Starting phenix.real_space_refine on Wed Dec 13 08:06:00 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l1q_23115/12_2023/7l1q_23115_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l1q_23115/12_2023/7l1q_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_23115/12_2023/7l1q_23115.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l1q_23115/12_2023/7l1q_23115.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l1q_23115/12_2023/7l1q_23115_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l1q_23115/12_2023/7l1q_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: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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: 11.81, per 1000 atoms: 0.49 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: 9.74 Conformation dependent library (CDL) restraints added in 4.4 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: 4.73 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: 7.28 Time building geometry restraints manager: 10.22 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: 0.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 4.840 Check model and map are aligned: 0.360 Set scattering table: 0.210 Process input model: 61.010 Find NCS groups from input model: 1.780 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: 0.000 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.990 ------------------------------------------------------------------------------- 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 : 2.622 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 outliers start: 65 outliers final: 13 residues processed: 1101 average time/residue: 0.4204 time to fit residues: 681.3555 Evaluate side-chains 984 residues out of total 2558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 971 time to evaluate : 2.622 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.2172 time to fit residues: 9.0273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 5.9990 chunk 130 optimal weight: 0.9980 chunk 80 optimal weight: 3.9990 chunk 158 optimal weight: 9.9990 chunk 125 optimal weight: 2.9990 chunk 242 optimal weight: 7.9990 chunk 94 optimal weight: 10.0000 chunk 147 optimal weight: 2.9990 chunk 180 optimal weight: 10.0000 chunk 281 optimal weight: 1.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 GLN A 113 GLN A 185 ASN A 397 GLN A 422 GLN A 433 GLN A 469 GLN A 470 HIS ** A 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 474 HIS B 488 ASN C 46 ASN C 69 ASN C 185 ASN D 33 GLN D 200 HIS D 259 GLN D 372 GLN D 412 GLN E 33 GLN ** E 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 177 GLN E 179 HIS E 259 GLN E 287 GLN E 371 GLN E 401 HIS ** E 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 419 GLN F 8 GLN F 33 GLN F 196 ASN F 287 GLN F 304 GLN F 330 ASN F 363 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 G 270 GLN Total number of N/Q/H flips: 41 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6719 moved from start: 0.2914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 24608 Z= 0.251 Angle : 0.703 15.018 33370 Z= 0.370 Chirality : 0.049 0.389 3840 Planarity : 0.005 0.061 4349 Dihedral : 9.311 86.659 3572 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.61 % Favored : 97.36 % Rotamer: Outliers : 5.82 % Allowed : 20.99 % Favored : 73.18 % 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: -0.01 (0.15), residues: 3104 helix: 0.53 (0.14), residues: 1260 sheet: 0.27 (0.23), residues: 502 loop : -0.52 (0.17), residues: 1342 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS A 470 PHE 0.027 0.002 PHE A 236 TYR 0.023 0.002 TYR G 103 ARG 0.012 0.001 ARG E 405 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1144 residues out of total 2558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 995 time to evaluate : 2.656 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 outliers start: 149 outliers final: 73 residues processed: 1055 average time/residue: 0.4190 time to fit residues: 655.5879 Evaluate side-chains 1033 residues out of total 2558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 960 time to evaluate : 2.693 Switching outliers to nearest non-outliers outliers start: 73 outliers final: 0 residues processed: 73 average time/residue: 0.2617 time to fit residues: 37.3167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 156 optimal weight: 9.9990 chunk 87 optimal weight: 3.9990 chunk 234 optimal weight: 3.9990 chunk 191 optimal weight: 9.9990 chunk 77 optimal weight: 0.9980 chunk 282 optimal weight: 0.9990 chunk 304 optimal weight: 0.9990 chunk 251 optimal weight: 3.9990 chunk 279 optimal weight: 0.1980 chunk 96 optimal weight: 6.9990 chunk 226 optimal weight: 9.