Starting phenix.real_space_refine on Mon Feb 19 08:57:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l1q_23115/02_2024/7l1q_23115_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l1q_23115/02_2024/7l1q_23115.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l1q_23115/02_2024/7l1q_23115.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l1q_23115/02_2024/7l1q_23115.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l1q_23115/02_2024/7l1q_23115_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l1q_23115/02_2024/7l1q_23115_updated.pdb" } resolution = 3.4 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= 0.049 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 18 5.49 5 Mg 6 5.21 5 S 78 5.16 5 C 15235 2.51 5 N 4214 2.21 5 O 4653 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 68": "OE1" <-> "OE2" Residue "A ARG 93": "NH1" <-> "NH2" Residue "A GLU 96": "OE1" <-> "OE2" Residue "A GLU 101": "OE1" <-> "OE2" Residue "A ASP 116": "OD1" <-> "OD2" Residue "A GLU 122": "OE1" <-> "OE2" Residue "A ARG 127": "NH1" <-> "NH2" Residue "A GLU 202": "OE1" <-> "OE2" Residue "A TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 262": "OD1" <-> "OD2" Residue "A ARG 271": "NH1" <-> "NH2" Residue "A GLU 272": "OE1" <-> "OE2" Residue "A ARG 296": "NH1" <-> "NH2" Residue "A ASP 306": "OD1" <-> "OD2" Residue "A ASP 339": "OD1" <-> "OD2" Residue "A PHE 343": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 350": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 390": "NH1" <-> "NH2" Residue "A ASP 401": "OD1" <-> "OD2" Residue "A ARG 412": "NH1" <-> "NH2" Residue "A ASP 423": "OD1" <-> "OD2" Residue "A TYR 438": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 442": "NH1" <-> "NH2" Residue "A ASP 447": "OD1" <-> "OD2" Residue "A ARG 454": "NH1" <-> "NH2" Residue "A PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 457": "OE1" <-> "OE2" Residue "A PHE 463": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 465": "OD1" <-> "OD2" Residue "A GLU 473": "OE1" <-> "OE2" Residue "B ASP 45": "OD1" <-> "OD2" Residue "B TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 122": "OE1" <-> "OE2" Residue "B ARG 140": "NH1" <-> "NH2" Residue "B GLU 144": "OE1" <-> "OE2" Residue "B ASP 170": "OD1" <-> "OD2" Residue "B ARG 171": "NH1" <-> "NH2" Residue "B TYR 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 206": "NH1" <-> "NH2" Residue "B ASP 219": "OD1" <-> "OD2" Residue "B PHE 236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 247": "OE1" <-> "OE2" Residue "B TYR 260": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 262": "OD1" <-> "OD2" Residue "B ARG 296": "NH1" <-> "NH2" Residue "B GLU 299": "OE1" <-> "OE2" Residue "B ASP 306": "OD1" <-> "OD2" Residue "B PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 320": "OE1" <-> "OE2" Residue "B ASP 325": "OD1" <-> "OD2" Residue "B ASP 347": "OD1" <-> "OD2" Residue "B ARG 365": "NH1" <-> "NH2" Residue "B ARG 383": "NH1" <-> "NH2" Residue "B ASP 385": "OD1" <-> "OD2" Residue "B GLU 391": "OE1" <-> "OE2" Residue "B PHE 395": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 401": "OD1" <-> "OD2" Residue "B ARG 412": "NH1" <-> "NH2" Residue "B GLU 418": "OE1" <-> "OE2" Residue "B ASP 423": "OD1" <-> "OD2" Residue "B GLU 451": "OE1" <-> "OE2" Residue "B ARG 454": "NH1" <-> "NH2" Residue "B ARG 455": "NH1" <-> "NH2" Residue "B PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 465": "OD1" <-> "OD2" Residue "B GLU 473": "OE1" <-> "OE2" Residue "C ASP 27": "OD1" <-> "OD2" Residue "C GLU 54": "OE1" <-> "OE2" Residue "C GLU 68": "OE1" <-> "OE2" Residue "C GLU 84": "OE1" <-> "OE2" Residue "C ASP 86": "OD1" <-> "OD2" Residue "C GLU 96": "OE1" <-> "OE2" Residue "C GLU 125": "OE1" <-> "OE2" Residue "C ARG 140": "NH1" <-> "NH2" Residue "C ASP 181": "OD1" <-> "OD2" Residue "C TYR 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 202": "OE1" <-> "OE2" Residue "C ARG 206": "NH1" <-> "NH2" Residue "C TYR 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 271": "NH1" <-> "NH2" Residue "C ARG 278": "NH1" <-> "NH2" Residue "C PHE 291": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 299": "OE1" <-> "OE2" Residue "C GLU 320": "OE1" <-> "OE2" Residue "C ASP 339": "OD1" <-> "OD2" Residue "C ARG 365": "NH1" <-> "NH2" Residue "C TYR 389": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 391": "OE1" <-> "OE2" Residue "C GLU 393": "OE1" <-> "OE2" 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 GLU 457": "OE1" <-> "OE2" 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 PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 37": "NH1" <-> "NH2" Residue "D ASP 43": "OD1" <-> "OD2" Residue "D GLU 75": "OE1" <-> "OE2" 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 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 TYR 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 246": "OD1" <-> "OD2" Residue "D PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 263": "OE1" <-> "OE2" Residue "D TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 315": "OD1" <-> "OD2" Residue "D ASP 326": "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 ASP 394": "OD1" <-> "OD2" Residue "D GLU 395": "OE1" <-> "OE2" Residue "D ASP 396": "OD1" <-> "OD2" Residue "D PHE 408": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 418": "OE1" <-> "OE2" Residue "D TYR 427": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 435": "NH1" <-> "NH2" Residue "D TYR 445": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 "E ARG 3": "NH1" <-> "NH2" Residue "E ASP 15": "OD1" <-> "OD2" Residue "E PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 39": "OE1" <-> "OE2" Residue "E ARG 72": "NH1" <-> "NH2" Residue "E GLU 89": "OE1" <-> "OE2" Residue "E GLU 101": "OE1" <-> "OE2" Residue "E GLU 106": "OE1" <-> "OE2" Residue "E ASP 108": "OD1" <-> "OD2" Residue "E ARG 114": "NH1" <-> "NH2" Residue "E GLU 136": "OE1" <-> "OE2" Residue "E PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 170": "OE1" <-> "OE2" Residue "E PHE 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 190": "OD1" <-> "OD2" Residue "E ASP 197": "OD1" <-> "OD2" Residue "E ASP 204": "OD1" <-> "OD2" Residue "E ARG 240": "NH1" <-> "NH2" Residue "E ASP 246": "OD1" <-> "OD2" Residue "E ASP 252": "OD1" <-> "OD2" Residue "E GLU 263": "OE1" <-> "OE2" Residue "E GLU 284": "OE1" <-> "OE2" Residue "E TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 322": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 357": "OE1" <-> "OE2" Residue "E GLU 361": "OE1" <-> "OE2" Residue "E ASP 382": "OD1" <-> "OD2" Residue "E ARG 402": "NH1" <-> "NH2" Residue "E ARG 404": "NH1" <-> "NH2" Residue "E PHE 409": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 414": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 418": "OE1" <-> "OE2" Residue "E GLU 450": "OE1" <-> "OE2" Residue "E ASP 451": "OD1" <-> "OD2" Residue "E PHE 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 454": "NH1" <-> "NH2" Residue "F ARG 5": "NH1" <-> "NH2" Residue "F PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 19": "OE1" <-> "OE2" Residue "F ARG 37": "NH1" <-> "NH2" Residue "F GLU 39": "OE1" <-> "OE2" Residue "F ASP 57": "OD1" <-> "OD2" Residue "F ASP 68": "OD1" <-> "OD2" Residue "F GLU 89": "OE1" <-> "OE2" Residue "F PHE 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 112": "OD1" <-> "OD2" Residue "F ARG 120": "NH1" <-> "NH2" 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 TYR 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 240": "NH1" <-> "NH2" Residue "F ASP 252": "OD1" <-> "OD2" Residue "F GLU 263": "OE1" <-> "OE2" Residue "F GLU 284": "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 357": "OE1" <-> "OE2" Residue "F GLU 362": "OE1" <-> "OE2" Residue "F GLU 379": "OE1" <-> "OE2" Residue "F ASP 382": "OD1" <-> "OD2" Residue "F ASP 396": "OD1" <-> "OD2" Residue "F ARG 402": "NH1" <-> "NH2" Residue "F ARG 404": "NH1" <-> "NH2" Residue "F GLU 418": "OE1" <-> "OE2" Residue "F PHE 420": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 439": "OE1" <-> "OE2" Residue "F GLU 460": "OE1" <-> "OE2" 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 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 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 GLU 154": "OE1" <-> "OE2" Residue "G ASP 169": "OD1" <-> "OD2" Residue "G GLU 170": "OE1" <-> "OE2" 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 225": "OE1" <-> "OE2" Residue "G GLU 256": "OE1" <-> "OE2" Residue "G TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 24204 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: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" 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: "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: 12.60, per 1000 atoms: 0.52 Number of scatterers: 24204 At special positions: 0 Unit cell: (141.12, 120.96, 131.88, 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 18 15.00 Mg 6 11.99 O 4653 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: 8.92 Conformation dependent library (CDL) restraints added in 4.3 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: 110 helices and 24 sheets defined 40.9% alpha, 11.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.48 Creating SS restraints... Processing helix chain 'A' and resid 151 through 156 Processing helix chain 'A' and resid 175 through 183 Processing helix chain 'A' and resid 202 through 214 Processing helix chain 'A' and resid 232 through 252 Proline residue: A 239 - end of helix removed outlier: 3.508A pdb=" N GLY A 246 " --> pdb=" O GLY A 242 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N TYR A 248 " --> pdb=" O ALA A 244 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N PHE A 249 " --> pdb=" O MET A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 276 Processing helix chain 'A' and resid 283 through 285 No H-bonds generated for 'chain 'A' and resid 283 through 285' Processing helix chain 'A' and resid 288 through 300 removed outlier: 3.680A pdb=" N HIS A 294 " --> pdb=" O PHE A 291 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N SER A 295 " --> pdb=" O TYR A 292 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LEU A 298 " --> pdb=" O SER A 295 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N GLU A 299 " --> pdb=" O ARG A 296 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ARG A 300 " --> pdb=" O LEU A 297 " (cutoff:3.500A) 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: 3.686A 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 398 removed outlier: 3.728A pdb=" N LYS A 377 " --> pdb=" O LYS A 373 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N VAL A 378 " --> pdb=" O ALA A 374 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N THR A 381 " --> pdb=" O LYS A 377 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLU A 391 " --> pdb=" O ALA A 387 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ALA A 394 " --> pdb=" O ARG A 390 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N PHE A 395 " --> pdb=" O GLU A 391 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N GLN A 397 " --> pdb=" O GLU A 393 " (cutoff:3.500A) removed outlier: 8.124A pdb=" N PHE A 398 " --> pdb=" O ALA A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 420 removed outlier: 4.012A pdb=" N LYS A 409 " --> pdb=" O ALA A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 442 Processing helix chain 'A' and resid 444 through 446 No H-bonds generated for 'chain 'A' and resid 444 through 446' Processing helix chain 'A' and resid 450 through 467 removed outlier: 4.974A pdb=" N ARG A 454 " --> pdb=" O GLU A 451 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N PHE A 456 " --> pdb=" O VAL A 453 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLU A 459 " --> pdb=" O PHE A 456 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N TYR A 461 " --> pdb=" O LYS A 458 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU A 462 " --> pdb=" O GLU A 459 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LEU A 464 " --> pdb=" O TYR A 461 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ASN A 467 " --> pdb=" O LEU A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 478 Processing helix chain 'A' and resid 484 through 497 removed outlier: 3.827A pdb=" N ASN A 488 " --> pdb=" O GLU A 484 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N LYS A 489 " --> pdb=" O ASP A 485 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N PHE A 494 " --> pdb=" O ALA A 490 " (cutoff:3.500A) 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 185 Processing helix chain 'B' and resid 202 through 214 removed outlier: 3.595A pdb=" N ARG B 213 " --> pdb=" O VAL B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 219 No H-bonds generated for 'chain 'B' and resid 217 through 219' Processing helix chain 'B' and resid 232 through 236 Processing helix chain 'B' and resid 238 through 252 removed outlier: 3.739A pdb=" N TYR B 248 " --> pdb=" O ALA B 244 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N PHE B 249 " --> pdb=" O MET B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 276 Processing helix chain 'B' and resid 283 through 285 No H-bonds generated for 'chain 'B' and resid 283 through 285' Processing helix chain 'B' and resid 288 through 300 removed outlier: 3.819A pdb=" N LEU B 293 " --> pdb=" O ILE B 290 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N HIS B 294 " --> pdb=" O PHE B 291 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU B 298 " --> pdb=" O SER B 295 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N GLU B 299 " --> pdb=" O ARG B 296 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ARG B 300 " --> pdb=" O LEU B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 337 removed outlier: 3.832A pdb=" N ILE B 337 " --> pdb=" O ASN B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 349 No H-bonds generated for 'chain 'B' and resid 346 through 349' Processing helix chain 'B' and resid 359 through 361 No H-bonds generated for 'chain 'B' and resid 359 through 361' Processing helix chain 'B' and resid 373 through 379 Processing helix chain 'B' and resid 382 through 398 removed outlier: 3.825A pdb=" N PHE B 398 " --> pdb=" O ALA B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 420 removed outlier: 3.622A pdb=" N ALA B 411 " --> pdb=" O GLN B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 441 Processing helix chain 'B' and resid 450 through 467 removed outlier: 3.888A pdb=" N ARG B 454 " --> pdb=" O VAL B 450 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N GLN B 466 " --> pdb=" O LEU B 462 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ASN B 467 " --> pdb=" O PHE B 463 " (cutoff:3.500A) Processing helix chain 'B' and resid 469 through 478 Processing helix chain 'B' and resid 484 through 497 removed outlier: 3.627A pdb=" N LYS B 496 " --> pdb=" O GLU B 492 " (cutoff:3.500A) Processing helix chain 'C' and resid 35 through 37 No H-bonds generated for 'chain 'C' and resid 35 through 37' Processing helix chain 'C' and resid 151 through 156 Processing helix chain 'C' and resid 175 through 187 removed outlier: 4.601A pdb=" N LYS C 187 " --> pdb=" O ILE C 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 214 Processing helix chain 'C' and resid 218 through 220 No H-bonds generated for 'chain 'C' and resid 218 through 220' Processing helix chain 'C' and resid 232 through 236 Processing helix chain 'C' and resid 238 through 252 removed outlier: 4.089A pdb=" N TYR C 248 " --> pdb=" O ALA C 244 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N PHE C 249 " --> pdb=" O MET C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 263 through 277 Processing helix chain 'C' and resid 290 through 298 Processing helix chain 'C' and resid 329 through 337 Processing helix chain 'C' and resid 346 through 351 removed outlier: 3.649A pdb=" N SER C 351 " --> pdb=" O ASP C 347 " (cutoff:3.500A) Processing helix chain 'C' and resid 373 through 396 removed outlier: 3.583A pdb=" N VAL C 378 " --> pdb=" O ALA C 374 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N THR C 381 " --> pdb=" O LYS C 377 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU C 384 " --> pdb=" O GLY C 380 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLU C 391 " --> pdb=" O ALA C 387 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N PHE C 395 " --> pdb=" O GLU C 391 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 419 Processing helix chain 'C' and resid 430 through 441 removed outlier: 3.796A pdb=" N LEU C 435 " --> pdb=" O GLU C 431 " (cutoff:3.500A) Processing helix chain 'C' and resid 452 through 466 removed outlier: 4.323A pdb=" N GLU C 457 " --> pdb=" O ARG C 454 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLU C 459 " --> pdb=" O PHE C 456 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N TYR C 461 " --> pdb=" O LYS C 458 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LEU C 462 " --> pdb=" O GLU C 459 " (cutoff:3.500A) Processing helix chain 'C' and resid 469 through 478 removed outlier: 3.635A pdb=" N THR C 477 " --> pdb=" O GLU C 473 " (cutoff:3.500A) Processing helix chain 'C' and resid 484 through 497 Processing helix chain 'D' and resid 140 through 145 Processing helix chain 'D' and resid 164 through 178 Processing helix chain 'D' and resid 192 through 204 removed outlier: 3.582A pdb=" N ASN D 196 " --> pdb=" O THR D 192 " (cutoff:3.500A) Processing helix chain 'D' and resid 208 through 210 No H-bonds generated for 'chain 'D' and resid 208 through 210' Processing helix chain 'D' and resid 222 through 243 removed outlier: 3.605A pdb=" N VAL D 228 " --> pdb=" O ALA D 224 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N ALA D 229 " --> pdb=" O ARG D 225 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N LEU D 230 " --> pdb=" O MET D 226 " (cutoff:3.500A) Processing helix chain 'D' and resid 255 through 268 Processing helix chain 'D' and resid 281 through 291 removed outlier: 4.254A pdb=" N ARG D 291 " --> pdb=" O GLN D 287 " (cutoff:3.500A) Processing helix chain 'D' and resid 316 through 322 Processing helix chain 'D' and resid 333 through 338 Processing helix chain 'D' and resid 361 through 378 Processing helix chain 'D' and resid 381 through 386 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 Processing helix chain 'D' and resid 416 through 420 Processing helix chain 'D' and resid 430 through 442 Processing helix chain 'D' and resid 444 through 447 removed outlier: 4.334A pdb=" N HIS D 447 " --> pdb=" O LYS D 444 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 444 through 447' Processing helix chain 'D' and resid 450 through 453 Processing helix chain 'D' and resid 459 through 469 Processing helix chain 'E' and resid 140 through 145 Processing helix chain 'E' and resid 165 through 177 Processing helix chain 'E' and resid 192 through 205 Processing helix chain 'E' and resid 222 through 241 removed outlier: 4.381A pdb=" N ALA E 229 " --> pdb=" O ARG E 225 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N LEU E 230 " --> pdb=" O MET E 226 