REVERT: C 451 GLU cc_start: 0.7627 (mp0) cc_final: 0.7180 (mp0) REVERT: C 473 GLU cc_start: 0.8051 (mm-30) cc_final: 0.7774 (mm-30) REVERT: C 496 LYS cc_start: 0.8531 (mttt) cc_final: 0.8008 (mttt) REVERT: D 5 ARG cc_start: 0.6159 (mtm-85) cc_final: 0.5894 (mtm-85) REVERT: D 7 ILE cc_start: 0.7594 (OUTLIER) cc_final: 0.7355 (mm) REVERT: D 10 MET cc_start: 0.6357 (mtm) cc_final: 0.5787 (mtm) REVERT: D 15 ASP cc_start: 0.6967 (m-30) cc_final: 0.6673 (m-30) REVERT: D 17 LYS cc_start: 0.7075 (tttt) cc_final: 0.6791 (tttm) REVERT: D 37 ARG cc_start: 0.6842 (mtm180) cc_final: 0.6349 (mtm180) REVERT: D 41 GLU cc_start: 0.6835 (mt-10) cc_final: 0.6075 (mt-10) REVERT: D 64 MET cc_start: 0.6772 (mmt) cc_final: 0.6453 (mmt) REVERT: D 74 MET cc_start: 0.7515 (mtt) cc_final: 0.7062 (mtt) REVERT: D 75 GLU cc_start: 0.7359 (tt0) cc_final: 0.6907 (tt0) REVERT: D 84 SER cc_start: 0.7849 (m) cc_final: 0.7412 (p) REVERT: D 96 PHE cc_start: 0.7390 (m-80) cc_final: 0.6810 (m-80) REVERT: D 101 GLU cc_start: 0.7164 (mt-10) cc_final: 0.6743 (mt-10) REVERT: D 114 ARG cc_start: 0.7283 (ttt180) cc_final: 0.6784 (ttp80) REVERT: D 116 ASP cc_start: 0.7086 (m-30) cc_final: 0.6462 (m-30) REVERT: D 120 ARG cc_start: 0.7246 (ttt90) cc_final: 0.6830 (ptm160) REVERT: D 133 GLU cc_start: 0.7286 (mt-10) cc_final: 0.6709 (mt-10) REVERT: D 169 GLN cc_start: 0.7356 (mt0) cc_final: 0.6894 (mm-40) REVERT: D 173 HIS cc_start: 0.8289 (t70) cc_final: 0.8061 (t70) REVERT: D 190 ASP cc_start: 0.6829 (m-30) cc_final: 0.5496 (m-30) REVERT: D 191 ARG cc_start: 0.6877 (OUTLIER) cc_final: 0.6555 (mtt-85) REVERT: D 197 ASP cc_start: 0.6903 (t0) cc_final: 0.6664 (t0) REVERT: D 214 VAL cc_start: 0.7485 (t) cc_final: 0.7008 (p) REVERT: D 227 ARG cc_start: 0.6709 (mmt180) cc_final: 0.6153 (mmt90) REVERT: D 237 GLU cc_start: 0.7077 (mt-10) cc_final: 0.6584 (mt-10) REVERT: D 241 ASP cc_start: 0.7086 (m-30) cc_final: 0.6741 (m-30) REVERT: D 246 ASP cc_start: 0.7494 (m-30) cc_final: 0.7009 (m-30) REVERT: D 252 ASP cc_start: 0.6428 (t0) cc_final: 0.5961 (t0) REVERT: D 284 GLU cc_start: 0.6090 (mt-10) cc_final: 0.5583 (mt-10) REVERT: D 285 MET cc_start: 0.6361 (ttm) cc_final: 0.6008 (ttm) REVERT: D 326 ASP cc_start: 0.7024 (m-30) cc_final: 0.6312 (m-30) REVERT: D 337 GLU cc_start: 0.7047 (mt-10) cc_final: 0.6784 (mt-10) REVERT: D 352 ARG cc_start: 0.7124 (mtp180) cc_final: 0.6873 (mtp180) REVERT: D 387 LEU cc_start: 0.7751 (mt) cc_final: 0.7517 (mp) REVERT: D 428 VAL cc_start: 0.8374 (t) cc_final: 0.8027 (m) REVERT: D 439 GLU cc_start: 0.7336 (mm-30) cc_final: 0.6686 (mm-30) REVERT: E 1 MET cc_start: 0.3488 (mmt) cc_final: 0.3080 (mmt) REVERT: E 5 ARG cc_start: 0.6453 (ptp-110) cc_final: 0.6129 (ptp-110) REVERT: E 10 MET cc_start: 0.6207 (ptp) cc_final: 0.5722 (ptp) REVERT: E 17 LYS cc_start: 0.7339 (tttt) cc_final: 0.6858 (ttmm) REVERT: E 89 GLU cc_start: 0.7388 (mm-30) cc_final: 0.7061 (mm-30) REVERT: E 91 THR cc_start: 0.7892 (p) cc_final: 0.7424 (t) REVERT: E 127 GLU cc_start: 0.6831 (mt-10) cc_final: 0.6474 (mt-10) REVERT: E 134 ILE cc_start: 0.8278 (mt) cc_final: 0.7956 (tt) REVERT: E 170 GLU cc_start: 0.7069 (tp30) cc_final: 0.6697 (tt0) REVERT: E 210 LYS cc_start: 0.7543 (mttt) cc_final: 0.7152 (mttt) REVERT: E 284 GLU cc_start: 0.5993 (mt-10) cc_final: 0.5671 (mt-10) REVERT: E 312 ASP cc_start: 0.7287 (t0) cc_final: 0.6843 (t0) REVERT: E 334 LYS cc_start: 0.7304 (mmmm) cc_final: 0.7082 (mmmm) REVERT: E 362 GLU cc_start: 0.7706 (pm20) cc_final: 0.7427 (pm20) REVERT: E 365 GLN cc_start: 0.7569 (mt0) cc_final: 0.7162 (mt0) REVERT: E 375 GLN cc_start: 0.7684 (tp-100) cc_final: 0.7386 (tp40) REVERT: E 387 LEU cc_start: 0.7262 (mt) cc_final: 0.6908 (mt) REVERT: E 391 GLU cc_start: 0.7613 (mt-10) cc_final: 0.7144 (mt-10) REVERT: E 402 ARG cc_start: 0.7587 (mmm-85) cc_final: 0.7085 (mtt-85) REVERT: E 405 ARG cc_start: 0.7486 (mpt180) cc_final: 0.7280 (mpt180) REVERT: E 407 GLN cc_start: 0.7589 (tt0) cc_final: 0.7134 (tp40) REVERT: E 431 LYS cc_start: 0.7660 (ptmm) cc_final: 0.7409 (ptmm) REVERT: E 435 ARG cc_start: 0.7411 (ttp80) cc_final: 0.6917 (ttp80) REVERT: E 438 LYS cc_start: 0.7746 (ttpt) cc_final: 0.6762 (ttpt) REVERT: E 439 GLU cc_start: 0.7623 (mm-30) cc_final: 0.6520 (mm-30) REVERT: E 441 LEU cc_start: 0.8315 (mt) cc_final: 0.8047 (mt) REVERT: E 442 GLU cc_start: 0.7755 (mt-10) cc_final: 0.7195 (mt-10) REVERT: E 445 TYR cc_start: 0.7532 (m-80) cc_final: 0.6725 (m-80) REVERT: E 446 ASP cc_start: 0.7453 (m-30) cc_final: 0.7167 (m-30) REVERT: E 450 GLU cc_start: 0.7765 (pm20) cc_final: 0.7205 (pm20) REVERT: E 461 GLU cc_start: 0.7421 (mt-10) cc_final: 0.7199 (mt-10) REVERT: F 3 ARG cc_start: 0.6793 (mtt180) cc_final: 0.6110 (mtt180) REVERT: F 5 ARG cc_start: 0.6044 (mmt180) cc_final: 0.5520 (mmt180) REVERT: F 8 GLN cc_start: 0.7319 (mt0) cc_final: 0.6877 (mt0) REVERT: F 10 MET cc_start: 0.7085 (mtm) cc_final: 0.6875 (mtm) REVERT: F 15 ASP cc_start: 0.6929 (m-30) cc_final: 0.6527 (m-30) REVERT: F 33 GLN cc_start: 0.7383 (mt0) cc_final: 0.7143 (mt0) REVERT: F 37 ARG cc_start: 0.7332 (ttm170) cc_final: 0.7104 (ttm170) REVERT: F 39 GLU cc_start: 0.7489 (mp0) cc_final: 0.7014 (mp0) REVERT: F 74 MET cc_start: 0.6797 (mtt) cc_final: 0.6324 (mtt) REVERT: F 75 GLU cc_start: 0.6841 (tt0) cc_final: 0.5018 (tt0) REVERT: F 89 GLU cc_start: 0.7580 (tp30) cc_final: 0.7291 (tp30) REVERT: F 114 ARG cc_start: 0.7458 (ttp-170) cc_final: 0.7079 (ttp80) REVERT: F 115 ARG cc_start: 0.7382 (mtt90) cc_final: 0.7065 (mtt90) REVERT: F 116 ASP cc_start: 0.7396 (m-30) cc_final: 0.7020 (m-30) REVERT: F 120 ARG cc_start: 0.7116 (ptm-80) cc_final: 0.6699 (ttp-110) REVERT: F 124 LYS cc_start: 0.7163 (mttm) cc_final: 0.6717 (mttm) REVERT: F 127 GLU cc_start: 0.7313 (mt-10) cc_final: 0.6790 (mt-10) REVERT: F 213 MET cc_start: 0.7308 (mtp) cc_final: 0.7006 (mtm) REVERT: F 220 GLU cc_start: 0.6832 (mm-30) cc_final: 0.6557 (mm-30) REVERT: F 237 GLU cc_start: 0.6470 (tt0) cc_final: 0.5963 (mt-10) REVERT: F 285 MET cc_start: 0.6821 (ttm) cc_final: 0.6549 (ttm) REVERT: F 290 GLU cc_start: 0.7325 (mm-30) cc_final: 0.7116 (mm-30) REVERT: F 300 ILE cc_start: 0.7677 (mt) cc_final: 0.7424 (tt) REVERT: F 303 ILE cc_start: 0.7569 (mt) cc_final: 0.7293 (mp) REVERT: F 345 ASP cc_start: 0.7244 (t70) cc_final: 0.6876 (t70) REVERT: F 389 MET cc_start: 0.7391 (mtm) cc_final: 0.7093 (mtm) REVERT: F 395 GLU cc_start: 0.6778 (pm20) cc_final: 0.6444 (pm20) REVERT: F 423 GLN cc_start: 0.7563 (pt0) cc_final: 0.7336 (pt0) REVERT: F 438 LYS cc_start: 0.7647 (tttt) cc_final: 0.7124 (tttt) REVERT: F 439 GLU cc_start: 0.7562 (mt-10) cc_final: 0.6801 (mt-10) REVERT: F 442 GLU cc_start: 0.7256 (mt-10) cc_final: 0.6604 (mt-10) REVERT: F 444 LYS cc_start: 0.7957 (tttt) cc_final: 0.7500 (tttt) REVERT: F 445 TYR cc_start: 0.8290 (m-80) cc_final: 0.7727 (m-80) REVERT: F 451 ASP cc_start: 0.7782 (m-30) cc_final: 0.7541 (m-30) REVERT: G 11 LYS cc_start: 0.7275 (tptt) cc_final: 0.6914 (tptt) REVERT: G 17 THR cc_start: 0.6442 (OUTLIER) cc_final: 0.6241 (t) REVERT: G 30 VAL cc_start: 0.7265 (t) cc_final: 0.7023 (t) REVERT: G 33 SER cc_start: 0.7797 (t) cc_final: 0.7327 (p) REVERT: G 39 GLU cc_start: 0.8422 (tt0) cc_final: 0.8174 (tp30) REVERT: G 54 GLU cc_start: 0.8787 (mt-10) cc_final: 0.8482 (mt-10) REVERT: G 70 MET cc_start: 0.7882 (mmm) cc_final: 0.7266 (mmm) REVERT: G 85 THR cc_start: 0.7634 (OUTLIER) cc_final: 0.7218 (t) REVERT: G 95 ASN cc_start: 0.7843 (m-40) cc_final: 0.7554 (m110) REVERT: G 115 GLU cc_start: 0.8119 (mm-30) cc_final: 0.7712 (mm-30) REVERT: G 116 TYR cc_start: 0.7549 (p90) cc_final: 0.7099 (p90) REVERT: G 134 MET cc_start: 0.6507 (mtm) cc_final: 0.5620 (mtm) REVERT: G 170 GLU cc_start: 0.6824 (tt0) cc_final: 0.6478 (tt0) REVERT: G 173 MET cc_start: 0.7008 (mtm) cc_final: 0.6748 (mtm) REVERT: G 185 GLU cc_start: 0.6562 (mm-30) cc_final: 0.6153 (mm-30) REVERT: G 188 GLU cc_start: 0.5752 (tt0) cc_final: 0.5490 (tt0) REVERT: G 223 TYR cc_start: 0.8125 (t80) cc_final: 0.7771 (t80) REVERT: G 225 GLU cc_start: 0.8572 (mt-10) cc_final: 0.8251 (mt-10) REVERT: G 227 LEU cc_start: 0.7949 (mm) cc_final: 0.7727 (mm) outliers start: 120 outliers final: 85 residues processed: 1143 average time/residue: 0.4202 time to fit residues: 698.4341 Evaluate side-chains 1150 residues out of total 2558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 1056 time to evaluate : 2.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 89 ARG Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 137 MET Chi-restraints excluded: chain B residue 144 GLU Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 306 ASP Chi-restraints excluded: chain B residue 375 MET Chi-restraints excluded: chain B residue 377 LYS Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 442 ARG Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 452 ASP Chi-restraints excluded: chain C residue 28 VAL Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 262 ASP Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 327 SER Chi-restraints excluded: chain C residue 332 THR Chi-restraints excluded: chain C residue 375 MET Chi-restraints excluded: chain C residue 450 VAL Chi-restraints excluded: chain C residue 470 HIS Chi-restraints excluded: chain D residue 2 THR Chi-restraints excluded: chain D residue 7 ILE Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 57 ASP Chi-restraints excluded: chain D residue 112 ASP Chi-restraints excluded: chain D residue 131 GLU Chi-restraints excluded: chain D residue 191 ARG Chi-restraints excluded: chain D residue 203 LYS Chi-restraints excluded: chain D residue 207 VAL Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 295 THR Chi-restraints excluded: chain D residue 299 SER Chi-restraints excluded: chain D residue 344 VAL Chi-restraints excluded: chain D residue 382 ASP Chi-restraints excluded: chain D residue 384 ILE Chi-restraints excluded: chain D residue 433 THR Chi-restraints excluded: chain D residue 456 VAL Chi-restraints excluded: chain E residue 67 THR Chi-restraints excluded: chain E residue 68 ASP Chi-restraints excluded: chain E residue 103 ILE Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 293 THR Chi-restraints excluded: chain E residue 328 THR Chi-restraints excluded: chain E residue 357 GLU Chi-restraints excluded: chain E residue 381 GLN Chi-restraints excluded: chain E residue 384 ILE Chi-restraints excluded: chain E residue 395 GLU Chi-restraints excluded: chain E residue 399 VAL Chi-restraints excluded: chain E residue 400 VAL Chi-restraints excluded: chain E residue 456 VAL Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 46 LEU Chi-restraints excluded: chain F residue 84 SER Chi-restraints excluded: chain F residue 98 VAL Chi-restraints excluded: chain F residue 106 GLU Chi-restraints excluded: chain F residue 183 SER Chi-restraints excluded: chain F residue 233 LEU Chi-restraints excluded: chain F residue 267 LEU Chi-restraints excluded: chain F residue 273 SER Chi-restraints excluded: chain F residue 322 PHE Chi-restraints excluded: chain F residue 378 LYS Chi-restraints excluded: chain F residue 462 VAL Chi-restraints excluded: chain G residue 13 ARG Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain G residue 22 GLN Chi-restraints excluded: chain G residue 23 ILE Chi-restraints excluded: chain G residue 83 VAL Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain G residue 101 LEU Chi-restraints excluded: chain G residue 148 SER Chi-restraints excluded: chain G residue 172 TYR Chi-restraints excluded: chain G residue 186 VAL Chi-restraints excluded: chain G residue 232 LEU Chi-restraints excluded: chain G residue 281 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 249 optimal weight: 0.9980 chunk 170 optimal weight: 7.9990 chunk 4 optimal weight: 3.9990 chunk 223 optimal weight: 5.9990 chunk 123 optimal weight: 0.8980 chunk 255 optimal weight: 9.9990 chunk 207 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 153 optimal weight: 0.9990 chunk 268 optimal weight: 6.9990 chunk 75 optimal weight: 10.0000 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 GLN ** A 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 33 GLN B 163 GLN B 333 ASN B 345 GLN B 371 GLN B 433 GLN C 172 GLN ** C 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 33 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6947 moved from start: 0.4014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 24604 Z= 0.314 Angle : 0.597 7.183 33364 Z= 0.318 Chirality : 0.046 0.162 3840 Planarity : 0.005 0.051 4349 Dihedral : 8.392 114.602 3575 Min Nonbonded Distance : 1.762 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 5.36 % Allowed : 23.73 % Favored : 70.