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 422 GLN A 474 HIS B 474 HIS C 407 GLN C 469 GLN D 200 HIS D 278 GLN E 8 GLN ** 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 289 GLN ** F 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 371 GLN ** G 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 107 GLN ** G 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6713 moved from start: 0.3634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 24608 Z= 0.206 Angle : 0.650 16.783 33370 Z= 0.332 Chirality : 0.046 0.250 3840 Planarity : 0.005 0.067 4349 Dihedral : 8.986 86.407 3572 Min Nonbonded Distance : 1.821 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.84 % Favored : 97.13 % Rotamer: Outliers : 3.05 % Allowed : 25.61 % Favored : 71.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.15), residues: 3104 helix: 0.68 (0.14), residues: 1260 sheet: 0.34 (0.23), residues: 501 loop : -0.54 (0.17), residues: 1343 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.014 0.001 HIS E 119 PHE 0.022 0.002 PHE G 129 TYR 0.022 0.001 TYR G 103 ARG 0.009 0.001 ARG C 140 *********************** 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 1064 residues out of total 2558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 986 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: symmetry clash outliers start: 78 outliers final: 43 residues processed: 1012 average time/residue: 0.4290 time to fit residues: 650.5683 Evaluate side-chains 1009 residues out of total 2558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 966 time to evaluate : 2.552 Switching outliers to nearest non-outliers outliers start: 43 outliers final: 0 residues processed: 43 average time/residue: 0.2677 time to fit residues: 24.7136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 278 optimal weight: 2.9990 chunk 212 optimal weight: 7.9990 chunk 146 optimal weight: 6.9990 chunk 31 optimal weight: 0.0470 chunk 134 optimal weight: 6.9990 chunk 189 optimal weight: 5.9990 chunk 283 optimal weight: 5.9990 chunk 299 optimal weight: 0.8980 chunk 147 optimal weight: 6.9990 chunk 268 optimal weight: 6.9990 chunk 80 optimal weight: 0.5980 overall best weight: 2.1082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 143 HIS ** C 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 407 GLN D 200 HIS ** D 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 259 GLN ** D 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 174 ASN ** E 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 174 ASN F 289 GLN F 324 HIS F 371 GLN ** G 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 107 GLN ** G 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6751 moved from start: 0.4198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 24608 Z= 0.240 Angle : 0.645 15.707 33370 Z= 0.333 Chirality : 0.047 0.261 3840 Planarity : 0.005 0.066 4349 Dihedral : 8.854 89.719 3572 Min Nonbonded Distance : 1.779 Molprobity Statistics. All-atom Clashscore : 12.94 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.41 % Favored : 96.55 % Rotamer: Outliers : 3.75 % Allowed : 27.64 % Favored : 68.61 % 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: -0.06 (0.15), residues: 3104 helix: 0.59 (0.14), residues: 1267 sheet: 0.28 (0.23), residues: 499 loop : -0.69 (0.17), residues: 1338 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS E 119 PHE 0.027 0.002 PHE D 255 TYR 0.024 0.002 TYR A 220 ARG 0.009 0.001 ARG C 383 *********************** 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 1090 residues out of total 2558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 994 time to evaluate : 2.770 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 outliers start: 96 outliers final: 52 residues processed: 1029 average time/residue: 0.3559 time to fit residues: 547.4530 Evaluate side-chains 1032 residues out of total 2558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 980 time to evaluate : 1.669 Switching outliers to nearest non-outliers outliers start: 52 outliers final: 0 residues processed: 52 average time/residue: 0.1710 time to fit residues: 18.2314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 249 optimal weight: 4.9990 chunk 170 optimal weight: 7.9990 chunk 4 optimal weight: 5.9990 chunk 223 optimal weight: 5.9990 chunk 123 optimal weight: 1.9990 chunk 255 optimal weight: 0.0980 chunk 207 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 153 optimal weight: 0.9990 chunk 268 optimal weight: 8.9990 chunk 75 optimal weight: 10.0000 overall best weight: 2.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 69 ASN ** C 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 407 GLN D 200 HIS ** D 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 304 GLN D 401 HIS D 413 ASN ** E 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 174 ASN F 8 GLN F 324 HIS F 371 GLN ** G 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 107 GLN ** G 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 270 GLN ** G 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6788 moved from start: 0.4674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 24608 Z= 0.294 Angle : 0.692 15.074 33370 Z= 0.356 Chirality : 0.048 0.256 3840 Planarity : 0.005 0.067 4349 Dihedral : 8.812 81.895 3572 Min Nonbonded Distance : 1.768 Molprobity Statistics. All-atom Clashscore : 15.41 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.99 % Favored : 95.97 % Rotamer: Outliers : 3.71 % Allowed : 29.52 % Favored : 66.