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU E 233 " --> pdb=" O ALA E 229 " (cutoff:3.500A) Processing helix chain 'E' and resid 255 through 268 Processing helix chain 'E' and resid 281 through 289 removed outlier: 3.654A pdb=" N LEU E 288 " --> pdb=" O GLU E 284 " (cutoff:3.500A) Processing helix chain 'E' and resid 316 through 324 removed outlier: 3.952A pdb=" N HIS E 324 " --> pdb=" O THR E 320 " (cutoff:3.500A) Processing helix chain 'E' and resid 333 through 336 No H-bonds generated for 'chain 'E' and resid 333 through 336' 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: 4.019A pdb=" N ASP E 382 " --> pdb=" O LYS E 378 " (cutoff:3.500A) Processing helix chain 'E' and resid 394 through 409 Processing helix chain 'E' and resid 415 through 420 Processing helix chain 'E' and resid 430 through 442 Processing helix chain 'E' and resid 444 through 447 removed outlier: 4.362A pdb=" N HIS E 447 " --> pdb=" O LYS E 444 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 444 through 447' Processing helix chain 'E' and resid 450 through 453 Processing helix chain 'E' and resid 459 through 469 removed outlier: 3.560A pdb=" N LYS E 467 " --> pdb=" O VAL E 463 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA E 468 " --> pdb=" O GLU E 464 " (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 144 Processing helix chain 'F' and resid 164 through 175 Processing helix chain 'F' and resid 192 through 204 Processing helix chain 'F' and resid 207 through 209 No H-bonds generated for 'chain 'F' and resid 207 through 209' Processing helix chain 'F' and resid 222 through 242 removed outlier: 4.292A pdb=" N ALA F 229 " --> pdb=" O ARG F 225 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N LEU F 230 " --> pdb=" O MET F 226 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N MET F 235 " --> pdb=" O THR F 231 " (cutoff:3.500A) Processing helix chain 'F' and resid 254 through 268 removed outlier: 3.593A pdb=" N GLN F 259 " --> pdb=" O ARG F 256 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N SER F 265 " --> pdb=" O SER F 262 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ALA F 266 " --> pdb=" O GLU F 263 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU F 267 " --> pdb=" O VAL F 264 " (cutoff:3.500A) Processing helix chain 'F' and resid 281 through 291 removed outlier: 3.824A pdb=" N ARG F 291 " --> pdb=" O GLN F 287 " (cutoff:3.500A) Processing helix chain 'F' and resid 316 through 321 removed outlier: 3.634A pdb=" N THR F 321 " --> pdb=" O ALA F 317 " (cutoff:3.500A) Processing helix chain 'F' and resid 333 through 338 removed outlier: 3.544A pdb=" N MET F 338 " --> pdb=" O LYS F 334 " (cutoff:3.500A) 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 387 removed outlier: 3.748A pdb=" N VAL F 366 " --> pdb=" O GLU F 362 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLU F 379 " --> pdb=" O GLN F 375 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ASP F 382 " --> pdb=" O LYS F 378 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ILE F 383 " --> pdb=" O GLU F 379 " (cutoff:3.500A) Processing helix chain 'F' and resid 389 through 391 No H-bonds generated for 'chain 'F' and resid 389 through 391' Processing helix chain 'F' and resid 394 through 409 removed outlier: 4.162A pdb=" N LEU F 398 " --> pdb=" O GLU F 395 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL F 399 " --> pdb=" O ASP F 396 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA F 403 " --> pdb=" O VAL F 400 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ARG F 404 " --> pdb=" O HIS F 401 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ILE F 406 " --> pdb=" O ALA F 403 " (cutoff:3.500A) Processing helix chain 'F' and resid 417 through 419 No H-bonds generated for 'chain 'F' and resid 417 through 419' Processing helix chain 'F' and resid 430 through 442 Processing helix chain 'F' and resid 459 through 468 Processing helix chain 'G' and resid 7 through 61 removed outlier: 4.164A pdb=" N THR G 12 " --> pdb=" O ARG G 8 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ARG G 13 " --> pdb=" O ASP G 9 " (cutoff:3.500A) Proline residue: G 47 - end of helix Processing helix chain 'G' and resid 94 through 110 removed outlier: 3.764A pdb=" N VAL G 98 " --> pdb=" O TYR G 94 " (cutoff:3.500A) Processing helix chain 'G' and resid 123 through 132 Processing helix chain 'G' and resid 149 through 164 removed outlier: 3.894A pdb=" N GLU G 154 " --> pdb=" O ALA G 150 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N ILE G 155 " --> pdb=" O ASP G 151 " (cutoff:3.500A) Processing helix chain 'G' and resid 212 through 286 Proline residue: G 221 - end of helix Processing sheet with id= A, first strand: chain 'A' and resid 88 through 90 removed outlier: 3.898A pdb=" N MET A 60 " --> pdb=" O LEU A 76 " (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 318 through 320 removed outlier: 6.533A pdb=" N ILE A 167 " --> pdb=" O VAL A 319 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N ILE A 342 " --> pdb=" O ILE A 168 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'A' and resid 221 through 227 removed outlier: 6.795A pdb=" N SER A 193 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 8.323A pdb=" N VAL A 224 " --> pdb=" O SER A 193 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N TYR A 195 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 8.174A pdb=" N ALA A 226 " --> pdb=" O TYR A 195 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N ALA A 197 " --> pdb=" O ALA A 226 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N THR A 314 " --> pdb=" O VAL A 258 " (cutoff:3.500A) removed outlier: 8.399A pdb=" N TYR A 260 " --> pdb=" O THR A 314 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N LEU A 316 " --> pdb=" O TYR A 260 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 29 through 34 removed outlier: 6.305A pdb=" N ARG A 40 " --> pdb=" O ILE A 32 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 30 through 35 removed outlier: 6.348A pdb=" N ARG B 40 " --> pdb=" O ILE B 32 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N VAL B 34 " --> pdb=" O ILE B 38 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ILE B 38 " --> pdb=" O VAL B 34 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ASN B 65 " --> pdb=" O GLY B 72 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N VAL B 74 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N ALA B 63 " --> pdb=" O VAL B 74 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N LEU B 76 " --> pdb=" O GLY B 61 " (cutoff:3.500A) removed outlier: 5.382A pdb=" N GLY B 61 " --> pdb=" O LEU B 76 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 96 through 99 removed outlier: 4.230A pdb=" N GLU B 125 " --> pdb=" O VAL B 99 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 341 through 344 removed outlier: 6.596A pdb=" N LEU B 166 " --> pdb=" O ILE B 342 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N LEU B 344 " --> pdb=" O LEU B 166 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N ILE B 168 " --> pdb=" O LEU B 344 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 222 through 226 removed outlier: 6.483A pdb=" N LEU B 257 " --> pdb=" O ILE B 194 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N VAL B 196 " --> pdb=" O LEU B 257 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N VAL B 259 " --> pdb=" O VAL B 196 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N ILE B 198 " --> pdb=" O VAL B 259 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N THR B 314 " --> pdb=" O VAL B 258 " (cutoff:3.500A) removed outlier: 8.178A pdb=" N TYR B 260 " --> pdb=" O THR B 314 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N LEU B 316 " --> pdb=" O TYR B 260 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 71 through 75 removed outlier: 3.955A pdb=" N ASN C 65 " --> pdb=" O GLY C 72 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N VAL C 74 " --> pdb=" O ALA C 63 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N ALA C 63 " --> pdb=" O VAL C 74 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N ARG C 40 " --> pdb=" O ILE C 32 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 96 through 99 Processing sheet with id= L, first strand: chain 'C' and resid 341 through 344 removed outlier: 6.525A pdb=" N LEU C 166 " --> pdb=" O ILE C 342 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N LEU C 344 " --> pdb=" O LEU C 166 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N ILE C 168 " --> pdb=" O LEU C 344 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 257 through 260 removed outlier: 6.671A pdb=" N THR C 314 " --> pdb=" O VAL C 258 " (cutoff:3.500A) removed outlier: 8.165A pdb=" N TYR C 260 " --> pdb=" O THR C 314 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N LEU C 316 " --> pdb=" O TYR C 260 " (cutoff:3.500A) No H-bonds generated for sheet with id= M Processing sheet with id= N, first strand: chain 'C' and resid 194 through 200 removed outlier: 6.585A pdb=" N ILE C 222 " --> pdb=" O TYR C 195 " (cutoff:3.500A) removed outlier: 7.922A pdb=" N ALA C 197 " --> pdb=" O ILE C 222 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N VAL C 224 " --> pdb=" O ALA C 197 " (cutoff:3.500A) removed outlier: 7.968A pdb=" N GLY C 199 " --> pdb=" O VAL C 224 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N ALA C 226 " --> pdb=" O GLY C 199 " (cutoff:3.500A) No H-bonds generated for sheet with id= N Processing sheet with id= O, first strand: chain 'D' and resid 6 through 10 removed outlier: 6.366A pdb=" N ASP D 15 " --> pdb=" O ILE D 7 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N VAL D 9 " --> pdb=" O VAL D 13 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N VAL D 13 " --> pdb=" O VAL D 9 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ILE D 62 " --> pdb=" O VAL D 50 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N VAL D 50 " --> pdb=" O ILE D 62 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 84 through 86 Processing sheet with id= Q, first strand: chain 'D' and resid 327 through 330 removed outlier: 3.721A pdb=" N ALA D 327 " --> pdb=" O LYS D 153 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N SER D 302 " --> pdb=" O ILE D 154 " (cutoff:3.500A) removed outlier: 7.894A pdb=" N LEU D 156 " --> pdb=" O SER D 302 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N GLN D 304 " --> pdb=" O LEU D 156 " (cutoff:3.500A) removed outlier: 8.090A pdb=" N GLY D 158 " --> pdb=" O GLN D 304 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N ILE D 306 " --> pdb=" O GLY D 158 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N LEU D 249 " --> pdb=" O ILE D 303 " (cutoff:3.500A) removed outlier: 8.256A pdb=" N ALA D 305 " --> pdb=" O LEU D 249 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N ILE D 251 " --> pdb=" O ALA D 305 " (cutoff:3.500A) removed outlier: 8.956A pdb=" N TYR D 307 " --> pdb=" O ILE D 251 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'E' and resid 75 through 77 removed outlier: 3.696A pdb=" N ARG E 5 " --> pdb=" O LYS E 17 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N ASP E 15 " --> pdb=" O ILE E 7 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N VAL E 9 " --> pdb=" O VAL E 13 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N VAL E 13 " --> pdb=" O VAL E 9 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N ILE E 62 " --> pdb=" O VAL E 50 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N VAL E 50 " --> pdb=" O ILE E 62 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'E' and resid 84 through 86 Processing sheet with id= T, first strand: chain 'E' and resid 327 through 331 removed outlier: 7.907A pdb=" N ILE E 154 " --> pdb=" O ILE E 300 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N SER E 302 " --> pdb=" O ILE E 154 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N LEU E 156 " --> pdb=" O SER E 302 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N GLN E 304 " --> pdb=" O LEU E 156 " (cutoff:3.500A) removed outlier: 8.513A pdb=" N GLY E 158 " --> pdb=" O GLN E 304 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N ILE E 306 " --> pdb=" O GLY E 158 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N VAL E 247 " --> pdb=" O THR E 301 " (cutoff:3.500A) removed outlier: 8.438A pdb=" N ILE E 303 " --> pdb=" O VAL E 247 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N LEU E 249 " --> pdb=" O ILE E 303 " (cutoff:3.500A) removed outlier: 8.337A pdb=" N ALA E 305 " --> pdb=" O LEU E 249 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N ILE E 251 " --> pdb=" O ALA E 305 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ALA E 212 " --> pdb=" O PHE E 185 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N GLY E 187 " --> pdb=" O ALA E 212 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N VAL E 214 " --> pdb=" O GLY E 187 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'F' and resid 6 through 10 removed outlier: 6.831A pdb=" N ASP F 15 " --> pdb=" O ILE F 7 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N VAL F 9 " --> pdb=" O VAL F 13 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N VAL F 13 " --> pdb=" O VAL F 9 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N ILE F 62 " --> pdb=" O VAL F 50 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N VAL F 50 " --> pdb=" O ILE F 62 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N ILE F 44 " --> pdb=" O HIS F 34 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N HIS F 34 " --> pdb=" O ILE F 44 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'F' and resid 84 through 86 Processing sheet with id= W, first strand: chain 'F' and resid 327 through 331 removed outlier: 7.883A pdb=" N ILE F 154 " --> pdb=" O ILE F 300 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N SER F 302 " --> pdb=" O ILE F 154 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N LEU F 156 " --> pdb=" O SER F 302 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N GLN F 304 " --> pdb=" O LEU F 156 " (cutoff:3.500A) removed outlier: 8.071A pdb=" N GLY F 158 " --> pdb=" O GLN F 304 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N ILE F 306 " --> pdb=" O GLY F 158 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N VAL F 247 " --> pdb=" O THR F 301 " (cutoff:3.500A) removed outlier: 8.086A pdb=" N ILE F 303 " --> pdb=" O VAL F 247 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N LEU F 249 " --> pdb=" O ILE F 303 " (cutoff:3.500A) removed outlier: 8.405A pdb=" N ALA F 305 " --> pdb=" O LEU F 249 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N ILE F 251 " --> pdb=" O ALA F 305 " (cutoff:3.500A) removed outlier: 8.997A pdb=" N TYR F 307 " --> pdb=" O ILE F 251 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ALA F 212 " --> pdb=" O PHE F 185 " (cutoff:3.500A) removed outlier: 8.207A pdb=" N GLY F 187 " --> pdb=" O ALA F 212 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N VAL F 214 " --> pdb=" O GLY F 187 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'G' and resid 189 through 192 removed outlier: 6.773A pdb=" N LEU G 171 " --> pdb=" O LEU G 191 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ILE G 84 " --> pdb=" O TYR G 174 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N VAL G 120 " --> pdb=" O ILE G 137 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N ASP G 139 " --> pdb=" O VAL G 120 " (cutoff:3.500A) 900 hydrogen bonds defined for protein. 2520 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: 6.97 Time building geometry restraints manager: 9.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 4497 1.32 - 1.44: 5579 1.44 - 1.57: 14350 1.57 - 1.69: 28 1.69 - 1.81: 154 Bond restraints: 24608 Sorted by residual: bond pdb=" C4 ATP A 600 " pdb=" C5 ATP A 600 " ideal model delta sigma weight residual 1.388 1.476 -0.088 1.00e-02 1.00e+04 7.83e+01 bond pdb=" C4 ATP B 600 " pdb=" C5 ATP B 600 " ideal model delta sigma weight residual 1.388 1.472 -0.084 1.00e-02 1.00e+04 7.13e+01 bond pdb=" C5 ATP A 600 " pdb=" C6 ATP A 600 " ideal model delta sigma weight residual 1.409 1.481 -0.072 1.00e-02 1.00e+04 5.18e+01 bond pdb=" C5 ATP B 600 " pdb=" C6 ATP B 600 " ideal model delta sigma weight residual 1.409 1.472 -0.063 1.00e-02 1.00e+04 3.93e+01 bond pdb=" C8 ATP B 600 " pdb=" N7 ATP B 600 " ideal model delta sigma weight residual 1.310 1.365 -0.055 1.00e-02 1.00e+04 3.03e+01 ... (remaining 24603 not shown) Histogram of bond angle deviations from ideal: 97.91 - 105.61: 695 105.61 - 113.32: 13042 113.32 - 121.02: 12283 121.02 - 128.73: 7227 128.73 - 136.44: 123 Bond angle restraints: 33370 Sorted by residual: angle pdb=" PB ATP B 600 " pdb=" O3B ATP B 600 " pdb=" PG ATP B 600 " ideal model delta sigma weight residual 139.87 118.94 20.93 1.00e+00 1.00e+00 4.38e+02 angle pdb=" PA ATP A 600 " pdb=" O3A ATP A 600 " pdb=" PB ATP A 600 " ideal model delta sigma weight residual 136.83 116.65 20.18 1.00e+00 1.00e+00 4.07e+02 angle pdb=" PB ATP E 501 " pdb=" O3B ATP E 501 " pdb=" PG ATP E 501 " ideal model delta sigma weight residual 139.87 121.88 17.99 1.00e+00 1.00e+00 3.24e+02 angle pdb=" PB ATP A 600 " pdb=" O3B ATP A 600 " pdb=" PG ATP A 600 " ideal model delta sigma weight residual 139.87 122.90 16.97 1.00e+00 1.00e+00 2.88e+02 angle pdb=" PB ATP C 602 " pdb=" O3B ATP C 602 " pdb=" PG ATP C 602 " ideal model delta sigma weight residual 139.87 122.97 16.90 1.00e+00 1.00e+00 2.86e+02 ... (remaining 33365 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.19: 13819 21.19 - 42.39: 997 42.39 - 63.58: 176 63.58 - 84.78: 45 84.78 - 105.97: 7 Dihedral angle restraints: 15044 sinusoidal: 6152 harmonic: 8892 Sorted by residual: dihedral pdb=" C THR B 204 " pdb=" N THR B 204 " pdb=" CA THR B 204 " pdb=" CB THR B 204 " ideal model delta harmonic sigma weight residual -122.00 -137.70 15.70 0 2.50e+00 1.60e-01 3.95e+01 dihedral pdb=" CA GLU C 284 " pdb=" C GLU C 284 " pdb=" N ALA C 285 " pdb=" CA ALA C 285 " ideal model delta harmonic sigma weight residual 180.00 151.59 28.41 0 5.00e+00 4.00e-02 3.23e+01 dihedral pdb=" CA GLY C 35 " pdb=" C GLY C 35 " pdb=" N ASP C 36 " pdb=" CA ASP C 36 " ideal model delta harmonic sigma weight residual 180.00 151.80 28.20 0 5.00e+00 4.00e-02 3.18e+01 ... (remaining 15041 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.101: 3338 0.101 - 0.203: 466 0.203 - 0.304: 28 0.304 - 0.406: 6 0.406 - 0.507: 2 Chirality restraints: 3840 Sorted by residual: chirality pdb=" CA THR B 204 " pdb=" N THR B 204 " pdb=" C THR B 204 " pdb=" CB THR B 204 " both_signs ideal model delta sigma weight residual False 2.53 2.02 0.51 2.00e-01 2.50e+01 6.42e+00 chirality pdb=" CA HIS A 425 " pdb=" N HIS A 425 " pdb=" C HIS A 425 " pdb=" CB HIS A 425 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.55e+00 chirality pdb=" CA ARG C 454 " pdb=" N ARG C 454 " pdb=" C ARG C 454 " pdb=" CB ARG C 454 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.63e+00 ... (remaining 3837 not shown) Planarity restraints: 4349 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 296 " -0.348 9.50e-02 1.11e+02 1.61e-01 3.64e+01 pdb=" NE ARG B 296 " -0.006 2.00e-02 2.50e+03 pdb=" CZ ARG B 296 " 0.084 2.00e-02 2.50e+03 pdb=" NH1 ARG B 296 " -0.023 2.00e-02 2.50e+03 pdb=" NH2 ARG B 296 " -0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 435 " 0.336 9.50e-02 1.11e+02 1.55e-01 3.04e+01 pdb=" NE ARG D 435 " 0.004 2.00e-02 2.50e+03 pdb=" CZ ARG D 435 " -0.074 2.00e-02 2.50e+03 pdb=" NH1 ARG D 435 " 0.020 2.00e-02 2.50e+03 pdb=" NH2 ARG D 435 " 0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 161 " 0.129 9.50e-02 1.11e+02 7.38e-02 2.83e+01 pdb=" NE ARG A 161 " -0.038 2.00e-02 2.50e+03 pdb=" CZ ARG A 161 " 0.087 2.00e-02 2.50e+03 pdb=" NH1 ARG A 161 " -0.031 2.00e-02 2.50e+03 pdb=" NH2 ARG A 161 " -0.024 2.00e-02 2.50e+03 ... (remaining 4346 not shown) Histogram of nonbonded interaction distances: 1.81 - 2.43: 24 2.43 - 3.04: 15008 3.04 - 3.66: 34598 3.66 - 4.28: 51970 4.28 - 4.90: 88168 Nonbonded interactions: 189768 Sorted by model distance: nonbonded pdb=" O2B ATP A 600 " pdb="MG MG A 601 " model vdw 1.807 2.170 nonbonded pdb=" OG1 THR F 165 " pdb="MG MG F 501 " model vdw 2.058 2.170 nonbonded pdb=" O1G ATP B 600 " pdb="MG MG B 601 " model vdw 2.067 2.170 nonbonded pdb=" OE1 GLU E 194 " pdb="MG MG E 502 " model vdw 2.151 2.170 nonbonded pdb=" O2G ATP E 501 " pdb="MG MG E 502 " model vdw 2.161 2.170 ... (remaining 189763 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) selection = (chain 'B' and resid 27 through 499) selection = (chain 'C' and resid 27 through 499) } ncs_group { reference = (chain 'D' and resid 2 through 470) selection = (chain 'E' and resid 2 through 470) selection = (chain 'F' and resid 2 through 470) } 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: 0.