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.15), residues: 3104 helix: 0.98 (0.15), residues: 1236 sheet: 0.06 (0.22), residues: 537 loop : -0.83 (0.17), residues: 1331 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS F 363 PHE 0.024 0.002 PHE G 45 TYR 0.026 0.002 TYR E 427 ARG 0.009 0.001 ARG C 415 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1223 residues out of total 2558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 1086 time to evaluate : 2.826 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 ARG cc_start: 0.7019 (ptt180) cc_final: 0.6702 (ptt180) REVERT: A 96 GLU cc_start: 0.6116 (mt-10) cc_final: 0.5832 (tt0) REVERT: A 125 GLU cc_start: 0.6418 (pt0) cc_final: 0.6191 (pt0) REVERT: A 140 ARG cc_start: 0.7311 (ttt-90) cc_final: 0.7025 (ttt90) REVERT: A 144 GLU cc_start: 0.7214 (pt0) cc_final: 0.6955 (pt0) REVERT: A 163 GLN cc_start: 0.7517 (tt0) cc_final: 0.7293 (tt0) REVERT: A 248 TYR cc_start: 0.7175 (t80) cc_final: 0.6941 (t80) REVERT: A 251 TYR cc_start: 0.7197 (m-80) cc_final: 0.6883 (m-80) REVERT: A 254 LYS cc_start: 0.7337 (mmtm) cc_final: 0.6974 (mmtm) REVERT: A 272 GLU cc_start: 0.6694 (tt0) cc_final: 0.6214 (tt0) REVERT: A 299 GLU cc_start: 0.7748 (mm-30) cc_final: 0.7258 (mm-30) REVERT: A 303 LYS cc_start: 0.7514 (tptp) cc_final: 0.7208 (tptp) REVERT: A 375 MET cc_start: 0.7269 (tpp) cc_final: 0.6584 (tpp) REVERT: A 376 LYS cc_start: 0.6862 (ttmm) cc_final: 0.6472 (ttmm) REVERT: A 402 LEU cc_start: 0.7465 (mt) cc_final: 0.7259 (mt) REVERT: A 421 LYS cc_start: 0.7509 (mttp) cc_final: 0.7276 (mttm) REVERT: A 426 GLN cc_start: 0.7205 (mm-40) cc_final: 0.6817 (mm-40) REVERT: A 486 ASP cc_start: 0.8246 (m-30) cc_final: 0.7961 (t0) REVERT: A 489 LYS cc_start: 0.7709 (tttt) cc_final: 0.7434 (tttt) REVERT: B 46 ASN cc_start: 0.6947 (m110) cc_final: 0.6608 (m110) REVERT: B 67 GLU cc_start: 0.6953 (mm-30) cc_final: 0.6534 (mm-30) REVERT: B 95 MET cc_start: 0.6857 (tpt) cc_final: 0.6300 (tpt) REVERT: B 101 GLU cc_start: 0.6797 (mp0) cc_final: 0.6543 (mp0) REVERT: B 144 GLU cc_start: 0.6913 (OUTLIER) cc_final: 0.5994 (pt0) REVERT: B 177 SER cc_start: 0.6330 (p) cc_final: 0.5852 (m) REVERT: B 181 ASP cc_start: 0.7374 (m-30) cc_final: 0.7160 (m-30) REVERT: B 200 GLN cc_start: 0.7852 (mm-40) cc_final: 0.7588 (mm110) REVERT: B 230 GLN cc_start: 0.7263 (mm-40) cc_final: 0.6979 (mt0) REVERT: B 261 ASP cc_start: 0.6259 (OUTLIER) cc_final: 0.6046 (m-30) REVERT: B 272 GLU cc_start: 0.6729 (tt0) cc_final: 0.6360 (tt0) REVERT: B 336 SER cc_start: 0.7624 (t) cc_final: 0.7413 (p) REVERT: B 361 LEU cc_start: 0.7855 (mt) cc_final: 0.7576 (mp) REVERT: B 378 VAL cc_start: 0.8076 (t) cc_final: 0.7874 (p) REVERT: B 418 GLU cc_start: 0.7453 (mm-30) cc_final: 0.7195 (mm-30) REVERT: B 449 PRO cc_start: 0.7434 (Cg_exo) cc_final: 0.7198 (Cg_endo) REVERT: B 467 ASN cc_start: 0.8276 (t0) cc_final: 0.7937 (t0) REVERT: B 479 LYS cc_start: 0.7062 (mptt) cc_final: 0.6538 (mptt) REVERT: C 34 VAL cc_start: 0.7845 (t) cc_final: 0.7606 (p) REVERT: C 62 MET cc_start: 0.6611 (ttt) cc_final: 0.6312 (ttp) REVERT: C 68 GLU cc_start: 0.7206 (mt-10) cc_final: 0.6816 (mt-10) REVERT: C 80 THR cc_start: 0.7945 (p) cc_final: 0.7697 (m) REVERT: C 127 ARG cc_start: 0.7352 (mtp85) cc_final: 0.6915 (mtp85) REVERT: C 137 MET cc_start: 0.7979 (mmm) cc_final: 0.7746 (mmm) REVERT: C 147 GLN cc_start: 0.7420 (mm-40) cc_final: 0.6884 (mm110) REVERT: C 181 ASP cc_start: 0.7574 (m-30) cc_final: 0.7240 (m-30) REVERT: C 185 ASN cc_start: 0.7849 (t0) cc_final: 0.7537 (t0) REVERT: C 196 VAL cc_start: 0.7716 (t) cc_final: 0.7403 (m) REVERT: C 254 LYS cc_start: 0.7383 (mmtm) cc_final: 0.7044 (mtmm) REVERT: C 262 ASP cc_start: 0.7118 (OUTLIER) cc_final: 0.6882 (t0) REVERT: C 272 GLU cc_start: 0.6918 (mt-10) cc_final: 0.6517 (mt-10) REVERT: C 278 ARG cc_start: 0.7710 (mtp85) cc_final: 0.7491 (mmm160) REVERT: C 314 THR cc_start: 0.7503 (OUTLIER) cc_final: 0.6969 (p) REVERT: C 354 ARG cc_start: 0.7159 (mtt90) cc_final: 0.6648 (mtt180) REVERT: C 361 LEU cc_start: 0.7670 (mp) cc_final: 0.7385 (mp) REVERT: C 376 LYS cc_start: 0.7479 (ttpt) cc_final: 0.7182 (ttpt) REVERT: C 451 GLU cc_start: 0.7667 (mp0) cc_final: 0.7185 (mp0) REVERT: C 473 GLU cc_start: 0.8059 (mm-30) cc_final: 0.7697 (mm-30) REVERT: C 496 LYS cc_start: 0.8509 (mttt) cc_final: 0.7977 (mttt) REVERT: D 5 ARG cc_start: 0.6166 (mtm-85) cc_final: 0.5902 (mtm-85) REVERT: D 7 ILE cc_start: 0.7600 (OUTLIER) cc_final: 0.7394 (mm) REVERT: D 10 MET cc_start: 0.6390 (mtm) cc_final: 0.5810 (mtm) REVERT: D 15 ASP cc_start: 0.6965 (m-30) cc_final: 0.6666 (m-30) REVERT: D 17 LYS cc_start: 0.7089 (tttt) cc_final: 0.6777 (tttm) REVERT: D 37 ARG cc_start: 0.6848 (mtm180) cc_final: 0.6339 (mtm180) REVERT: D 41 GLU cc_start: 0.6766 (mt-10) cc_final: 0.5975 (mt-10) REVERT: D 64 MET cc_start: 0.6773 (mmt) cc_final: 0.6418 (mmt) REVERT: D 74 MET cc_start: 0.7540 (mtt) cc_final: 0.7302 (mtt) REVERT: D 75 GLU cc_start: 0.7354 (tt0) cc_final: 0.6896 (tt0) REVERT: D 96 PHE cc_start: 0.7363 (m-80) cc_final: 0.6721 (m-80) REVERT: D 101 GLU cc_start: 0.7146 (mt-10) cc_final: 0.6731 (mt-10) REVERT: D 114 ARG cc_start: 0.7321 (ttt180) cc_final: 0.6864 (ttp80) REVERT: D 116 ASP cc_start: 0.7055 (m-30) cc_final: 0.6450 (m-30) REVERT: D 120 ARG cc_start: 0.7295 (ttt90) cc_final: 0.6854 (ptm160) REVERT: D 133 GLU cc_start: 0.7290 (mt-10) cc_final: 0.6707 (mt-10) REVERT: D 169 GLN cc_start: 0.7343 (mt0) cc_final: 0.6917 (mm-40) REVERT: D 190 ASP cc_start: 0.6817 (m-30) cc_final: 0.5493 (m-30) REVERT: D 197 ASP cc_start: 0.6929 (t0) cc_final: 0.6706 (t0) REVERT: D 214 VAL cc_start: 0.7554 (t) cc_final: 0.7067 (p) REVERT: D 237 GLU cc_start: 0.7127 (mt-10) cc_final: 0.6640 (mt-10) REVERT: D 241 ASP cc_start: 0.7161 (m-30) cc_final: 0.6874 (m-30) REVERT: D 246 ASP cc_start: 0.7511 (m-30) cc_final: 0.7049 (m-30) REVERT: D 252 ASP cc_start: 0.6455 (t0) cc_final: 0.5945 (t0) REVERT: D 270 ARG cc_start: 0.7523 (mtt180) cc_final: 0.6932 (mtt-85) REVERT: D 284 GLU cc_start: 0.6066 (mt-10) cc_final: 0.5530 (mt-10) REVERT: D 285 MET cc_start: 0.6402 (ttm) cc_final: 0.6076 (ttm) REVERT: D 326 ASP cc_start: 0.7011 (m-30) cc_final: 0.6330 (m-30) REVERT: D 337 GLU cc_start: 0.7014 (mt-10) cc_final: 0.6745 (mt-10) REVERT: D 352 ARG cc_start: 0.7118 (mtp180) cc_final: 0.6838 (mtp180) REVERT: D 387 LEU cc_start: 0.7753 (mt) cc_final: 0.7551 (mp) REVERT: D 415 HIS cc_start: 0.8034 (m-70) cc_final: 0.7831 (m90) REVERT: D 428 VAL cc_start: 0.8340 (OUTLIER) cc_final: 0.7995 (m) REVERT: D 439 GLU cc_start: 0.7376 (mm-30) cc_final: 0.6692 (mm-30) REVERT: E 1 MET cc_start: 0.3466 (mmt) cc_final: 0.3186 (mmt) REVERT: E 3 ARG cc_start: 0.6744 (mtm-85) cc_final: 0.6292 (mtm-85) REVERT: E 5 ARG cc_start: 0.6460 (ptp-110) cc_final: 0.6088 (ptp-110) REVERT: E 10 MET cc_start: 0.6226 (ptp) cc_final: 0.5855 (ptp) REVERT: E 17 LYS cc_start: 0.7362 (tttt) cc_final: 0.6860 (ttmm) REVERT: E 31 LYS cc_start: 0.7593 (mmtt) cc_final: 0.7179 (mmtt) REVERT: E 43 ASP cc_start: 0.6727 (m-30) cc_final: 0.6277 (m-30) REVERT: E 89 GLU cc_start: 0.7343 (mm-30) cc_final: 0.7001 (mm-30) REVERT: E 91 THR cc_start: 0.7855 (p) cc_final: 0.7408 (t) REVERT: E 104 ASP cc_start: 0.7446 (m-30) cc_final: 0.7054 (m-30) REVERT: E 127 GLU cc_start: 0.6848 (mt-10) cc_final: 0.6510 (mt-10) REVERT: E 134 ILE cc_start: 0.8281 (mt) cc_final: 0.7965 (tt) REVERT: E 170 GLU cc_start: 0.7116 (tp30) cc_final: 0.6700 (tt0) REVERT: E 178 GLU cc_start: 0.7042 (mm-30) cc_final: 0.6538 (mt-10) REVERT: E 203 LYS cc_start: 0.7561 (tppt) cc_final: 0.7351 (tppt) REVERT: E 210 LYS cc_start: 0.7573 (mttt) cc_final: 0.7186 (mttt) REVERT: E 280 THR cc_start: 0.5816 (p) cc_final: 0.5476 (m) REVERT: E 311 ASP cc_start: 0.7213 (OUTLIER) cc_final: 0.6942 (m-30) REVERT: E 334 LYS cc_start: 0.7336 (mmmm) cc_final: 0.7089 (mmmm) REVERT: E 362 GLU cc_start: 0.7722 (pm20) cc_final: 0.7442 (pm20) REVERT: E 365 GLN cc_start: 0.7580 (mt0) cc_final: 0.7201 (mt0) REVERT: E 375 GLN cc_start: 0.7716 (tp-100) cc_final: 0.7495 (tp40) REVERT: E 387 LEU cc_start: 0.7239 (mt) cc_final: 0.6922 (mt) REVERT: E 391 GLU cc_start: 0.7657 (mt-10) cc_final: 0.7196 (mt-10) REVERT: E 401 HIS cc_start: 0.7528 (OUTLIER) cc_final: 0.6346 (t70) REVERT: E 402 ARG cc_start: 0.7596 (mmm-85) cc_final: 0.7108 (mtt-85) REVERT: E 405 ARG cc_start: 0.7519 (mpt180) cc_final: 0.7037 (mmt-90) REVERT: E 407 GLN cc_start: 0.7431 (tt0) cc_final: 0.7016 (tp40) REVERT: E 431 LYS cc_start: 0.7733 (ptmm) cc_final: 0.7231 (ptmm) REVERT: E 435 ARG cc_start: 0.7442 (ttp80) cc_final: 0.6590 (ttp80) REVERT: E 438 LYS cc_start: 0.7744 (ttpt) cc_final: 0.6748 (ttpt) REVERT: E 439 GLU cc_start: 0.7614 (mm-30) cc_final: 0.6529 (mm-30) REVERT: E 441 LEU cc_start: 0.8312 (mt) cc_final: 0.7993 (mt) REVERT: E 442 GLU cc_start: 0.7726 (mt-10) cc_final: 0.7168 (mt-10) REVERT: E 445 TYR cc_start: 0.7541 (m-80) cc_final: 0.6722 (m-80) REVERT: E 446 ASP cc_start: 0.7502 (m-30) cc_final: 0.7213 (m-30) REVERT: E 450 GLU cc_start: 0.7794 (pm20) cc_final: 0.7268 (pm20) REVERT: E 461 GLU cc_start: 0.7436 (mt-10) cc_final: 0.7220 (mt-10) REVERT: E 469 MET cc_start: 0.7507 (mmm) cc_final: 0.7053 (mmm) REVERT: F 5 ARG cc_start: 0.6059 (mmt180) cc_final: 0.5519 (mmt180) REVERT: F 8 GLN cc_start: 0.7362 (mt0) cc_final: 0.6883 (mt0) REVERT: F 15 ASP cc_start: 0.6930 (m-30) cc_final: 0.6560 (m-30) REVERT: F 33 GLN cc_start: 0.7399 (mt0) cc_final: 0.7184 (mt0) REVERT: F 37 ARG cc_start: 0.7347 (ttm170) cc_final: 0.7117 (ttm170) REVERT: F 39 GLU cc_start: 0.7528 (mp0) cc_final: 0.7114 (mp0) REVERT: F 74 MET cc_start: 0.6813 (mtt) cc_final: 0.6335 (mtt) REVERT: F 75 GLU cc_start: 0.6888 (tt0) cc_final: 0.5123 (tt0) REVERT: F 89 GLU cc_start: 0.7615 (tp30) cc_final: 0.7337 (tp30) REVERT: F 114 ARG cc_start: 0.7507 (ttp-170) cc_final: 0.7158 (ttp80) REVERT: F 115 ARG cc_start: 0.7417 (mtt90) cc_final: 0.7047 (mtt90) REVERT: F 116 ASP cc_start: 0.7428 (m-30) cc_final: 0.7082 (m-30) REVERT: F 124 LYS cc_start: 0.7162 (mttm) cc_final: 0.6747 (mttm) REVERT: F 127 GLU cc_start: 0.7322 (mt-10) cc_final: 0.6786 (mt-10) REVERT: F 213 MET cc_start: 0.7315 (mtp) cc_final: 0.6787 (mtp) REVERT: F 218 MET cc_start: 0.7541 (mtm) cc_final: 0.7280 (mtp) REVERT: F 220 GLU cc_start: 0.6852 (mm-30) cc_final: 0.6569 (mm-30) REVERT: F 237 GLU cc_start: 0.6494 (tt0) cc_final: 0.6050 (mt-10) REVERT: F 290 GLU cc_start: 0.7354 (mm-30) cc_final: 0.7130 (mm-30) REVERT: F 300 ILE cc_start: 0.7666 (mt) cc_final: 0.7435 (tt) REVERT: F 303 ILE cc_start: 0.7574 (mt) cc_final: 0.7302 (mp) REVERT: F 337 GLU cc_start: 0.7185 (mt-10) cc_final: 0.6977 (mm-30) REVERT: F 345 ASP cc_start: 0.7337 (t70) cc_final: 0.6919 (t70) REVERT: F 389 MET cc_start: 0.7361 (mtm) cc_final: 0.6962 (mtm) REVERT: F 395 GLU cc_start: 0.6739 (pm20) cc_final: 0.6453 (pm20) REVERT: F 438 LYS cc_start: 0.7632 (tttt) cc_final: 0.7101 (tttt) REVERT: F 439 GLU cc_start: 0.7628 (mt-10) cc_final: 0.6916 (mt-10) REVERT: F 442 GLU cc_start: 0.7253 (mt-10) cc_final: 0.6610 (mt-10) REVERT: F 444 LYS cc_start: 0.7950 (tttt) cc_final: 0.7695 (tttt) REVERT: F 445 TYR cc_start: 0.8269 (m-80) cc_final: 0.7692 (m-80) REVERT: F 448 LEU cc_start: 0.8110 (mm) cc_final: 0.7779 (mp) REVERT: F 451 ASP cc_start: 0.7779 (m-30) cc_final: 0.7539 (m-30) REVERT: G 11 LYS cc_start: 0.7292 (tptt) cc_final: 0.6966 (tptt) REVERT: G 28 GLU cc_start: 0.7485 (tt0) cc_final: 0.7167 (tt0) REVERT: G 39 GLU cc_start: 0.8420 (tt0) cc_final: 0.8166 (tp30) REVERT: G 54 GLU cc_start: 0.8777 (mt-10) cc_final: 0.8485 (mt-10) REVERT: G 70 MET cc_start: 0.7886 (mmm) cc_final: 0.7267 (mmm) REVERT: G 85 THR cc_start: 0.7741 (OUTLIER) cc_final: 0.7322 (t) REVERT: G 95 ASN cc_start: 0.7875 (m-40) cc_final: 0.7580 (m110) REVERT: G 105 THR cc_start: 0.7493 (m) cc_final: 0.7241 (t) REVERT: G 115 GLU cc_start: 0.8111 (mm-30) cc_final: 0.7732 (mm-30) REVERT: G 116 TYR cc_start: 0.7547 (p90) cc_final: 0.7262 (p90) REVERT: G 170 GLU cc_start: 0.6859 (tt0) cc_final: 0.6529 (tt0) REVERT: G 173 MET cc_start: 0.6939 (mtm) cc_final: 0.6694 (mtm) REVERT: G 185 GLU cc_start: 0.6544 (mm-30) cc_final: 0.6149 (mm-30) REVERT: G 188 GLU cc_start: 0.5714 (OUTLIER) cc_final: 0.5438 (tt0) REVERT: G 223 TYR cc_start: 0.8095 (t80) cc_final: 0.7748 (t80) REVERT: G 225 GLU cc_start: 0.8554 (mt-10) cc_final: 0.8221 (mt-10) REVERT: G 227 LEU cc_start: 0.7923 (mm) cc_final: 0.7695 (mm) REVERT: G 244 MET cc_start: 0.7255 (ttm) cc_final: 0.7019 (ttp) outliers start: 137 outliers final: 97 residues processed: 1135 average time/residue: 0.4458 time to fit residues: 737.1982 Evaluate side-chains 1180 residues out of total 2558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 1073 time to evaluate : 2.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 60 MET Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 320 GLU Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 491 ILE Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 89 ARG Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 137 MET Chi-restraints excluded: chain B residue 144 GLU Chi-restraints excluded: chain B residue 201 LYS Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 261 ASP Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 327 SER Chi-restraints excluded: chain B residue 333 ASN Chi-restraints excluded: chain B residue 375 MET Chi-restraints excluded: chain B residue 377 LYS Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 452 ASP Chi-restraints excluded: chain C residue 28 VAL Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 262 ASP Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 327 SER Chi-restraints excluded: chain C residue 332 THR Chi-restraints excluded: chain C residue 375 MET Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 450 VAL Chi-restraints excluded: chain C residue 470 HIS Chi-restraints excluded: chain C residue 486 ASP Chi-restraints excluded: chain D residue 2 THR Chi-restraints excluded: chain D residue 7 ILE Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 57 ASP Chi-restraints excluded: chain D residue 112 ASP Chi-restraints excluded: chain D residue 131 GLU Chi-restraints excluded: chain D residue 203 LYS Chi-restraints excluded: chain D residue 207 VAL Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 295 THR Chi-restraints excluded: chain D residue 323 SER Chi-restraints excluded: chain D residue 334 LYS Chi-restraints excluded: chain D residue 344 VAL Chi-restraints excluded: chain D residue 382 ASP Chi-restraints excluded: chain D residue 384 ILE Chi-restraints excluded: chain D residue 423 GLN Chi-restraints excluded: chain D residue 428 VAL Chi-restraints excluded: chain D residue 456 VAL Chi-restraints excluded: chain E residue 67 THR Chi-restraints excluded: chain E residue 68 ASP Chi-restraints excluded: chain E residue 103 ILE Chi-restraints excluded: chain E residue 136 GLU Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 265 SER Chi-restraints excluded: chain E residue 293 THR Chi-restraints excluded: chain E residue 311 ASP Chi-restraints excluded: chain E residue 328 THR Chi-restraints excluded: chain E residue 349 SER Chi-restraints excluded: chain E residue 357 GLU Chi-restraints excluded: chain E residue 384 ILE Chi-restraints excluded: chain E residue 400 VAL Chi-restraints excluded: chain E residue 401 HIS Chi-restraints excluded: chain E residue 421 THR Chi-restraints excluded: chain E residue 456 VAL Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 46 LEU Chi-restraints excluded: chain F residue 84 SER Chi-restraints excluded: chain F residue 98 VAL Chi-restraints excluded: chain F residue 106 GLU Chi-restraints excluded: chain F residue 183 SER Chi-restraints excluded: chain F residue 233 LEU Chi-restraints excluded: chain F residue 267 LEU Chi-restraints excluded: chain F residue 281 LEU Chi-restraints excluded: chain F residue 329 THR Chi-restraints excluded: chain F residue 330 ASN Chi-restraints excluded: chain F residue 351 SER Chi-restraints excluded: chain F residue 378 LYS Chi-restraints excluded: chain F residue 384 ILE Chi-restraints excluded: chain F residue 455 LEU Chi-restraints excluded: chain F residue 462 VAL Chi-restraints excluded: chain G residue 13 ARG Chi-restraints excluded: chain G residue 22 GLN Chi-restraints excluded: chain G residue 23 ILE Chi-restraints excluded: chain G residue 83 VAL Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain G residue 101 LEU Chi-restraints excluded: chain G residue 148 SER Chi-restraints excluded: chain G residue 172 TYR Chi-restraints excluded: chain G residue 186 VAL Chi-restraints excluded: chain G residue 188 GLU Chi-restraints excluded: chain G residue 232 LEU Chi-restraints excluded: chain G residue 281 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 100 optimal weight: 1.9990 chunk 269 optimal weight: 4.9990 chunk 59 optimal weight: 5.9990 chunk 175 optimal weight: 0.8980 chunk 73 optimal weight: 2.9990 chunk 299 optimal weight: 7.9990 chunk 248 optimal weight: 10.0000 chunk 138 optimal weight: 9.9990 chunk 24 optimal weight: 0.6980 chunk 99 optimal weight: 5.9990 chunk 157 optimal weight: 0.8980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 GLN B 333 ASN ** B 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 172 GLN ** C 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 119 HIS ** F 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 40 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6934 moved from start: 0.4201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 24604 Z= 0.206 Angle : 0.548 6.911 33364 Z= 0.288 Chirality : 0.044 0.144 3840 Planarity : 0.005 0.050 4349 Dihedral : 8.120 105.447 3575 Min Nonbonded Distance : 1.830 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 4.42 % Allowed : 25.06 % Favored : 70.