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.15), residues: 3104 helix: 0.32 (0.14), residues: 1264 sheet: 0.24 (0.23), residues: 517 loop : -0.72 (0.17), residues: 1323 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.002 HIS E 119 PHE 0.028 0.002 PHE B 460 TYR 0.024 0.002 TYR G 229 ARG 0.009 0.001 ARG B 476 *********************** 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 1096 residues out of total 2558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 1001 time to evaluate : 3.023 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 outliers start: 95 outliers final: 46 residues processed: 1029 average time/residue: 0.4031 time to fit residues: 618.8363 Evaluate side-chains 1022 residues out of total 2558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 976 time to evaluate : 2.631 Switching outliers to nearest non-outliers outliers start: 46 outliers final: 0 residues processed: 46 average time/residue: 0.2587 time to fit residues: 24.7026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 100 optimal weight: 4.9990 chunk 269 optimal weight: 5.9990 chunk 59 optimal weight: 8.9990 chunk 175 optimal weight: 3.9990 chunk 73 optimal weight: 0.8980 chunk 299 optimal weight: 5.9990 chunk 248 optimal weight: 7.9990 chunk 138 optimal weight: 8.9990 chunk 24 optimal weight: 5.9990 chunk 99 optimal weight: 7.9990 chunk 157 optimal weight: 0.6980 overall best weight: 3.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 433 GLN C 407 GLN ** D 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 372 GLN F 22 HIS F 174 ASN ** F 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 95 ASN G 107 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: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6812 moved from start: 0.5047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 24608 Z= 0.341 Angle : 0.727 14.115 33370 Z= 0.376 Chirality : 0.049 0.252 3840 Planarity : 0.005 0.068 4349 Dihedral : 8.821 83.043 3572 Min Nonbonded Distance : 1.737 Molprobity Statistics. All-atom Clashscore : 16.40 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.15 % Favored : 94.81 % Rotamer: Outliers : 3.32 % Allowed : 30.49 % Favored : 66.18 % 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: 0.09 (0.14), residues: 1264 sheet: 0.19 (0.24), residues: 493 loop : -0.94 (0.17), residues: 1347 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.002 HIS F 179 PHE 0.038 0.002 PHE B 460 TYR 0.023 0.002 TYR G 103 ARG 0.008 0.001 ARG B 476 *********************** 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 1047 residues out of total 2558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 962 time to evaluate : 2.558 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 outliers start: 85 outliers final: 56 residues processed: 989 average time/residue: 0.4159 time to fit residues: 612.0451 Evaluate side-chains 1013 residues out of total 2558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 957 time to evaluate : 3.330 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 56 outliers final: 1 residues processed: 56 average time/residue: 0.2403 time to fit residues: 28.3708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 289 optimal weight: 7.9990 chunk 33 optimal weight: 0.9990 chunk 170 optimal weight: 9.9990 chunk 219 optimal weight: 0.5980 chunk 169 optimal weight: 4.9990 chunk 252 optimal weight: 3.9990 chunk 167 optimal weight: 3.9990 chunk 298 optimal weight: 0.6980 chunk 186 optimal weight: 8.9990 chunk 182 optimal weight: 0.9980 chunk 137 optimal weight: 4.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 GLN ** B 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 426 GLN ** B 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 407 GLN ** D 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 278 GLN ** E 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 219 ASN F 174 ASN ** G 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 40 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: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6745 moved from start: 0.5211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 24608 Z= 0.213 Angle : 0.666 13.647 33370 Z= 0.339 Chirality : 0.046 0.229 3840 Planarity : 0.005 0.066 4349 Dihedral : 8.426 83.044 3572 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 14.36 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.90 % Favored : 96.07 % Rotamer: Outliers : 2.23 % Allowed : 32.02 % Favored : 65.