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 4.830 Check model and map are aligned: 0.340 Set scattering table: 0.190 Process input model: 62.180 Find NCS groups from input model: 1.710 Set up NCS constraints: 0.100 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:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6633 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 : 0.008 0.105 24608 Z= 0.521 Angle : 1.295 20.929 33370 Z= 0.838 Chirality : 0.068 0.507 3840 Planarity : 0.011 0.161 4349 Dihedral : 15.526 105.970 9354 Min Nonbonded Distance : 1.807 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.70 % Favored : 96.13 % Rotamer: Outliers : 2.54 % Allowed : 12.24 % Favored : 85.22 % Cbeta Deviations : 0.21 % 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: -0.80 (0.14), residues: 3104 helix: -0.40 (0.13), residues: 1253 sheet: -0.16 (0.22), residues: 500 loop : -0.63 (0.16), residues: 1351 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.013 0.003 HIS C 425 PHE 0.057 0.005 PHE A 236 TYR 0.054 0.007 TYR C 438 ARG 0.089 0.011 ARG A 161 *********************** 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 1127 residues out of total 2558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 1062 time to evaluate : 2.726 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 ILE cc_start: 0.7669 (mm) cc_final: 0.7371 (tt) REVERT: A 190 ASN cc_start: 0.7620 (m-40) cc_final: 0.7234 (m-40) REVERT: A 214 LYS cc_start: 0.7555 (tttt) cc_final: 0.7302 (tttt) REVERT: A 333 ASN cc_start: 0.7541 (t0) cc_final: 0.7303 (t0) REVERT: A 415 ARG cc_start: 0.7852 (mtt90) cc_final: 0.7505 (mtt90) REVERT: A 417 VAL cc_start: 0.8583 (t) cc_final: 0.8352 (m) REVERT: A 420 LEU cc_start: 0.8207 (mp) cc_final: 0.7912 (mt) REVERT: A 432 LYS cc_start: 0.7861 (mttt) cc_final: 0.7137 (mtpp) REVERT: A 456 PHE cc_start: 0.7658 (t80) cc_final: 0.7399 (t80) REVERT: B 32 ILE cc_start: 0.8331 (tt) cc_final: 0.7889 (tt) REVERT: B 45 ASP cc_start: 0.6433 (p0) cc_final: 0.6207 (p0) REVERT: B 88 VAL cc_start: 0.8178 (OUTLIER) cc_final: 0.7909 (p) REVERT: B 150 ILE cc_start: 0.8228 (mt) cc_final: 0.7330 (mt) REVERT: B 154 ASP cc_start: 0.7528 (m-30) cc_final: 0.7204 (m-30) REVERT: B 175 LYS cc_start: 0.7543 (mtmm) cc_final: 0.7065 (mtmm) REVERT: B 184 ILE cc_start: 0.7744 (mt) cc_final: 0.7505 (tp) REVERT: B 230 GLN cc_start: 0.6724 (mm-40) cc_final: 0.6459 (mm-40) REVERT: B 243 VAL cc_start: 0.7452 (m) cc_final: 0.7237 (t) REVERT: B 373 LYS cc_start: 0.7641 (ttmt) cc_final: 0.7149 (ttmt) REVERT: B 377 LYS cc_start: 0.7910 (mttp) cc_final: 0.7596 (mttp) REVERT: B 424 LEU cc_start: 0.7913 (tp) cc_final: 0.7657 (tp) REVERT: B 452 ASP cc_start: 0.6625 (m-30) cc_final: 0.6388 (t0) REVERT: B 470 HIS cc_start: 0.7689 (p90) cc_final: 0.7414 (p-80) REVERT: C 202 GLU cc_start: 0.6807 (tt0) cc_final: 0.6550 (tt0) REVERT: C 206 ARG cc_start: 0.7191 (ttt180) cc_final: 0.6851 (tpp-160) REVERT: C 227 SER cc_start: 0.7186 (p) cc_final: 0.6584 (p) REVERT: C 434 VAL cc_start: 0.7791 (m) cc_final: 0.7445 (p) REVERT: C 452 ASP cc_start: 0.7178 (m-30) cc_final: 0.6960 (m-30) REVERT: C 474 HIS cc_start: 0.6663 (t70) cc_final: 0.6315 (t70) REVERT: C 480 ASP cc_start: 0.6697 (t0) cc_final: 0.6357 (t0) REVERT: D 18 PHE cc_start: 0.7504 (m-80) cc_final: 0.7130 (m-80) REVERT: D 35 LYS cc_start: 0.7908 (ttmt) cc_final: 0.7700 (ttmt) REVERT: D 44 ILE cc_start: 0.7474 (tp) cc_final: 0.7230 (tp) REVERT: D 45 ASP cc_start: 0.6683 (t0) cc_final: 0.6178 (t0) REVERT: D 66 SER cc_start: 0.6800 (t) cc_final: 0.6524 (m) REVERT: D 104 ASP cc_start: 0.7583 (p0) cc_final: 0.6976 (p0) REVERT: D 191 ARG cc_start: 0.6989 (OUTLIER) cc_final: 0.6678 (mtt180) REVERT: D 213 MET cc_start: 0.7084 (mtp) cc_final: 0.6867 (mtp) REVERT: D 271 MET cc_start: 0.6352 (mtt) cc_final: 0.5522 (mtt) REVERT: D 275 VAL cc_start: 0.8418 (t) cc_final: 0.8096 (t) REVERT: D 308 VAL cc_start: 0.8668 (t) cc_final: 0.8432 (m) REVERT: D 333 ARG cc_start: 0.6760 (ttm110) cc_final: 0.6558 (ttm110) REVERT: D 334 LYS cc_start: 0.7477 (ttpt) cc_final: 0.7167 (ttpt) REVERT: D 401 HIS cc_start: 0.6358 (t70) cc_final: 0.5405 (t70) REVERT: D 405 ARG cc_start: 0.7057 (mpt180) cc_final: 0.6646 (mpt180) REVERT: D 441 LEU cc_start: 0.8432 (mt) cc_final: 0.8190 (mp) REVERT: D 464 GLU cc_start: 0.7391 (tp30) cc_final: 0.7023 (tp30) REVERT: E 10 MET cc_start: 0.5754 (mtp) cc_final: 0.5433 (mtp) REVERT: E 44 ILE cc_start: 0.6401 (tp) cc_final: 0.6162 (tp) REVERT: E 92 LEU cc_start: 0.6890 (OUTLIER) cc_final: 0.6627 (mt) REVERT: E 101 GLU cc_start: 0.6779 (OUTLIER) cc_final: 0.6551 (mp0) REVERT: E 136 GLU cc_start: 0.5764 (tt0) cc_final: 0.5480 (tt0) REVERT: E 168 ILE cc_start: 0.8685 (mm) cc_final: 0.8453 (mm) REVERT: E 197 ASP cc_start: 0.6279 (t0) cc_final: 0.6020 (t0) REVERT: E 201 GLU cc_start: 0.6676 (tp30) cc_final: 0.6202 (tp30) REVERT: E 207 VAL cc_start: 0.7471 (t) cc_final: 0.7196 (p) REVERT: E 372 GLN cc_start: 0.7623 (mt0) cc_final: 0.7305 (mt0) REVERT: E 389 MET cc_start: 0.7091 (mmm) cc_final: 0.6845 (mmm) REVERT: E 405 ARG cc_start: 0.7391 (mpt180) cc_final: 0.7188 (mpt180) REVERT: E 410 LEU cc_start: 0.8395 (mt) cc_final: 0.8175 (mt) REVERT: E 411 SER cc_start: 0.7834 (m) cc_final: 0.7548 (p) REVERT: E 419 GLN cc_start: 0.7452 (pt0) cc_final: 0.6862 (pm20) REVERT: E 432 GLU cc_start: 0.6463 (mm-30) cc_final: 0.5443 (mm-30) REVERT: E 450 GLU cc_start: 0.7008 (OUTLIER) cc_final: 0.6320 (pm20) REVERT: E 453 PHE cc_start: 0.7865 (m-80) cc_final: 0.7590 (m-80) REVERT: E 469 MET cc_start: 0.5663 (mmm) cc_final: 0.5352 (mmm) REVERT: F 38 ASN cc_start: 0.7681 (t0) cc_final: 0.7258 (t0) REVERT: F 39 GLU cc_start: 0.6959 (pp20) cc_final: 0.6727 (pp20) REVERT: F 47 THR cc_start: 0.6921 (t) cc_final: 0.6711 (p) REVERT: F 77 ILE cc_start: 0.6162 (OUTLIER) cc_final: 0.5684 (mt) REVERT: F 240 ARG cc_start: 0.5653 (OUTLIER) cc_final: 0.5324 (ppt90) REVERT: F 241 ASP cc_start: 0.7103 (m-30) cc_final: 0.6702 (m-30) REVERT: F 285 MET cc_start: 0.6887 (ttp) cc_final: 0.6530 (ttt) REVERT: F 331 LEU cc_start: 0.7754 (mt) cc_final: 0.7352 (mt) REVERT: F 366 VAL cc_start: 0.7550 (t) cc_final: 0.7017 (p) REVERT: F 377 TYR cc_start: 0.7842 (t80) cc_final: 0.7493 (t80) REVERT: F 438 LYS cc_start: 0.7942 (tttt) cc_final: 0.7651 (tttt) REVERT: F 456 VAL cc_start: 0.6235 (p) cc_final: 0.5750 (m) REVERT: G 12 THR cc_start: 0.8066 (p) cc_final: 0.7845 (t) REVERT: G 19 LYS cc_start: 0.8018 (mptt) cc_final: 0.7731 (mptt) REVERT: G 43 LYS cc_start: 0.8519 (ttpt) cc_final: 0.8253 (ttpt) REVERT: G 48 TYR cc_start: 0.7508 (t80) cc_final: 0.7266 (t80) REVERT: G 49 MET cc_start: 0.7640 (mmt) cc_final: 0.7430 (mmt) REVERT: G 70 MET cc_start: 0.7766 (mmp) cc_final: 0.7475 (mmp) REVERT: G 97 ASN cc_start: 0.7656 (m-40) cc_final: 0.6845 (m-40) REVERT: G 148 SER cc_start: 0.8579 (m) cc_final: 0.8346 (p) REVERT: G 149 PHE cc_start: 0.6840 (t80) cc_final: 0.6640 (t80) REVERT: G 222 GLN cc_start: 0.7570 (mt0) cc_final: 0.7337 (mt0) REVERT: G 265 TYR cc_start: 0.7740 (t80) cc_final: 0.7035 (t80) REVERT: G 269 ARG cc_start: 0.7140 (ttp80) cc_final: 0.6762 (ttp80) REVERT: G 270 GLN cc_start: 0.7319 (mt0) cc_final: 0.6930 (mt0) REVERT: G 275 GLN cc_start: 0.7426 (tp40) cc_final: 0.6321 (tp40) REVERT: G 279 GLU cc_start: 0.6698 (mm-30) cc_final: 0.6452 (mm-30) outliers start: 65 outliers final: 13 residues processed: 1101 average time/residue: 0.4090 time to fit residues: 661.9837 Evaluate side-chains 1004 residues out of total 2558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 984 time to evaluate : 2.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 306 ASP Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 177 GLN Chi-restraints excluded: chain D residue 191 ARG Chi-restraints excluded: chain D residue 426 SER Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain E residue 101 GLU Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 450 GLU Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 68 ASP Chi-restraints excluded: chain F residue 77 ILE Chi-restraints excluded: chain F residue 166 VAL Chi-restraints excluded: chain F residue 240 ARG Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 322 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 261 optimal weight: 0.9990 chunk 234 optimal weight: 6.9990 chunk 130 optimal weight: 0.9980 chunk 80 optimal weight: 3.9990 chunk 158 optimal weight: 9.9990 chunk 125 optimal weight: 3.9990 chunk 242 optimal weight: 3.9990 chunk 94 optimal weight: 10.0000 chunk 147 optimal weight: 3.9990 chunk 180 optimal weight: 10.0000 chunk 281 optimal weight: 5.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 GLN A 113 GLN A 185 ASN ** A 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 422 GLN A 433 GLN A 469 GLN A 470 HIS ** A 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 69 ASN B 470 HIS B 474 HIS B 488 ASN C 46 ASN C 69 ASN C 185 ASN D 33 GLN D 200 HIS ** D 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 259 GLN D 372 GLN D 381 GLN D 419 GLN E 33 GLN ** E 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 177 GLN E 259 GLN E 371 GLN ** E 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 8 GLN F 33 GLN F 174 ASN F 196 ASN F 287 GLN F 304 GLN ** F 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 330 ASN ** F 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 401 HIS F 423 GLN G 22 GLN G 41 ASN ** G 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 107 GLN G 146 GLN G 184 GLN G 266 ASN Total number of N/Q/H flips: 39 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6763 moved from start: 0.3045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 24608 Z= 0.304 Angle : 0.730 14.449 33370 Z= 0.384 Chirality : 0.050 0.231 3840 Planarity : 0.005 0.060 4349 Dihedral : 9.648 87.915 3611 Min Nonbonded Distance : 1.642 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.77 % Favored : 97.20 % Rotamer: Outliers : 6.14 % Allowed : 19.66 % Favored : 74.20 % 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: 0.39 (0.14), residues: 1248 sheet: 0.22 (0.23), residues: 498 loop : -0.61 (0.17), residues: 1358 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.002 HIS F 53 PHE 0.028 0.002 PHE A 236 TYR 0.023 0.002 TYR G 103 ARG 0.014 0.001 ARG A 278 *********************** 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 1177 residues out of total 2558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 157 poor density : 1020 time to evaluate : 2.636 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: symmetry clash revert: symmetry clash REVERT: A 31 VAL cc_start: 0.7494 (t) cc_final: 0.6786 (m) REVERT: A 87 GLU cc_start: 0.6789 (mm-30) cc_final: 0.6564 (mm-30) REVERT: A 154 ASP cc_start: 0.7723 (m-30) cc_final: 0.7451 (m-30) REVERT: A 156 LEU cc_start: 0.7359 (OUTLIER) cc_final: 0.7115 (mp) REVERT: A 190 ASN cc_start: 0.7501 (m-40) cc_final: 0.7097 (m-40) REVERT: A 272 GLU cc_start: 0.6891 (tt0) cc_final: 0.6649 (tt0) REVERT: A 296 ARG cc_start: 0.7317 (ttp-110) cc_final: 0.7111 (ttp-170) REVERT: A 365 ARG cc_start: 0.7142 (OUTLIER) cc_final: 0.6875 (mtt-85) REVERT: A 375 MET cc_start: 0.6493 (ttm) cc_final: 0.6193 (ttm) REVERT: A 415 ARG cc_start: 0.7882 (mtt90) cc_final: 0.7504 (mtt90) REVERT: A 417 VAL cc_start: 0.8540 (t) cc_final: 0.8337 (m) REVERT: A 424 LEU cc_start: 0.7794 (tp) cc_final: 0.7022 (tp) REVERT: A 432 LYS cc_start: 0.8001 (mttt) cc_final: 0.7218 (mtpp) REVERT: A 448 ILE cc_start: 0.7414 (mp) cc_final: 0.7047 (mp) REVERT: A 466 GLN cc_start: 0.7452 (mt0) cc_final: 0.7161 (mt0) REVERT: B 80 THR cc_start: 0.7989 (p) cc_final: 0.7723 (m) REVERT: B 93 ARG cc_start: 0.6476 (mmm160) cc_final: 0.6262 (mmm160) REVERT: B 303 LYS cc_start: 0.6786 (tptt) cc_final: 0.6563 (tptt) REVERT: B 305 SER cc_start: 0.6920 (m) cc_final: 0.6657 (m) REVERT: B 373 LYS cc_start: 0.7518 (ttmt) cc_final: 0.6899 (ttmt) REVERT: B 377 LYS cc_start: 0.8026 (mttp) cc_final: 0.7591 (mttp) REVERT: B 419 VAL cc_start: 0.8243 (t) cc_final: 0.8033 (p) REVERT: B 423 ASP cc_start: 0.7298 (OUTLIER) cc_final: 0.7095 (p0) REVERT: B 458 LYS cc_start: 0.6821 (tmmt) cc_final: 0.6572 (mttp) REVERT: B 463 PHE cc_start: 0.8099 (t80) cc_final: 0.7808 (t80) REVERT: B 469 GLN cc_start: 0.8189 (mm-40) cc_final: 0.7713 (mm-40) REVERT: B 470 HIS cc_start: 0.7656 (p-80) cc_final: 0.7424 (p-80) REVERT: B 477 THR cc_start: 0.7837 (m) cc_final: 0.7440 (p) REVERT: C 206 ARG cc_start: 0.7211 (ttt180) cc_final: 0.6893 (tpp80) REVERT: C 265 LYS cc_start: 0.7686 (mttp) cc_final: 0.7375 (mttp) REVERT: C 298 LEU cc_start: 0.8307 (OUTLIER) cc_final: 0.8092 (mt) REVERT: C 389 TYR cc_start: 0.7936 (t80) cc_final: 0.7655 (t80) REVERT: C 431 GLU cc_start: 0.7089 (pt0) cc_final: 0.6516 (pt0) REVERT: C 433 GLN cc_start: 0.7804 (mt0) cc_final: 0.7563 (mt0) REVERT: C 459 GLU cc_start: 0.7342 (mt-10) cc_final: 0.7001 (mt-10) REVERT: D 8 GLN cc_start: 0.6861 (tt0) cc_final: 0.6638 (tt0) REVERT: D 18 PHE cc_start: 0.7294 (m-80) cc_final: 0.6881 (m-80) REVERT: D 35 LYS cc_start: 0.7817 (ttmt) cc_final: 0.7605 (ttmt) REVERT: D 104 ASP cc_start: 0.7415 (p0) cc_final: 0.6853 (p0) REVERT: D 106 GLU cc_start: 0.6532 (mt-10) cc_final: 0.6235 (mt-10) REVERT: D 177 GLN cc_start: 0.7366 (OUTLIER) cc_final: 0.7025 (mp10) REVERT: D 183 SER cc_start: 0.7940 (m) cc_final: 0.7739 (m) REVERT: D 202 MET cc_start: 0.6498 (mmt) cc_final: 0.6216 (mmt) REVERT: D 207 VAL cc_start: 0.8518 (t) cc_final: 0.7709 (p) REVERT: D 227 ARG cc_start: 0.6354 (mmt180) cc_final: 0.6070 (mmt180) REVERT: D 242 GLU cc_start: 0.6678 (mm-30) cc_final: 0.6467 (mm-30) REVERT: D 256 ARG cc_start: 0.7875 (mtm-85) cc_final: 0.7651 (mtt90) REVERT: D 267 LEU cc_start: 0.7768 (mm) cc_final: 0.7199 (mt) REVERT: D 294 SER cc_start: 0.7259 (t) cc_final: 0.6709 (p) REVERT: D 308 VAL cc_start: 0.8824 (t) cc_final: 0.8573 (m) REVERT: D 314 THR cc_start: 0.8421 (p) cc_final: 0.8150 (m) REVERT: D 333 ARG cc_start: 0.6665 (ttm110) cc_final: 0.6440 (ttm110) REVERT: D 347 LEU cc_start: 0.7483 (OUTLIER) cc_final: 0.7121 (mt) REVERT: D 386 ILE cc_start: 0.7819 (OUTLIER) cc_final: 0.7460 (mt) REVERT: D 418 GLU cc_start: 0.7317 (mt-10) cc_final: 0.6865 (mp0) REVERT: D 441 LEU cc_start: 0.8599 (mt) cc_final: 0.8355 (mp) REVERT: D 464 GLU cc_start: 0.7360 (tp30) cc_final: 0.7041 (tp30) REVERT: E 92 LEU cc_start: 0.7039 (OUTLIER) cc_final: 0.6832 (mt) REVERT: E 101 GLU cc_start: 0.7140 (OUTLIER) cc_final: 0.6847 (mp0) REVERT: E 188 VAL cc_start: 0.7236 (t) cc_final: 0.7026 (p) REVERT: E 197 ASP cc_start: 0.6313 (t0) cc_final: 0.6025 (t0) REVERT: E 199 TYR cc_start: 0.7925 (t80) cc_final: 0.7173 (t80) REVERT: E 256 ARG cc_start: 0.7405 (mmt180) cc_final: 0.7192 (tpp-160) REVERT: E 291 ARG cc_start: 0.6561 (OUTLIER) cc_final: 0.6218 (tpp80) REVERT: E 369 LYS cc_start: 0.8089 (mtmm) cc_final: 0.7881 (mttm) REVERT: E 372 GLN cc_start: 0.7627 (mt0) cc_final: 0.7239 (mt0) REVERT: E 380 LEU cc_start: 0.8051 (tp) cc_final: 0.7589 (pp) REVERT: E 384 ILE cc_start: 0.8291 (mt) cc_final: 0.7554 (mt) REVERT: E 410 LEU cc_start: 0.8379 (mt) cc_final: 0.8178 (mt) REVERT: E 412 GLN cc_start: 0.6616 (tp40) cc_final: 0.6405 (tp-100) REVERT: E 469 MET cc_start: 0.5596 (mmm) cc_final: 0.5269 (mmm) REVERT: F 38 ASN cc_start: 0.7783 (t0) cc_final: 0.7459 (t0) REVERT: F 202 MET cc_start: 0.6109 (mmp) cc_final: 0.5744 (mmp) REVERT: F 240 ARG cc_start: 0.5587 (OUTLIER) cc_final: 0.5352 (ppt90) REVERT: F 241 ASP cc_start: 0.7017 (m-30) cc_final: 0.6062 (m-30) REVERT: F 256 ARG cc_start: 0.7625 (mmt180) cc_final: 0.7399 (mpt180) REVERT: F 285 MET cc_start: 0.6997 (ttp) cc_final: 0.6488 (ttp) REVERT: F 331 LEU cc_start: 0.7800 (mt) cc_final: 0.7254 (mp) REVERT: F 389 MET cc_start: 0.6323 (mmm) cc_final: 0.6011 (mmm) REVERT: F 456 VAL cc_start: 0.6703 (p) cc_final: 0.6402 (m) REVERT: F 458 ARG cc_start: 0.6543 (ttp-110) cc_final: 0.6286 (mtp-110) REVERT: G 11 LYS cc_start: 0.8766 (tptt) cc_final: 0.8234 (tppt) REVERT: G 15 ASN cc_start: 0.8440 (m-40) cc_final: 0.8139 (m110) REVERT: G 33 SER cc_start: 0.8327 (t) cc_final: 0.8088 (p) REVERT: G 43 LYS cc_start: 0.8556 (ttpt) cc_final: 0.8297 (ttpt) REVERT: G 48 TYR cc_start: 0.7611 (t80) cc_final: 0.7353 (t80) REVERT: G 94 TYR cc_start: 0.6941 (t80) cc_final: 0.6550 (t80) REVERT: G 97 ASN cc_start: 0.7780 (m-40) cc_final: 0.7575 (m-40) REVERT: G 104 GLN cc_start: 0.8184 (mt0) cc_final: 0.7912 (mt0) REVERT: G 132 ARG cc_start: 0.7782 (mmp80) cc_final: 0.7362 (mmm-85) REVERT: G 148 SER cc_start: 0.8685 (m) cc_final: 0.8295 (p) REVERT: G 174 TYR cc_start: 0.7064 (m-80) cc_final: 0.5542 (m-80) REVERT: G 176 ASN cc_start: 0.7043 (m-40) cc_final: 0.6735 (m-40) REVERT: G 222 GLN cc_start: 0.7850 (mt0) cc_final: 0.7633 (mt0) REVERT: G 239 GLU cc_start: 0.7521 (tt0) cc_final: 0.7246 (tt0) REVERT: G 269 ARG cc_start: 0.7358 (ttp80) cc_final: 0.7013 (ttp80) REVERT: G 275 GLN cc_start: 0.7571 (tp40) cc_final: 0.6318 (tp40) REVERT: G 279 GLU cc_start: 0.6925 (mm-30) cc_final: 0.6439 (mm-30) outliers start: 157 outliers final: 74 residues processed: 1087 average time/residue: 0.4045 time to fit residues: 650.4244 Evaluate side-chains 1070 residues out of total 2558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 985 time to evaluate : 2.