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.83 % 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: 0.22 (0.15), residues: 3104 helix: 1.15 (0.15), residues: 1237 sheet: 0.17 (0.22), residues: 546 loop : -0.78 (0.17), residues: 1321 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS F 363 PHE 0.018 0.001 PHE G 45 TYR 0.020 0.001 TYR C 248 ARG 0.006 0.000 ARG E 115 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1203 residues out of total 2558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 1090 time to evaluate : 2.631 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 ARG cc_start: 0.6908 (ptt180) cc_final: 0.6635 (ptt180) REVERT: A 96 GLU cc_start: 0.6276 (mt-10) cc_final: 0.5998 (tt0) REVERT: A 125 GLU cc_start: 0.6504 (OUTLIER) cc_final: 0.6285 (pt0) REVERT: A 140 ARG cc_start: 0.7305 (ttt-90) cc_final: 0.7013 (ttt90) REVERT: A 147 GLN cc_start: 0.7532 (mm-40) cc_final: 0.7321 (mm110) REVERT: A 248 TYR cc_start: 0.7165 (t80) cc_final: 0.6947 (t80) REVERT: A 251 TYR cc_start: 0.7148 (m-80) cc_final: 0.6819 (m-80) REVERT: A 254 LYS cc_start: 0.7341 (mmtm) cc_final: 0.6975 (mmtm) REVERT: A 272 GLU cc_start: 0.6696 (tt0) cc_final: 0.6200 (tt0) REVERT: A 299 GLU cc_start: 0.7740 (mm-30) cc_final: 0.7248 (mm-30) REVERT: A 303 LYS cc_start: 0.7495 (tptp) cc_final: 0.7221 (tptp) REVERT: A 375 MET cc_start: 0.7232 (tpp) cc_final: 0.6561 (tpp) REVERT: A 376 LYS cc_start: 0.6780 (ttmm) cc_final: 0.6451 (ttmm) REVERT: A 421 LYS cc_start: 0.7455 (mttp) cc_final: 0.7221 (mttm) REVERT: A 486 ASP cc_start: 0.8251 (m-30) cc_final: 0.7961 (t0) REVERT: A 489 LYS cc_start: 0.7755 (tttt) cc_final: 0.7471 (tttt) REVERT: B 46 ASN cc_start: 0.7012 (m110) cc_final: 0.6669 (m110) REVERT: B 67 GLU cc_start: 0.6933 (mm-30) cc_final: 0.6538 (mm-30) REVERT: B 95 MET cc_start: 0.6853 (tpt) cc_final: 0.6585 (tpp) REVERT: B 101 GLU cc_start: 0.6805 (mp0) cc_final: 0.6550 (mp0) REVERT: B 113 GLN cc_start: 0.6934 (mm-40) cc_final: 0.6619 (mm-40) REVERT: B 144 GLU cc_start: 0.6907 (OUTLIER) cc_final: 0.5867 (pt0) REVERT: B 177 SER cc_start: 0.6285 (p) cc_final: 0.5788 (m) REVERT: B 200 GLN cc_start: 0.7779 (mm-40) cc_final: 0.7517 (mm-40) REVERT: B 230 GLN cc_start: 0.7264 (mm-40) cc_final: 0.6968 (mt0) REVERT: B 261 ASP cc_start: 0.6217 (OUTLIER) cc_final: 0.6012 (m-30) REVERT: B 265 LYS cc_start: 0.6700 (mttp) cc_final: 0.6434 (mttp) REVERT: B 272 GLU cc_start: 0.6728 (tt0) cc_final: 0.6380 (tt0) REVERT: B 336 SER cc_start: 0.7571 (t) cc_final: 0.7355 (p) REVERT: B 361 LEU cc_start: 0.7904 (mt) cc_final: 0.7522 (mp) REVERT: B 373 LYS cc_start: 0.7470 (ttpp) cc_final: 0.7264 (ttpp) REVERT: B 418 GLU cc_start: 0.7448 (mm-30) cc_final: 0.7213 (mm-30) REVERT: B 442 ARG cc_start: 0.7626 (OUTLIER) cc_final: 0.7019 (mmp80) REVERT: B 449 PRO cc_start: 0.7342 (Cg_exo) cc_final: 0.7094 (Cg_endo) REVERT: B 479 LYS cc_start: 0.7030 (mptt) cc_final: 0.6473 (mptt) REVERT: C 34 VAL cc_start: 0.7849 (t) cc_final: 0.7618 (p) REVERT: C 62 MET cc_start: 0.6594 (ttt) cc_final: 0.6271 (ttp) REVERT: C 68 GLU cc_start: 0.7209 (tt0) cc_final: 0.6869 (mt-10) REVERT: C 80 THR cc_start: 0.7933 (p) cc_final: 0.7696 (m) REVERT: C 127 ARG cc_start: 0.7343 (mtp85) cc_final: 0.6902 (mtp85) REVERT: C 137 MET cc_start: 0.7946 (mmm) cc_final: 0.7726 (mmm) REVERT: C 147 GLN cc_start: 0.7396 (mm-40) cc_final: 0.6792 (mm-40) REVERT: C 165 GLU cc_start: 0.7848 (tp30) cc_final: 0.7602 (tp30) REVERT: C 171 ARG cc_start: 0.7379 (ptm-80) cc_final: 0.7029 (ptm-80) REVERT: C 181 ASP cc_start: 0.7554 (m-30) cc_final: 0.7211 (m-30) REVERT: C 185 ASN cc_start: 0.7843 (t0) cc_final: 0.7536 (t0) REVERT: C 196 VAL cc_start: 0.7703 (t) cc_final: 0.7381 (m) REVERT: C 222 ILE cc_start: 0.7272 (mt) cc_final: 0.6991 (mt) REVERT: C 262 ASP cc_start: 0.7102 (OUTLIER) cc_final: 0.6890 (t0) REVERT: C 272 GLU cc_start: 0.6907 (mt-10) cc_final: 0.6501 (mt-10) REVERT: C 314 THR cc_start: 0.7482 (OUTLIER) cc_final: 0.6974 (p) REVERT: C 349 PHE cc_start: 0.7640 (t80) cc_final: 0.7389 (t80) REVERT: C 354 ARG cc_start: 0.7107 (mtt90) cc_final: 0.6590 (mtt90) REVERT: C 361 LEU cc_start: 0.7652 (mp) cc_final: 0.7369 (mp) REVERT: C 421 LYS cc_start: 0.7146 (mttp) cc_final: 0.6945 (mttm) REVERT: C 451 GLU cc_start: 0.7664 (mp0) cc_final: 0.7205 (mp0) REVERT: C 469 GLN cc_start: 0.7929 (tp40) cc_final: 0.7628 (mm-40) REVERT: C 473 GLU cc_start: 0.8036 (mm-30) cc_final: 0.7746 (mm-30) REVERT: C 496 LYS cc_start: 0.8493 (mttt) cc_final: 0.7964 (mttt) REVERT: D 7 ILE cc_start: 0.7563 (OUTLIER) cc_final: 0.7352 (mm) REVERT: D 10 MET cc_start: 0.6334 (mtm) cc_final: 0.5787 (mtm) REVERT: D 15 ASP cc_start: 0.6959 (m-30) cc_final: 0.6664 (m-30) REVERT: D 17 LYS cc_start: 0.7055 (tttt) cc_final: 0.6729 (tttm) REVERT: D 26 ILE cc_start: 0.8116 (mt) cc_final: 0.7837 (mp) REVERT: D 37 ARG cc_start: 0.6822 (mtm180) cc_final: 0.6286 (mtm180) REVERT: D 41 GLU cc_start: 0.6693 (mt-10) cc_final: 0.5833 (mt-10) REVERT: D 64 MET cc_start: 0.6753 (mmt) cc_final: 0.6433 (mmt) REVERT: D 74 MET cc_start: 0.7505 (mtt) cc_final: 0.7245 (mtt) REVERT: D 75 GLU cc_start: 0.7322 (tt0) cc_final: 0.6852 (tt0) REVERT: D 96 PHE cc_start: 0.7338 (m-80) cc_final: 0.6708 (m-80) REVERT: D 101 GLU cc_start: 0.7163 (mt-10) cc_final: 0.6745 (mt-10) REVERT: D 114 ARG cc_start: 0.7314 (ttt180) cc_final: 0.6876 (ttp80) REVERT: D 116 ASP cc_start: 0.7087 (m-30) cc_final: 0.6471 (m-30) REVERT: D 120 ARG cc_start: 0.7257 (ttt90) cc_final: 0.6799 (ptm160) REVERT: D 133 GLU cc_start: 0.7274 (mt-10) cc_final: 0.6697 (mt-10) REVERT: D 169 GLN cc_start: 0.7337 (mt0) cc_final: 0.6927 (mm-40) REVERT: D 190 ASP cc_start: 0.6821 (m-30) cc_final: 0.5693 (m-30) REVERT: D 197 ASP cc_start: 0.6928 (t0) cc_final: 0.6703 (t0) REVERT: D 213 MET cc_start: 0.7424 (mtm) cc_final: 0.6891 (mtp) REVERT: D 214 VAL cc_start: 0.7516 (t) cc_final: 0.7019 (p) REVERT: D 237 GLU cc_start: 0.7058 (mt-10) cc_final: 0.6558 (mt-10) REVERT: D 241 ASP cc_start: 0.7098 (m-30) cc_final: 0.6802 (m-30) REVERT: D 246 ASP cc_start: 0.7504 (m-30) cc_final: 0.7047 (m-30) REVERT: D 252 ASP cc_start: 0.6429 (t0) cc_final: 0.5948 (t0) REVERT: D 284 GLU cc_start: 0.6052 (mt-10) cc_final: 0.5513 (mt-10) REVERT: D 285 MET cc_start: 0.6280 (ttm) cc_final: 0.5928 (ttm) REVERT: D 326 ASP cc_start: 0.6998 (m-30) cc_final: 0.6322 (m-30) REVERT: D 337 GLU cc_start: 0.7004 (mt-10) cc_final: 0.6786 (mt-10) REVERT: D 352 ARG cc_start: 0.7121 (mtp180) cc_final: 0.6836 (mtp180) REVERT: D 428 VAL cc_start: 0.8329 (OUTLIER) cc_final: 0.7977 (m) REVERT: D 439 GLU cc_start: 0.7386 (mm-30) cc_final: 0.6700 (mm-30) REVERT: D 464 GLU cc_start: 0.7616 (tp30) cc_final: 0.7401 (tp30) REVERT: D 467 LYS cc_start: 0.8152 (tttt) cc_final: 0.7894 (tttp) REVERT: E 1 MET cc_start: 0.3447 (mmt) cc_final: 0.3164 (mmt) REVERT: E 3 ARG cc_start: 0.6712 (mtm-85) cc_final: 0.6329 (mtm-85) REVERT: E 5 ARG cc_start: 0.6413 (ptp-110) cc_final: 0.5991 (ptp-110) REVERT: E 10 MET cc_start: 0.6159 (ptp) cc_final: 0.5851 (ptp) REVERT: E 17 LYS cc_start: 0.7294 (tttt) cc_final: 0.6862 (tttt) REVERT: E 31 LYS cc_start: 0.7573 (mmtt) cc_final: 0.7152 (mmtt) REVERT: E 89 GLU cc_start: 0.7367 (mm-30) cc_final: 0.7019 (mm-30) REVERT: E 91 THR cc_start: 0.7839 (p) cc_final: 0.7397 (t) REVERT: E 101 GLU cc_start: 0.6851 (mt-10) cc_final: 0.6526 (mp0) REVERT: E 104 ASP cc_start: 0.7413 (m-30) cc_final: 0.7067 (m-30) REVERT: E 127 GLU cc_start: 0.6829 (mt-10) cc_final: 0.6467 (mt-10) REVERT: E 134 ILE cc_start: 0.8257 (mt) cc_final: 0.7952 (tt) REVERT: E 149 ILE cc_start: 0.7653 (mt) cc_final: 0.7381 (mm) REVERT: E 170 GLU cc_start: 0.7149 (tp30) cc_final: 0.6706 (tt0) REVERT: E 178 GLU cc_start: 0.7060 (mm-30) cc_final: 0.6444 (mt-10) REVERT: E 203 LYS cc_start: 0.7563 (tppt) cc_final: 0.7358 (tppt) REVERT: E 210 LYS cc_start: 0.7563 (mttt) cc_final: 0.7184 (mttt) REVERT: E 334 LYS cc_start: 0.7340 (mmmm) cc_final: 0.7128 (mmmm) REVERT: E 362 GLU cc_start: 0.7750 (pm20) cc_final: 0.7497 (pm20) REVERT: E 365 GLN cc_start: 0.7542 (mt0) cc_final: 0.7166 (mt0) REVERT: E 375 GLN cc_start: 0.7779 (tp-100) cc_final: 0.7522 (tp40) REVERT: E 391 GLU cc_start: 0.7661 (mt-10) cc_final: 0.7446 (mt-10) REVERT: E 402 ARG cc_start: 0.7581 (mmm-85) cc_final: 0.7149 (mtt-85) REVERT: E 407 GLN cc_start: 0.7488 (tt0) cc_final: 0.7050 (tp40) REVERT: E 431 LYS cc_start: 0.7704 (ptmm) cc_final: 0.7215 (ptmm) REVERT: E 435 ARG cc_start: 0.7439 (ttp80) cc_final: 0.6535 (ttp80) REVERT: E 438 LYS cc_start: 0.7730 (ttpt) cc_final: 0.6712 (ttpt) REVERT: E 439 GLU cc_start: 0.7624 (mm-30) cc_final: 0.6493 (mm-30) REVERT: E 441 LEU cc_start: 0.8310 (mt) cc_final: 0.8000 (mt) REVERT: E 442 GLU cc_start: 0.7682 (mt-10) cc_final: 0.7145 (mt-10) REVERT: E 445 TYR cc_start: 0.7522 (m-80) cc_final: 0.6658 (m-80) REVERT: E 446 ASP cc_start: 0.7536 (m-30) cc_final: 0.7202 (m-30) REVERT: E 450 GLU cc_start: 0.7786 (pm20) cc_final: 0.7270 (pm20) REVERT: E 469 MET cc_start: 0.7524 (mmm) cc_final: 0.7049 (mmm) REVERT: F 5 ARG cc_start: 0.6037 (mmt180) cc_final: 0.5513 (mmt180) REVERT: F 8 GLN cc_start: 0.7314 (mt0) cc_final: 0.6854 (mt0) REVERT: F 15 ASP cc_start: 0.6908 (m-30) cc_final: 0.6565 (m-30) REVERT: F 33 GLN cc_start: 0.7386 (mt0) cc_final: 0.7172 (mt0) REVERT: F 37 ARG cc_start: 0.7351 (ttm170) cc_final: 0.7125 (ttm170) REVERT: F 39 GLU cc_start: 0.7607 (mp0) cc_final: 0.7174 (mp0) REVERT: F 54 LEU cc_start: 0.7792 (OUTLIER) cc_final: 0.7479 (mp) REVERT: F 74 MET cc_start: 0.6793 (mtt) cc_final: 0.6316 (mtt) REVERT: F 75 GLU cc_start: 0.6875 (tt0) cc_final: 0.5144 (tt0) REVERT: F 89 GLU cc_start: 0.7685 (tp30) cc_final: 0.7407 (tp30) REVERT: F 114 ARG cc_start: 0.7523 (ttp-170) cc_final: 0.7278 (ttp80) REVERT: F 115 ARG cc_start: 0.7402 (mtt90) cc_final: 0.7079 (mtt90) REVERT: F 116 ASP cc_start: 0.7419 (m-30) cc_final: 0.7163 (m-30) REVERT: F 124 LYS cc_start: 0.7103 (mttm) cc_final: 0.6717 (mttm) REVERT: F 127 GLU cc_start: 0.7273 (mt-10) cc_final: 0.6778 (mt-10) REVERT: F 213 MET cc_start: 0.7281 (mtp) cc_final: 0.6768 (mtp) REVERT: F 220 GLU cc_start: 0.6814 (mm-30) cc_final: 0.6583 (mm-30) REVERT: F 237 GLU cc_start: 0.6497 (tt0) cc_final: 0.6031 (mt-10) REVERT: F 290 GLU cc_start: 0.7354 (mm-30) cc_final: 0.7135 (mm-30) REVERT: F 300 ILE cc_start: 0.7615 (mt) cc_final: 0.7405 (tt) REVERT: F 303 ILE cc_start: 0.7566 (mt) cc_final: 0.7290 (mp) REVERT: F 337 GLU cc_start: 0.7197 (mt-10) cc_final: 0.6962 (mm-30) REVERT: F 345 ASP cc_start: 0.7346 (t70) cc_final: 0.6928 (t70) REVERT: F 389 MET cc_start: 0.7358 (mtm) cc_final: 0.7114 (mtm) REVERT: F 395 GLU cc_start: 0.6827 (pm20) cc_final: 0.6472 (pm20) REVERT: F 438 LYS cc_start: 0.7609 (tttt) cc_final: 0.7076 (tttt) REVERT: F 439 GLU cc_start: 0.7612 (mt-10) cc_final: 0.6869 (mt-10) REVERT: F 442 GLU cc_start: 0.7253 (mt-10) cc_final: 0.6587 (mt-10) REVERT: F 444 LYS cc_start: 0.7957 (tttt) cc_final: 0.7731 (tttt) REVERT: F 445 TYR cc_start: 0.8319 (m-80) cc_final: 0.7758 (m-80) REVERT: F 451 ASP cc_start: 0.7776 (m-30) cc_final: 0.7516 (m-30) REVERT: G 11 LYS cc_start: 0.7259 (tptt) cc_final: 0.6929 (tptt) REVERT: G 28 GLU cc_start: 0.7484 (tt0) cc_final: 0.7178 (tt0) REVERT: G 54 GLU cc_start: 0.8785 (mt-10) cc_final: 0.8509 (mt-10) REVERT: G 70 MET cc_start: 0.7853 (mmm) cc_final: 0.7206 (mmm) REVERT: G 81 TYR cc_start: 0.7197 (m-80) cc_final: 0.6896 (m-80) REVERT: G 85 THR cc_start: 0.7741 (OUTLIER) cc_final: 0.7352 (t) REVERT: G 95 ASN cc_start: 0.7878 (m-40) cc_final: 0.7537 (m-40) REVERT: G 115 GLU cc_start: 0.8109 (mm-30) cc_final: 0.7738 (mm-30) REVERT: G 116 TYR cc_start: 0.7515 (p90) cc_final: 0.7135 (p90) REVERT: G 173 MET cc_start: 0.6977 (mtm) cc_final: 0.6704 (mtm) REVERT: G 184 GLN cc_start: 0.6923 (mp10) cc_final: 0.6582 (mp10) REVERT: G 185 GLU cc_start: 0.6578 (mm-30) cc_final: 0.6140 (mm-30) REVERT: G 188 GLU cc_start: 0.5706 (OUTLIER) cc_final: 0.5456 (tt0) REVERT: G 223 TYR cc_start: 0.8056 (t80) cc_final: 0.7696 (t80) REVERT: G 225 GLU cc_start: 0.8498 (mt-10) cc_final: 0.8168 (mt-10) REVERT: G 227 LEU cc_start: 0.7916 (mm) cc_final: 0.7693 (mm) REVERT: G 244 MET cc_start: 0.7241 (ttm) cc_final: 0.6918 (ttp) outliers start: 113 outliers final: 87 residues processed: 1130 average time/residue: 0.4308 time to fit residues: 707.1693 Evaluate side-chains 1178 residues out of total 2558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 1080 time to evaluate : 2.