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.15), residues: 3104 helix: 0.36 (0.14), residues: 1269 sheet: 0.23 (0.24), residues: 510 loop : -0.69 (0.17), residues: 1325 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.012 0.001 HIS F 179 PHE 0.035 0.002 PHE A 494 TYR 0.020 0.001 TYR G 103 ARG 0.010 0.001 ARG G 37 *********************** 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 1017 residues out of total 2558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 960 time to evaluate : 2.649 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 outliers start: 57 outliers final: 33 residues processed: 977 average time/residue: 0.4134 time to fit residues: 601.9855 Evaluate side-chains 972 residues out of total 2558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 939 time to evaluate : 2.669 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 0 residues processed: 33 average time/residue: 0.2923 time to fit residues: 20.0963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 184 optimal weight: 5.9990 chunk 119 optimal weight: 5.9990 chunk 178 optimal weight: 2.9990 chunk 90 optimal weight: 10.0000 chunk 58 optimal weight: 6.9990 chunk 57 optimal weight: 0.9980 chunk 189 optimal weight: 4.9990 chunk 203 optimal weight: 0.0570 chunk 147 optimal weight: 6.9990 chunk 27 optimal weight: 9.9990 chunk 234 optimal weight: 4.9990 overall best weight: 2.8104 ------------------------------------------------------------------------------- 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 433 GLN ** B 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 488 ASN ** D 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 372 GLN F 40 ASN F 174 ASN ** F 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 259 GLN ** F 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 40 GLN G 41 ASN ** G 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 107 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: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6793 moved from start: 0.5400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 24608 Z= 0.307 Angle : 0.726 12.954 33370 Z= 0.372 Chirality : 0.049 0.221 3840 Planarity : 0.005 0.065 4349 Dihedral : 8.490 84.794 3572 Min Nonbonded Distance : 1.745 Molprobity Statistics. All-atom Clashscore : 16.65 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.51 % Favored : 94.46 % Rotamer: Outliers : 1.92 % Allowed : 33.50 % Favored : 64.58 % 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: -0.45 (0.15), residues: 3104 helix: 0.14 (0.14), residues: 1272 sheet: 0.22 (0.24), residues: 492 loop : -0.82 (0.17), residues: 1340 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.011 0.001 HIS F 179 PHE 0.026 0.002 PHE C 463 TYR 0.023 0.002 TYR B 389 ARG 0.011 0.001 ARG E 333 *********************** 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 1005 residues out of total 2558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 956 time to evaluate : 2.614 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 outliers start: 49 outliers final: 34 residues processed: 969 average time/residue: 0.4224 time to fit residues: 609.6028 Evaluate side-chains 981 residues out of total 2558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 947 time to evaluate : 2.639 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 0 residues processed: 34 average time/residue: 0.2572 time to fit residues: 19.7203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 271 optimal weight: 0.7980 chunk 286 optimal weight: 6.9990 chunk 261 optimal weight: 6.9990 chunk 278 optimal weight: 0.5980 chunk 167 optimal weight: 6.9990 chunk 121 optimal weight: 5.9990 chunk 218 optimal weight: 8.9990 chunk 85 optimal weight: 1.9990 chunk 251 optimal weight: 7.9990 chunk 263 optimal weight: 5.9990 chunk 277 optimal weight: 0.8980 overall best weight: 2.0584 ------------------------------------------------------------------------------- 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** A 433 GLN ** B 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 341 GLN ** B 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 488 ASN D 196 ASN ** D 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 174 ASN ** F 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 95 ASN ** 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: 0.6766 moved from start: 0.5524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 24608 Z= 0.260 Angle : 0.714 14.283 33370 Z= 0.364 Chirality : 0.048 0.221 3840 Planarity : 0.005 0.065 4349 Dihedral : 8.365 87.098 3572 Min Nonbonded Distance : 1.795 Molprobity Statistics. All-atom Clashscore : 16.32 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.96 % Favored : 95.01 % Rotamer: Outliers : 1.21 % Allowed : 34.17 % Favored : 64.62 % 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: -0.37 (0.15), residues: 3104 helix: 0.22 (0.14), residues: 1265 sheet: 0.27 (0.24), residues: 485 loop : -0.78 (0.17), residues: 1354 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.011 0.001 HIS F 179 PHE 0.041 0.002 PHE B 494 TYR 0.030 0.002 TYR B 389 ARG 0.013 0.001 ARG E 333 *********************** 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 970 residues out of total 2558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 939 time to evaluate : 2.488 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 outliers start: 31 outliers final: 18 residues processed: 947 average time/residue: 0.4195 time to fit residues: 591.7520 Evaluate side-chains 949 residues out of total 2558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 931 time to evaluate : 2.822 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.2870 time to fit residues: 12.9646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 182 optimal weight: 0.5980 chunk 294 optimal weight: 8.9990 chunk 179 optimal weight: 6.9990 chunk 139 optimal weight: 0.9980 chunk 204 optimal weight: 1.9990 chunk 308 optimal weight: 7.9990 chunk 284 optimal weight: 0.9980 chunk 245 optimal weight: 0.0050 chunk 25 optimal weight: 0.9990 chunk 189 optimal weight: 0.9980 chunk 150 optimal weight: 8.9990 overall best weight: 0.7194 ------------------------------------------------------------------------------- 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** B 147 GLN B 341 GLN ** B 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 474 HIS B 488 ASN D 174 ASN D 217 GLN E 173 HIS F 174 ASN ** F 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 95 ASN ** 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: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6698 moved from start: 0.5673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 24608 Z= 0.186 Angle : 0.698 18.774 33370 Z= 0.349 Chirality : 0.046 0.224 3840 Planarity : 0.005 0.065 4349 Dihedral : 7.914 87.030 3572 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 14.43 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.83 % Favored : 96.13 % Rotamer: Outliers : 0.51 % Allowed : 35.26 % Favored : 64.23 % 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: -0.21 (0.15), residues: 3104 helix: 0.37 (0.14), residues: 1267 sheet: 0.29 (0.23), residues: 493 loop : -0.69 (0.17), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.001 HIS F 179 PHE 0.029 0.002 PHE B 494 TYR 0.027 0.001 TYR B 389 ARG 0.010 0.001 ARG B 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 955 residues out of total 2558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 942 time to evaluate : 2.707 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 outliers start: 13 outliers final: 9 residues processed: 945 average time/residue: 0.4131 time to fit residues: 582.7491 Evaluate side-chains 943 residues out of total 2558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 934 time to evaluate : 2.862 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.3248 time to fit residues: 8.7860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 5.9990 chunk 75 optimal weight: 0.0070 chunk 226 optimal weight: 3.9990 chunk 36 optimal weight: 9.9990 chunk 68 optimal weight: 4.9990 chunk 246 optimal weight: 3.9990 chunk 103 optimal weight: 9.9990 chunk 252 optimal weight: 0.5980 chunk 31 optimal weight: 10.0000 chunk 45 optimal weight: 9.9990 overall best weight: 2.7204 ------------------------------------------------------------------------------- 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** ** B 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 185 ASN D 419 GLN ** E 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 95 ASN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.141892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.123771 restraints weight = 40287.645| |-----------------------------------------------------------------------------| r_work (start): 0.3727 rms_B_bonded: 3.12 r_work: 0.3578 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7305 moved from start: 0.5792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 24608 Z= 0.305 Angle : 0.753 18.245 33370 Z= 0.384 Chirality : 0.049 0.217 3840 Planarity : 0.005 0.065 4349 Dihedral : 8.163 85.823 3572 Min Nonbonded Distance : 1.743 Molprobity Statistics. All-atom Clashscore : 17.88 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.54 % Favored : 94.43 % Rotamer: Outliers : 0.98 % Allowed : 35.97 % Favored : 63.06 % 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: 0.20 (0.14), residues: 1258 sheet: 0.10 (0.24), residues: 476 loop : -0.78 (0.17), residues: 1370 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.012 0.001 HIS F 179 PHE 0.049 0.002 PHE B 494 TYR 0.029 0.002 TYR G 94 ARG 0.010 0.001 ARG G 189 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9212.41 seconds wall clock time: 163 minutes 55.28 seconds (9835.28 seconds total)