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 339 ASP Chi-restraints excluded: chain A residue 365 ARG Chi-restraints excluded: chain A residue 391 GLU Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 397 GLN Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 451 GLU Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 46 ASN Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 236 PHE Chi-restraints excluded: chain B residue 245 MET Chi-restraints excluded: chain B residue 284 GLU Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 338 THR Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain B residue 385 ASP Chi-restraints excluded: chain B residue 423 ASP Chi-restraints excluded: chain B residue 444 PHE Chi-restraints excluded: chain C residue 46 ASN Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 54 GLU Chi-restraints excluded: chain C residue 67 GLU Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 141 SER Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain C residue 417 VAL Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain C residue 491 ILE Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 153 LYS Chi-restraints excluded: chain D residue 177 GLN Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 254 ILE Chi-restraints excluded: chain D residue 322 PHE Chi-restraints excluded: chain D residue 347 LEU Chi-restraints excluded: chain D residue 373 THR Chi-restraints excluded: chain D residue 386 ILE Chi-restraints excluded: chain D residue 465 LYS Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain E residue 101 GLU Chi-restraints excluded: chain E residue 210 LYS Chi-restraints excluded: chain E residue 226 MET Chi-restraints excluded: chain E residue 231 THR Chi-restraints excluded: chain E residue 291 ARG Chi-restraints excluded: chain E residue 294 SER Chi-restraints excluded: chain E residue 314 THR Chi-restraints excluded: chain E residue 322 PHE Chi-restraints excluded: chain E residue 328 THR Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 396 ASP Chi-restraints excluded: chain F residue 68 ASP Chi-restraints excluded: chain F residue 74 MET Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain F residue 172 ILE Chi-restraints excluded: chain F residue 240 ARG Chi-restraints excluded: chain F residue 302 SER Chi-restraints excluded: chain F residue 322 PHE Chi-restraints excluded: chain F residue 390 ASP Chi-restraints excluded: chain F residue 400 VAL Chi-restraints excluded: chain F residue 406 ILE Chi-restraints excluded: chain F residue 416 VAL Chi-restraints excluded: chain F residue 464 GLU Chi-restraints excluded: chain G residue 107 GLN Chi-restraints excluded: chain G residue 127 SER Chi-restraints excluded: chain G residue 146 GLN Chi-restraints excluded: chain G residue 151 ASP Chi-restraints excluded: chain G residue 273 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 156 optimal weight: 6.9990 chunk 87 optimal weight: 0.7980 chunk 234 optimal weight: 9.9990 chunk 191 optimal weight: 8.9990 chunk 77 optimal weight: 0.7980 chunk 282 optimal weight: 9.9990 chunk 304 optimal weight: 6.9990 chunk 251 optimal weight: 0.9980 chunk 279 optimal weight: 7.9990 chunk 96 optimal weight: 4.9990 chunk 226 optimal weight: 9.9990 overall best weight: 2.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 474 HIS ** C 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 469 GLN D 200 HIS ** D 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 304 GLN ** E 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 174 ASN ** F 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 363 HIS F 371 GLN G 107 GLN ** G 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6795 moved from start: 0.3806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 24608 Z= 0.303 Angle : 0.682 15.442 33370 Z= 0.358 Chirality : 0.048 0.231 3840 Planarity : 0.005 0.078 4349 Dihedral : 9.528 85.667 3590 Min Nonbonded Distance : 1.790 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.61 % Favored : 96.36 % Rotamer: Outliers : 6.06 % Allowed : 24.16 % Favored : 69.78 % 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: 0.34 (0.14), residues: 1256 sheet: 0.13 (0.24), residues: 496 loop : -0.70 (0.17), residues: 1352 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.002 HIS F 53 PHE 0.022 0.002 PHE D 255 TYR 0.027 0.002 TYR G 103 ARG 0.009 0.001 ARG C 383 *********************** 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 1154 residues out of total 2558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 155 poor density : 999 time to evaluate : 2.527 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: symmetry clash revert: symmetry clash REVERT: A 87 GLU cc_start: 0.6813 (mm-30) cc_final: 0.6496 (mm-30) REVERT: A 333 ASN cc_start: 0.7834 (t0) cc_final: 0.7618 (t0) REVERT: A 415 ARG cc_start: 0.7745 (mtt90) cc_final: 0.7187 (mtt90) REVERT: A 424 LEU cc_start: 0.7451 (tp) cc_final: 0.6786 (tp) REVERT: A 432 LYS cc_start: 0.7935 (mttt) cc_final: 0.7265 (mtpp) REVERT: A 448 ILE cc_start: 0.7511 (OUTLIER) cc_final: 0.6940 (mm) REVERT: A 466 GLN cc_start: 0.7467 (mt0) cc_final: 0.7174 (mt0) REVERT: A 496 LYS cc_start: 0.8454 (mmtt) cc_final: 0.8235 (mmtt) REVERT: B 38 ILE cc_start: 0.7793 (mp) cc_final: 0.7548 (mt) REVERT: B 80 THR cc_start: 0.7943 (p) cc_final: 0.7723 (m) REVERT: B 93 ARG cc_start: 0.6658 (mmm160) cc_final: 0.6429 (mmm160) REVERT: B 113 GLN cc_start: 0.6923 (tp40) cc_final: 0.6713 (tp-100) REVERT: B 136 VAL cc_start: 0.5981 (p) cc_final: 0.4850 (m) REVERT: B 154 ASP cc_start: 0.7704 (m-30) cc_final: 0.7218 (m-30) REVERT: B 373 LYS cc_start: 0.7560 (ttmt) cc_final: 0.7124 (ttmt) REVERT: B 463 PHE cc_start: 0.8027 (t80) cc_final: 0.7700 (t80) REVERT: B 469 GLN cc_start: 0.8058 (mm-40) cc_final: 0.7609 (mm-40) REVERT: B 470 HIS cc_start: 0.7699 (p-80) cc_final: 0.7496 (p90) REVERT: C 206 ARG cc_start: 0.7237 (ttt180) cc_final: 0.6923 (tpp80) REVERT: C 265 LYS cc_start: 0.7651 (mttp) cc_final: 0.7405 (mttp) REVERT: C 389 TYR cc_start: 0.8068 (t80) cc_final: 0.7775 (t80) REVERT: C 459 GLU cc_start: 0.7290 (mt-10) cc_final: 0.7026 (mt-10) REVERT: C 467 ASN cc_start: 0.7156 (m-40) cc_final: 0.6864 (m-40) REVERT: D 35 LYS cc_start: 0.7866 (ttmt) cc_final: 0.7646 (ttmt) REVERT: D 104 ASP cc_start: 0.7085 (p0) cc_final: 0.6438 (p0) REVERT: D 120 ARG cc_start: 0.6656 (OUTLIER) cc_final: 0.6388 (ptt-90) REVERT: D 154 ILE cc_start: 0.7571 (mm) cc_final: 0.7321 (mt) REVERT: D 178 GLU cc_start: 0.7758 (tm-30) cc_final: 0.7420 (tm-30) REVERT: D 185 PHE cc_start: 0.7952 (t80) cc_final: 0.7659 (t80) REVERT: D 202 MET cc_start: 0.6620 (mmt) cc_final: 0.6320 (mmt) REVERT: D 207 VAL cc_start: 0.8558 (t) cc_final: 0.7518 (p) REVERT: D 227 ARG cc_start: 0.6411 (mmt180) cc_final: 0.5992 (mmt180) REVERT: D 242 GLU cc_start: 0.6625 (mm-30) cc_final: 0.6396 (mm-30) REVERT: D 256 ARG cc_start: 0.7867 (mtm-85) cc_final: 0.7663 (mtt90) REVERT: D 267 LEU cc_start: 0.7807 (mm) cc_final: 0.7236 (mt) REVERT: D 314 THR cc_start: 0.8357 (p) cc_final: 0.8147 (m) REVERT: D 386 ILE cc_start: 0.7824 (pt) cc_final: 0.7453 (mt) REVERT: D 441 LEU cc_start: 0.8595 (mt) cc_final: 0.8361 (mp) REVERT: D 464 GLU cc_start: 0.7387 (tp30) cc_final: 0.7054 (tp30) REVERT: E 27 TYR cc_start: 0.7175 (m-80) cc_final: 0.6867 (m-80) REVERT: E 101 GLU cc_start: 0.7077 (OUTLIER) cc_final: 0.6846 (mp0) REVERT: E 125 PHE cc_start: 0.6847 (t80) cc_final: 0.6562 (t80) REVERT: E 188 VAL cc_start: 0.7287 (t) cc_final: 0.7044 (p) REVERT: E 197 ASP cc_start: 0.6356 (t0) cc_final: 0.5979 (t0) REVERT: E 199 TYR cc_start: 0.7904 (t80) cc_final: 0.6916 (t80) REVERT: E 203 LYS cc_start: 0.8055 (tppp) cc_final: 0.7389 (tppp) REVERT: E 369 LYS cc_start: 0.8138 (mtmm) cc_final: 0.7892 (mttt) REVERT: E 372 GLN cc_start: 0.7610 (mt0) cc_final: 0.7167 (mt0) REVERT: E 378 LYS cc_start: 0.8119 (OUTLIER) cc_final: 0.7706 (tmmm) REVERT: E 380 LEU cc_start: 0.8063 (tp) cc_final: 0.7673 (pp) REVERT: E 384 ILE cc_start: 0.8181 (mt) cc_final: 0.7683 (mt) REVERT: E 469 MET cc_start: 0.5731 (mmm) cc_final: 0.5473 (mmm) REVERT: F 38 ASN cc_start: 0.7724 (t0) cc_final: 0.7507 (t0) REVERT: F 156 LEU cc_start: 0.7564 (mm) cc_final: 0.7196 (mt) REVERT: F 201 GLU cc_start: 0.6742 (tp30) cc_final: 0.6516 (tp30) REVERT: F 202 MET cc_start: 0.6120 (mmp) cc_final: 0.5757 (mmp) REVERT: F 240 ARG cc_start: 0.5625 (OUTLIER) cc_final: 0.5383 (ppt90) REVERT: F 241 ASP cc_start: 0.7030 (m-30) cc_final: 0.6227 (m-30) REVERT: F 256 ARG cc_start: 0.7682 (mmt180) cc_final: 0.7439 (mmt-90) REVERT: F 285 MET cc_start: 0.7052 (ttp) cc_final: 0.6557 (ttp) REVERT: F 389 MET cc_start: 0.6454 (mmm) cc_final: 0.6123 (mmm) REVERT: F 442 GLU cc_start: 0.7138 (mt-10) cc_final: 0.6745 (mt-10) REVERT: F 456 VAL cc_start: 0.7018 (p) cc_final: 0.6594 (m) REVERT: G 11 LYS cc_start: 0.8764 (tptt) cc_final: 0.8311 (tppt) REVERT: G 15 ASN cc_start: 0.8420 (m-40) cc_final: 0.8140 (m110) REVERT: G 33 SER cc_start: 0.8304 (t) cc_final: 0.7979 (p) REVERT: G 43 LYS cc_start: 0.8447 (ttpt) cc_final: 0.8160 (ttpt) REVERT: G 48 TYR cc_start: 0.7576 (t80) cc_final: 0.7306 (t80) REVERT: G 94 TYR cc_start: 0.7032 (t80) cc_final: 0.6605 (t80) REVERT: G 97 ASN cc_start: 0.7818 (m-40) cc_final: 0.7604 (m-40) REVERT: G 132 ARG cc_start: 0.7830 (mmp80) cc_final: 0.7352 (mmm-85) REVERT: G 148 SER cc_start: 0.8626 (m) cc_final: 0.8271 (p) REVERT: G 176 ASN cc_start: 0.7162 (m-40) cc_final: 0.6957 (m-40) REVERT: G 222 GLN cc_start: 0.7866 (mt0) cc_final: 0.7603 (mt0) REVERT: G 239 GLU cc_start: 0.7556 (tt0) cc_final: 0.7295 (tt0) REVERT: G 267 ARG cc_start: 0.7741 (OUTLIER) cc_final: 0.7525 (ttm-80) REVERT: G 269 ARG cc_start: 0.7434 (ttp80) cc_final: 0.7050 (ttp80) REVERT: G 275 GLN cc_start: 0.7629 (tp40) cc_final: 0.7207 (tp40) REVERT: G 279 GLU cc_start: 0.6879 (mm-30) cc_final: 0.6671 (mm-30) outliers start: 155 outliers final: 108 residues processed: 1057 average time/residue: 0.4091 time to fit residues: 641.7692 Evaluate side-chains 1091 residues out of total 2558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 977 time to evaluate : 2.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 339 ASP Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 45 ASP Chi-restraints excluded: chain B residue 46 ASN Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 236 PHE Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 245 MET Chi-restraints excluded: chain B residue 284 GLU Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 339 ASP Chi-restraints excluded: chain B residue 364 SER Chi-restraints excluded: chain B residue 423 ASP Chi-restraints excluded: chain B residue 444 PHE Chi-restraints excluded: chain B residue 452 ASP Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 46 ASN Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 54 GLU Chi-restraints excluded: chain C residue 62 MET Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 141 SER Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 177 SER Chi-restraints excluded: chain C residue 214 LYS Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 306 ASP Chi-restraints excluded: chain C residue 417 VAL Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain C residue 487 LEU Chi-restraints excluded: chain C residue 491 ILE Chi-restraints excluded: chain D residue 43 ASP Chi-restraints excluded: chain D residue 120 ARG Chi-restraints excluded: chain D residue 130 THR Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 153 LYS Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 254 ILE Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 273 SER Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain D residue 322 PHE Chi-restraints excluded: chain D residue 394 ASP Chi-restraints excluded: chain D residue 398 LEU Chi-restraints excluded: chain D residue 399 VAL Chi-restraints excluded: chain E residue 47 THR Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 74 MET Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain E residue 101 GLU Chi-restraints excluded: chain E residue 112 ASP Chi-restraints excluded: chain E residue 124 LYS Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain E residue 143 ASP Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 293 THR Chi-restraints excluded: chain E residue 294 SER Chi-restraints excluded: chain E residue 314 THR Chi-restraints excluded: chain E residue 322 PHE Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 378 LYS Chi-restraints excluded: chain E residue 396 ASP Chi-restraints excluded: chain E residue 441 LEU Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 68 ASP Chi-restraints excluded: chain F residue 74 MET Chi-restraints excluded: chain F residue 134 ILE Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain F residue 172 ILE Chi-restraints excluded: chain F residue 190 ASP Chi-restraints excluded: chain F residue 226 MET Chi-restraints excluded: chain F residue 240 ARG Chi-restraints excluded: chain F residue 295 THR Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 302 SER Chi-restraints excluded: chain F residue 322 PHE Chi-restraints excluded: chain F residue 379 GLU Chi-restraints excluded: chain F residue 390 ASP Chi-restraints excluded: chain F residue 400 VAL Chi-restraints excluded: chain F residue 406 ILE Chi-restraints excluded: chain F residue 416 VAL Chi-restraints excluded: chain G residue 88 ARG Chi-restraints excluded: chain G residue 107 GLN Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 127 SER Chi-restraints excluded: chain G residue 146 GLN Chi-restraints excluded: chain G residue 151 ASP Chi-restraints excluded: chain G residue 232 LEU Chi-restraints excluded: chain G residue 260 THR Chi-restraints excluded: chain G residue 267 ARG Chi-restraints excluded: chain G residue 273 ILE Chi-restraints excluded: chain G residue 277 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 278 optimal weight: 3.9990 chunk 212 optimal weight: 4.9990 chunk 146 optimal weight: 9.9990 chunk 31 optimal weight: 0.0170 chunk 134 optimal weight: 6.9990 chunk 189 optimal weight: 5.9990 chunk 283 optimal weight: 2.9990 chunk 299 optimal weight: 4.9990 chunk 147 optimal weight: 0.8980 chunk 268 optimal weight: 2.9990 chunk 80 optimal weight: 0.4980 overall best weight: 1.4822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 422 GLN ** A 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 143 HIS ** B 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 426 GLN B 474 HIS C 143 HIS C 230 GLN C 407 GLN C 433 GLN D 200 HIS ** D 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 8 GLN F 40 ASN F 174 ASN F 259 GLN F 324 HIS F 371 GLN F 401 HIS G 107 GLN ** G 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6745 moved from start: 0.4173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 24608 Z= 0.196 Angle : 0.620 15.354 33370 Z= 0.318 Chirality : 0.045 0.228 3840 Planarity : 0.005 0.067 4349 Dihedral : 9.019 83.256 3587 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.19 % Favored : 96.78 % Rotamer: Outliers : 5.79 % Allowed : 26.43 % Favored : 67.79 % 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: -0.03 (0.15), residues: 3104 helix: 0.64 (0.14), residues: 1255 sheet: 0.20 (0.23), residues: 511 loop : -0.65 (0.17), residues: 1338 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.001 HIS D 401 PHE 0.023 0.002 PHE E 255 TYR 0.023 0.001 TYR G 103 ARG 0.010 0.001 ARG E 405 *********************** 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 1128 residues out of total 2558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 980 time to evaluate : 2.587 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 GLU cc_start: 0.6803 (mm-30) cc_final: 0.6525 (mm-30) REVERT: A 181 ASP cc_start: 0.6931 (m-30) cc_final: 0.6684 (m-30) REVERT: A 349 PHE cc_start: 0.7944 (t80) cc_final: 0.7736 (t80) REVERT: A 415 ARG cc_start: 0.7597 (mtt90) cc_final: 0.7099 (mtt90) REVERT: A 424 LEU cc_start: 0.7386 (tp) cc_final: 0.7077 (tp) REVERT: A 432 LYS cc_start: 0.7893 (mttt) cc_final: 0.7639 (mttt) REVERT: A 448 ILE cc_start: 0.7489 (OUTLIER) cc_final: 0.7049 (mm) REVERT: A 466 GLN cc_start: 0.7410 (mt0) cc_final: 0.7102 (mt0) REVERT: A 496 LYS cc_start: 0.8535 (mmtt) cc_final: 0.8326 (mmtt) REVERT: B 38 ILE cc_start: 0.7826 (mp) cc_final: 0.7566 (mt) REVERT: B 62 MET cc_start: 0.5772 (ttt) cc_final: 0.5545 (ttp) REVERT: B 96 GLU cc_start: 0.7272 (mt-10) cc_final: 0.7048 (mt-10) REVERT: B 127 ARG cc_start: 0.7066 (ttm-80) cc_final: 0.6856 (tpt-90) REVERT: B 181 ASP cc_start: 0.6951 (t70) cc_final: 0.6655 (t70) REVERT: B 341 GLN cc_start: 0.6793 (pt0) cc_final: 0.6579 (pt0) REVERT: B 371 GLN cc_start: 0.5803 (mt0) cc_final: 0.5596 (mt0) REVERT: B 373 LYS cc_start: 0.7478 (ttmt) cc_final: 0.6996 (ttmt) REVERT: B 460 PHE cc_start: 0.7105 (t80) cc_final: 0.6826 (t80) REVERT: B 463 PHE cc_start: 0.8034 (t80) cc_final: 0.7788 (t80) REVERT: B 469 GLN cc_start: 0.8056 (mm-40) cc_final: 0.7653 (mm-40) REVERT: B 470 HIS cc_start: 0.7715 (p-80) cc_final: 0.7482 (p-80) REVERT: C 161 ARG cc_start: 0.6585 (mtt180) cc_final: 0.6270 (mmt90) REVERT: C 206 ARG cc_start: 0.7217 (ttt180) cc_final: 0.6890 (tpp80) REVERT: C 389 TYR cc_start: 0.8026 (t80) cc_final: 0.7744 (t80) REVERT: C 459 GLU cc_start: 0.7232 (mt-10) cc_final: 0.6980 (mt-10) REVERT: C 467 ASN cc_start: 0.7110 (m110) cc_final: 0.6876 (m-40) REVERT: D 35 LYS cc_start: 0.7871 (ttmt) cc_final: 0.7468 (ttmt) REVERT: D 154 ILE cc_start: 0.7550 (mm) cc_final: 0.7324 (mt) REVERT: D 185 PHE cc_start: 0.7937 (t80) cc_final: 0.7696 (t80) REVERT: D 202 MET cc_start: 0.6635 (mmt) cc_final: 0.6282 (mmt) REVERT: D 207 VAL cc_start: 0.8652 (t) cc_final: 0.7469 (p) REVERT: D 256 ARG cc_start: 0.7821 (mtm-85) cc_final: 0.7578 (mtt90) REVERT: D 267 LEU cc_start: 0.7721 (mm) cc_final: 0.7151 (mt) REVERT: D 334 LYS cc_start: 0.7123 (ttpt) cc_final: 0.6886 (ttpt) REVERT: D 381 GLN cc_start: 0.7219 (pm20) cc_final: 0.6993 (pm20) REVERT: D 386 ILE cc_start: 0.7813 (pt) cc_final: 0.7502 (mt) REVERT: D 441 LEU cc_start: 0.8559 (mt) cc_final: 0.8352 (mp) REVERT: D 464 GLU cc_start: 0.7355 (tp30) cc_final: 0.7023 (tp30) REVERT: E 26 ILE cc_start: 0.8601 (mt) cc_final: 0.8385 (tt) REVERT: E 197 ASP cc_start: 0.6369 (t0) cc_final: 0.5988 (t0) REVERT: E 199 TYR cc_start: 0.7895 (t80) cc_final: 0.6944 (t80) REVERT: E 203 LYS cc_start: 0.8010 (tppp) cc_final: 0.7230 (tppp) REVERT: E 369 LYS cc_start: 0.8121 (mtmm) cc_final: 0.7882 (mttt) REVERT: E 372 GLN cc_start: 0.7548 (mt0) cc_final: 0.7070 (mt0) REVERT: E 378 LYS cc_start: 0.8098 (OUTLIER) cc_final: 0.7729 (tmmm) REVERT: E 380 LEU cc_start: 0.8111 (tp) cc_final: 0.7676 (tp) REVERT: E 384 ILE cc_start: 0.8101 (mt) cc_final: 0.7900 (mt) REVERT: E 435 ARG cc_start: 0.6053 (ttp80) cc_final: 0.5724 (ttp80) REVERT: E 469 MET cc_start: 0.5723 (mmm) cc_final: 0.5406 (mmm) REVERT: F 38 ASN cc_start: 0.7537 (t0) cc_final: 0.7313 (t0) REVERT: F 202 MET cc_start: 0.6023 (mmp) cc_final: 0.5626 (mmp) REVERT: F 241 ASP cc_start: 0.7023 (m-30) cc_final: 0.6179 (m-30) REVERT: F 256 ARG cc_start: 0.7648 (mmt180) cc_final: 0.7440 (mmt-90) REVERT: F 285 MET cc_start: 0.7051 (ttp) cc_final: 0.6527 (ttp) REVERT: F 389 MET cc_start: 0.6406 (mmm) cc_final: 0.6083 (mmm) REVERT: F 442 GLU cc_start: 0.7071 (mt-10) cc_final: 0.6743 (mt-10) REVERT: F 456 VAL cc_start: 0.6836 (OUTLIER) cc_final: 0.6449 (m) REVERT: F 458 ARG cc_start: 0.6443 (ttp-110) cc_final: 0.6222 (mtm110) REVERT: G 15 ASN cc_start: 0.8393 (m-40) cc_final: 0.8137 (m110) REVERT: G 19 LYS cc_start: 0.8093 (mptt) cc_final: 0.7774 (mptt) REVERT: G 37 ARG cc_start: 0.7368 (ttp80) cc_final: 0.6747 (ttp80) REVERT: G 43 LYS cc_start: 0.8328 (ttpt) cc_final: 0.8018 (ttpt) REVERT: G 48 TYR cc_start: 0.7528 (t80) cc_final: 0.7245 (t80) REVERT: G 97 ASN cc_start: 0.7712 (m-40) cc_final: 0.7408 (m-40) REVERT: G 132 ARG cc_start: 0.7853 (mmp80) cc_final: 0.7406 (mmm-85) REVERT: G 146 GLN cc_start: 0.7165 (OUTLIER) cc_final: 0.6943 (pp30) REVERT: G 148 SER cc_start: 0.8688 (m) cc_final: 0.8362 (p) REVERT: G 183 GLN cc_start: 0.7317 (pp30) cc_final: 0.6404 (pp30) REVERT: G 222 GLN cc_start: 0.7813 (mt0) cc_final: 0.7534 (mt0) REVERT: G 239 GLU cc_start: 0.7496 (tt0) cc_final: 0.7231 (tt0) REVERT: G 267 ARG cc_start: 0.7705 (OUTLIER) cc_final: 0.7489 (ttm-80) REVERT: G 269 ARG cc_start: 0.7458 (ttp80) cc_final: 0.7036 (ttp80) REVERT: G 279 GLU cc_start: 0.6775 (mm-30) cc_final: 0.6565 (mm-30) outliers start: 148 outliers final: 102 residues processed: 1031 average time/residue: 0.4281 time to fit residues: 658.4530 Evaluate side-chains 1066 residues out of total 2558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 959 time to evaluate : 2.