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 54 GLU Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 89 ARG Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 144 GLU Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 261 ASP Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 327 SER Chi-restraints excluded: chain B residue 333 ASN Chi-restraints excluded: chain B residue 375 MET Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 442 ARG Chi-restraints excluded: chain B residue 452 ASP Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 262 ASP Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 332 THR Chi-restraints excluded: chain C residue 375 MET Chi-restraints excluded: chain C residue 450 VAL Chi-restraints excluded: chain C residue 470 HIS Chi-restraints excluded: chain C residue 486 ASP Chi-restraints excluded: chain D residue 2 THR Chi-restraints excluded: chain D residue 7 ILE Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 57 ASP Chi-restraints excluded: chain D residue 112 ASP Chi-restraints excluded: chain D residue 131 GLU Chi-restraints excluded: chain D residue 203 LYS Chi-restraints excluded: chain D residue 207 VAL Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 295 THR Chi-restraints excluded: chain D residue 323 SER Chi-restraints excluded: chain D residue 344 VAL Chi-restraints excluded: chain D residue 382 ASP Chi-restraints excluded: chain D residue 384 ILE Chi-restraints excluded: chain D residue 423 GLN Chi-restraints excluded: chain D residue 428 VAL Chi-restraints excluded: chain D residue 456 VAL Chi-restraints excluded: chain E residue 57 ASP Chi-restraints excluded: chain E residue 67 THR Chi-restraints excluded: chain E residue 103 ILE Chi-restraints excluded: chain E residue 136 GLU Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 226 MET Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 265 SER Chi-restraints excluded: chain E residue 349 SER Chi-restraints excluded: chain E residue 357 GLU Chi-restraints excluded: chain E residue 381 GLN Chi-restraints excluded: chain E residue 384 ILE Chi-restraints excluded: chain E residue 400 VAL Chi-restraints excluded: chain E residue 456 VAL Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 46 LEU Chi-restraints excluded: chain F residue 54 LEU Chi-restraints excluded: chain F residue 84 SER Chi-restraints excluded: chain F residue 98 VAL Chi-restraints excluded: chain F residue 106 GLU Chi-restraints excluded: chain F residue 134 ILE Chi-restraints excluded: chain F residue 149 ILE Chi-restraints excluded: chain F residue 170 GLU Chi-restraints excluded: chain F residue 183 SER Chi-restraints excluded: chain F residue 233 LEU Chi-restraints excluded: chain F residue 273 SER Chi-restraints excluded: chain F residue 281 LEU Chi-restraints excluded: chain F residue 329 THR Chi-restraints excluded: chain F residue 330 ASN Chi-restraints excluded: chain F residue 351 SER Chi-restraints excluded: chain F residue 384 ILE Chi-restraints excluded: chain F residue 464 GLU Chi-restraints excluded: chain G residue 13 ARG Chi-restraints excluded: chain G residue 22 GLN Chi-restraints excluded: chain G residue 23 ILE Chi-restraints excluded: chain G residue 83 VAL Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain G residue 101 LEU Chi-restraints excluded: chain G residue 148 SER Chi-restraints excluded: chain G residue 186 VAL Chi-restraints excluded: chain G residue 188 GLU Chi-restraints excluded: chain G residue 232 LEU Chi-restraints excluded: chain G residue 281 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 289 optimal weight: 8.9990 chunk 33 optimal weight: 6.9990 chunk 170 optimal weight: 7.9990 chunk 219 optimal weight: 5.9990 chunk 169 optimal weight: 2.9990 chunk 252 optimal weight: 4.9990 chunk 167 optimal weight: 2.9990 chunk 298 optimal weight: 5.9990 chunk 186 optimal weight: 4.9990 chunk 182 optimal weight: 6.9990 chunk 137 optimal weight: 0.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 GLN A 345 GLN B 333 ASN ** B 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 433 GLN C 172 GLN ** C 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 474 HIS E 119 HIS ** F 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6963 moved from start: 0.4343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 24604 Z= 0.397 Angle : 0.639 7.604 33364 Z= 0.340 Chirality : 0.048 0.178 3840 Planarity : 0.005 0.055 4349 Dihedral : 8.371 93.045 3575 Min Nonbonded Distance : 1.738 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 5.28 % Allowed : 25.33 % Favored : 69.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.15), residues: 3104 helix: 0.82 (0.14), residues: 1239 sheet: -0.07 (0.22), residues: 545 loop : -0.94 (0.17), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS D 173 PHE 0.017 0.002 PHE A 236 TYR 0.022 0.002 TYR E 427 ARG 0.009 0.001 ARG E 115 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1249 residues out of total 2558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 1114 time to evaluate : 2.670 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 ASN cc_start: 0.7952 (m-40) cc_final: 0.7746 (m-40) REVERT: A 93 ARG cc_start: 0.6850 (ptt180) cc_final: 0.6549 (ptt180) REVERT: A 96 GLU cc_start: 0.6452 (mt-10) cc_final: 0.6128 (tt0) REVERT: A 140 ARG cc_start: 0.7331 (ttt-90) cc_final: 0.7053 (ttt90) REVERT: A 144 GLU cc_start: 0.7330 (pt0) cc_final: 0.7089 (pt0) REVERT: A 248 TYR cc_start: 0.7096 (t80) cc_final: 0.6863 (t80) REVERT: A 251 TYR cc_start: 0.7301 (m-80) cc_final: 0.6946 (m-80) REVERT: A 254 LYS cc_start: 0.7375 (mmtm) cc_final: 0.7025 (mmtm) REVERT: A 272 GLU cc_start: 0.6690 (tt0) cc_final: 0.6223 (tt0) REVERT: A 299 GLU cc_start: 0.7748 (mm-30) cc_final: 0.7249 (mm-30) REVERT: A 375 MET cc_start: 0.7233 (tpp) cc_final: 0.6562 (tpp) REVERT: A 376 LYS cc_start: 0.6932 (ttmm) cc_final: 0.6619 (ttmm) REVERT: A 385 ASP cc_start: 0.7267 (OUTLIER) cc_final: 0.6966 (t0) REVERT: A 426 GLN cc_start: 0.7315 (mm-40) cc_final: 0.6947 (mm-40) REVERT: A 478 THR cc_start: 0.7497 (OUTLIER) cc_final: 0.7268 (t) REVERT: A 489 LYS cc_start: 0.7850 (tttt) cc_final: 0.7576 (tttt) REVERT: B 46 ASN cc_start: 0.7028 (m110) cc_final: 0.6699 (m110) REVERT: B 67 GLU cc_start: 0.6874 (mm-30) cc_final: 0.6372 (mm-30) REVERT: B 95 MET cc_start: 0.6834 (tpt) cc_final: 0.6256 (tpt) REVERT: B 101 GLU cc_start: 0.6860 (mp0) cc_final: 0.6552 (mp0) REVERT: B 113 GLN cc_start: 0.7072 (mm-40) cc_final: 0.6764 (mm-40) REVERT: B 137 MET cc_start: 0.7607 (OUTLIER) cc_final: 0.7291 (mtm) REVERT: B 144 GLU cc_start: 0.6921 (OUTLIER) cc_final: 0.5907 (pt0) REVERT: B 200 GLN cc_start: 0.7766 (mm-40) cc_final: 0.7429 (mm-40) REVERT: B 230 GLN cc_start: 0.7254 (mm-40) cc_final: 0.6977 (mt0) REVERT: B 265 LYS cc_start: 0.6727 (mttp) cc_final: 0.6451 (mttp) REVERT: B 272 GLU cc_start: 0.6727 (tt0) cc_final: 0.6398 (tt0) REVERT: B 327 SER cc_start: 0.7639 (OUTLIER) cc_final: 0.7378 (p) REVERT: B 373 LYS cc_start: 0.7529 (ttpp) cc_final: 0.7310 (ttpp) REVERT: B 418 GLU cc_start: 0.7431 (mm-30) cc_final: 0.7166 (mm-30) REVERT: B 442 ARG cc_start: 0.7653 (OUTLIER) cc_final: 0.7254 (mmp80) REVERT: B 449 PRO cc_start: 0.7575 (Cg_exo) cc_final: 0.7369 (Cg_endo) REVERT: C 34 VAL cc_start: 0.7891 (t) cc_final: 0.7639 (p) REVERT: C 62 MET cc_start: 0.6653 (ttt) cc_final: 0.6289 (ttp) REVERT: C 68 GLU cc_start: 0.7234 (tt0) cc_final: 0.6882 (mt-10) REVERT: C 80 THR cc_start: 0.7924 (p) cc_final: 0.7679 (m) REVERT: C 96 GLU cc_start: 0.6711 (mt-10) cc_final: 0.6398 (mt-10) REVERT: C 127 ARG cc_start: 0.7386 (mtp85) cc_final: 0.6933 (mtp85) REVERT: C 137 MET cc_start: 0.7975 (mmm) cc_final: 0.7751 (mmm) REVERT: C 147 GLN cc_start: 0.7420 (mm-40) cc_final: 0.6919 (mm110) REVERT: C 181 ASP cc_start: 0.7510 (m-30) cc_final: 0.7169 (m-30) REVERT: C 185 ASN cc_start: 0.7857 (t0) cc_final: 0.7532 (t0) REVERT: C 196 VAL cc_start: 0.7675 (t) cc_final: 0.7362 (m) REVERT: C 254 LYS cc_start: 0.7740 (mtmm) cc_final: 0.7381 (mtmm) REVERT: C 262 ASP cc_start: 0.7164 (m-30) cc_final: 0.6928 (t0) REVERT: C 272 GLU cc_start: 0.6925 (mt-10) cc_final: 0.6527 (mt-10) REVERT: C 314 THR cc_start: 0.7500 (OUTLIER) cc_final: 0.6974 (p) REVERT: C 354 ARG cc_start: 0.7087 (mtt90) cc_final: 0.6556 (mtt90) REVERT: C 361 LEU cc_start: 0.7644 (mp) cc_final: 0.7341 (mp) REVERT: C 376 LYS cc_start: 0.7532 (ttpt) cc_final: 0.7127 (tppt) REVERT: C 451 GLU cc_start: 0.7608 (mp0) cc_final: 0.7140 (mp0) REVERT: C 469 GLN cc_start: 0.7933 (tp40) cc_final: 0.7588 (mm-40) REVERT: C 473 GLU cc_start: 0.8077 (mm-30) cc_final: 0.7785 (mm-30) REVERT: D 5 ARG cc_start: 0.6155 (mtm-85) cc_final: 0.5913 (mtm-85) REVERT: D 7 ILE cc_start: 0.7588 (OUTLIER) cc_final: 0.7345 (mm) REVERT: D 10 MET cc_start: 0.6479 (mtm) cc_final: 0.5936 (mtm) REVERT: D 15 ASP cc_start: 0.6949 (m-30) cc_final: 0.6647 (m-30) REVERT: D 17 LYS cc_start: 0.7086 (tttt) cc_final: 0.6773 (tttm) REVERT: D 37 ARG cc_start: 0.6813 (mtm180) cc_final: 0.6321 (mtm180) REVERT: D 41 GLU cc_start: 0.6698 (mt-10) cc_final: 0.5892 (mt-10) REVERT: D 64 MET cc_start: 0.6805 (mmt) cc_final: 0.6450 (mmt) REVERT: D 74 MET cc_start: 0.7552 (mtt) cc_final: 0.7331 (mtt) REVERT: D 75 GLU cc_start: 0.7326 (tt0) cc_final: 0.6862 (tt0) REVERT: D 101 GLU cc_start: 0.7195 (mt-10) cc_final: 0.6768 (mt-10) REVERT: D 114 ARG cc_start: 0.7303 (ttt180) cc_final: 0.6878 (ttp80) REVERT: D 116 ASP cc_start: 0.7059 (m-30) cc_final: 0.6430 (m-30) REVERT: D 120 ARG cc_start: 0.7321 (ttt90) cc_final: 0.6921 (ptm160) REVERT: D 169 GLN cc_start: 0.7333 (mt0) cc_final: 0.6924 (mm-40) REVERT: D 190 ASP cc_start: 0.6809 (m-30) cc_final: 0.5551 (m-30) REVERT: D 197 ASP cc_start: 0.6972 (t0) cc_final: 0.6735 (t0) REVERT: D 214 VAL cc_start: 0.7526 (t) cc_final: 0.7029 (p) REVERT: D 237 GLU cc_start: 0.7123 (mt-10) cc_final: 0.6640 (mt-10) REVERT: D 241 ASP cc_start: 0.7161 (m-30) cc_final: 0.6874 (m-30) REVERT: D 246 ASP cc_start: 0.7532 (m-30) cc_final: 0.7087 (m-30) REVERT: D 252 ASP cc_start: 0.6455 (t0) cc_final: 0.5926 (t0) REVERT: D 270 ARG cc_start: 0.7490 (mtt180) cc_final: 0.6843 (mtt-85) REVERT: D 273 SER cc_start: 0.7040 (t) cc_final: 0.6380 (p) REVERT: D 284 GLU cc_start: 0.6098 (mt-10) cc_final: 0.5527 (mt-10) REVERT: D 285 MET cc_start: 0.6374 (ttm) cc_final: 0.6032 (ttm) REVERT: D 352 ARG cc_start: 0.7129 (mtp180) cc_final: 0.6816 (mtp180) REVERT: D 426 SER cc_start: 0.8473 (m) cc_final: 0.8181 (p) REVERT: D 428 VAL cc_start: 0.8330 (OUTLIER) cc_final: 0.7973 (m) REVERT: D 439 GLU cc_start: 0.7413 (mm-30) cc_final: 0.6699 (mm-30) REVERT: D 467 LYS cc_start: 0.8167 (tttt) cc_final: 0.7901 (tttp) REVERT: E 1 MET cc_start: 0.3635 (mmt) cc_final: 0.3352 (mmt) REVERT: E 3 ARG cc_start: 0.6724 (mtm-85) cc_final: 0.6290 (mtm-85) REVERT: E 5 ARG cc_start: 0.6433 (ptp-110) cc_final: 0.6009 (ptp-110) REVERT: E 10 MET cc_start: 0.6410 (ptp) cc_final: 0.6062 (ptp) REVERT: E 17 LYS cc_start: 0.7319 (tttt) cc_final: 0.6816 (ttmm) REVERT: E 31 LYS cc_start: 0.7574 (mmtt) cc_final: 0.7146 (mmtt) REVERT: E 43 ASP cc_start: 0.6720 (m-30) cc_final: 0.6259 (m-30) REVERT: E 71 ILE cc_start: 0.7578 (mt) cc_final: 0.7192 (mp) REVERT: E 89 GLU cc_start: 0.7297 (mm-30) cc_final: 0.6955 (mm-30) REVERT: E 91 THR cc_start: 0.7835 (p) cc_final: 0.7386 (t) REVERT: E 101 GLU cc_start: 0.6945 (mt-10) cc_final: 0.6576 (mp0) REVERT: E 104 ASP cc_start: 0.7439 (m-30) cc_final: 0.7153 (m-30) REVERT: E 127 GLU cc_start: 0.6849 (mt-10) cc_final: 0.6491 (mt-10) REVERT: E 134 ILE cc_start: 0.8332 (mt) cc_final: 0.8003 (tt) REVERT: E 170 GLU cc_start: 0.7133 (tp30) cc_final: 0.6694 (tt0) REVERT: E 178 GLU cc_start: 0.7110 (mm-30) cc_final: 0.6617 (mt-10) REVERT: E 210 LYS cc_start: 0.7553 (mttt) cc_final: 0.7191 (mttt) REVERT: E 270 ARG cc_start: 0.7037 (mtt90) cc_final: 0.6780 (mtt180) REVERT: E 285 MET cc_start: 0.6591 (tpp) cc_final: 0.6321 (tpp) REVERT: E 311 ASP cc_start: 0.7190 (OUTLIER) cc_final: 0.6943 (m-30) REVERT: E 334 LYS cc_start: 0.7363 (mmmm) cc_final: 0.7108 (mmmm) REVERT: E 362 GLU cc_start: 0.7755 (pm20) cc_final: 0.7502 (pm20) REVERT: E 365 GLN cc_start: 0.7601 (mt0) cc_final: 0.7187 (mt0) REVERT: E 375 GLN cc_start: 0.7800 (tp-100) cc_final: 0.7544 (tp40) REVERT: E 401 HIS cc_start: 0.7768 (OUTLIER) cc_final: 0.7123 (t-90) REVERT: E 402 ARG cc_start: 0.7599 (mmm-85) cc_final: 0.7147 (mtt-85) REVERT: E 405 ARG cc_start: 0.7536 (OUTLIER) cc_final: 0.7297 (mmt-90) REVERT: E 407 GLN cc_start: 0.7480 (tt0) cc_final: 0.7026 (tp40) REVERT: E 431 LYS cc_start: 0.7757 (ptmm) cc_final: 0.7273 (ptmm) REVERT: E 435 ARG cc_start: 0.7486 (ttp80) cc_final: 0.6552 (ttp80) REVERT: E 438 LYS cc_start: 0.7759 (ttpt) cc_final: 0.6698 (ttpt) REVERT: E 439 GLU cc_start: 0.7622 (mm-30) cc_final: 0.6503 (mm-30) REVERT: E 441 LEU cc_start: 0.8300 (mt) cc_final: 0.7975 (mt) REVERT: E 442 GLU cc_start: 0.7729 (mt-10) cc_final: 0.7013 (mt-10) REVERT: E 445 TYR cc_start: 0.7529 (m-80) cc_final: 0.6673 (m-80) REVERT: E 450 GLU cc_start: 0.7805 (pm20) cc_final: 0.7289 (pm20) REVERT: E 469 MET cc_start: 0.7607 (mmm) cc_final: 0.7139 (mmm) REVERT: F 5 ARG cc_start: 0.6070 (mmt180) cc_final: 0.5510 (mmt180) REVERT: F 8 GLN cc_start: 0.7402 (mt0) cc_final: 0.7005 (mt0) REVERT: F 15 ASP cc_start: 0.6931 (m-30) cc_final: 0.6575 (m-30) REVERT: F 33 GLN cc_start: 0.7423 (mt0) cc_final: 0.7208 (mt0) REVERT: F 37 ARG cc_start: 0.7359 (ttm170) cc_final: 0.7142 (ttm170) REVERT: F 39 GLU cc_start: 0.7576 (mp0) cc_final: 0.7163 (mp0) REVERT: F 74 MET cc_start: 0.6836 (mtt) cc_final: 0.6347 (mtt) REVERT: F 75 GLU cc_start: 0.6916 (tt0) cc_final: 0.5214 (tt0) REVERT: F 89 GLU cc_start: 0.7666 (tp30) cc_final: 0.7387 (tp30) REVERT: F 114 ARG cc_start: 0.7550 (ttp-170) cc_final: 0.7303 (ttp80) REVERT: F 115 ARG cc_start: 0.7492 (mtt90) cc_final: 0.7101 (mtt90) REVERT: F 116 