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 190 ASN Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 339 ASP Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain A residue 485 ASP Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 45 ASP Chi-restraints excluded: chain B residue 46 ASN Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 132 ARG Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 236 PHE Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 245 MET Chi-restraints excluded: chain B residue 284 GLU Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 385 ASP Chi-restraints excluded: chain B residue 423 ASP Chi-restraints excluded: chain B residue 444 PHE Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 62 MET Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 141 SER Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 214 LYS Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain C residue 306 ASP Chi-restraints excluded: chain C residue 407 GLN Chi-restraints excluded: chain C residue 417 VAL Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain C residue 484 GLU Chi-restraints excluded: chain C residue 487 LEU Chi-restraints excluded: chain C residue 491 ILE Chi-restraints excluded: chain D residue 130 THR Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 153 LYS Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 254 ILE Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 273 SER Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain D residue 322 PHE Chi-restraints excluded: chain D residue 374 LEU Chi-restraints excluded: chain D residue 442 GLU Chi-restraints excluded: chain E residue 57 ASP Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 112 ASP Chi-restraints excluded: chain E residue 124 LYS Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain E residue 200 HIS Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 273 SER Chi-restraints excluded: chain E residue 293 THR Chi-restraints excluded: chain E residue 322 PHE Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 378 LYS Chi-restraints excluded: chain E residue 383 ILE Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 41 GLU Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 68 ASP Chi-restraints excluded: chain F residue 74 MET Chi-restraints excluded: chain F residue 134 ILE Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain F residue 172 ILE Chi-restraints excluded: chain F residue 190 ASP Chi-restraints excluded: chain F residue 258 THR Chi-restraints excluded: chain F residue 295 THR Chi-restraints excluded: chain F residue 328 THR Chi-restraints excluded: chain F residue 398 LEU Chi-restraints excluded: chain F residue 400 VAL Chi-restraints excluded: chain F residue 406 ILE Chi-restraints excluded: chain F residue 416 VAL Chi-restraints excluded: chain F residue 456 VAL Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain G residue 27 MET Chi-restraints excluded: chain G residue 32 THR Chi-restraints excluded: chain G residue 88 ARG Chi-restraints excluded: chain G residue 107 GLN Chi-restraints excluded: chain G residue 146 GLN Chi-restraints excluded: chain G residue 151 ASP Chi-restraints excluded: chain G residue 267 ARG Chi-restraints excluded: chain G residue 273 ILE Chi-restraints excluded: chain G residue 277 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 249 optimal weight: 6.9990 chunk 170 optimal weight: 5.9990 chunk 4 optimal weight: 10.0000 chunk 223 optimal weight: 8.9990 chunk 123 optimal weight: 8.9990 chunk 255 optimal weight: 3.9990 chunk 207 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 153 optimal weight: 7.9990 chunk 268 optimal weight: 9.9990 chunk 75 optimal weight: 8.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 53 HIS D 200 HIS ** D 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 259 GLN ** D 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 146 GLN ** G 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6881 moved from start: 0.4864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.119 24608 Z= 0.505 Angle : 0.808 13.344 33370 Z= 0.433 Chirality : 0.053 0.278 3840 Planarity : 0.006 0.071 4349 Dihedral : 9.312 84.903 3576 Min Nonbonded Distance : 1.658 Molprobity Statistics. All-atom Clashscore : 19.14 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.15 % Favored : 93.81 % Rotamer: Outliers : 8.60 % Allowed : 26.47 % Favored : 64.93 % 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: -1.02 (0.15), residues: 3104 helix: -0.33 (0.14), residues: 1255 sheet: -0.17 (0.24), residues: 500 loop : -1.09 (0.17), residues: 1349 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.011 0.002 HIS D 200 PHE 0.025 0.003 PHE F 250 TYR 0.030 0.003 TYR G 103 ARG 0.011 0.001 ARG C 171 *********************** 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 1199 residues out of total 2558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 220 poor density : 979 time to evaluate : 2.615 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: symmetry clash REVERT: A 87 GLU cc_start: 0.6770 (mm-30) cc_final: 0.6552 (mm-30) REVERT: A 154 ASP cc_start: 0.7874 (m-30) cc_final: 0.7608 (t0) REVERT: A 176 THR cc_start: 0.7548 (OUTLIER) cc_final: 0.6899 (p) REVERT: A 181 ASP cc_start: 0.6958 (m-30) cc_final: 0.6674 (m-30) REVERT: A 300 ARG cc_start: 0.7113 (OUTLIER) cc_final: 0.6389 (mtp85) REVERT: A 424 LEU cc_start: 0.7326 (tp) cc_final: 0.7074 (tp) REVERT: A 432 LYS cc_start: 0.8039 (mttt) cc_final: 0.7818 (mttt) REVERT: A 448 ILE cc_start: 0.7596 (OUTLIER) cc_final: 0.7388 (mm) REVERT: A 466 GLN cc_start: 0.7571 (mt0) cc_final: 0.7255 (mt0) REVERT: A 476 ARG cc_start: 0.7452 (tpm170) cc_final: 0.7207 (tpp-160) REVERT: B 38 ILE cc_start: 0.7969 (mp) cc_final: 0.7730 (mt) REVERT: B 181 ASP cc_start: 0.6970 (t70) cc_final: 0.6715 (t70) REVERT: B 272 GLU cc_start: 0.7235 (tt0) cc_final: 0.6892 (tt0) REVERT: B 341 GLN cc_start: 0.6880 (pt0) cc_final: 0.6656 (pt0) REVERT: B 458 LYS cc_start: 0.7250 (tmmt) cc_final: 0.6838 (mttp) REVERT: B 470 HIS cc_start: 0.7776 (p-80) cc_final: 0.7565 (p-80) REVERT: C 52 LEU cc_start: 0.7522 (OUTLIER) cc_final: 0.7280 (mt) REVERT: C 206 ARG cc_start: 0.7351 (ttt180) cc_final: 0.6990 (tpp80) REVERT: C 377 LYS cc_start: 0.7897 (tttp) cc_final: 0.7577 (tttp) REVERT: C 389 TYR cc_start: 0.8150 (t80) cc_final: 0.7728 (t80) REVERT: C 407 GLN cc_start: 0.7917 (mt0) cc_final: 0.7612 (mt0) REVERT: C 418 GLU cc_start: 0.6294 (mm-30) cc_final: 0.6079 (mt-10) REVERT: C 433 GLN cc_start: 0.7977 (mt0) cc_final: 0.7753 (mt0) REVERT: D 35 LYS cc_start: 0.7892 (ttmt) cc_final: 0.7611 (ttmt) REVERT: D 120 ARG cc_start: 0.6686 (OUTLIER) cc_final: 0.6474 (ptt-90) REVERT: D 154 ILE cc_start: 0.7726 (mm) cc_final: 0.7432 (mt) REVERT: D 178 GLU cc_start: 0.8254 (tm-30) cc_final: 0.7853 (tm-30) REVERT: D 202 MET cc_start: 0.6800 (mmt) cc_final: 0.6478 (mmt) REVERT: D 207 VAL cc_start: 0.8634 (t) cc_final: 0.7240 (p) REVERT: D 227 ARG cc_start: 0.6547 (mmt180) cc_final: 0.6228 (mmt180) REVERT: D 378 LYS cc_start: 0.8210 (tttt) cc_final: 0.7862 (mmmm) REVERT: D 386 ILE cc_start: 0.7980 (pt) cc_final: 0.7707 (mp) REVERT: D 428 VAL cc_start: 0.5984 (OUTLIER) cc_final: 0.4838 (p) REVERT: D 439 GLU cc_start: 0.6177 (mm-30) cc_final: 0.5968 (mm-30) REVERT: D 441 LEU cc_start: 0.8604 (mt) cc_final: 0.8395 (mp) REVERT: D 464 GLU cc_start: 0.7516 (tp30) cc_final: 0.7163 (tp30) REVERT: E 112 ASP cc_start: 0.7062 (OUTLIER) cc_final: 0.6810 (m-30) REVERT: E 170 GLU cc_start: 0.8365 (tt0) cc_final: 0.8125 (mt-10) REVERT: E 291 ARG cc_start: 0.7199 (mtt180) cc_final: 0.6967 (mtt180) REVERT: E 333 ARG cc_start: 0.7162 (ttm-80) cc_final: 0.6933 (ttm-80) REVERT: E 369 LYS cc_start: 0.8154 (mtmm) cc_final: 0.7950 (mttm) REVERT: E 378 LYS cc_start: 0.8175 (OUTLIER) cc_final: 0.7779 (tmmm) REVERT: E 380 LEU cc_start: 0.8154 (tp) cc_final: 0.7813 (pp) REVERT: E 435 ARG cc_start: 0.6238 (ttp80) cc_final: 0.5903 (ttp80) REVERT: E 458 ARG cc_start: 0.7248 (ttm110) cc_final: 0.6966 (ptm-80) REVERT: E 469 MET cc_start: 0.5787 (mmm) cc_final: 0.5519 (mmm) REVERT: F 38 ASN cc_start: 0.7550 (t0) cc_final: 0.7292 (t0) REVERT: F 202 MET cc_start: 0.6147 (mmp) cc_final: 0.5821 (mmp) REVERT: F 226 MET cc_start: 0.4656 (OUTLIER) cc_final: 0.4287 (mtm) REVERT: F 240 ARG cc_start: 0.5824 (OUTLIER) cc_final: 0.5296 (ppt90) REVERT: F 285 MET cc_start: 0.7158 (ttp) cc_final: 0.6679 (ttp) REVERT: F 389 MET cc_start: 0.6613 (mmm) cc_final: 0.6183 (mmm) REVERT: F 442 GLU cc_start: 0.7104 (mt-10) cc_final: 0.6781 (mt-10) REVERT: G 15 ASN cc_start: 0.8436 (m-40) cc_final: 0.8054 (m110) REVERT: G 33 SER cc_start: 0.8339 (t) cc_final: 0.8131 (p) REVERT: G 37 ARG cc_start: 0.7649 (ttp80) cc_final: 0.7377 (ttp80) REVERT: G 43 LYS cc_start: 0.8427 (ttpt) cc_final: 0.8119 (ttpt) REVERT: G 48 TYR cc_start: 0.7583 (t80) cc_final: 0.7255 (t80) REVERT: G 183 GLN cc_start: 0.7545 (pp30) cc_final: 0.6795 (pp30) REVERT: G 222 GLN cc_start: 0.8006 (mt0) cc_final: 0.7685 (mt0) REVERT: G 239 GLU cc_start: 0.7662 (tt0) cc_final: 0.7448 (tt0) REVERT: G 269 ARG cc_start: 0.7498 (ttp80) cc_final: 0.7088 (ttp80) REVERT: G 279 GLU cc_start: 0.6819 (mm-30) cc_final: 0.6392 (mm-30) outliers start: 220 outliers final: 151 residues processed: 1065 average time/residue: 0.3988 time to fit residues: 628.9026 Evaluate side-chains 1125 residues out of total 2558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 161 poor density : 964 time to evaluate : 2.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 132 ARG Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 190 ASN Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 265 LYS Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 300 ARG Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 339 ASP Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 391 GLU Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 422 GLN Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 33 GLN Chi-restraints excluded: chain B residue 45 ASP Chi-restraints excluded: chain B residue 46 ASN Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 147 GLN Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 236 PHE Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 245 MET Chi-restraints excluded: chain B residue 252 LYS Chi-restraints excluded: chain B residue 284 GLU Chi-restraints excluded: chain B residue 289 ASP Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 339 ASP Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain B residue 372 ILE Chi-restraints excluded: chain B residue 423 ASP Chi-restraints excluded: chain B residue 444 PHE Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 46 ASN Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 143 HIS Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 177 SER Chi-restraints excluded: chain C residue 214 LYS Chi-restraints excluded: chain C residue 219 ASP Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 252 LYS Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 381 THR Chi-restraints excluded: chain C residue 417 VAL Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain C residue 487 LEU Chi-restraints excluded: chain C residue 491 ILE Chi-restraints excluded: chain D residue 67 THR Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 120 ARG Chi-restraints excluded: chain D residue 130 THR Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 153 LYS Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 254 ILE Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 273 SER Chi-restraints excluded: chain D residue 374 LEU Chi-restraints excluded: chain D residue 392 LEU Chi-restraints excluded: chain D residue 398 LEU Chi-restraints excluded: chain D residue 399 VAL Chi-restraints excluded: chain D residue 428 VAL Chi-restraints excluded: chain D residue 442 GLU Chi-restraints excluded: chain D residue 447 HIS Chi-restraints excluded: chain E residue 57 ASP Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 64 MET Chi-restraints excluded: chain E residue 68 ASP Chi-restraints excluded: chain E residue 112 ASP Chi-restraints excluded: chain E residue 124 LYS Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 143 ASP Chi-restraints excluded: chain E residue 218 MET Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 293 THR Chi-restraints excluded: chain E residue 294 SER Chi-restraints excluded: chain E residue 300 ILE Chi-restraints excluded: chain E residue 322 PHE Chi-restraints excluded: chain E residue 323 SER Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 378 LYS Chi-restraints excluded: chain E residue 441 LEU Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 23 LEU Chi-restraints excluded: chain F residue 39 GLU Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 68 ASP Chi-restraints excluded: chain F residue 74 MET Chi-restraints excluded: chain F residue 120 ARG Chi-restraints excluded: chain F residue 134 ILE Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain F residue 154 ILE Chi-restraints excluded: chain F residue 172 ILE Chi-restraints excluded: chain F residue 190 ASP Chi-restraints excluded: chain F residue 226 MET Chi-restraints excluded: chain F residue 234 THR Chi-restraints excluded: chain F residue 240 ARG Chi-restraints excluded: chain F residue 258 THR Chi-restraints excluded: chain F residue 295 THR Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 302 SER Chi-restraints excluded: chain F residue 328 THR Chi-restraints excluded: chain F residue 381 GLN Chi-restraints excluded: chain F residue 398 LEU Chi-restraints excluded: chain F residue 400 VAL Chi-restraints excluded: chain F residue 406 ILE Chi-restraints excluded: chain F residue 410 LEU Chi-restraints excluded: chain F residue 416 VAL Chi-restraints excluded: chain F residue 441 LEU Chi-restraints excluded: chain F residue 448 LEU Chi-restraints excluded: chain F residue 456 VAL Chi-restraints excluded: chain F residue 464 GLU Chi-restraints excluded: chain G residue 27 MET Chi-restraints excluded: chain G residue 28 GLU Chi-restraints excluded: chain G residue 36 ASN Chi-restraints excluded: chain G residue 127 SER Chi-restraints excluded: chain G residue 146 GLN Chi-restraints excluded: chain G residue 151 ASP Chi-restraints excluded: chain G residue 227 LEU Chi-restraints excluded: chain G residue 232 LEU Chi-restraints excluded: chain G residue 260 THR Chi-restraints excluded: chain G residue 264 SER Chi-restraints excluded: chain G residue 273 ILE Chi-restraints excluded: chain G residue 274 THR Chi-restraints excluded: chain G residue 277 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 100 optimal weight: 8.9990 chunk 269 optimal weight: 0.6980 chunk 59 optimal weight: 4.9990 chunk 175 optimal weight: 6.9990 chunk 73 optimal weight: 0.7980 chunk 299 optimal weight: 0.9980 chunk 248 optimal weight: 7.9990 chunk 138 optimal weight: 10.0000 chunk 24 optimal weight: 4.9990 chunk 99 optimal weight: 3.9990 chunk 157 optimal weight: 0.7980 overall best weight: 1.4582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 426 GLN ** A 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 174 ASN ** D 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 243 GLN ** D 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 22 HIS F 174 ASN F 259 GLN F 401 HIS G 107 GLN G 146 GLN ** G 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6776 moved from start: 0.4966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 24608 Z= 0.216 Angle : 0.646 13.431 33370 Z= 0.333 Chirality : 0.046 0.252 3840 Planarity : 0.005 0.070 4349 Dihedral : 8.730 85.807 3576 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 14.30 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.87 % Favored : 96.10 % Rotamer: Outliers : 6.61 % Allowed : 29.55 % Favored : 63.84 % 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: -0.39 (0.15), residues: 3104 helix: 0.33 (0.14), residues: 1261 sheet: 0.04 (0.23), residues: 526 loop : -0.87 (0.17), residues: 1317 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.012 0.001 HIS D 401 PHE 0.028 0.002 PHE B 460 TYR 0.031 0.002 TYR G 103 ARG 0.009 0.001 ARG G 132 *********************** 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 1136 residues out of total 2558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 169 poor density : 967 time to evaluate : 2.462 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 LEU cc_start: 0.7633 (OUTLIER) cc_final: 0.7372 (mp) REVERT: A 87 GLU cc_start: 0.6797 (mm-30) cc_final: 0.6552 (mm-30) REVERT: A 181 ASP cc_start: 0.6812 (m-30) cc_final: 0.6485 (m-30) REVERT: A 424 LEU cc_start: 0.7311 (tp) cc_final: 0.6949 (tp) REVERT: A 466 GLN cc_start: 0.7549 (mt0) cc_final: 0.7283 (mt0) REVERT: A 496 LYS cc_start: 0.8405 (mmtt) cc_final: 0.8158 (mmtt) REVERT: B 38 ILE cc_start: 0.7856 (mp) cc_final: 0.7600 (mt) REVERT: B 96 GLU cc_start: 0.6713 (mt-10) cc_final: 0.5961 (mt-10) REVERT: B 181 ASP cc_start: 0.6817 (t70) cc_final: 0.6523 (t70) REVERT: B 284 GLU cc_start: 0.7704 (OUTLIER) cc_final: 0.7359 (mt-10) REVERT: B 341 GLN cc_start: 0.6827 (pt0) cc_final: 0.6531 (pt0) REVERT: B 373 LYS cc_start: 0.7505 (ttmt) cc_final: 0.7060 (ttmt) REVERT: B 432 LYS cc_start: 0.8354 (OUTLIER) cc_final: 0.7767 (mttt) REVERT: B 458 LYS cc_start: 0.7245 (tmmt) cc_final: 0.6907 (mttp) REVERT: B 460 PHE cc_start: 0.7115 (t80) cc_final: 0.6911 (t80) REVERT: B 463 PHE cc_start: 0.8022 (t80) cc_final: 0.7789 (t80) REVERT: C 161 ARG cc_start: 0.6601 (mtt180) cc_final: 0.6355 (mmt90) REVERT: C 206 ARG cc_start: 0.7186 (ttt180) cc_final: 0.6916 (tpp80) REVERT: C 214 LYS cc_start: 0.7839 (OUTLIER) cc_final: 0.7561 (mtpt) REVERT: C 377 LYS cc_start: 0.7831 (tttp) cc_final: 0.7507 (tttp) REVERT: C 389 TYR cc_start: 0.8029 (t80) cc_final: 0.7755 (t80) REVERT: C 433 GLN cc_start: 0.7731 (mt0) cc_final: 0.7525 (mt0) REVERT: D 35 LYS cc_start: 0.7903 (ttmt) cc_final: 0.7619 (ttmt) REVERT: D 124 LYS cc_start: 0.7493 (mmmm) cc_final: 0.7194 (mmmm) REVERT: D 154 ILE cc_start: 0.7591 (mm) cc_final: 0.7326 (mt) REVERT: D 157 PHE cc_start: 0.6819 (m-10) cc_final: 0.6308 (m-80) REVERT: D 202 MET cc_start: 0.6707 (mmt) cc_final: 0.6331 (mmt) REVERT: D 207 VAL cc_start: 0.8643 (t) cc_final: 0.7242 (p) REVERT: D 267 LEU cc_start: 0.7686 (mm) cc_final: 0.7074 (mt) REVERT: D 338 MET cc_start: 0.5875 (mpp) cc_final: 0.5412 (mpp) REVERT: D 378 LYS cc_start: 0.8182 (tttt) cc_final: 0.7716 (mmmm) REVERT: D 386 ILE cc_start: 0.7889 (pt) cc_final: 0.7542 (mt) REVERT: D 396 ASP cc_start: 0.7328 (m-30) cc_final: 0.7123 (m-30) REVERT: D 428 VAL cc_start: 0.5966 (OUTLIER) cc_final: 0.4869 (p) REVERT: D 441 LEU cc_start: 0.8586 (mt) cc_final: 0.8371 (mp) REVERT: D 464 GLU cc_start: 0.7376 (tp30) cc_final: 0.7059 (tp30) REVERT: D 465 LYS cc_start: 0.8163 (tttt) cc_final: 0.7919 (tttt) REVERT: E 26 ILE cc_start: 0.8576 (mt) cc_final: 0.8362 (tt) REVERT: E 112 ASP cc_start: 0.7085 (OUTLIER) cc_final: 0.6809 (m-30) REVERT: E 168 ILE cc_start: 0.8644 (mm) cc_final: 0.8384 (tp) REVERT: E 203 LYS cc_start: 0.8245 (tppp) cc_final: 0.7895 (tppp) REVERT: E 291 ARG cc_start: 0.7104 (mtt180) cc_final: 0.6559 (ttm170) REVERT: E 333 ARG cc_start: 0.7115 (ttm-80) cc_final: 0.6895 (ttm-80) REVERT: E 378 LYS cc_start: 0.8097 (OUTLIER) cc_final: 0.7723 (tmmm) REVERT: E 380 LEU cc_start: 0.8108 (tp) cc_final: 0.7879 (pp) REVERT: E 435 ARG cc_start: 0.6096 (ttp80) cc_final: 0.5762 (ttp80) REVERT: E 458 ARG cc_start: 0.6935 (ttm110) cc_final: 0.6677 (ptm-80) REVERT: E 469 MET cc_start: 0.5739 (OUTLIER) cc_final: 0.5504 (mmm) REVERT: F 38 ASN cc_start: 0.7445 (t0) cc_final: 0.7237 (t0) REVERT: F 202 MET cc_start: 0.6047 (mmp) cc_final: 0.5683 (mmp) REVERT: F 227 ARG cc_start: 0.6516 (mmt-90) cc_final: 0.6196 (mpt180) REVERT: F 240 ARG cc_start: 0.5364 (OUTLIER) cc_final: 0.4903 (ppt90) REVERT: F 285 MET cc_start: 0.7039 (ttp) cc_final: 0.6550 (ttp) REVERT: F 389 MET cc_start: 0.6487 (mmm) cc_final: 0.6108 (mmm) REVERT: F 442 GLU cc_start: 0.7076 (mt-10) cc_final: 0.6798 (mt-10) REVERT: F 456 VAL cc_start: 0.7153 (OUTLIER) cc_final: 0.6762 (m) REVERT: G 19 LYS cc_start: 0.8131 (mptt) cc_final: 0.7901 (mptt) REVERT: G 37 ARG cc_start: 0.7437 (ttp80) cc_final: 0.7086 (ttp80) REVERT: G 43 LYS cc_start: 0.8257 (ttpt) cc_final: 0.7935 (ttpt) REVERT: G 48 TYR cc_start: 0.7560 (t80) cc_final: 0.7265 (t80) REVERT: G 103 TYR cc_start: 0.7513 (t80) cc_final: 0.7286 (t80) REVERT: G 148 SER cc_start: 0.8667 (m) cc_final: 0.8379 (p) REVERT: G 183 GLN cc_start: 0.7333 (pp30) cc_final: 0.6541 (pp30) REVERT: G 222 GLN cc_start: 0.7921 (mt0) cc_final: 0.7614 (mt0) REVERT: G 239 GLU cc_start: 0.7468 (tt0) cc_final: 0.7224 (tt0) REVERT: G 248 LYS cc_start: 0.8050 (ttmm) cc_final: 0.7677 (ttmm) REVERT: G 269 ARG cc_start: 0.7475 (ttp80) cc_final: 0.7063 (ttp80) REVERT: G 279 GLU cc_start: 0.6646 (mm-30) cc_final: 0.6241 (mm-30) outliers start: 169 outliers final: 122 residues processed: 1031 average time/residue: 0.4025 time to fit residues: 621.6184 Evaluate side-chains 1093 residues out of total 2558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 961 time to evaluate : 2.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 190 ASN Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain A residue 339 ASP Chi-restraints excluded: chain A residue 391 GLU Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 422 GLN Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 485 ASP Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 45 ASP Chi-restraints excluded: chain B residue 46 ASN Chi-restraints excluded: chain B residue 132 ARG Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain B residue 236 PHE Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 245 MET Chi-restraints excluded: chain B residue 284 GLU Chi-restraints excluded: chain B residue 289 ASP Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 299 GLU Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain B residue 372 ILE Chi-restraints excluded: chain B residue 385 ASP Chi-restraints excluded: chain B residue 432 LYS Chi-restraints excluded: chain B residue 444 PHE Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 177 SER Chi-restraints excluded: chain C residue 214 LYS Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 252 LYS Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain C residue 417 VAL Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 487 LEU Chi-restraints excluded: chain C residue 491 ILE Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 120 ARG Chi-restraints excluded: chain D residue 130 THR Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 153 LYS Chi-restraints excluded: chain D residue 170 GLU Chi-restraints excluded: chain D residue 174 ASN Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 254 ILE Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 273 SER Chi-restraints excluded: chain D residue 314 THR Chi-restraints excluded: chain D residue 321 THR Chi-restraints excluded: chain D residue 322 PHE Chi-restraints excluded: chain D residue 374 LEU Chi-restraints excluded: chain D residue 392 LEU Chi-restraints excluded: chain D residue 428 VAL Chi-restraints excluded: chain D residue 442 GLU Chi-restraints excluded: chain E residue 47 THR Chi-restraints excluded: chain E residue 57 ASP Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 74 MET Chi-restraints excluded: chain E residue 112 ASP Chi-restraints excluded: chain E residue 214 VAL Chi-restraints excluded: chain E residue 218 MET Chi-restraints excluded: chain E residue 226 MET Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 294 SER Chi-restraints excluded: chain E residue 314 THR Chi-restraints excluded: chain E residue 322 PHE Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 378 LYS Chi-restraints excluded: chain E residue 391 GLU Chi-restraints excluded: chain E residue 469 MET Chi-restraints excluded: chain F residue 14 VAL Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 39 GLU Chi-restraints excluded: chain F residue 41 GLU Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 68 ASP Chi-restraints excluded: chain F residue 74 MET Chi-restraints excluded: chain F residue 90 VAL Chi-restraints excluded: chain F residue 120 ARG Chi-restraints excluded: chain F residue 134 ILE Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain F residue 172 ILE Chi-restraints excluded: chain F residue 190 ASP Chi-restraints excluded: chain F residue 240 ARG Chi-restraints excluded: chain F residue 295 THR Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 379 GLU Chi-restraints excluded: chain F residue 387 LEU Chi-restraints excluded: chain F residue 398 LEU Chi-restraints excluded: chain F residue 400 VAL Chi-restraints excluded: chain F residue 410 LEU Chi-restraints excluded: chain F residue 416 VAL Chi-restraints excluded: chain F residue 456 VAL Chi-restraints excluded: chain F residue 464 GLU Chi-restraints excluded: chain G residue 27 MET Chi-restraints excluded: chain G residue 39 GLU Chi-restraints excluded: chain G residue 88 ARG Chi-restraints excluded: chain G residue 107 GLN Chi-restraints excluded: chain G residue 127 SER Chi-restraints excluded: chain G residue 146 GLN Chi-restraints excluded: chain G residue 151 ASP Chi-restraints excluded: chain G residue 153 LYS Chi-restraints excluded: chain G residue 190 LYS Chi-restraints excluded: chain G residue 232 LEU Chi-restraints excluded: chain G residue 260 THR Chi-restraints excluded: chain G residue 264 SER Chi-restraints excluded: chain G residue 273 ILE Chi-restraints excluded: chain G residue 277 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 289 optimal weight: 10.0000 chunk 33 optimal weight: 8.9990 chunk 170 optimal weight: 3.9990 chunk 219 optimal weight: 2.9990 chunk 169 optimal weight: 5.9990 chunk 252 optimal weight: 4.9990 chunk 167 optimal weight: 4.9990 chunk 298 optimal weight: 5.9990 chunk 186 optimal weight: 0.7980 chunk 182 optimal weight: 0.9990 chunk 137 optimal weight: 4.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 GLN ** A 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 425 HIS B 69 ASN C 143 HIS C 407 GLN D 174 ASN D 177 GLN ** D 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 8 GLN E 179 HIS F 174 ASN ** F 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6813 moved from start: 0.5186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 24608 Z= 0.301 Angle : 0.689 14.037 33370 Z= 0.356 Chirality : 0.048 0.239 3840 Planarity : 0.005 0.067 4349 Dihedral : 8.682 89.751 3576 Min Nonbonded Distance : 1.747 Molprobity Statistics. All-atom Clashscore : 16.34 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.80 % Favored : 94.17 % Rotamer: Outliers : 7.04 % Allowed : 30.22 % Favored : 62.74 % 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: -0.48 (0.15), residues: 3104 helix: 0.27 (0.14), residues: 1256 sheet: -0.00 (0.23), residues: 509 loop : -0.92 (0.17), residues: 1339 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.011 0.002 HIS F 179 PHE 0.025 0.002 PHE B 460 TYR 0.025 0.002 TYR G 103 ARG 0.013 0.001 ARG A 171 *********************** 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 1137 residues out of total 2558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 180 poor density : 957 time to evaluate : 2.735 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 LEU cc_start: 0.7710 (OUTLIER) cc_final: 0.7458 (mp) REVERT: A 87 GLU cc_start: 0.6771 (mm-30) cc_final: 0.6547 (mm-30) REVERT: A 181 ASP cc_start: 0.6831 (m-30) cc_final: 0.6604 (m-30) REVERT: A 230 GLN cc_start: 0.7534 (OUTLIER) cc_final: 0.7289 (mm-40) REVERT: A 317 PRO cc_start: 0.8292 (Cg_endo) cc_final: 0.8084 (Cg_exo) REVERT: A 466 GLN cc_start: 0.7595 (mt0) cc_final: 0.7357 (mt0) REVERT: A 496 LYS cc_start: 0.8454 (mmtt) cc_final: 0.8216 (mmtt) REVERT: B 136 VAL cc_start: 0.5872 (p) cc_final: 0.4689 (m) REVERT: B 181 ASP cc_start: 0.6825 (t70) cc_final: 0.6563 (t70) REVERT: B 341 GLN cc_start: 0.6811 (pt0) cc_final: 0.6552 (pt0) REVERT: B 373 LYS cc_start: 0.7498 (ttmt) cc_final: 0.7021 (ttmt) REVERT: B 432 LYS cc_start: 0.8322 (OUTLIER) cc_final: 0.7763 (mttt) REVERT: B 458 LYS cc_start: 0.7329 (tmmt) cc_final: 0.7003 (mttp) REVERT: B 460 PHE cc_start: 0.7175 (t80) cc_final: 0.6965 (t80) REVERT: C 206 ARG cc_start: 0.7247 (ttt180) cc_final: 0.7031 (tpp-160) REVERT: C 214 LYS cc_start: 0.7819 (OUTLIER) cc_final: 0.7547 (mtpt) REVERT: C 377 LYS cc_start: 0.7909 (tttp) cc_final: 0.7580 (tttp) REVERT: C 389 TYR cc_start: 0.8064 (t80) cc_final: 0.7765 (t80) REVERT: C 424 LEU cc_start: 0.8290 (tp) cc_final: 0.8066 (tp) REVERT: C 433 GLN cc_start: 0.7840 (mt0) cc_final: 0.7604 (mt0) REVERT: C 435 LEU cc_start: 0.7953 (OUTLIER) cc_final: 0.7708 (mm) REVERT: D 35 LYS cc_start: 0.7842 (ttmt) cc_final: 0.7538 (ttmt) REVERT: D 154 ILE cc_start: 0.7636 (mm) cc_final: 0.7401 (mt) REVERT: D 157 PHE cc_start: 0.6900 (m-10) cc_final: 0.6315 (m-80) REVERT: D 178 GLU cc_start: 0.8040 (tm-30) cc_final: 0.7808 (tm-30) REVERT: D 202 MET cc_start: 0.6750 (mmt) cc_final: 0.6375 (mmt) REVERT: D 207 VAL cc_start: 0.8649 (t) cc_final: 0.7235 (p) REVERT: D 220 GLU cc_start: 0.6862 (mp0) cc_final: 0.6650 (mp0) REVERT: D 267 LEU cc_start: 0.7819 (mm) cc_final: 0.7224 (mt) REVERT: D 340 ILE cc_start: 0.8593 (pt) cc_final: 0.8218 (mm) REVERT: D 378 LYS cc_start: 0.8170 (tttt) cc_final: 0.7829 (mmmm) REVERT: D 386 ILE cc_start: 0.7937 (pt) cc_final: 0.7669 (mp) REVERT: D 396 ASP cc_start: 0.7371 (m-30) cc_final: 0.7120 (m-30) REVERT: D 428 VAL cc_start: 0.5995 (OUTLIER) cc_final: 0.4882 (p) REVERT: D 464 GLU cc_start: 0.7401 (tp30) cc_final: 0.7072 (tp30) REVERT: D 465 LYS cc_start: 0.8253 (tttt) cc_final: 0.8004 (tttt) REVERT: E 26 ILE cc_start: 0.8550 (mt) cc_final: 0.8323 (tt) REVERT: E 112 ASP cc_start: 0.7082 (OUTLIER) cc_final: 0.6825 (m-30) REVERT: E 291 ARG cc_start: 0.7167 (mtt180) cc_final: 0.6795 (mtt180) REVERT: E 333 ARG cc_start: 0.7087 (ttm-80) cc_final: 0.6863 (ttm-80) REVERT: E 361 GLU cc_start: 0.7379 (mm-30) cc_final: 0.6825 (mm-30) REVERT: E 365 GLN cc_start: 0.7921 (pt0) cc_final: 0.7528 (pm20) REVERT: E 369 LYS cc_start: 0.8026 (mttt) cc_final: 0.7709 (mtmm) REVERT: E 380 LEU cc_start: 0.8123 (tp) cc_final: 0.7877 (pp) REVERT: E 435 ARG cc_start: 0.6168 (ttp80) cc_final: 0.5837 (ttp80) REVERT: E 458 ARG cc_start: 0.6928 (ttm110) cc_final: 0.6688 (ptm-80) REVERT: E 469 MET cc_start: 0.5778 (OUTLIER) cc_final: 0.5540 (mmm) REVERT: F 38 ASN cc_start: 0.7534 (t0) cc_final: 0.7306 (t0) REVERT: F 234 THR cc_start: 0.7667 (OUTLIER) cc_final: 0.6988 (t) REVERT: F 285 MET cc_start: 0.7171 (ttp) cc_final: 0.6688 (ttp) REVERT: F 389 MET cc_start: 0.6443 (mmm) cc_final: 0.6052 (mmm) REVERT: F 390 ASP cc_start: 0.6913 (p0) cc_final: 0.6712 (p0) REVERT: F 442 GLU cc_start: 0.7079 (mt-10) cc_final: 0.6817 (mt-10) REVERT: F 456 VAL cc_start: 0.7167 (OUTLIER) cc_final: 0.6681 (m) REVERT: G 15 ASN cc_start: 0.8253 (m-40) cc_final: 0.7925 (m110) REVERT: G 19 LYS cc_start: 0.8136 (mptt) cc_final: 0.7875 (mptt) REVERT: G 37 ARG cc_start: 0.7480 (ttp80) cc_final: 0.7144 (ttp80) REVERT: G 48 TYR cc_start: 0.7600 (t80) cc_final: 0.7269 (t80) REVERT: G 70 MET cc_start: 0.7953 (mmp) cc_final: 0.7409 (mmp) REVERT: G 103 TYR cc_start: 0.7744 (t80) cc_final: 0.7193 (t80) REVERT: G 131 LYS cc_start: 0.8311 (ttmm) cc_final: 0.8058 (ttmm) REVERT: G 132 ARG cc_start: 0.8011 (mmp80) cc_final: 0.7336 (mmm-85) REVERT: G 146 GLN cc_start: 0.7207 (OUTLIER) cc_final: 0.6792 (pp30) REVERT: G 148 SER cc_start: 0.8619 (m) cc_final: 0.8256 (p) REVERT: G 183 GLN cc_start: 0.7446 (pp30) cc_final: 0.6735 (pp30) REVERT: G 189 ARG cc_start: 0.6266 (mpt90) cc_final: 0.6059 (mpt90) REVERT: G 194 LEU cc_start: 0.5386 (OUTLIER) cc_final: 0.5124 (tm) REVERT: G 222 GLN cc_start: 0.7976 (mt0) cc_final: 0.7708 (mt0) REVERT: G 239 GLU cc_start: 0.7533 (tt0) cc_final: 0.7303 (tt0) REVERT: G 269 ARG cc_start: 0.7489 (ttp80) cc_final: 0.7096 (ttp80) REVERT: G 279 GLU cc_start: 0.6645 (mm-30) cc_final: 0.6251 (mm-30) outliers start: 180 outliers final: 133 residues processed: 1024 average time/residue: 0.3969 time to fit residues: 606.9502 Evaluate side-chains 1090 residues out of total 2558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 145 poor density : 945 time to evaluate : 2.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 190 ASN Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 230 GLN Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 339 ASP Chi-restraints excluded: chain A residue 391 GLU Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 422 GLN Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 33 GLN Chi-restraints excluded: chain B residue 45 ASP Chi-restraints excluded: chain B residue 46 ASN Chi-restraints excluded: chain B residue 87 GLU Chi-restraints excluded: chain B residue 132 ARG Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 236 PHE Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 245 MET Chi-restraints excluded: chain B residue 272 GLU Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 284 GLU Chi-restraints excluded: chain B residue 289 ASP Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 372 ILE Chi-restraints excluded: chain B residue 432 LYS Chi-restraints excluded: chain B residue 444 PHE Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain C residue 46 ASN Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 177 SER Chi-restraints excluded: chain C residue 214 LYS Chi-restraints excluded: chain C residue 219 ASP Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 252 LYS Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 381 THR Chi-restraints excluded: chain C residue 407 GLN Chi-restraints excluded: chain C residue 417 VAL Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 120 ARG Chi-restraints excluded: chain D residue 130 THR Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 153 LYS Chi-restraints excluded: chain D residue 170 GLU Chi-restraints excluded: chain D residue 174 ASN Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 251 ILE Chi-restraints excluded: chain D residue 254 ILE Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 273 SER Chi-restraints excluded: chain D residue 314 THR Chi-restraints excluded: chain D residue 321 THR Chi-restraints excluded: chain D residue 328 THR Chi-restraints excluded: chain D residue 361 GLU Chi-restraints excluded: chain D residue 374 LEU Chi-restraints excluded: chain D residue 392 LEU Chi-restraints excluded: chain D residue 428 VAL Chi-restraints excluded: chain D residue 442 GLU Chi-restraints excluded: chain E residue 7 ILE Chi-restraints excluded: chain E residue 57 ASP Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 68 ASP Chi-restraints excluded: chain E residue 74 MET Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain E residue 96 PHE Chi-restraints excluded: chain E residue 112 ASP Chi-restraints excluded: chain E residue 218 MET Chi-restraints excluded: chain E residue 226 MET Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 273 SER Chi-restraints excluded: chain E residue 294 SER Chi-restraints excluded: chain E residue 300 ILE Chi-restraints excluded: chain E residue 311 ASP Chi-restraints excluded: chain E residue 314 THR Chi-restraints excluded: chain E residue 322 PHE Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 396 ASP Chi-restraints excluded: chain E residue 413 ASN Chi-restraints excluded: chain E residue 469 MET Chi-restraints excluded: chain F residue 14 VAL Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 39 GLU Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 68 ASP Chi-restraints excluded: chain F residue 74 MET Chi-restraints excluded: chain F residue 84 SER Chi-restraints excluded: chain F residue 90 VAL Chi-restraints excluded: chain F residue 103 ILE Chi-restraints excluded: chain F residue 120 ARG Chi-restraints excluded: chain F residue 134 ILE Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain F residue 172 ILE Chi-restraints excluded: chain F residue 190 ASP Chi-restraints excluded: chain F residue 234 THR Chi-restraints excluded: chain F residue 240 ARG Chi-restraints excluded: chain F residue 295 THR Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 387 LEU Chi-restraints excluded: chain F residue 398 LEU Chi-restraints excluded: chain F residue 400 VAL Chi-restraints excluded: chain F residue 410 LEU Chi-restraints excluded: chain F residue 416 VAL Chi-restraints excluded: chain F residue 440 ILE Chi-restraints excluded: chain F residue 456 VAL Chi-restraints excluded: chain F residue 464 GLU Chi-restraints excluded: chain G residue 27 MET Chi-restraints excluded: chain G residue 39 GLU Chi-restraints excluded: chain G residue 88 ARG Chi-restraints excluded: chain G residue 127 SER Chi-restraints excluded: chain G residue 146 GLN Chi-restraints excluded: chain G residue 151 ASP Chi-restraints excluded: chain G residue 