ASP cc_start: 0.7444 (m-30) cc_final: 0.7201 (m-30) REVERT: F 124 LYS cc_start: 0.7162 (mttm) cc_final: 0.6736 (mttm) REVERT: F 127 GLU cc_start: 0.7307 (mt-10) cc_final: 0.6776 (mt-10) REVERT: F 213 MET cc_start: 0.7323 (mtp) cc_final: 0.6799 (mtp) REVERT: F 218 MET cc_start: 0.7567 (mtm) cc_final: 0.7344 (mtp) REVERT: F 220 GLU cc_start: 0.6840 (mm-30) cc_final: 0.6595 (mm-30) REVERT: F 237 GLU cc_start: 0.6502 (tt0) cc_final: 0.6046 (mt-10) REVERT: F 290 GLU cc_start: 0.7398 (mm-30) cc_final: 0.7172 (mm-30) REVERT: F 300 ILE cc_start: 0.7653 (mt) cc_final: 0.7448 (tt) REVERT: F 303 ILE cc_start: 0.7570 (mt) cc_final: 0.7289 (mp) REVERT: F 345 ASP cc_start: 0.7376 (t70) cc_final: 0.6943 (t70) REVERT: F 389 MET cc_start: 0.7355 (mtm) cc_final: 0.7022 (mtm) REVERT: F 397 LYS cc_start: 0.7172 (tttm) cc_final: 0.6864 (tttm) REVERT: F 439 GLU cc_start: 0.7653 (mt-10) cc_final: 0.6922 (mt-10) REVERT: F 442 GLU cc_start: 0.7272 (mt-10) cc_final: 0.6623 (mt-10) REVERT: F 444 LYS cc_start: 0.7953 (tttt) cc_final: 0.7704 (tttt) REVERT: F 445 TYR cc_start: 0.8271 (m-80) cc_final: 0.7689 (m-80) REVERT: F 451 ASP cc_start: 0.7786 (m-30) cc_final: 0.7530 (m-30) REVERT: G 11 LYS cc_start: 0.7299 (tptt) cc_final: 0.6671 (tptt) REVERT: G 15 ASN cc_start: 0.7397 (m-40) cc_final: 0.7071 (m-40) REVERT: G 28 GLU cc_start: 0.7485 (tt0) cc_final: 0.7174 (tt0) REVERT: G 33 SER cc_start: 0.7806 (t) cc_final: 0.7446 (p) REVERT: G 54 GLU cc_start: 0.8812 (mt-10) cc_final: 0.8559 (mt-10) REVERT: G 70 MET cc_start: 0.7836 (mmm) cc_final: 0.7193 (mmm) REVERT: G 85 THR cc_start: 0.7811 (OUTLIER) cc_final: 0.7367 (t) REVERT: G 95 ASN cc_start: 0.7887 (m-40) cc_final: 0.7599 (m110) REVERT: G 105 THR cc_start: 0.7490 (m) cc_final: 0.7263 (t) REVERT: G 115 GLU cc_start: 0.8106 (mm-30) cc_final: 0.7733 (mm-30) REVERT: G 116 TYR cc_start: 0.7564 (p90) cc_final: 0.7308 (p90) REVERT: G 173 MET cc_start: 0.6934 (mtm) cc_final: 0.6668 (mtm) REVERT: G 184 GLN cc_start: 0.6883 (mp10) cc_final: 0.6588 (mp10) REVERT: G 185 GLU cc_start: 0.6594 (mm-30) cc_final: 0.6184 (mm-30) REVERT: G 188 GLU cc_start: 0.5630 (OUTLIER) cc_final: 0.5377 (tt0) REVERT: G 223 TYR cc_start: 0.8136 (t80) cc_final: 0.7757 (t80) REVERT: G 225 GLU cc_start: 0.8575 (mt-10) cc_final: 0.8257 (mt-10) REVERT: G 227 LEU cc_start: 0.7922 (mm) cc_final: 0.7700 (mm) REVERT: G 244 MET cc_start: 0.7242 (ttm) cc_final: 0.6977 (ttp) outliers start: 135 outliers final: 95 residues processed: 1171 average time/residue: 0.4292 time to fit residues: 728.5511 Evaluate side-chains 1213 residues out of total 2558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 1104 time to evaluate : 2.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 54 GLU Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 373 LYS Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 385 ASP Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 491 ILE Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 137 MET Chi-restraints excluded: chain B residue 144 GLU Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 201 LYS Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 261 ASP Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 327 SER Chi-restraints excluded: chain B residue 333 ASN Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 442 ARG Chi-restraints excluded: chain B residue 452 ASP Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 327 SER Chi-restraints excluded: chain C residue 332 THR Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 450 VAL Chi-restraints excluded: chain C residue 470 HIS Chi-restraints excluded: chain D residue 2 THR Chi-restraints excluded: chain D residue 7 ILE Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 49 GLU Chi-restraints excluded: chain D residue 57 ASP Chi-restraints excluded: chain D residue 112 ASP Chi-restraints excluded: chain D residue 131 GLU Chi-restraints excluded: chain D residue 203 LYS Chi-restraints excluded: chain D residue 207 VAL Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 265 SER Chi-restraints excluded: chain D residue 295 THR Chi-restraints excluded: chain D residue 299 SER Chi-restraints excluded: chain D residue 323 SER Chi-restraints excluded: chain D residue 344 VAL Chi-restraints excluded: chain D residue 382 ASP Chi-restraints excluded: chain D residue 384 ILE Chi-restraints excluded: chain D residue 423 GLN Chi-restraints excluded: chain D residue 428 VAL Chi-restraints excluded: chain D residue 456 VAL Chi-restraints excluded: chain E residue 57 ASP Chi-restraints excluded: chain E residue 68 ASP Chi-restraints excluded: chain E residue 103 ILE Chi-restraints excluded: chain E residue 136 GLU Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 265 SER Chi-restraints excluded: chain E residue 293 THR Chi-restraints excluded: chain E residue 311 ASP Chi-restraints excluded: chain E residue 349 SER Chi-restraints excluded: chain E residue 357 GLU Chi-restraints excluded: chain E residue 400 VAL Chi-restraints excluded: chain E residue 401 HIS Chi-restraints excluded: chain E residue 405 ARG Chi-restraints excluded: chain E residue 456 VAL Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 46 LEU Chi-restraints excluded: chain F residue 84 SER Chi-restraints excluded: chain F residue 98 VAL Chi-restraints excluded: chain F residue 106 GLU Chi-restraints excluded: chain F residue 134 ILE Chi-restraints excluded: chain F residue 149 ILE Chi-restraints excluded: chain F residue 168 ILE Chi-restraints excluded: chain F residue 183 SER Chi-restraints excluded: chain F residue 233 LEU Chi-restraints excluded: chain F residue 258 THR Chi-restraints excluded: chain F residue 265 SER Chi-restraints excluded: chain F residue 273 SER Chi-restraints excluded: chain F residue 281 LEU Chi-restraints excluded: chain F residue 311 ASP Chi-restraints excluded: chain F residue 329 THR Chi-restraints excluded: chain F residue 330 ASN Chi-restraints excluded: chain F residue 351 SER Chi-restraints excluded: chain F residue 384 ILE Chi-restraints excluded: chain F residue 455 LEU Chi-restraints excluded: chain F residue 462 VAL Chi-restraints excluded: chain G residue 13 ARG Chi-restraints excluded: chain G residue 22 GLN Chi-restraints excluded: chain G residue 83 VAL Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain G residue 101 LEU Chi-restraints excluded: chain G residue 148 SER Chi-restraints excluded: chain G residue 154 GLU Chi-restraints excluded: chain G residue 172 TYR Chi-restraints excluded: chain G residue 186 VAL Chi-restraints excluded: chain G residue 188 GLU Chi-restraints excluded: chain G residue 232 LEU Chi-restraints excluded: chain G residue 281 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 184 optimal weight: 0.9980 chunk 119 optimal weight: 0.7980 chunk 178 optimal weight: 5.9990 chunk 90 optimal weight: 6.9990 chunk 58 optimal weight: 4.9990 chunk 57 optimal weight: 5.9990 chunk 189 optimal weight: 1.9990 chunk 203 optimal weight: 2.9990 chunk 147 optimal weight: 0.8980 chunk 27 optimal weight: 0.9980 chunk 234 optimal weight: 7.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 GLN A 345 GLN B 333 ASN ** B 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 433 GLN C 172 GLN ** C 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 447 HIS ** F 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 36 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6934 moved from start: 0.4494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 24604 Z= 0.181 Angle : 0.547 7.682 33364 Z= 0.285 Chirality : 0.043 0.159 3840 Planarity : 0.005 0.055 4349 Dihedral : 7.981 89.387 3575 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 4.14 % Allowed : 26.58 % Favored : 69.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.15), residues: 3104 helix: 1.13 (0.15), residues: 1241 sheet: 0.14 (0.22), residues: 544 loop : -0.78 (0.17), residues: 1319 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS D 447 PHE 0.020 0.001 PHE C 494 TYR 0.021 0.001 TYR C 248 ARG 0.008 0.000 ARG D 193 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1186 residues out of total 2558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 1080 time to evaluate : 2.711 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 GLU cc_start: 0.6391 (mt-10) cc_final: 0.6087 (tt0) REVERT: A 140 ARG cc_start: 0.7286 (ttt-90) cc_final: 0.6988 (ttt90) REVERT: A 251 TYR cc_start: 0.7182 (m-80) cc_final: 0.6882 (m-80) REVERT: A 254 LYS cc_start: 0.7379 (mmtm) cc_final: 0.6988 (mmtm) REVERT: A 272 GLU cc_start: 0.6711 (tt0) cc_final: 0.6208 (tt0) REVERT: A 296 ARG cc_start: 0.7205 (mtm-85) cc_final: 0.6876 (mtm-85) REVERT: A 299 GLU cc_start: 0.7714 (mm-30) cc_final: 0.7210 (mm-30) REVERT: A 375 MET cc_start: 0.7209 (tpp) cc_final: 0.6566 (tpp) REVERT: A 376 LYS cc_start: 0.6870 (ttmm) cc_final: 0.6517 (mtmm) REVERT: A 385 ASP cc_start: 0.7278 (OUTLIER) cc_final: 0.6987 (t0) REVERT: A 426 GLN cc_start: 0.7349 (mm-40) cc_final: 0.7042 (mm-40) REVERT: A 478 THR cc_start: 0.7421 (t) cc_final: 0.7198 (t) REVERT: A 489 LYS cc_start: 0.7829 (tttt) cc_final: 0.7558 (tttt) REVERT: A 494 PHE cc_start: 0.7445 (t80) cc_final: 0.7199 (t80) REVERT: B 46 ASN cc_start: 0.6983 (m110) cc_final: 0.6681 (m110) REVERT: B 67 GLU cc_start: 0.6902 (mm-30) cc_final: 0.6443 (mm-30) REVERT: B 95 MET cc_start: 0.6805 (tpt) cc_final: 0.6422 (mmm) REVERT: B 101 GLU cc_start: 0.6877 (mp0) cc_final: 0.6584 (mp0) REVERT: B 103 LEU cc_start: 0.7541 (tp) cc_final: 0.7109 (tp) REVERT: B 113 GLN cc_start: 0.7092 (mm-40) cc_final: 0.6775 (mm-40) REVERT: B 144 GLU cc_start: 0.6972 (pt0) cc_final: 0.5932 (pt0) REVERT: B 200 GLN cc_start: 0.7773 (mm-40) cc_final: 0.7383 (mm-40) REVERT: B 230 GLN cc_start: 0.7236 (mm-40) cc_final: 0.6955 (mt0) REVERT: B 261 ASP cc_start: 0.6155 (OUTLIER) cc_final: 0.5935 (m-30) REVERT: B 265 LYS cc_start: 0.6722 (mttp) cc_final: 0.6372 (mttp) REVERT: B 272 GLU cc_start: 0.6725 (tt0) cc_final: 0.6390 (tt0) REVERT: B 442 ARG cc_start: 0.7609 (OUTLIER) cc_final: 0.7216 (mmt-90) REVERT: B 449 PRO cc_start: 0.7482 (Cg_exo) cc_final: 0.7259 (Cg_endo) REVERT: B 479 LYS cc_start: 0.7074 (mptt) cc_final: 0.6521 (mptt) REVERT: C 34 VAL cc_start: 0.7841 (t) cc_final: 0.7627 (p) REVERT: C 62 MET cc_start: 0.6587 (ttt) cc_final: 0.6257 (ttp) REVERT: C 68 GLU cc_start: 0.7208 (tt0) cc_final: 0.6904 (mt-10) REVERT: C 80 THR cc_start: 0.7912 (p) cc_final: 0.7667 (m) REVERT: C 96 GLU cc_start: 0.6713 (mt-10) cc_final: 0.6392 (mt-10) REVERT: C 127 ARG cc_start: 0.7359 (mtp85) cc_final: 0.6905 (mtp85) REVERT: C 137 MET cc_start: 0.7941 (mmm) cc_final: 0.7714 (mmm) REVERT: C 147 GLN cc_start: 0.7394 (mm-40) cc_final: 0.6921 (mm110) REVERT: C 171 ARG cc_start: 0.7384 (ptm-80) cc_final: 0.7038 (ptm-80) REVERT: C 181 ASP cc_start: 0.7522 (m-30) cc_final: 0.7183 (m-30) REVERT: C 185 ASN cc_start: 0.7816 (t0) cc_final: 0.7510 (t0) REVERT: C 196 VAL cc_start: 0.7668 (t) cc_final: 0.7347 (m) REVERT: C 222 ILE cc_start: 0.7264 (mt) cc_final: 0.6991 (mt) REVERT: C 254 LYS cc_start: 0.7539 (mtmm) cc_final: 0.7193 (mtmm) REVERT: C 262 ASP cc_start: 0.7123 (OUTLIER) cc_final: 0.6914 (t0) REVERT: C 272 GLU cc_start: 0.6893 (mt-10) cc_final: 0.6488 (mt-10) REVERT: C 314 THR cc_start: 0.7473 (OUTLIER) cc_final: 0.6998 (p) REVERT: C 354 ARG cc_start: 0.7087 (mtt90) cc_final: 0.6613 (mtt90) REVERT: C 361 LEU cc_start: 0.7613 (mp) cc_final: 0.7301 (mp) REVERT: C 376 LYS cc_start: 0.7488 (ttpt) cc_final: 0.7235 (ttpt) REVERT: C 451 GLU cc_start: 0.7615 (mp0) cc_final: 0.7144 (mp0) REVERT: C 469 GLN cc_start: 0.7960 (tp40) cc_final: 0.7611 (mm-40) REVERT: C 473 GLU cc_start: 0.8021 (mm-30) cc_final: 0.7737 (mm-30) REVERT: D 7 ILE cc_start: 0.7596 (OUTLIER) cc_final: 0.7374 (mm) REVERT: D 10 MET cc_start: 0.6351 (mtm) cc_final: 0.5821 (mtm) REVERT: D 15 ASP cc_start: 0.6950 (m-30) cc_final: 0.6666 (m-30) REVERT: D 17 LYS cc_start: 0.7044 (tttt) cc_final: 0.6666 (tttm) REVERT: D 26 ILE cc_start: 0.8175 (mt) cc_final: 0.7872 (mp) REVERT: D 37 ARG cc_start: 0.6773 (mtm180) cc_final: 0.6241 (mtm180) REVERT: D 41 GLU cc_start: 0.6582 (mt-10) cc_final: 0.5711 (mt-10) REVERT: D 64 MET cc_start: 0.6738 (mmt) cc_final: 0.6412 (mmt) REVERT: D 74 MET cc_start: 0.7498 (mtt) cc_final: 0.7233 (mtt) REVERT: D 75 GLU cc_start: 0.7295 (tt0) cc_final: 0.6831 (tt0) REVERT: D 96 PHE cc_start: 0.7328 (m-80) cc_final: 0.6650 (m-80) REVERT: D 101 GLU cc_start: 0.7157 (mt-10) cc_final: 0.6728 (mt-10) REVERT: D 114 ARG cc_start: 0.7320 (ttt180) cc_final: 0.6798 (ttp80) REVERT: D 116 ASP cc_start: 0.7071 (m-30) cc_final: 0.6392 (m-30) REVERT: D 120 ARG cc_start: 0.7243 (ttt90) cc_final: 0.6832 (ptm160) REVERT: D 169 GLN cc_start: 0.7322 (mt0) cc_final: 0.6924 (mm-40) REVERT: D 190 ASP cc_start: 0.6819 (m-30) cc_final: 0.5691 (m-30) REVERT: D 197 ASP cc_start: 0.6941 (t0) cc_final: 0.6711 (t0) REVERT: D 213 MET cc_start: 0.7412 (mtm) cc_final: 0.6862 (mtp) REVERT: D 214 VAL cc_start: 0.7480 (t) cc_final: 0.6977 (p) REVERT: D 237 GLU cc_start: 0.7062 (mt-10) cc_final: 0.6554 (mt-10) REVERT: D 241 ASP cc_start: 0.7055 (m-30) cc_final: 0.6760 (m-30) REVERT: D 246 ASP cc_start: 0.7478 (m-30) cc_final: 0.7050 (m-30) REVERT: D 252 ASP cc_start: 0.6450 (t0) cc_final: 0.5965 (t0) REVERT: D 270 ARG cc_start: 0.7499 (mtt180) cc_final: 0.6852 (mtt-85) REVERT: D 284 GLU cc_start: 0.6036 (mt-10) cc_final: 0.5429 (mt-10) REVERT: D 285 MET cc_start: 0.6246 (ttm) cc_final: 0.5892 (ttm) REVERT: D 352 ARG cc_start: 0.7143 (mtp180) cc_final: 0.6793 (mtp180) REVERT: D 428 VAL cc_start: 0.8404 (OUTLIER) cc_final: 0.8094 (m) REVERT: D 439 GLU cc_start: 0.7423 (mm-30) cc_final: 0.6678 (mm-30) REVERT: E 1 MET cc_start: 0.3617 (mmt) cc_final: 0.3336 (mmt) REVERT: E 3 ARG cc_start: 0.6704 (mtm-85) cc_final: 0.6272 (mtm-85) REVERT: E 5 ARG cc_start: 0.6453 (ptp-110) cc_final: 0.5959 (ptp-110) REVERT: E 10 MET cc_start: 0.6153 (ptp) cc_final: 0.5864 (ptp) REVERT: E 17 LYS cc_start: 0.7254 (tttt) cc_final: 0.6830 (ttmm) REVERT: E 31 LYS cc_start: 0.7579 (mmtt) cc_final: 0.7134 (mmtt) REVERT: E 89 GLU cc_start: 0.7333 (mm-30) cc_final: 0.7008 (mm-30) REVERT: E 91 THR cc_start: 