194 LEU Chi-restraints excluded: chain G residue 232 LEU Chi-restraints excluded: chain G residue 233 LEU Chi-restraints excluded: chain G residue 260 THR Chi-restraints excluded: chain G residue 273 ILE Chi-restraints excluded: chain G residue 277 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 184 optimal weight: 6.9990 chunk 119 optimal weight: 5.9990 chunk 178 optimal weight: 0.2980 chunk 90 optimal weight: 10.0000 chunk 58 optimal weight: 0.6980 chunk 57 optimal weight: 7.9990 chunk 189 optimal weight: 5.9990 chunk 203 optimal weight: 4.9990 chunk 147 optimal weight: 0.9990 chunk 27 optimal weight: 6.9990 chunk 234 optimal weight: 6.9990 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 GLN A 143 HIS ** A 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 488 ASN C 407 GLN D 173 HIS D 174 ASN D 196 ASN ** D 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 146 GLN ** G 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6806 moved from start: 0.5309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 24608 Z= 0.286 Angle : 0.690 16.346 33370 Z= 0.353 Chirality : 0.048 0.291 3840 Planarity : 0.005 0.115 4349 Dihedral : 8.603 88.647 3576 Min Nonbonded Distance : 1.773 Molprobity Statistics. All-atom Clashscore : 16.20 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.35 % Favored : 94.62 % Rotamer: Outliers : 6.92 % Allowed : 30.06 % Favored : 63.02 % 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: -0.46 (0.15), residues: 3104 helix: 0.27 (0.14), residues: 1263 sheet: 0.12 (0.24), residues: 478 loop : -0.93 (0.17), residues: 1363 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.012 0.002 HIS A 425 PHE 0.025 0.002 PHE C 343 TYR 0.035 0.002 TYR G 103 ARG 0.019 0.001 ARG C 171 *********************** 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 1125 residues out of total 2558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 177 poor density : 948 time to evaluate : 2.838 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 LEU cc_start: 0.7733 (OUTLIER) cc_final: 0.7457 (mp) REVERT: A 87 GLU cc_start: 0.6761 (mm-30) cc_final: 0.6554 (mm-30) REVERT: A 230 GLN cc_start: 0.7529 (OUTLIER) cc_final: 0.7288 (mm-40) REVERT: A 317 PRO cc_start: 0.8291 (Cg_endo) cc_final: 0.8081 (Cg_exo) REVERT: A 420 LEU cc_start: 0.8201 (OUTLIER) cc_final: 0.7701 (mm) REVERT: A 466 GLN cc_start: 0.7636 (mt0) cc_final: 0.7395 (mt0) REVERT: A 496 LYS cc_start: 0.8558 (mmtt) cc_final: 0.8322 (mmtt) REVERT: B 136 VAL cc_start: 0.5928 (p) cc_final: 0.4752 (m) REVERT: B 181 ASP cc_start: 0.6848 (t70) cc_final: 0.6559 (t70) REVERT: B 341 GLN cc_start: 0.6822 (pt0) cc_final: 0.6550 (pt0) REVERT: B 373 LYS cc_start: 0.7474 (ttmt) cc_final: 0.7010 (ttmt) REVERT: B 432 LYS cc_start: 0.8389 (OUTLIER) cc_final: 0.7774 (mttt) REVERT: B 458 LYS cc_start: 0.7374 (tmmt) cc_final: 0.7066 (mttm) REVERT: B 460 PHE cc_start: 0.7167 (t80) cc_final: 0.6966 (t80) REVERT: B 476 ARG cc_start: 0.7953 (ptp-110) cc_final: 0.7467 (ptp-110) REVERT: B 488 ASN cc_start: 0.7932 (m110) cc_final: 0.7712 (m110) REVERT: C 214 LYS cc_start: 0.7812 (OUTLIER) cc_final: 0.7539 (mtpt) REVERT: C 377 LYS cc_start: 0.7950 (tttp) cc_final: 0.7741 (tttp) REVERT: C 389 TYR cc_start: 0.8068 (t80) cc_final: 0.7769 (t80) REVERT: C 424 LEU cc_start: 0.8268 (tp) cc_final: 0.8039 (tp) REVERT: C 433 GLN cc_start: 0.7845 (mt0) cc_final: 0.7619 (mt0) REVERT: C 435 LEU cc_start: 0.7954 (OUTLIER) cc_final: 0.7713 (mm) REVERT: C 444 PHE cc_start: 0.7208 (m-80) cc_final: 0.7002 (m-80) REVERT: D 35 LYS cc_start: 0.7838 (ttmt) cc_final: 0.7534 (ttmt) REVERT: D 124 LYS cc_start: 0.7484 (mmmm) cc_final: 0.7182 (mmmm) REVERT: D 154 ILE cc_start: 0.7663 (mm) cc_final: 0.7370 (mt) REVERT: D 202 MET cc_start: 0.6756 (mmt) cc_final: 0.6430 (mmt) REVERT: D 207 VAL cc_start: 0.8632 (t) cc_final: 0.7203 (p) REVERT: D 220 GLU cc_start: 0.6865 (mp0) cc_final: 0.6661 (mp0) REVERT: D 267 LEU cc_start: 0.7817 (mm) cc_final: 0.7217 (mt) REVERT: D 340 ILE cc_start: 0.8610 (pt) cc_final: 0.8217 (mm) REVERT: D 378 LYS cc_start: 0.8159 (tttt) cc_final: 0.7820 (mmmm) REVERT: D 386 ILE cc_start: 0.7944 (pt) cc_final: 0.7698 (mp) REVERT: D 396 ASP cc_start: 0.7327 (m-30) cc_final: 0.7111 (m-30) REVERT: D 428 VAL cc_start: 0.5965 (OUTLIER) cc_final: 0.4842 (p) REVERT: D 464 GLU cc_start: 0.7392 (tp30) cc_final: 0.7049 (tp30) REVERT: D 465 LYS cc_start: 0.8259 (tttt) cc_final: 0.8015 (tttt) REVERT: E 26 ILE cc_start: 0.8572 (mt) cc_final: 0.8343 (tt) REVERT: E 112 ASP cc_start: 0.7091 (OUTLIER) cc_final: 0.6830 (m-30) REVERT: E 202 MET cc_start: 0.6825 (ttt) cc_final: 0.6603 (ttt) REVERT: E 291 ARG cc_start: 0.7148 (mtt180) cc_final: 0.6805 (mtt180) REVERT: E 333 ARG cc_start: 0.7090 (ttm-80) cc_final: 0.6853 (ttm-80) REVERT: E 361 GLU cc_start: 0.7339 (mm-30) cc_final: 0.6768 (mm-30) REVERT: E 365 GLN cc_start: 0.7904 (pt0) cc_final: 0.7521 (pm20) REVERT: E 369 LYS cc_start: 0.8018 (mttt) cc_final: 0.7712 (mtmm) REVERT: E 378 LYS cc_start: 0.8146 (OUTLIER) cc_final: 0.7737 (tmmm) REVERT: E 380 LEU cc_start: 0.8125 (tp) cc_final: 0.7889 (pp) REVERT: E 435 ARG cc_start: 0.6156 (ttp80) cc_final: 0.5835 (ttp80) REVERT: E 458 ARG cc_start: 0.6952 (ttm110) cc_final: 0.6693 (ptm-80) REVERT: E 465 LYS cc_start: 0.8534 (tttp) cc_final: 0.7797 (tttp) REVERT: E 469 MET cc_start: 0.5799 (OUTLIER) cc_final: 0.5392 (mmm) REVERT: F 38 ASN cc_start: 0.7503 (t0) cc_final: 0.7275 (t0) REVERT: F 234 THR cc_start: 0.7636 (OUTLIER) cc_final: 0.6954 (t) REVERT: F 285 MET cc_start: 0.7156 (ttp) cc_final: 0.6657 (ttp) REVERT: F 389 MET cc_start: 0.6656 (mmm) cc_final: 0.6263 (mmm) REVERT: F 442 GLU cc_start: 0.7050 (mt-10) cc_final: 0.6813 (mt-10) REVERT: G 15 ASN cc_start: 0.8247 (m-40) cc_final: 0.7917 (m110) REVERT: G 19 LYS cc_start: 0.8138 (mptt) cc_final: 0.7883 (mptt) REVERT: G 37 ARG cc_start: 0.7481 (ttp80) cc_final: 0.7146 (ttp80) REVERT: G 48 TYR cc_start: 0.7601 (t80) cc_final: 0.7257 (t80) REVERT: G 70 MET cc_start: 0.7946 (mmp) cc_final: 0.7451 (mmt) REVERT: G 103 TYR cc_start: 0.7633 (t80) cc_final: 0.6949 (t80) REVERT: G 131 LYS cc_start: 0.8293 (ttmm) cc_final: 0.8059 (ttmm) REVERT: G 132 ARG cc_start: 0.7971 (mmp80) cc_final: 0.7169 (mmm-85) REVERT: G 148 SER cc_start: 0.8620 (m) cc_final: 0.8242 (p) REVERT: G 153 LYS cc_start: 0.7580 (tttm) cc_final: 0.7287 (tttm) REVERT: G 183 GLN cc_start: 0.7462 (pp30) cc_final: 0.6712 (pp30) REVERT: G 194 LEU cc_start: 0.5319 (OUTLIER) cc_final: 0.5060 (tm) REVERT: G 222 GLN cc_start: 0.7980 (mt0) cc_final: 0.7753 (mt0) REVERT: G 239 GLU cc_start: 0.7527 (tt0) cc_final: 0.7306 (tt0) REVERT: G 244 MET cc_start: 0.7228 (ttp) cc_final: 0.6973 (ttp) REVERT: G 248 LYS cc_start: 0.8100 (ttmm) cc_final: 0.7703 (ttmm) REVERT: G 269 ARG cc_start: 0.7509 (ttp80) cc_final: 0.7110 (ttp80) REVERT: G 279 GLU cc_start: 0.6589 (mm-30) cc_final: 0.6206 (mm-30) outliers start: 177 outliers final: 144 residues processed: 1012 average time/residue: 0.4053 time to fit residues: 613.2332 Evaluate side-chains 1106 residues out of total 2558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 156 poor density : 950 time to evaluate : 2.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 190 ASN Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 230 GLN Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 339 ASP Chi-restraints excluded: chain A residue 391 GLU Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 409 LYS Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 422 GLN Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 485 ASP Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 45 ASP Chi-restraints excluded: chain B residue 46 ASN Chi-restraints excluded: chain B residue 84 GLU Chi-restraints excluded: chain B residue 132 ARG Chi-restraints excluded: chain B residue 147 GLN Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 229 SER Chi-restraints excluded: chain B residue 236 PHE Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 245 MET Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 284 GLU Chi-restraints excluded: chain B residue 289 ASP Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 339 ASP Chi-restraints excluded: chain B residue 372 ILE Chi-restraints excluded: chain B residue 432 LYS Chi-restraints excluded: chain B residue 444 PHE Chi-restraints excluded: chain B residue 452 ASP Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain C residue 46 ASN Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 172 GLN Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 177 SER Chi-restraints excluded: chain C residue 214 LYS Chi-restraints excluded: chain C residue 219 ASP Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 252 LYS Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 339 ASP Chi-restraints excluded: chain C residue 381 THR Chi-restraints excluded: chain C residue 407 GLN Chi-restraints excluded: chain C residue 417 VAL Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain C residue 440 LEU Chi-restraints excluded: chain C residue 491 ILE Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 120 ARG Chi-restraints excluded: chain D residue 130 THR Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 153 LYS Chi-restraints excluded: chain D residue 170 GLU Chi-restraints excluded: chain D residue 172 ILE Chi-restraints excluded: chain D residue 174 ASN Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 251 ILE Chi-restraints excluded: chain D residue 254 ILE Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 273 SER Chi-restraints excluded: chain D residue 314 THR Chi-restraints excluded: chain D residue 321 THR Chi-restraints excluded: chain D residue 328 THR Chi-restraints excluded: chain D residue 361 GLU Chi-restraints excluded: chain D residue 374 LEU Chi-restraints excluded: chain D residue 392 LEU Chi-restraints excluded: chain D residue 428 VAL Chi-restraints excluded: chain D residue 442 GLU Chi-restraints excluded: chain E residue 7 ILE Chi-restraints excluded: chain E residue 57 ASP Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 68 ASP Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain E residue 96 PHE Chi-restraints excluded: chain E residue 112 ASP Chi-restraints excluded: chain E residue 213 MET Chi-restraints excluded: chain E residue 218 MET Chi-restraints excluded: chain E residue 226 MET Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 273 SER Chi-restraints excluded: chain E residue 293 THR Chi-restraints excluded: chain E residue 294 SER Chi-restraints excluded: chain E residue 300 ILE Chi-restraints excluded: chain E residue 311 ASP Chi-restraints excluded: chain E residue 314 THR Chi-restraints excluded: chain E residue 322 PHE Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 378 LYS Chi-restraints excluded: chain E residue 389 MET Chi-restraints excluded: chain E residue 391 GLU Chi-restraints excluded: chain E residue 469 MET Chi-restraints excluded: chain F residue 14 VAL Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 39 GLU Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 68 ASP Chi-restraints excluded: chain F residue 74 MET Chi-restraints excluded: chain F residue 90 VAL Chi-restraints excluded: chain F residue 120 ARG Chi-restraints excluded: chain F residue 134 ILE Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain F residue 172 ILE Chi-restraints excluded: chain F residue 190 ASP Chi-restraints excluded: chain F residue 234 THR Chi-restraints excluded: chain F residue 295 THR Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 387 LEU Chi-restraints excluded: chain F residue 398 LEU Chi-restraints excluded: chain F residue 400 VAL Chi-restraints excluded: chain F residue 410 LEU Chi-restraints excluded: chain F residue 416 VAL Chi-restraints excluded: chain F residue 440 ILE Chi-restraints excluded: chain F residue 464 GLU Chi-restraints excluded: chain G residue 27 MET Chi-restraints excluded: chain G residue 88 ARG Chi-restraints excluded: chain G residue 127 SER Chi-restraints excluded: chain G residue 146 GLN Chi-restraints excluded: chain G residue 151 ASP Chi-restraints excluded: chain G residue 190 LYS Chi-restraints excluded: chain G residue 194 LEU Chi-restraints excluded: chain G residue 227 LEU Chi-restraints excluded: chain G residue 232 LEU Chi-restraints excluded: chain G residue 233 LEU Chi-restraints excluded: chain G residue 264 SER Chi-restraints excluded: chain G residue 273 ILE Chi-restraints excluded: chain G residue 277 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 271 optimal weight: 2.9990 chunk 286 optimal weight: 8.9990 chunk 261 optimal weight: 5.9990 chunk 278 optimal weight: 7.9990 chunk 167 optimal weight: 5.9990 chunk 121 optimal weight: 0.8980 chunk 218 optimal weight: 10.0000 chunk 85 optimal weight: 2.9990 chunk 251 optimal weight: 5.9990 chunk 263 optimal weight: 6.9990 chunk 277 optimal weight: 0.9980 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 GLN C 407 GLN D 174 ASN ** D 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 413 ASN E 8 GLN ** E 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 174 ASN F 217 GLN ** F 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6812 moved from start: 0.5435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 24608 Z= 0.302 Angle : 0.704 18.317 33370 Z= 0.361 Chirality : 0.048 0.262 3840 Planarity : 0.005 0.077 4349 Dihedral : 8.512 79.450 3576 Min Nonbonded Distance : 1.760 Molprobity Statistics. All-atom Clashscore : 16.52 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.99 % Favored : 93.98 % Rotamer: Outliers : 6.88 % Allowed : 30.49 % Favored : 62.63 % 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: -0.56 (0.15), residues: 3104 helix: 0.21 (0.14), residues: 1261 sheet: -0.01 (0.24), residues: 464 loop : -0.96 (0.17), residues: 1379 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.012 0.002 HIS D 401 PHE 0.036 0.002 PHE A 494 TYR 0.037 0.002 TYR G 103 ARG 0.016 0.001 ARG C 171 *********************** 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 1132 residues out of total 2558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 176 poor density : 956 time to evaluate : 2.718 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: symmetry clash REVERT: A 44 LEU cc_start: 0.7799 (OUTLIER) cc_final: 0.7574 (mp) REVERT: A 87 GLU cc_start: 0.6755 (mm-30) cc_final: 0.6543 (mm-30) REVERT: A 176 THR cc_start: 0.7394 (OUTLIER) cc_final: 0.6703 (p) REVERT: A 230 GLN cc_start: 0.7541 (OUTLIER) cc_final: 0.7302 (mm-40) REVERT: A 300 ARG cc_start: 0.6998 (OUTLIER) cc_final: 0.6404 (mtp85) REVERT: A 317 PRO cc_start: 0.8315 (Cg_endo) cc_final: 0.8110 (Cg_exo) REVERT: A 420 LEU cc_start: 0.8190 (OUTLIER) cc_final: 0.7686 (mm) REVERT: A 466 GLN cc_start: 0.7611 (mt0) cc_final: 0.7382 (mt0) REVERT: A 496 LYS cc_start: 0.8573 (mmtt) cc_final: 0.8341 (mmtt) REVERT: B 122 GLU cc_start: 0.6621 (mm-30) cc_final: 0.6331 (mm-30) REVERT: B 136 VAL cc_start: 0.5975 (p) cc_final: 0.4771 (m) REVERT: B 181 ASP cc_start: 0.6837 (t70) cc_final: 0.6567 (t70) REVERT: B 341 GLN cc_start: 0.6827 (pt0) cc_final: 0.6528 (pt0) REVERT: B 373 LYS cc_start: 0.7471 (ttmt) cc_final: 0.7000 (ttmt) REVERT: B 418 GLU cc_start: 0.6235 (pt0) cc_final: 0.6011 (mt-10) REVERT: B 432 LYS cc_start: 0.8373 (mttt) cc_final: 0.7746 (mttt) REVERT: B 458 LYS cc_start: 0.7381 (tmmt) cc_final: 0.7049 (mttp) REVERT: B 460 PHE cc_start: 0.7197 (t80) cc_final: 0.6966 (t80) REVERT: B 476 ARG cc_start: 0.8000 (ptp-110) cc_final: 0.7729 (ptp-110) REVERT: C 191 MET cc_start: 0.5811 (tpp) cc_final: 0.5534 (tpp) REVERT: C 214 LYS cc_start: 0.7777 (OUTLIER) cc_final: 0.7506 (mtpt) REVERT: C 377 LYS cc_start: 0.7953 (tttp) cc_final: 0.7686 (tttp) REVERT: C 389 TYR cc_start: 0.8055 (t80) cc_final: 0.7745 (t80) REVERT: C 424 LEU cc_start: 0.8274 (tp) cc_final: 0.8057 (tp) REVERT: D 35 LYS cc_start: 0.7849 (ttmt) cc_final: 0.7544 (ttmt) REVERT: D 124 LYS cc_start: 0.7506 (mmmm) cc_final: 0.7177 (mmmm) REVERT: D 154 ILE cc_start: 0.7679 (mm) cc_final: 0.7391 (mt) REVERT: D 202 MET cc_start: 0.6784 (mmt) cc_final: 0.6468 (mmt) REVERT: D 207 VAL cc_start: 0.8625 (t) cc_final: 0.7212 (p) REVERT: D 267 LEU cc_start: 0.7825 (mm) cc_final: 0.7217 (mt) REVERT: D 340 ILE cc_start: 0.8541 (pt) cc_final: 0.8242 (mm) REVERT: D 386 ILE cc_start: 0.7926 (pt) cc_final: 0.7612 (mp) REVERT: D 396 ASP cc_start: 0.7351 (m-30) cc_final: 0.7111 (m-30) REVERT: D 428 VAL cc_start: 0.5993 (OUTLIER) cc_final: 0.4870 (p) REVERT: D 450 GLU cc_start: 0.6928 (pt0) cc_final: 0.6674 (pt0) REVERT: D 464 GLU cc_start: 0.7415 (tp30) cc_final: 0.7065 (tp30) REVERT: D 465 LYS cc_start: 0.8280 (tttt) cc_final: 0.8007 (tttt) REVERT: E 26 ILE cc_start: 0.8526 (mt) cc_final: 0.8297 (tt) REVERT: E 112 ASP cc_start: 0.7073 (OUTLIER) cc_final: 0.6837 (m-30) REVERT: E 202 MET cc_start: 0.6905 (ttt) cc_final: 0.6652 (ttt) REVERT: E 291 ARG cc_start: 0.7136 (mtt180) cc_final: 0.6803 (mtt180) REVERT: E 333 ARG cc_start: 0.7098 (ttm-80) cc_final: 0.6852 (ttm-80) REVERT: E 369 LYS cc_start: 0.8001 (mttt) cc_final: 0.7689 (mtmm) REVERT: E 378 LYS cc_start: 0.8148 (OUTLIER) cc_final: 0.7745 (tmmm) REVERT: E 380 LEU cc_start: 0.8125 (tp) cc_final: 0.7897 (pp) REVERT: E 435 ARG cc_start: 0.6126 (ttp80) cc_final: 0.5800 (ttp80) REVERT: E 446 ASP cc_start: 0.7672 (m-30) cc_final: 0.7431 (m-30) REVERT: E 458 ARG cc_start: 0.6942 (ttm110) cc_final: 0.6677 (ptm-80) REVERT: E 465 LYS cc_start: 0.8543 (tttp) cc_final: 0.7886 (tttp) REVERT: E 469 MET cc_start: 0.5792 (OUTLIER) cc_final: 0.5545 (mmm) REVERT: F 38 ASN cc_start: 0.7502 (t0) cc_final: 0.7279 (t0) REVERT: F 202 MET cc_start: 0.6116 (mmp) cc_final: 0.5821 (mmp) REVERT: F 234 THR cc_start: 0.7623 (OUTLIER) cc_final: 0.6979 (t) REVERT: F 257 PHE cc_start: 0.7912 (t80) cc_final: 0.7685 (t80) REVERT: F 285 MET cc_start: 0.7182 (ttp) cc_final: 0.6669 (ttp) REVERT: F 389 MET cc_start: 0.6698 (mmm) cc_final: 0.6219 (mmm) REVERT: F 390 ASP cc_start: 0.6876 (p0) cc_final: 0.6483 (p0) REVERT: F 442 GLU cc_start: 0.7054 (mt-10) cc_final: 0.6836 (mt-10) REVERT: F 444 LYS cc_start: 0.7736 (tttt) cc_final: 0.7505 (tttt) REVERT: G 15 ASN cc_start: 0.8251 (m-40) cc_final: 0.7908 (m110) REVERT: G 19 LYS cc_start: 0.8149 (mptt) cc_final: 0.7864 (mptt) REVERT: G 37 ARG cc_start: 0.7511 (ttp80) cc_final: 0.7187 (ttp80) REVERT: G 48 TYR cc_start: 0.7622 (t80) cc_final: 0.7240 (t80) REVERT: G 70 MET cc_start: 0.7951 (mmp) cc_final: 0.7418 (mmp) REVERT: G 103 TYR cc_start: 0.7637 (t80) cc_final: 0.7038 (t80) REVERT: G 131 LYS cc_start: 0.8295 (ttmm) cc_final: 0.8065 (ttmm) REVERT: G 132 ARG cc_start: 0.7982 (mmp80) cc_final: 0.7223 (mmm-85) REVERT: G 146 GLN cc_start: 0.7332 (OUTLIER) cc_final: 0.7118 (pp30) REVERT: G 148 SER cc_start: 0.8682 (m) cc_final: 0.8310 (p) REVERT: G 153 LYS cc_start: 0.7586 (tttm) cc_final: 0.7322 (tttm) REVERT: G 183 GLN cc_start: 0.7475 (pp30) cc_final: 0.6738 (pp30) REVERT: G 222 GLN cc_start: 0.7991 (mt0) cc_final: 0.7757 (mt0) REVERT: G 239 GLU cc_start: 0.7555 (tt0) cc_final: 0.7333 (tt0) REVERT: G 244 MET cc_start: 0.7236 (ttp) cc_final: 0.6954 (ttp) REVERT: G 269 ARG cc_start: 0.7509 (ttp80) cc_final: 0.7117 (ttp80) REVERT: G 279 GLU cc_start: 0.6569 (mm-30) cc_final: 0.6219 (mm-30) outliers start: 176 outliers final: 143 residues processed: 1023 average time/residue: 0.3952 time to fit residues: 606.6486 Evaluate side-chains 1110 residues out of total 2558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 155 poor density : 955 time to evaluate : 2.