0.7823 (p) cc_final: 0.7397 (t) REVERT: E 101 GLU cc_start: 0.6904 (mt-10) cc_final: 0.6528 (mp0) REVERT: E 127 GLU cc_start: 0.6822 (mt-10) cc_final: 0.6464 (mt-10) REVERT: E 134 ILE cc_start: 0.8322 (mt) cc_final: 0.7980 (tt) REVERT: E 149 ILE cc_start: 0.7676 (mt) cc_final: 0.7380 (mm) REVERT: E 170 GLU cc_start: 0.7227 (tp30) cc_final: 0.6770 (tt0) REVERT: E 178 GLU cc_start: 0.7095 (mm-30) cc_final: 0.6565 (mt-10) REVERT: E 210 LYS cc_start: 0.7598 (mttt) cc_final: 0.7239 (mttt) REVERT: E 270 ARG cc_start: 0.7001 (mtt90) cc_final: 0.6796 (mtt180) REVERT: E 285 MET cc_start: 0.6638 (tpp) cc_final: 0.6363 (tpp) REVERT: E 334 LYS cc_start: 0.7338 (mmmm) cc_final: 0.7086 (mmmm) REVERT: E 362 GLU cc_start: 0.7770 (pm20) cc_final: 0.7514 (pm20) REVERT: E 365 GLN cc_start: 0.7525 (mt0) cc_final: 0.7132 (mt0) REVERT: E 375 GLN cc_start: 0.7766 (tp-100) cc_final: 0.7494 (tp40) REVERT: E 402 ARG cc_start: 0.7558 (mmm-85) cc_final: 0.7163 (mtt-85) REVERT: E 407 GLN cc_start: 0.7500 (tt0) cc_final: 0.7031 (tp40) REVERT: E 435 ARG cc_start: 0.7462 (ttp80) cc_final: 0.6504 (ttp80) REVERT: E 438 LYS cc_start: 0.7735 (ttpt) cc_final: 0.6660 (ttpt) REVERT: E 439 GLU cc_start: 0.7577 (mm-30) cc_final: 0.6459 (mm-30) REVERT: E 441 LEU cc_start: 0.8224 (mt) cc_final: 0.7997 (mt) REVERT: E 442 GLU cc_start: 0.7654 (mt-10) cc_final: 0.7040 (mt-10) REVERT: E 445 TYR cc_start: 0.7476 (m-80) cc_final: 0.6619 (m-80) REVERT: E 450 GLU cc_start: 0.7799 (pm20) cc_final: 0.7266 (pm20) REVERT: E 469 MET cc_start: 0.7562 (mmm) cc_final: 0.7084 (mmm) REVERT: F 5 ARG cc_start: 0.6061 (mmt180) cc_final: 0.5520 (mmt180) REVERT: F 8 GLN cc_start: 0.7303 (mt0) cc_final: 0.6869 (mt0) REVERT: F 15 ASP cc_start: 0.6901 (m-30) cc_final: 0.6539 (m-30) REVERT: F 37 ARG cc_start: 0.7352 (ttm170) cc_final: 0.7140 (ttm170) REVERT: F 39 GLU cc_start: 0.7589 (mp0) cc_final: 0.7180 (mp0) REVERT: F 54 LEU cc_start: 0.7777 (mt) cc_final: 0.7463 (mp) REVERT: F 74 MET cc_start: 0.6771 (mtt) cc_final: 0.6300 (mtt) REVERT: F 75 GLU cc_start: 0.6914 (tt0) cc_final: 0.5214 (tt0) REVERT: F 89 GLU cc_start: 0.7719 (tp30) cc_final: 0.7432 (tp30) REVERT: F 114 ARG cc_start: 0.7562 (ttp-170) cc_final: 0.7119 (ttp80) REVERT: F 115 ARG cc_start: 0.7432 (mtt90) cc_final: 0.7087 (mtt90) REVERT: F 116 ASP cc_start: 0.7371 (m-30) cc_final: 0.6922 (m-30) REVERT: F 120 ARG cc_start: 0.7104 (ptm-80) cc_final: 0.6810 (tmm-80) REVERT: F 124 LYS cc_start: 0.7027 (mttm) cc_final: 0.6666 (mttm) REVERT: F 127 GLU cc_start: 0.7202 (mt-10) cc_final: 0.6670 (mt-10) REVERT: F 213 MET cc_start: 0.7251 (mtp) cc_final: 0.6761 (mtp) REVERT: F 218 MET cc_start: 0.7447 (mtm) cc_final: 0.7181 (mtp) REVERT: F 220 GLU cc_start: 0.6839 (mm-30) cc_final: 0.6599 (mm-30) REVERT: F 237 GLU cc_start: 0.6489 (tt0) cc_final: 0.5918 (mt-10) REVERT: F 290 GLU cc_start: 0.7371 (mm-30) cc_final: 0.7152 (mm-30) REVERT: F 303 ILE cc_start: 0.7591 (mt) cc_final: 0.7305 (mp) REVERT: F 337 GLU cc_start: 0.7179 (mm-30) cc_final: 0.6939 (mm-30) REVERT: F 345 ASP cc_start: 0.7373 (t70) cc_final: 0.6929 (t70) REVERT: F 389 MET cc_start: 0.7352 (mtm) cc_final: 0.6987 (mtm) REVERT: F 439 GLU cc_start: 0.7592 (mt-10) cc_final: 0.6894 (mt-10) REVERT: F 442 GLU cc_start: 0.7251 (mt-10) cc_final: 0.6590 (mt-10) REVERT: F 444 LYS cc_start: 0.7964 (tttt) cc_final: 0.7746 (tttt) REVERT: F 445 TYR cc_start: 0.8318 (m-80) cc_final: 0.7757 (m-80) REVERT: F 451 ASP cc_start: 0.7755 (m-30) cc_final: 0.7512 (m-30) REVERT: G 28 GLU cc_start: 0.7456 (tt0) cc_final: 0.7154 (tt0) REVERT: G 33 SER cc_start: 0.7677 (t) cc_final: 0.7331 (p) REVERT: G 54 GLU cc_start: 0.8795 (mt-10) cc_final: 0.8555 (mt-10) REVERT: G 70 MET cc_start: 0.7814 (mmm) cc_final: 0.7147 (mmm) REVERT: G 81 TYR cc_start: 0.7151 (m-80) cc_final: 0.6839 (m-80) REVERT: G 85 THR cc_start: 0.7788 (OUTLIER) cc_final: 0.7388 (t) REVERT: G 95 ASN cc_start: 0.7814 (m-40) cc_final: 0.7479 (m-40) REVERT: G 115 GLU cc_start: 0.8122 (mm-30) cc_final: 0.7777 (mm-30) REVERT: G 116 TYR cc_start: 0.7517 (p90) cc_final: 0.7156 (p90) REVERT: G 173 MET cc_start: 0.6975 (mtm) cc_final: 0.6660 (mtm) REVERT: G 184 GLN cc_start: 0.6939 (mp10) cc_final: 0.6594 (mp10) REVERT: G 185 GLU cc_start: 0.6594 (mm-30) cc_final: 0.6121 (mm-30) REVERT: G 188 GLU cc_start: 0.5662 (OUTLIER) cc_final: 0.5428 (tt0) REVERT: G 223 TYR cc_start: 0.8091 (t80) cc_final: 0.7712 (t80) REVERT: G 225 GLU cc_start: 0.8522 (mt-10) cc_final: 0.8196 (mt-10) REVERT: G 227 LEU cc_start: 0.7843 (mm) cc_final: 0.7607 (mm) REVERT: G 244 MET cc_start: 0.7245 (ttm) cc_final: 0.6961 (ttp) outliers start: 106 outliers final: 86 residues processed: 1125 average time/residue: 0.4368 time to fit residues: 715.7082 Evaluate side-chains 1172 residues out of total 2558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 1077 time to evaluate : 3.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 54 GLU Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 385 ASP Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 261 ASP Chi-restraints excluded: chain B residue 327 SER Chi-restraints excluded: chain B residue 333 ASN Chi-restraints excluded: chain B residue 375 MET Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 442 ARG Chi-restraints excluded: chain B residue 452 ASP Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 262 ASP Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 332 THR Chi-restraints excluded: chain C residue 450 VAL Chi-restraints excluded: chain C residue 458 LYS Chi-restraints excluded: chain C residue 470 HIS Chi-restraints excluded: chain C residue 486 ASP Chi-restraints excluded: chain D residue 2 THR Chi-restraints excluded: chain D residue 7 ILE Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 49 GLU Chi-restraints excluded: chain D residue 57 ASP Chi-restraints excluded: chain D residue 112 ASP Chi-restraints excluded: chain D residue 203 LYS Chi-restraints excluded: chain D residue 207 VAL Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 295 THR Chi-restraints excluded: chain D residue 299 SER Chi-restraints excluded: chain D residue 323 SER Chi-restraints excluded: chain D residue 334 LYS Chi-restraints excluded: chain D residue 382 ASP Chi-restraints excluded: chain D residue 384 ILE Chi-restraints excluded: chain D residue 423 GLN Chi-restraints excluded: chain D residue 428 VAL Chi-restraints excluded: chain D residue 456 VAL Chi-restraints excluded: chain E residue 57 ASP Chi-restraints excluded: chain E residue 103 ILE Chi-restraints excluded: chain E residue 136 GLU Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 265 SER Chi-restraints excluded: chain E residue 293 THR Chi-restraints excluded: chain E residue 349 SER Chi-restraints excluded: chain E residue 357 GLU Chi-restraints excluded: chain E residue 381 GLN Chi-restraints excluded: chain E residue 384 ILE Chi-restraints excluded: chain E residue 395 GLU Chi-restraints excluded: chain E residue 456 VAL Chi-restraints excluded: chain F residue 7 ILE Chi-restraints excluded: chain F residue 46 LEU Chi-restraints excluded: chain F residue 90 VAL Chi-restraints excluded: chain F residue 98 VAL Chi-restraints excluded: chain F residue 106 GLU Chi-restraints excluded: chain F residue 183 SER Chi-restraints excluded: chain F residue 233 LEU Chi-restraints excluded: chain F residue 258 THR Chi-restraints excluded: chain F residue 265 SER Chi-restraints excluded: chain F residue 267 LEU Chi-restraints excluded: chain F residue 273 SER Chi-restraints excluded: chain F residue 281 LEU Chi-restraints excluded: chain F residue 292 ILE Chi-restraints excluded: chain F residue 322 PHE Chi-restraints excluded: chain F residue 351 SER Chi-restraints excluded: chain F residue 384 ILE Chi-restraints excluded: chain F residue 455 LEU Chi-restraints excluded: chain F residue 462 VAL Chi-restraints excluded: chain F residue 464 GLU Chi-restraints excluded: chain G residue 22 GLN Chi-restraints excluded: chain G residue 36 ASN Chi-restraints excluded: chain G residue 83 VAL Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain G residue 101 LEU Chi-restraints excluded: chain G residue 148 SER Chi-restraints excluded: chain G residue 186 VAL Chi-restraints excluded: chain G residue 188 GLU Chi-restraints excluded: chain G residue 232 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 271 optimal weight: 7.9990 chunk 286 optimal weight: 0.9980 chunk 261 optimal weight: 7.9990 chunk 278 optimal weight: 0.3980 chunk 167 optimal weight: 1.9990 chunk 121 optimal weight: 7.9990 chunk 218 optimal weight: 0.8980 chunk 85 optimal weight: 2.9990 chunk 251 optimal weight: 3.9990 chunk 263 optimal weight: 6.9990 chunk 277 optimal weight: 3.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 433 GLN ** B 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 333 ASN B 433 GLN C 70 ASN C 172 GLN ** C 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 474 HIS D 34 HIS F 28 ASN ** G 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6938 moved from start: 0.4568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 24604 Z= 0.208 Angle : 0.555 7.691 33364 Z= 0.289 Chirality : 0.044 0.162 3840 Planarity : 0.005 0.053 4349 Dihedral : 7.875 87.780 3575 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 4.14 % Allowed : 26.97 % Favored : 68.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.15), residues: 3104 helix: 1.18 (0.15), residues: 1241 sheet: 0.16 (0.22), residues: 550 loop : -0.76 (0.17), residues: 1313 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS D 173 PHE 0.016 0.001 PHE C 494 TYR 0.019 0.001 TYR C 248 ARG 0.009 0.000 ARG E 115 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1186 residues out of total 2558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 1080 time to evaluate : 2.594 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 VAL cc_start: 0.7612 (t) cc_final: 0.7380 (m) REVERT: A 57 ASN cc_start: 0.7915 (m-40) cc_final: 0.7666 (m-40) REVERT: A 96 GLU cc_start: 0.6338 (mt-10) cc_final: 0.6079 (tt0) REVERT: A 140 ARG cc_start: 0.7309 (ttt-90) cc_final: 0.6985 (ttt90) REVERT: A 144 GLU cc_start: 0.7297 (pt0) cc_final: 0.7013 (pt0) REVERT: A 147 GLN cc_start: 0.7474 (mm-40) cc_final: 0.7223 (mm110) REVERT: A 248 TYR cc_start: 0.7081 (t80) cc_final: 0.6716 (t80) REVERT: A 251 TYR cc_start: 0.7222 (m-80) cc_final: 0.6931 (m-80) REVERT: A 254 LYS cc_start: 0.7400 (mmtm) cc_final: 0.7009 (mmtm) REVERT: A 272 GLU cc_start: 0.6705 (tt0) cc_final: 0.6210 (tt0) REVERT: A 299 GLU cc_start: 0.7724 (mm-30) cc_final: 0.7213 (mm-30) REVERT: A 375 MET cc_start: 0.7148 (tpp) cc_final: 0.6506 (tpp) REVERT: A 376 LYS cc_start: 0.6870 (ttmm) cc_final: 0.6573 (mtmm) REVERT: A 385 ASP cc_start: 0.7303 (OUTLIER) cc_final: 0.7011 (t0) REVERT: A 421 LYS cc_start: 0.7352 (mttm) cc_final: 0.6906 (mttm) REVERT: A 426 GLN cc_start: 0.7361 (mm-40) cc_final: 0.7070 (mm-40) REVERT: A 478 THR cc_start: 0.7417 (t) cc_final: 0.7201 (t) REVERT: A 489 LYS cc_start: 0.7848 (tttt) cc_final: 0.7584 (tttt) REVERT: B 46 ASN cc_start: 0.7056 (m110) cc_final: 0.6762 (m110) REVERT: B 67 GLU cc_start: 0.6883 (mm-30) cc_final: 0.6427 (mm-30) REVERT: B 95 MET cc_start: 0.6843 (tpt) cc_final: 0.6427 (mmm) REVERT: B 101 GLU cc_start: 0.6881 (mp0) cc_final: 0.6584 (mp0) REVERT: B 103 LEU cc_start: 0.7541 (tp) cc_final: 0.7102 (tp) REVERT: B 113 GLN cc_start: 0.7093 (mm-40) cc_final: 0.6776 (mm-40) REVERT: B 144 GLU cc_start: 0.6952 (pt0) cc_final: 0.5930 (pt0) REVERT: B 200 GLN cc_start: 0.7782 (mm-40) cc_final: 0.7377 (mm-40) REVERT: B 230 GLN cc_start: 0.7228 (mm-40) cc_final: 0.6957 (mt0) REVERT: B 261 ASP cc_start: 0.6170 (OUTLIER) cc_final: 0.5952 (m-30) REVERT: B 265 LYS cc_start: 0.6691 (mttp) cc_final: 0.6340 (mttp) REVERT: B 272 GLU cc_start: 0.6717 (tt0) cc_final: 0.6384 (tt0) REVERT: B 428 ILE cc_start: 0.7661 (mt) cc_final: 0.7453 (mt) REVERT: B 442 ARG cc_start: 0.7627 (OUTLIER) cc_final: 0.7262 (mmt-90) REVERT: B 449 PRO cc_start: 0.7465 (Cg_exo) cc_final: 0.7247 (Cg_endo) REVERT: B 467 ASN cc_start: 0.8239 (m-40) cc_final: 0.8011 (m-40) REVERT: B 479 LYS cc_start: 0.6950 (mptt) cc_final: 0.6433 (mptt) REVERT: C 34 VAL cc_start: 0.7841 (t) cc_final: 0.7623 (p) REVERT: C 62 MET cc_start: 0.6570 (ttt) cc_final: 0.6213 (ttp) REVERT: C 68 GLU cc_start: 0.7223 (tt0) cc_final: 0.6920 (mt-10) REVERT: C 80 THR cc_start: 0.7912 (p) cc_final: 0.7678 (m) REVERT: C 96 GLU cc_start: 0.6722 (mt-10) cc_final: 0.6404 (mt-10) REVERT: C 127 ARG cc_start: 0.7367 (mtp85) cc_final: 0.6915 (mtp85) REVERT: C 137 MET cc_start: 0.7940 (mmm) cc_final: 0.7715 (mmm) REVERT: C 147 GLN cc_start: 0.7413 (mm-40) cc_final: 0.6931 (mm110) REVERT: C 171 ARG cc_start: 0.7385 (ptm-80) cc_final: 0.7039 (ptm-80) REVERT: C 181 ASP cc_start: 0.7539 (m-30) cc_final: 0.7198 (m-30) REVERT: C 185 ASN cc_start: 0.7826 (t0) cc_final: 0.7510 (t0) REVERT: C 196 VAL cc_start: 0.7660 (t) cc_final: 0.7338 (m) REVERT: C 222 ILE cc_start: 0.7264 (mt) cc_final: 0.6989 (mt) REVERT: C 254 LYS cc_start: 0.7545 (mtmm) cc_final: 0.7195 (mtmm) REVERT: C 262 ASP cc_start: 0.7149 (OUTLIER) cc_final: 0.6928 (t0) REVERT: C 272 GLU cc_start: 0.6906 (mt-10) cc_final: 0.6488 (mt-10) REVERT: C 314 THR cc_start: 0.7463 (OUTLIER) cc_final: 0.6997 (p) REVERT: C 354 ARG cc_start: 0.7079 (mtt90) cc_final: 0.6610 (mtt90) REVERT: C 361 LEU cc_start: 0.7575 (mp) cc_final: 0.7285 (mp) REVERT: C 376 LYS cc_start: 0.7521 (ttpt) cc_final: 0.7266 (ttpt) REVERT: C 451 GLU cc_start: 0.7617 (mp0) cc_final: 0.7145 (mp0) REVERT: C 469 GLN cc_start: 0.7945 (tp40) cc_final: 0.7606 (mm-40) REVERT: C 473 GLU cc_start: 0.8022 (mm-30) cc_final: 0.7738 (mm-30) REVERT: D 7 ILE cc_start: 0.7593 (OUTLIER) cc_final: 0.7349 (mm) REVERT: D 10 MET cc_start: 0.6362 (mtm) cc_final: 0.5837 (mtm) REVERT: D 15 ASP cc_start: 0.6959 (m-30) cc_final: 0.6665 (m-30) REVERT: D 17 LYS cc_start: 0.7051 (tttt) cc_final: 0.6622 (tttm) REVERT: D 26 ILE cc_start: 0.8158 (mt) cc_final: 0.7859 (mp) REVERT: D 41 GLU cc_start: 0.6607 (mt-10) cc_final: 0.6023 (mt-10) REVERT: D 64 MET cc_start: 0.6756 (mmt) cc_final: 0.6430 (mmt) REVERT: D 74 MET cc_start: 0.7506 (mtt) cc_final: 0.7238 (mtt) REVERT: D 75 GLU cc_start: 0.7279 (tt0) cc_final: 0.6818 (tt0) REVERT: D 101 GLU cc_start: 0.7147 (mt-10) cc_final: 0.6718 (mt-10) REVERT: D 114 ARG cc_start: 0.7330 (ttt180) cc_final: 0.6808 (ttp80) REVERT: D 116 ASP cc_start: 0.7073 (m-30) cc_final: 0.6398 (m-30) REVERT: D 120 ARG cc_start: 0.7259 (ttt90) cc_final: 0.6852 (ptm160) REVERT: D 133 GLU cc_start: 0.7202 (mt-10) cc_final: 0.6634 (mt-10) REVERT: D 169 GLN cc_start: 0.7331 (mt0) cc_final: 0.6939 (mm-40) REVERT: D 190 ASP cc_start: 0.6831 (m-30) cc_final: 0.5680 (m-30) REVERT: D 197 ASP cc_start: 0.6946 (t0) cc_final: 0.6728 (t70) REVERT: D 213 MET cc_start: 0.7418 (mtm) cc_final: 0.6977 (mtp) REVERT: D 214 VAL cc_start: 0.7491 (t) cc_final: 0.6962 (p) REVERT: D 237 GLU cc_start: 0.7036 (mt-10) cc_final: 0.6516 (mt-10) REVERT: D 241 ASP cc_start: 0.7105 (m-30) cc_final: 0.6825 (m-30) REVERT: D 246 ASP cc_start: 0.7480 (m-30) cc_final: 0.7060 (m-30) REVERT: D 252 ASP cc_start: 0.6493 (t0) cc_final: 0.5981 (t0) REVERT: D 270 ARG cc_start: 0.7488 (mtt180) cc_final: 0.6837 (mtt-85) REVERT: D 284 GLU cc_start: 0.6064 (mt-10) cc_final: 0.5468 (mt-10) REVERT: D 285 MET cc_start: 0.6273 (ttm) cc_final: 0.5923 (ttm) REVERT: D 304 GLN cc_start: 0.7310 (mt0) cc_final: 0.7056 (mt0) REVERT: D 352 ARG cc_start: 0.7149 (mtp180) cc_final: 0.6802 (mtp180) REVERT: D 428 VAL cc_start: 0.8429 (OUTLIER) cc_final: 0.8133 (m) REVERT: D 439 GLU cc_start: 0.7419 (mm-30) cc_final: 0.6683 (mm-30) REVERT: E 1 MET cc_start: 0.3624 (mmt) cc_final: 0.3323 (mmt) REVERT: E 3 ARG cc_start: 0.6708 (mtm-85) cc_final: 0.6285 (mtm-85) REVERT: E 5 ARG cc_start: 0.6448 (ptp-110) cc_final: 0.6000 (ptp-110) REVERT: E 10 MET cc_start: 0.6262 (ptp) cc_final: 0.5986 (ptp) REVERT: E 17 LYS cc_start: 0.7266 (tttt) cc_final: 0.6797 (ttmm) REVERT: E 31 LYS cc_start: 0.7578 (mmtt) cc_final: 0.7139 (mmtt) REVERT: E 89 GLU cc_start: 0.7328 (mm-30) cc_final: 0.6996 (mm-30) REVERT: E 91 THR cc_start: 0.7826 (p) cc_final: 0.7396 (t) REVERT: E 101 GLU cc_start: 0.6958 (mt-10) cc_final: 0.6589 (mp0) REVERT: E 127 GLU cc_start: 0.6858 (mt-10) cc_final: 0.6478 (mt-10) REVERT: E 134 ILE cc_start: 0.8315 (mt) cc_final: 0.7976 (tt) REVERT: E 149 ILE cc_start: 0.7672 (mt) cc_final: 0.7373 (mm) REVERT: E 170 GLU cc_start: 0.7244 (tp30) cc_final: 0.6783 (tt0) REVERT: E 178 GLU cc_start: 0.7068 (mm-30) cc_final: 0.6581 (mt-10) REVERT: E 210 LYS cc_start: 0.7590 (mttt) cc_final: 0.7311 (mttt) REVERT: E 270 ARG cc_start: 0.7003 (mtt90) cc_final: 0.6795 (mtt180) REVERT: E 285 MET cc_start: 0.6631 (tpp) cc_final: 0.6355 (tpp) REVERT: E 334 LYS cc_start: 0.7342 (mmmm) cc_final: 0.7089 (mmmm) REVERT: E 354 LEU cc_start: 0.7608 (tp) cc_final: 0.7339 (tt) REVERT: E 365 GLN cc_start: 0.7522 (mt0) cc_final: 0.7136 (mt0) REVERT: E 375 GLN cc_start: 0.7778 (tp-100) cc_final: 0.7514 (tp40) REVERT: E 376 ARG cc_start: 0.7883 (tpt170) cc_final: 0.7536 (tpt170) REVERT: E 402 ARG cc_start: 0.7579 (mmm-85) cc_final: 0.7176 (mtt-85) REVERT: E 405 ARG cc_start: 0.7538 (OUTLIER) cc_final: 0.7265 (mpt180) REVERT: E 407 GLN cc_start: 0.7524 (tt0) cc_final: 0.7033 (tp40) REVERT: E 423 GLN cc_start: 0.7502 (mm-40) cc_final: 0.7195 (mt0) REVERT: E 435 ARG cc_start: 0.7476 (ttp80) cc_final: 0.6461 (ttp80) REVERT: E 438 LYS cc_start: 0.7732 (ttpt) cc_final: 0.6649 (ttpt) REVERT: E 439 GLU cc_start: 0.7579 (mm-30) cc_final: 0.6462 (mm-30) REVERT: E 441 LEU cc_start: 0.8221 (mt) cc_final: 0.7949 (mt) REVERT: E 442 GLU cc_start: 0.7647 (mt-10) cc_final: 0.7082 (mt-10) REVERT: E 445 TYR cc_start: 0.7447 (m-80) cc_final: 0.6611 (m-80) REVERT: E 450 GLU cc_start: 0.7801 (pm20) cc_final: 0.7264 (pm20) REVERT: E 469 MET cc_start: 0.7568 (mmm) cc_final: 0.7089 (mmm) REVERT: F 5 ARG cc_start: 0.6057 (mmt180) cc_final: 0.5518 (mmt180) REVERT: F 8 GLN cc_start: 0.7360 (mt0) cc_final: 0.6904 (mt0) REVERT: F 15 ASP cc_start: 0.6909 (m-30) cc_final: 0.6549 (m-30) REVERT: F 37 ARG cc_start: 0.7354 (ttm170) cc_final: 0.7140 (ttm170) REVERT: F 39 GLU cc_start: 0.7596 (mp0) cc_final: 0.7181 (mp0) REVERT: F 54 LEU cc_start: 0.7777 (OUTLIER) cc_final: 0.7452 (mp) REVERT: F 74 MET cc_start: 0.6779 (mtt) cc_final: 0.6296 (mtt) REVERT: F 75 GLU cc_start: 0.6927 (tt0) cc_final: 0.5292 (tt0) REVERT: F 89 GLU cc_start: 0.7778 (tp30) cc_final: 0.7496 (tp30) REVERT: F 114 ARG cc_start: 0.7573 (ttp-170) cc_final: 0.7139 (ttp80) REVERT: F 115 ARG cc_start: 0.7450 (mtt90) cc_final: 0.7127 (mtt90) REVERT: F 116 ASP cc_start: 0.7380 (m-30) cc_final: 0.6948 (m-30) REVERT: F 124 LYS cc_start: 0.6963 (mttm) cc_final: 0.6620 (mttm) REVERT: F 127 GLU cc_start: 0.7135 (mt-10) cc_final: 0.6615 (mt-10) REVERT: F 213 MET cc_start: 0.7266 (mtp) cc_final: 0.6759 (mtp) REVERT: F 218 MET cc_start: 0.7435 (mtm) cc_final: 0.7182 (mtp) REVERT: F 220 GLU cc_start: 0.6835 (mm-30) cc_final: 0.6586 (mm-30) REVERT: F 237 GLU cc_start: 0.6487 (tt0) cc_final: 0.6080 (mt-10) REVERT: F 290 GLU cc_start: 0.7384 (mm-30) cc_final: 0.7165 (mm-30) REVERT: F 303 ILE cc_start: 0.7580 (mt) cc_final: 0.7306 (mp) REVERT: F 345 ASP cc_start: 0.7359 (t70) cc_final: 0.6923 (t70) REVERT: F 389 MET cc_start: 0.7328 (mtm) cc_final: 0.6991 (mtm) REVERT: F 397 LYS cc_start: 0.7092 (tttm) cc_final: 0.6824 (tttm) REVERT: F 401 HIS cc_start: 0.6644 (t-90) cc_final: 0.6316 (t-90) REVERT: F 439 GLU cc_start: 0.7581 (mt-10) cc_final: 0.6900 (mt-10) REVERT: F 442 GLU cc_start: 0.7240 (mt-10) cc_final: 0.6583 (mt-10) REVERT: F 444 LYS cc_start: 0.7974 (tttt) cc_final: 0.7759 (tttt) REVERT: F 445 TYR cc_start: 0.8310 (m-80) cc_final: 0.7775 (m-80) REVERT: F 451 ASP cc_start: 0.7789 (m-30) cc_final: 0.7548 (m-30) REVERT: G 28 GLU cc_start: 0.7466 (tt0) cc_final: 0.7154 (tt0) REVERT: G 54 GLU cc_start: 0.8799 (mt-10) cc_final: 0.8564 (mt-10) REVERT: G 70 MET cc_start: 0.7809 (mmm) cc_final: 0.7137 (mmm) REVERT: G 85 THR cc_start: 0.7789 (OUTLIER) cc_final: 0.7405 (t) REVERT: G 95 ASN cc_start: 0.7846 (m-40) cc_final: 0.7569 (m110) REVERT: G 115 GLU cc_start: 0.8095 (mm-30) cc_final: 0.7746 (mm-30) REVERT: G 116 TYR cc_start: 0.7525 (p90) cc_final: 0.7286 (p90) REVERT: G 173 MET cc_start: 0.7022 (mtm) cc_final: 0.6681 (mtm) REVERT: G 184 GLN cc_start: 0.6970 (mp10) cc_final: 0.6604 (mp10) REVERT: G 185 GLU cc_start: 0.6623 (mm-30) cc_final: 0.6123 (mm-30) REVERT: G 188 GLU cc_start: 0.5659 (OUTLIER) cc_final: 0.5425 (tt0) REVERT: G 223 TYR cc_start: 0.8098 (t80) cc_final: 0.7735 (t80) REVERT: G 225 GLU cc_start: 0.8516 (mt-10) cc_final: 0.8199 (mt-10) REVERT: G 227 LEU cc_start: 0.7841 (mm) cc_final: 0.7599 (mm) REVERT: G 244 MET cc_start: 0.7241 (ttm) cc_final: 0.6908 (ttp) outliers start: 106 outliers final: 88 residues processed: 1127 average time/residue: 0.4420 time to fit residues: 724.7295 Evaluate side-chains 1173 residues out of total 2558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 1074 time to evaluate : 2.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 54 GLU Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 385 ASP Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 261 ASP Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 327 SER Chi-restraints excluded: chain B residue 333 ASN Chi-restraints excluded: chain B residue 375 MET Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 442 ARG Chi-restraints excluded: chain B residue 452 ASP Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 36 ASP Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 70 ASN Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 262 ASP Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 327 SER Chi-restraints excluded: chain C residue 332 THR Chi-restraints excluded: chain C residue 450 VAL Chi-restraints excluded: chain C residue 458 LYS Chi-restraints excluded: chain C residue 470 HIS Chi-restraints excluded: chain C residue 486 ASP Chi-restraints excluded: chain D residue 2 THR Chi-restraints excluded: chain D residue 7 ILE Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 49 GLU Chi-restraints excluded: chain D residue 57 ASP Chi-restraints excluded: chain D residue 66 SER Chi-restraints excluded: chain D residue 112 ASP Chi-restraints excluded: chain D residue 131 GLU Chi-restraints excluded: chain D residue 203 LYS Chi-restraints excluded: chain D residue 207 VAL Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 295 THR Chi-restraints excluded: chain D residue 299 SER Chi-restraints excluded: chain D residue 323 SER Chi-restraints excluded: chain D residue 382 ASP Chi-restraints excluded: chain D residue 384 ILE Chi-restraints excluded: chain D residue 419 GLN Chi-restraints excluded: chain D residue 423 GLN Chi-restraints excluded: chain D residue 428 VAL Chi-restraints excluded: chain D residue 456 VAL Chi-restraints excluded: chain E residue 57 ASP Chi-restraints excluded: chain E residue 103 ILE Chi-restraints excluded: chain E residue 136 GLU Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 265 SER Chi-restraints excluded: chain E residue 293 THR Chi-restraints excluded: chain E residue 349 SER Chi-restraints excluded: chain E residue 357 GLU Chi-restraints excluded: chain E residue 381 GLN Chi-restraints excluded: chain E residue 384 ILE Chi-restraints excluded: chain E residue 395 GLU Chi-restraints excluded: chain E residue 405 ARG Chi-restraints excluded: chain E residue 456 VAL Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 46 LEU Chi-restraints excluded: chain F residue 54 LEU Chi-restraints excluded: chain F residue 84 SER Chi-restraints excluded: chain F residue 90 VAL Chi-restraints excluded: chain F residue 98 VAL Chi-restraints excluded: chain F residue 106 GLU Chi-restraints excluded: chain F residue 183 SER Chi-restraints excluded: chain F residue 233 LEU Chi-restraints excluded: chain F residue 258 THR Chi-restraints excluded: chain F residue 273 SER Chi-restraints excluded: chain F residue 281 LEU Chi-restraints excluded: chain F residue 351 SER Chi-restraints excluded: chain F residue 384 ILE Chi-restraints excluded: chain F residue 462 VAL Chi-restraints excluded: chain G residue 22 GLN Chi-restraints excluded: chain G residue 83 VAL Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain G residue 101 LEU Chi-restraints excluded: chain G residue 127 SER Chi-restraints excluded: chain G residue 146 GLN Chi-restraints excluded: chain G residue 148 SER Chi-restraints excluded: chain G residue 186 VAL Chi-restraints excluded: chain G residue 188 GLU Chi-restraints excluded: chain G residue 232 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 182 optimal weight: 0.9980 chunk 294 optimal weight: 0.7980 chunk 179 optimal weight: 6.9990 chunk 139 optimal weight: 3.9990 chunk 204 optimal weight: 8.9990 chunk 308 optimal weight: 3.9990 chunk 284 optimal weight: 2.9990 chunk 245 optimal weight: 3.9990 chunk 25 optimal weight: 6.9990 chunk 189 optimal weight: 0.9990 chunk 150 optimal weight: 0.5980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 172 GLN A 345 GLN ** B 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 433 GLN C 172 GLN ** C 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 36 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6935 moved from start: 0.4611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 24604 Z= 0.198 Angle : 0.558 7.885 33364 Z= 0.290 Chirality : 0.044 0.170 3840 Planarity : 0.005 0.092 4349 Dihedral : 7.815 87.620 3574 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 4.18 % Allowed : 27.29 % Favored : 68.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.83 % 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: 0.27 (0.15), residues: 3104 helix: 1.17 (0.15), residues: 1242 sheet: 0.21 (0.22), residues: 550 loop : -0.74 (0.17), residues: 1312 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS D 173 PHE 0.021 0.001 PHE E 408 TYR 0.019 0.001 TYR C 248 ARG 0.014 0.001 ARG F 405 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1185 residues out of total 2558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 1078 time to evaluate : 2.846 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 VAL cc_start: 0.7607 (t) cc_final: 0.7371 (m) REVERT: A 57 ASN cc_start: 0.7918 (m-40) cc_final: 0.7657 (m-40) REVERT: A 83 LYS cc_start: 0.6344 (mttp) cc_final: 0.6105 (mttm) REVERT: A 96 GLU cc_start: 0.6336 (mt-10) cc_final: 0.6085 (tt0) REVERT: A 140 ARG cc_start: 0.7308 (ttt-90) cc_final: 0.6983 (ttt90) REVERT: A 147 GLN cc_start: 0.7473 (mm-40) cc_final: 0.7234 (mm110) REVERT: A 248 TYR cc_start: 0.7089 (t80) cc_final: 0.6733 (t80) REVERT: A 251 TYR cc_start: 0.7212 (m-80) cc_final: 0.6916 (m-80) REVERT: A 254 LYS cc_start: 0.7406 (mmtm) cc_final: 0.7021 (mmtm) REVERT: A 272 GLU cc_start: 0.6705 (tt0) cc_final: 0.6208 (tt0) REVERT: A 299 GLU cc_start: 0.7723 (mm-30) cc_final: 0.7218 (mm-30) REVERT: A 375 MET cc_start: 0.7143 (tpp) cc_final: 0.6501 (tpp) REVERT: A 376 LYS cc_start: 0.6866 (ttmm) cc_final: 0.6571 (mtmm) REVERT: A 385 ASP cc_start: 0.7299 (OUTLIER) cc_final: 0.7010 (t0) REVERT: A 421 LYS cc_start: 0.7337 (mttm) cc_final: 0.6889 (mttm) REVERT: A 426 GLN cc_start: 0.7360 (mm-40) cc_final: 0.7085 (mm-40) REVERT: A 478 THR cc_start: 0.7418 (t) cc_final: 0.7161 (t) REVERT: A 480 ASP cc_start: 0.6427 (t0) cc_final: 0.6222 (m-30) REVERT: A 487 LEU cc_start: 0.7899 (mp) cc_final: 0.7582 (mm) REVERT: A 489 LYS cc_start: 0.7838 (tttt) cc_final: 0.7574 (tttt) REVERT: B 46 ASN cc_start: 0.7066 (m110) cc_final: 0.6772 (m110) REVERT: B 67 GLU cc_start: 0.6877 (mm-30) cc_final: 0.6485 (mm-30) REVERT: B 95 MET cc_start: 0.6862 (tpt) cc_final: 0.6445 (mmm) REVERT: B 101 GLU cc_start: 0.6846 (mp0) cc_final: 0.6560 (mp0) REVERT: B 103 LEU cc_start: 0.7535 (tp) cc_final: 0.7100 (tp) REVERT: B 113 GLN cc_start: 0.7091 (mm-40) cc_final: 0.6775 (mm-40) REVERT: B 144 GLU cc_start: 0.6955 (pt0) cc_final: 0.5931 (pt0) REVERT: B 200 GLN cc_start: 0.7766 (mm-40) cc_final: 0.7345 (mm-40) REVERT: B 230 GLN cc_start: 0.7224 (mm-40) cc_final: 0.6950 (mt0) REVERT: B 261 ASP cc_start: 0.6160 (OUTLIER) cc_final: 0.5939 (m-30) REVERT: B 265 LYS cc_start: 0.6688 (mttp) cc_final: 0.6356 (mttp) REVERT: B 272 GLU cc_start: 0.6717 (tt0) cc_final: 0.6384 (tt0) REVERT: B 442 ARG cc_start: 0.7623 (OUTLIER) cc_final: 0.7253 (mmt-90) REVERT: B 449 PRO cc_start: 0.7455 (Cg_exo) cc_final: 0.7237 (Cg_endo) REVERT: B 467 ASN cc_start: 0.8231 (m-40) cc_final: 0.8001 (m-40) REVERT: B 479 LYS cc_start: 0.6948 (mptt) cc_final: 0.6425 (mptt) REVERT: C 34 VAL cc_start: 0.7842 (t) cc_final: 0.7625 (p) REVERT: C 62 MET cc_start: 0.6565 (ttt) cc_final: 0.6209 (ttp) REVERT: C 68 GLU cc_start: 0.7230 (tt0) cc_final: 0.6934 (mt-10) REVERT: C 80 THR cc_start: 0.7909 (p) cc_final: 0.7678 (m) REVERT: C 96 GLU cc_start: 0.6724 (mt-10) cc_final: 0.6406 (mt-10) REVERT: C 127 ARG cc_start: 0.7366 (mtp85) cc_final: 0.6915 (mtp85) REVERT: C 137 MET cc_start: 0.7937 (mmm) cc_final: 0.7714 (mmm) REVERT: C 147 GLN cc_start: 0.7405 (mm-40) cc_final: 0.6933 (mm110) REVERT: C 171 ARG cc_start: 0.7387 (ptm-80) cc_final: 0.7042 (ptm-80) REVERT: C 181 ASP cc_start: 0.7535 (m-30) cc_final: 0.7193 (m-30) REVERT: C 185 ASN cc_start: 0.7824 (t0) cc_final: 0.7508 (t0) REVERT: C 196 VAL cc_start: 0.7656 (t) cc_final: 0.7335 (m) REVERT: C 222 ILE cc_start: 0.7252 (mt) cc_final: 0.6973 (mt) REVERT: C 254 LYS cc_start: 0.7531 (mtmm) cc_final: 0.7182 (mtmm) REVERT: C 262 ASP cc_start: 0.7152 (OUTLIER) cc_final: 0.6933 (t0) REVERT: C 272 GLU cc_start: 0.6902 (mt-10) cc_final: 0.6484 (mt-10) REVERT: C 314 THR cc_start: 0.7460 (OUTLIER) cc_final: 0.7000 (p) REVERT: C 354 ARG cc_start: 0.7075 (mtt90) cc_final: 0.6625 (mtt90) REVERT: C 361 LEU cc_start: 0.7621 (mp) cc_final: 0.7362 (mp) REVERT: C 376 LYS cc_start: 0.7521 (ttpt) cc_final: 0.7269 (ttpt) REVERT: C 451 GLU cc_start: 0.7620 (mp0) cc_final: 0.7150 (mp0) REVERT: C 469 GLN cc_start: 0.7950 (tp40) cc_final: 0.7595 (mm-40) REVERT: C 473 GLU cc_start: 0.8020 (mm-30) cc_final: 0.7742 (mm-30) REVERT: D 7 ILE cc_start: 0.7593 (OUTLIER) cc_final: 0.7354 (mm) REVERT: D 10 MET cc_start: 0.6346 (mtm) cc_final: 0.5821 (mtm) REVERT: D 15 ASP cc_start: 0.6938 (m-30) cc_final: 0.6643 (m-30) REVERT: D 17 LYS cc_start: 0.7057 (tttt) cc_final: 0.6615 (tttm) REVERT: D 26 ILE cc_start: 0.8160 (mt) cc_final: 0.7858 (mp) REVERT: D 41 GLU cc_start: 0.6587 (mt-10) cc_final: 0.6007 (mt-10) REVERT: D 64 MET cc_start: 0.6750 (mmt) cc_final: 0.6424 (mmt) REVERT: D 74 MET cc_start: 0.7502 (mtt) cc_final: 0.7237 (mtt) REVERT: D 75 GLU cc_start: 0.7278 (tt0) cc_final: 0.6812 (tt0) REVERT: D 101 GLU cc_start: 0.7134 (mt-10) cc_final: 0.6705 (mt-10) REVERT: D 114 ARG cc_start: 0.7329 (ttt180) cc_final: 0.6805 (ttp80) REVERT: D 116 ASP cc_start: 0.7073 (m-30) cc_final: 0.6400 (m-30) REVERT: D 120 ARG cc_start: 0.7256 (ttt90) cc_final: 0.6850 (ptm160) REVERT: D 169 GLN cc_start: 0.7322 (mt0) cc_final: 0.6933 (mm-40) REVERT: D 190 ASP cc_start: 0.6836 (m-30) cc_final: 0.5678 (m-30) REVERT: D 197 ASP cc_start: 0.6941 (t0) cc_final: 0.6728 (t70) REVERT: D 213 MET cc_start: 0.7413 (mtm) cc_final: 0.6975 (mtp) REVERT: D 214 VAL cc_start: 0.7482 (t) cc_final: 0.6958 (p) REVERT: D 237 GLU cc_start: 0.7020 (mt-10) cc_final: 0.6500 (mt-10) REVERT: D 241 ASP cc_start: 0.7093 (m-30) cc_final: 0.6816 (m-30) REVERT: D 246 ASP cc_start: 0.7461 (m-30) cc_final: 0.7037 (m-30) REVERT: D 252 ASP cc_start: 0.6508 (t0) cc_final: 0.5992 (t0) REVERT: D 270 ARG cc_start: 0.7487 (mtt180) cc_final: 0.6837 (mtt-85) REVERT: D 284 GLU cc_start: 0.6056 (mt-10) cc_final: 0.5463 (mt-10) REVERT: D 285 MET cc_start: 0.6256 (ttm) cc_final: 0.5905 (ttm) REVERT: D 352 ARG cc_start: 0.7146 (mtp180) cc_final: 0.6793 (mtp180) REVERT: D 428 VAL cc_start: 0.8429 (OUTLIER) cc_final: 0.8139 (m) REVERT: D 439 GLU cc_start: 0.7423 (mm-30) cc_final: 0.7220 (mm-30) REVERT: E 1 MET cc_start: 0.3629 (mmt) cc_final: 0.3319 (mmt) REVERT: E 3 ARG cc_start: 0.6713 (mtm-85) cc_final: 0.6287 (mtm-85) REVERT: E 5 ARG cc_start: 0.6444 (ptp-110) cc_final: 0.5995 (ptp-110) REVERT: E 10 MET cc_start: 0.6176 (ptp) cc_final: 0.5935 (ptp) REVERT: E 17 LYS cc_start: 0.7270 (tttt) cc_final: 0.6790 (ttmm) REVERT: E 31 LYS cc_start: 0.7571 (mmtt) cc_final: 0.7133 (mmtt) REVERT: E 89 GLU cc_start: 0.7311 (mm-30) cc_final: 0.6985 (mm-30) REVERT: E 91 THR cc_start: 0.7815 (p) cc_final: 0.7387 (t) REVERT: E 101 GLU cc_start: 0.6945 (mt-10) cc_final: 0.6574 (mp0) REVERT: E 127 GLU cc_start: 0.6858 (mt-10) cc_final: 0.6479 (mt-10) REVERT: E 134 ILE cc_start: 0.8296 (mt) cc_final: 0.7958 (tt) REVERT: E 149 ILE cc_start: 0.7670 (mt) cc_final: 0.7372 (mm) REVERT: E 170 GLU cc_start: 0.7247 (tp30) cc_final: 0.6786 (tt0) REVERT: E 178 GLU cc_start: 0.7032 (mm-30) cc_final: 0.6553 (mt-10) REVERT: E 210 LYS cc_start: 0.7585 (mttt) cc_final: 0.7304 (mttt) REVERT: E 285 MET cc_start: 0.6628 (tpp) cc_final: 0.6351 (tpp) REVERT: E 334 LYS cc_start: 0.7342 (mmmm) cc_final: 0.7089 (mmmm) REVERT: E 354 LEU cc_start: 0.7605 (tp) cc_final: 0.7336 (tt) REVERT: E 365 GLN cc_start: 0.7518 (mt0) cc_final: 0.7131 (mt0) REVERT: E 375 GLN cc_start: 0.7784 (tp-100) cc_final: 0.7521 (tp40) REVERT: E 376 ARG cc_start: 0.7884 (tpt170) cc_final: 0.7546 (tpt170) REVERT: E 402 ARG cc_start: 0.7570 (mmm-85) cc_final: 0.7197 (mtt-85) REVERT: E 405 ARG cc_start: 0.7455 (OUTLIER) cc_final: 0.7142 (mpt180) REVERT: E 423 GLN cc_start: 0.7500 (mm-40) cc_final: 0.7232 (mt0) REVERT: E 435 ARG cc_start: 0.7462 (ttp80) cc_final: 0.6450 (ttp80) REVERT: E 438 LYS cc_start: 0.7730 (ttpt) cc_final: 0.6645 (ttpt) REVERT: E 439 GLU cc_start: 0.7578 (mm-30) cc_final: 0.6455 (mm-30) REVERT: E 441 LEU cc_start: 0.8222 (mt) cc_final: 0.7989 (mt) REVERT: E 442 GLU cc_start: 0.7625 (mt-10) cc_final: 0.7022 (mt-10) REVERT: E 445 TYR cc_start: 0.7456 (m-80) cc_final: 0.6613 (m-80) REVERT: E 450 GLU cc_start: 0.7774 (pm20) cc_final: 0.7254 (pm20) REVERT: E 469 MET cc_start: 0.7566 (mmm) cc_final: 0.7087 (mmm) REVERT: F 5 ARG cc_start: 0.6053 (mmt180) cc_final: 0.5516 (mmt180) REVERT: F 8 GLN cc_start: 0.7318 (mt0) cc_final: 0.6829 (mt0) REVERT: F 15 ASP cc_start: 0.6902 (m-30) cc_final: 0.6375 (m-30) REVERT: F 37 ARG cc_start: 0.7353 (ttm170) cc_final: 0.7139 (ttm170) REVERT: F 39 GLU cc_start: 0.7599 (mp0) cc_final: 0.7163 (mp0) REVERT: F 54 LEU cc_start: 0.7771 (OUTLIER) cc_final: 0.7442 (mp) REVERT: F 74 MET cc_start: 0.6783 (mtt) cc_final: 0.6295 (mtt) REVERT: F 75 GLU cc_start: 0.6935 (tt0) cc_final: 0.5298 (tt0) REVERT: F 89 GLU cc_start: 0.7783 (tp30) cc_final: 0.7493 (tp30) REVERT: F 114 ARG cc_start: 0.7575 (ttp-170) cc_final: 0.7143 (ttp80) REVERT: F 115 ARG cc_start: 0.7445 (mtt90) cc_final: 0.7128 (mtt90) REVERT: F 116 ASP cc_start: 0.7353 (m-30) cc_final: 0.6934 (m-30) REVERT: F 120 ARG cc_start: 0.7134 (tmm-80) cc_final: 0.6803 (ptm160) REVERT: F 124 LYS cc_start: 0.6892 (mttm) cc_final: 0.6584 (mttm) REVERT: F 127 GLU cc_start: 0.7086 (mt-10) cc_final: 0.6569 (mt-10) REVERT: F 213 MET cc_start: 0.7257 (mtp) cc_final: 0.6747 (mtp) REVERT: F 218 MET cc_start: 0.7424 (mtm) cc_final: 0.7168 (mtp) REVERT: F 220 GLU cc_start: 0.6841 (mm-30) cc_final: 0.6614 (mm-30) REVERT: F 290 GLU cc_start: 0.7386 (mm-30) cc_final: 0.7163 (mm-30) REVERT: F 303 ILE cc_start: 0.7579 (mt) cc_final: 0.7307 (mp) REVERT: F 345 ASP cc_start: 0.7349 (t70) cc_final: 0.6917 (t70) REVERT: F 389 MET cc_start: 0.7338 (mtm) cc_final: 0.6952 (mtm) REVERT: F 439 GLU cc_start: 0.7575 (mt-10) cc_final: 0.6891 (mt-10) REVERT: F 442 GLU cc_start: 0.7236 (mt-10) cc_final: 0.6575 (mt-10) REVERT: F 444 LYS cc_start: 0.7977 (tttt) cc_final: 0.7761 (tttt) REVERT: F 445 TYR cc_start: 0.8290 (m-80) cc_final: 0.7700 (m-80) REVERT: F 451 ASP cc_start: 0.7787 (m-30) cc_final: 0.7555 (m-30) REVERT: G 28 GLU cc_start: 0.7468 (tt0) cc_final: 0.7168 (tt0) REVERT: G 54 GLU cc_start: 0.8790 (mt-10) cc_final: 0.8553 (mt-10) REVERT: G 70 MET cc_start: 0.7809 (mmm) cc_final: 0.7129 (mmm) REVERT: G 85 THR cc_start: 0.7787 (OUTLIER) cc_final: 0.7407 (t) REVERT: G 95 ASN cc_start: 0.7861 (m-40) cc_final: 0.7601 (m110) REVERT: G 115 GLU cc_start: 0.8097 (mm-30) cc_final: 0.7752 (mm-30) REVERT: G 116 TYR cc_start: 0.7528 (p90) cc_final: 0.7294 (p90) REVERT: G 142 ARG cc_start: 0.7430 (mmm-85) cc_final: 0.7017 (mmm-85) REVERT: G 173 MET cc_start: 0.7017 (mtm) cc_final: 0.6680 (mtm) REVERT: G 184 GLN cc_start: 0.6995 (mp10) cc_final: 0.6661 (mp10) REVERT: G 185 GLU cc_start: 0.6607 (mm-30) cc_final: 0.6090 (mm-30) REVERT: G 188 GLU cc_start: 0.5646 (OUTLIER) cc_final: 0.5415 (tt0) REVERT: G 223 TYR cc_start: 0.8096 (t80) cc_final: 0.7726 (t80) REVERT: G 225 GLU cc_start: 0.8513 (mt-10) cc_final: 0.8192 (mt-10) REVERT: G 227 LEU cc_start: 0.7836 (mm) cc_final: 0.7588 (mm) REVERT: G 244 MET cc_start: 0.7248 (ttm) cc_final: 0.6934 (ttp) outliers start: 107 outliers final: 87 residues processed: 1122 average time/residue: 0.4506 time to fit residues: 738.4431 Evaluate side-chains 1171 residues out of total 2558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 1073 time to evaluate : 2.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 54 GLU Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 373 LYS Chi-restraints excluded: chain A residue 385 ASP Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 491 ILE Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 261 ASP Chi-restraints excluded: chain B residue 375 MET Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 442 ARG Chi-restraints excluded: chain B residue 452 ASP Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 36 ASP Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 262 ASP Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 327 SER Chi-restraints excluded: chain C residue 332 THR Chi-restraints excluded: chain C residue 450 VAL Chi-restraints excluded: chain C residue 470 HIS Chi-restraints excluded: chain C residue 486 ASP Chi-restraints excluded: chain D residue 2 THR Chi-restraints excluded: chain D residue 7 ILE Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 49 GLU Chi-restraints excluded: chain D residue 57 ASP Chi-restraints excluded: chain D residue 66 SER Chi-restraints excluded: chain D residue 112 ASP Chi-restraints excluded: chain D residue 131 GLU Chi-restraints excluded: chain D residue 203 LYS Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 295 THR Chi-restraints excluded: chain D residue 299 SER Chi-restraints excluded: chain D residue 323 SER Chi-restraints excluded: chain D residue 344 VAL Chi-restraints excluded: chain D residue 382 ASP Chi-restraints excluded: chain D residue 384 ILE Chi-restraints excluded: chain D residue 419 GLN Chi-restraints excluded: chain D residue 423 GLN Chi-restraints excluded: chain D residue 428 VAL Chi-restraints excluded: chain D residue 456 VAL Chi-restraints excluded: chain E residue 57 ASP Chi-restraints excluded: chain E residue 103 ILE Chi-restraints excluded: chain E residue 136 GLU Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 265 SER Chi-restraints excluded: chain E residue 293 THR Chi-restraints excluded: chain E residue 314 THR Chi-restraints excluded: chain E residue 357 GLU Chi-restraints excluded: chain E residue 381 GLN Chi-restraints excluded: chain E residue 384 ILE Chi-restraints excluded: chain E residue 395 GLU Chi-restraints excluded: chain E residue 405 ARG Chi-restraints excluded: chain E residue 456 VAL Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 46 LEU Chi-restraints excluded: chain F residue 54 LEU Chi-restraints excluded: chain F residue 84 SER Chi-restraints excluded: chain F residue 90 VAL Chi-restraints excluded: chain F residue 98 VAL Chi-restraints excluded: chain F residue 106 GLU Chi-restraints excluded: chain F residue 183 SER Chi-restraints excluded: chain F residue 233 LEU Chi-restraints excluded: chain F residue 258 THR Chi-restraints excluded: chain F residue 267 LEU Chi-restraints excluded: chain F residue 273 SER Chi-restraints excluded: chain F residue 281 LEU Chi-restraints excluded: chain F residue 351 SER Chi-restraints excluded: chain F residue 384 ILE Chi-restraints excluded: chain F residue 455 LEU Chi-restraints excluded: chain F residue 462 VAL Chi-restraints excluded: chain G residue 22 GLN Chi-restraints excluded: chain G residue 83 VAL Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain G residue 101 LEU Chi-restraints excluded: chain G residue 146 GLN Chi-restraints excluded: chain G residue 148 SER Chi-restraints excluded: chain G residue 186 VAL Chi-restraints excluded: chain G residue 188 GLU Chi-restraints excluded: chain G residue 232 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 195 optimal weight: 6.9990 chunk 261 optimal weight: 6.9990 chunk 75 optimal weight: 0.6980 chunk 226 optimal weight: 0.8980 chunk 36 optimal weight: 6.9990 chunk 68 optimal weight: 0.5980 chunk 246 optimal weight: 9.9990 chunk 103 optimal weight: 0.0270 chunk 252 optimal weight: 8.9990 chunk 31 optimal weight: 6.9990 chunk 45 optimal weight: 4.9990 overall best weight: 1.4440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 GLN A 172 GLN ** B 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 433 GLN C 172 GLN ** C 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 365 GLN G 36 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.129594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.114617 restraints weight = 35216.307| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 2.20 r_work: 0.3345 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3177 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.4679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 24604 Z= 0.209 Angle : 0.557 8.035 33364 Z= 0.289 Chirality : 0.044 0.161 3840 Planarity : 0.005 0.055 4349 Dihedral : 7.692 86.558 3574 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 4.03 % Allowed : 27.44 % Favored : 68.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.83 % 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 (0.15), residues: 3104 helix: 1.15 (0.15), residues: 1249 sheet: 0.23 (0.22), residues: 550 loop : -0.73 (0.17), residues: 1305 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS D 173 PHE 0.022 0.001 PHE A 494 TYR 0.019 0.001 TYR C 248 ARG 0.009 0.000 ARG E 115 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10392.07 seconds wall clock time: 184 minutes 0.60 seconds (11040.60 seconds total)