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 181 ASP Chi-restraints excluded: chain A residue 190 ASN Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 230 GLN Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 300 ARG Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 339 ASP Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 391 GLU Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 409 LYS Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 422 GLN Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 485 ASP Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 45 ASP Chi-restraints excluded: chain B residue 46 ASN Chi-restraints excluded: chain B residue 84 GLU Chi-restraints excluded: chain B residue 87 GLU Chi-restraints excluded: chain B residue 132 ARG Chi-restraints excluded: chain B residue 137 MET Chi-restraints excluded: chain B residue 147 GLN Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 236 PHE Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 245 MET Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 284 GLU Chi-restraints excluded: chain B residue 289 ASP Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 339 ASP Chi-restraints excluded: chain B residue 372 ILE Chi-restraints excluded: chain B residue 444 PHE Chi-restraints excluded: chain B residue 452 ASP Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain C residue 46 ASN Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 172 GLN Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 177 SER Chi-restraints excluded: chain C residue 214 LYS Chi-restraints excluded: chain C residue 219 ASP Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 252 LYS Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 339 ASP Chi-restraints excluded: chain C residue 381 THR Chi-restraints excluded: chain C residue 407 GLN Chi-restraints excluded: chain C residue 417 VAL Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain C residue 440 LEU Chi-restraints excluded: chain C residue 489 LYS Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 120 ARG Chi-restraints excluded: chain D residue 130 THR Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 153 LYS Chi-restraints excluded: chain D residue 170 GLU Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 251 ILE Chi-restraints excluded: chain D residue 254 ILE Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 273 SER Chi-restraints excluded: chain D residue 314 THR Chi-restraints excluded: chain D residue 321 THR Chi-restraints excluded: chain D residue 328 THR Chi-restraints excluded: chain D residue 361 GLU Chi-restraints excluded: chain D residue 374 LEU Chi-restraints excluded: chain D residue 392 LEU Chi-restraints excluded: chain D residue 428 VAL Chi-restraints excluded: chain D residue 442 GLU Chi-restraints excluded: chain D residue 448 LEU Chi-restraints excluded: chain E residue 7 ILE Chi-restraints excluded: chain E residue 57 ASP Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 68 ASP Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain E residue 96 PHE Chi-restraints excluded: chain E residue 112 ASP Chi-restraints excluded: chain E residue 218 MET Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 273 SER Chi-restraints excluded: chain E residue 293 THR Chi-restraints excluded: chain E residue 294 SER Chi-restraints excluded: chain E residue 300 ILE Chi-restraints excluded: chain E residue 311 ASP Chi-restraints excluded: chain E residue 322 PHE Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 378 LYS Chi-restraints excluded: chain E residue 389 MET Chi-restraints excluded: chain E residue 396 ASP Chi-restraints excluded: chain E residue 469 MET Chi-restraints excluded: chain F residue 14 VAL Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 39 GLU Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 67 THR Chi-restraints excluded: chain F residue 68 ASP Chi-restraints excluded: chain F residue 74 MET Chi-restraints excluded: chain F residue 84 SER Chi-restraints excluded: chain F residue 90 VAL Chi-restraints excluded: chain F residue 103 ILE Chi-restraints excluded: chain F residue 120 ARG Chi-restraints excluded: chain F residue 134 ILE Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain F residue 172 ILE Chi-restraints excluded: chain F residue 190 ASP Chi-restraints excluded: chain F residue 234 THR Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 387 LEU Chi-restraints excluded: chain F residue 398 LEU Chi-restraints excluded: chain F residue 400 VAL Chi-restraints excluded: chain F residue 410 LEU Chi-restraints excluded: chain F residue 416 VAL Chi-restraints excluded: chain F residue 440 ILE Chi-restraints excluded: chain F residue 464 GLU Chi-restraints excluded: chain G residue 27 MET Chi-restraints excluded: chain G residue 88 ARG Chi-restraints excluded: chain G residue 127 SER Chi-restraints excluded: chain G residue 146 GLN Chi-restraints excluded: chain G residue 151 ASP Chi-restraints excluded: chain G residue 227 LEU Chi-restraints excluded: chain G residue 233 LEU Chi-restraints excluded: chain G residue 273 ILE Chi-restraints excluded: chain G residue 277 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 182 optimal weight: 5.9990 chunk 294 optimal weight: 8.9990 chunk 179 optimal weight: 0.9980 chunk 139 optimal weight: 0.3980 chunk 204 optimal weight: 4.9990 chunk 308 optimal weight: 4.9990 chunk 284 optimal weight: 4.9990 chunk 245 optimal weight: 10.0000 chunk 25 optimal weight: 0.9980 chunk 189 optimal weight: 2.9990 chunk 150 optimal weight: 7.9990 overall best weight: 2.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 GLN B 422 GLN ** B 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 488 ASN C 407 GLN D 174 ASN ** D 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 174 ASN ** F 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 15 ASN G 146 GLN ** G 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6785 moved from start: 0.5533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 24608 Z= 0.255 Angle : 0.693 18.758 33370 Z= 0.352 Chirality : 0.047 0.264 3840 Planarity : 0.005 0.069 4349 Dihedral : 8.311 77.171 3576 Min Nonbonded Distance : 1.801 Molprobity Statistics. All-atom Clashscore : 16.03 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.12 % Favored : 94.85 % Rotamer: Outliers : 6.14 % Allowed : 31.59 % Favored : 62.28 % 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: -0.43 (0.15), residues: 3104 helix: 0.34 (0.14), residues: 1263 sheet: 0.09 (0.25), residues: 463 loop : -0.93 (0.17), residues: 1378 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.012 0.001 HIS D 401 PHE 0.032 0.002 PHE A 494 TYR 0.038 0.002 TYR G 103 ARG 0.013 0.001 ARG C 171 ********************** 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 1115 residues out of total 2558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 157 poor density : 958 time to evaluate : 2.575 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 230 GLN cc_start: 0.7518 (OUTLIER) cc_final: 0.7281 (mm-40) REVERT: A 317 PRO cc_start: 0.8279 (Cg_endo) cc_final: 0.8062 (Cg_exo) REVERT: A 420 LEU cc_start: 0.8157 (OUTLIER) cc_final: 0.7651 (mm) REVERT: A 466 GLN cc_start: 0.7618 (mt0) cc_final: 0.7391 (mt0) REVERT: A 496 LYS cc_start: 0.8594 (mmtt) cc_final: 0.8329 (mmtt) REVERT: B 122 GLU cc_start: 0.6615 (mm-30) cc_final: 0.6325 (mm-30) REVERT: B 136 VAL cc_start: 0.5953 (p) cc_final: 0.4769 (m) REVERT: B 181 ASP cc_start: 0.6825 (t70) cc_final: 0.6522 (t70) REVERT: B 341 GLN cc_start: 0.6848 (pt0) cc_final: 0.6539 (pt0) REVERT: B 373 LYS cc_start: 0.7455 (ttmt) cc_final: 0.7007 (ttmt) REVERT: B 432 LYS cc_start: 0.8341 (mttt) cc_final: 0.7678 (mttt) REVERT: B 458 LYS cc_start: 0.7365 (tmmt) cc_final: 0.7058 (mttp) REVERT: B 460 PHE cc_start: 0.7156 (t80) cc_final: 0.6803 (t80) REVERT: B 476 ARG cc_start: 0.8132 (ptp-110) cc_final: 0.7827 (ptp-110) REVERT: B 494 PHE cc_start: 0.7698 (t80) cc_final: 0.6668 (t80) REVERT: C 150 ILE cc_start: 0.8234 (mp) cc_final: 0.7983 (mt) REVERT: C 191 MET cc_start: 0.5789 (tpp) cc_final: 0.5515 (tpp) REVERT: C 214 LYS cc_start: 0.7775 (OUTLIER) cc_final: 0.7508 (mtpt) REVERT: C 219 ASP cc_start: 0.5992 (OUTLIER) cc_final: 0.5644 (p0) REVERT: C 377 LYS cc_start: 0.7936 (tttp) cc_final: 0.7677 (tttp) REVERT: C 389 TYR cc_start: 0.8033 (t80) cc_final: 0.7746 (t80) REVERT: C 424 LEU cc_start: 0.8284 (tp) cc_final: 0.8057 (tp) REVERT: D 8 GLN cc_start: 0.6516 (tt0) cc_final: 0.5819 (tt0) REVERT: D 35 LYS cc_start: 0.7843 (ttmt) cc_final: 0.7548 (ttmt) REVERT: D 124 LYS cc_start: 0.7501 (mmmm) cc_final: 0.7173 (mmmm) REVERT: D 154 ILE cc_start: 0.7666 (mm) cc_final: 0.7385 (mt) REVERT: D 178 GLU cc_start: 0.8146 (tm-30) cc_final: 0.7754 (tm-30) REVERT: D 202 MET cc_start: 0.6668 (mmt) cc_final: 0.6434 (mmt) REVERT: D 207 VAL cc_start: 0.8645 (t) cc_final: 0.7689 (p) REVERT: D 340 ILE cc_start: 0.8482 (pt) cc_final: 0.8181 (mm) REVERT: D 365 GLN cc_start: 0.6954 (mp10) cc_final: 0.6715 (mp10) REVERT: D 378 LYS cc_start: 0.8068 (tttt) cc_final: 0.7744 (mmmm) REVERT: D 386 ILE cc_start: 0.7915 (pt) cc_final: 0.7638 (mp) REVERT: D 396 ASP cc_start: 0.7305 (m-30) cc_final: 0.7085 (m-30) REVERT: D 428 VAL cc_start: 0.5991 (OUTLIER) cc_final: 0.4872 (p) REVERT: D 450 GLU cc_start: 0.6932 (pt0) cc_final: 0.6645 (pt0) REVERT: D 464 GLU cc_start: 0.7396 (tp30) cc_final: 0.7048 (tp30) REVERT: D 465 LYS cc_start: 0.8277 (tttt) cc_final: 0.8009 (tttt) REVERT: E 26 ILE cc_start: 0.8559 (mt) cc_final: 0.8329 (tt) REVERT: E 202 MET cc_start: 0.6875 (ttt) cc_final: 0.6554 (ttt) REVERT: E 291 ARG cc_start: 0.7118 (mtt180) cc_final: 0.6776 (mtt180) REVERT: E 333 ARG cc_start: 0.7087 (ttm-80) cc_final: 0.6845 (ttm-80) REVERT: E 369 LYS cc_start: 0.8002 (mttt) cc_final: 0.7676 (mtmm) REVERT: E 378 LYS cc_start: 0.8129 (OUTLIER) cc_final: 0.7716 (tmmm) REVERT: E 380 LEU cc_start: 0.8122 (tp) cc_final: 0.7894 (pp) REVERT: E 435 ARG cc_start: 0.6168 (ttp80) cc_final: 0.5866 (ttp80) REVERT: E 446 ASP cc_start: 0.7642 (m-30) cc_final: 0.7387 (m-30) REVERT: E 458 ARG cc_start: 0.6925 (ttm110) cc_final: 0.6699 (ptm-80) REVERT: E 465 LYS cc_start: 0.8550 (tttp) cc_final: 0.7828 (tttp) REVERT: E 469 MET cc_start: 0.5776 (OUTLIER) cc_final: 0.5501 (mmm) REVERT: F 38 ASN cc_start: 0.7484 (t0) cc_final: 0.7258 (t0) REVERT: F 202 MET cc_start: 0.6071 (mmp) cc_final: 0.5866 (mmp) REVERT: F 234 THR cc_start: 0.7648 (OUTLIER) cc_final: 0.6986 (t) REVERT: F 257 PHE cc_start: 0.7852 (t80) cc_final: 0.7632 (t80) REVERT: F 285 MET cc_start: 0.7145 (ttp) cc_final: 0.6629 (ttp) REVERT: F 444 LYS cc_start: 0.7723 (tttt) cc_final: 0.7484 (tttt) REVERT: G 15 ASN cc_start: 0.8196 (m110) cc_final: 0.7959 (m110) REVERT: G 19 LYS cc_start: 0.8141 (mptt) cc_final: 0.7867 (mptt) REVERT: G 37 ARG cc_start: 0.7473 (ttp80) cc_final: 0.7113 (ttp80) REVERT: G 48 TYR cc_start: 0.7586 (t80) cc_final: 0.7186 (t80) REVERT: G 70 MET cc_start: 0.7954 (mmp) cc_final: 0.7395 (mmp) REVERT: G 103 TYR cc_start: 0.7619 (t80) cc_final: 0.6990 (t80) REVERT: G 131 LYS cc_start: 0.8261 (ttmm) cc_final: 0.8035 (ttmm) REVERT: G 132 ARG cc_start: 0.7967 (mmp80) cc_final: 0.7209 (mmm-85) REVERT: G 148 SER cc_start: 0.8641 (m) cc_final: 0.8293 (p) REVERT: G 153 LYS cc_start: 0.7551 (tttm) cc_final: 0.7325 (tttm) REVERT: G 183 GLN cc_start: 0.7432 (pp30) cc_final: 0.6745 (pp30) REVERT: G 222 GLN cc_start: 0.7988 (mt0) cc_final: 0.7757 (mt0) REVERT: G 239 GLU cc_start: 0.7521 (tt0) cc_final: 0.7296 (tt0) REVERT: G 244 MET cc_start: 0.7202 (ttp) cc_final: 0.6900 (ttp) REVERT: G 269 ARG cc_start: 0.7525 (ttp80) cc_final: 0.7120 (ttp80) REVERT: G 279 GLU cc_start: 0.6578 (mm-30) cc_final: 0.6201 (mm-30) outliers start: 157 outliers final: 133 residues processed: 1014 average time/residue: 0.3857 time to fit residues: 586.0280 Evaluate side-chains 1093 residues out of total 2558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 952 time to evaluate : 2.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 181 ASP Chi-restraints excluded: chain A residue 190 ASN Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 230 GLN Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 339 ASP Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 391 GLU Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 409 LYS Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 422 GLN Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 485 ASP Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 45 ASP Chi-restraints excluded: chain B residue 46 ASN Chi-restraints excluded: chain B residue 60 MET Chi-restraints excluded: chain B residue 87 GLU Chi-restraints excluded: chain B residue 132 ARG Chi-restraints excluded: chain B residue 137 MET Chi-restraints excluded: chain B residue 147 GLN Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 229 SER Chi-restraints excluded: chain B residue 236 PHE Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 245 MET Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 284 GLU Chi-restraints excluded: chain B residue 289 ASP Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 339 ASP Chi-restraints excluded: chain B residue 372 ILE Chi-restraints excluded: chain B residue 385 ASP Chi-restraints excluded: chain B residue 423 ASP Chi-restraints excluded: chain B residue 444 PHE Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain C residue 46 ASN Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 113 GLN Chi-restraints excluded: chain C residue 172 GLN Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 177 SER Chi-restraints excluded: chain C residue 214 LYS Chi-restraints excluded: chain C residue 219 ASP Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 252 LYS Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 339 ASP Chi-restraints excluded: chain C residue 381 THR Chi-restraints excluded: chain C residue 407 GLN Chi-restraints excluded: chain C residue 417 VAL Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 120 ARG Chi-restraints excluded: chain D residue 130 THR Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 153 LYS Chi-restraints excluded: chain D residue 170 GLU Chi-restraints excluded: chain D residue 254 ILE Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 273 SER Chi-restraints excluded: chain D residue 314 THR Chi-restraints excluded: chain D residue 321 THR Chi-restraints excluded: chain D residue 328 THR Chi-restraints excluded: chain D residue 361 GLU Chi-restraints excluded: chain D residue 374 LEU Chi-restraints excluded: chain D residue 428 VAL Chi-restraints excluded: chain D residue 442 GLU Chi-restraints excluded: chain D residue 448 LEU Chi-restraints excluded: chain E residue 7 ILE Chi-restraints excluded: chain E residue 57 ASP Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 68 ASP Chi-restraints excluded: chain E residue 96 PHE Chi-restraints excluded: chain E residue 218 MET Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 294 SER Chi-restraints excluded: chain E residue 300 ILE Chi-restraints excluded: chain E residue 311 ASP Chi-restraints excluded: chain E residue 322 PHE Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 378 LYS Chi-restraints excluded: chain E residue 389 MET Chi-restraints excluded: chain E residue 391 GLU Chi-restraints excluded: chain E residue 469 MET Chi-restraints excluded: chain F residue 14 VAL Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 39 GLU Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 67 THR Chi-restraints excluded: chain F residue 74 MET Chi-restraints excluded: chain F residue 84 SER Chi-restraints excluded: chain F residue 90 VAL Chi-restraints excluded: chain F residue 120 ARG Chi-restraints excluded: chain F residue 134 ILE Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain F residue 172 ILE Chi-restraints excluded: chain F residue 190 ASP Chi-restraints excluded: chain F residue 234 THR Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 387 LEU Chi-restraints excluded: chain F residue 398 LEU Chi-restraints excluded: chain F residue 400 VAL Chi-restraints excluded: chain F residue 410 LEU Chi-restraints excluded: chain F residue 416 VAL Chi-restraints excluded: chain F residue 440 ILE Chi-restraints excluded: chain F residue 464 GLU Chi-restraints excluded: chain G residue 27 MET Chi-restraints excluded: chain G residue 88 ARG Chi-restraints excluded: chain G residue 127 SER Chi-restraints excluded: chain G residue 146 GLN Chi-restraints excluded: chain G residue 151 ASP Chi-restraints excluded: chain G residue 233 LEU Chi-restraints excluded: chain G residue 260 THR Chi-restraints excluded: chain G residue 273 ILE Chi-restraints excluded: chain G residue 277 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 195 optimal weight: 10.0000 chunk 261 optimal weight: 8.9990 chunk 75 optimal weight: 3.9990 chunk 226 optimal weight: 0.0370 chunk 36 optimal weight: 9.9990 chunk 68 optimal weight: 0.6980 chunk 246 optimal weight: 7.9990 chunk 103 optimal weight: 9.9990 chunk 252 optimal weight: 8.9990 chunk 31 optimal weight: 0.8980 chunk 45 optimal weight: 0.9980 overall best weight: 1.3260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 GLN ** B 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 407 GLN D 174 ASN D 217 GLN D 419 GLN E 8 GLN E 173 HIS ** E 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 219 ASN F 174 ASN ** F 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 401 HIS ** G 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.143095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.124853 restraints weight = 40157.744| |-----------------------------------------------------------------------------| r_work (start): 0.3745 rms_B_bonded: 3.14 r_work: 0.3596 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7291 moved from start: 0.5637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 24608 Z= 0.213 Angle : 0.681 18.058 33370 Z= 0.342 Chirality : 0.047 0.246 3840 Planarity : 0.005 0.071 4349 Dihedral : 8.021 75.502 3574 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 14.73 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.90 % Favored : 95.07 % Rotamer: Outliers : 5.36 % Allowed : 32.64 % Favored : 62.00 % 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: -0.32 (0.15), residues: 3104 helix: 0.45 (0.15), residues: 1266 sheet: 0.12 (0.24), residues: 473 loop : -0.89 (0.17), residues: 1365 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.011 0.001 HIS D 401 PHE 0.027 0.002 PHE A 494 TYR 0.039 0.001 TYR G 103 ARG 0.011 0.001 ARG C 171 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9412.40 seconds wall clock time: 167 minutes 32.87 seconds (10052.87 seconds total)