Starting phenix.real_space_refine (version: 1.21rc1) on Tue Jul 11 18:51:52 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l1s_23117/07_2023/7l1s_23117_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l1s_23117/07_2023/7l1s_23117.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l1s_23117/07_2023/7l1s_23117.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l1s_23117/07_2023/7l1s_23117.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l1s_23117/07_2023/7l1s_23117_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l1s_23117/07_2023/7l1s_23117_updated.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.047 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 16 5.49 5 Mg 5 5.21 5 S 78 5.16 5 C 15225 2.51 5 N 4209 2.21 5 O 4643 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 27": "OD1" <-> "OD2" Residue "A ASP 45": "OD1" <-> "OD2" Residue "A GLU 68": "OE1" <-> "OE2" Residue "A GLU 84": "OE1" <-> "OE2" Residue "A ASP 86": "OD1" <-> "OD2" Residue "A GLU 130": "OE1" <-> "OE2" Residue "A ARG 140": "NH1" <-> "NH2" Residue "A ASP 181": "OD1" <-> "OD2" Residue "A ARG 206": "NH1" <-> "NH2" Residue "A TYR 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 271": "NH1" <-> "NH2" Residue "A GLU 299": "OE1" <-> "OE2" Residue "A GLU 320": "OE1" <-> "OE2" Residue "A ASP 325": "OD1" <-> "OD2" Residue "A ASP 339": "OD1" <-> "OD2" Residue "A ASP 347": "OD1" <-> "OD2" Residue "A PHE 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 365": "NH1" <-> "NH2" Residue "A GLU 393": "OE1" <-> "OE2" Residue "A PHE 395": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 403": "OD1" <-> "OD2" Residue "A ARG 412": "NH1" <-> "NH2" Residue "A TYR 438": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 442": "NH1" <-> "NH2" Residue "A ASP 447": "OD1" <-> "OD2" Residue "A ASP 452": "OD1" <-> "OD2" Residue "A ARG 454": "NH1" <-> "NH2" Residue "A PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 463": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 484": "OE1" <-> "OE2" Residue "A ASP 485": "OD1" <-> "OD2" Residue "A ASP 486": "OD1" <-> "OD2" Residue "B ASP 27": "OD1" <-> "OD2" Residue "B ASP 45": "OD1" <-> "OD2" Residue "B GLU 68": "OE1" <-> "OE2" Residue "B GLU 84": "OE1" <-> "OE2" Residue "B ASP 86": "OD1" <-> "OD2" Residue "B GLU 87": "OE1" <-> "OE2" Residue "B GLU 130": "OE1" <-> "OE2" Residue "B ARG 140": "NH1" <-> "NH2" Residue "B ASP 181": "OD1" <-> "OD2" Residue "B ARG 206": "NH1" <-> "NH2" Residue "B TYR 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 271": "NH1" <-> "NH2" Residue "B GLU 299": "OE1" <-> "OE2" Residue "B GLU 320": "OE1" <-> "OE2" Residue "B ASP 339": "OD1" <-> "OD2" Residue "B ASP 347": "OD1" <-> "OD2" Residue "B ARG 365": "NH1" <-> "NH2" Residue "B GLU 393": "OE1" <-> "OE2" Residue "B ASP 401": "OD1" <-> "OD2" Residue "B ASP 403": "OD1" <-> "OD2" Residue "B ARG 412": "NH1" <-> "NH2" Residue "B TYR 438": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 442": "NH1" <-> "NH2" Residue "B PHE 444": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 447": "OD1" <-> "OD2" Residue "B ASP 452": "OD1" <-> "OD2" Residue "B ARG 454": "NH1" <-> "NH2" Residue "B PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 463": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 484": "OE1" <-> "OE2" Residue "B ASP 485": "OD1" <-> "OD2" Residue "B ASP 486": "OD1" <-> "OD2" Residue "C ASP 27": "OD1" <-> "OD2" Residue "C ASP 45": "OD1" <-> "OD2" Residue "C GLU 68": "OE1" <-> "OE2" Residue "C GLU 84": "OE1" <-> "OE2" Residue "C ASP 86": "OD1" <-> "OD2" Residue "C GLU 130": "OE1" <-> "OE2" Residue "C ARG 140": "NH1" <-> "NH2" Residue "C ASP 181": "OD1" <-> "OD2" Residue "C TYR 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 206": "NH1" <-> "NH2" Residue "C TYR 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 271": "NH1" <-> "NH2" Residue "C GLU 299": "OE1" <-> "OE2" Residue "C GLU 320": "OE1" <-> "OE2" Residue "C ASP 339": "OD1" <-> "OD2" Residue "C ASP 347": "OD1" <-> "OD2" Residue "C ARG 365": "NH1" <-> "NH2" Residue "C GLU 393": "OE1" <-> "OE2" Residue "C PHE 395": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 403": "OD1" <-> "OD2" Residue "C ARG 412": "NH1" <-> "NH2" Residue "C TYR 438": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 442": "NH1" <-> "NH2" Residue "C PHE 444": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 447": "OD1" <-> "OD2" Residue "C ASP 452": "OD1" <-> "OD2" Residue "C ARG 454": "NH1" <-> "NH2" Residue "C PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 463": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 484": "OE1" <-> "OE2" Residue "C ASP 485": "OD1" <-> "OD2" Residue "C ASP 486": "OD1" <-> "OD2" Residue "D ARG 5": "NH1" <-> "NH2" Residue "D ASP 15": "OD1" <-> "OD2" Residue "D ARG 37": "NH1" <-> "NH2" Residue "D ASP 43": "OD1" <-> "OD2" Residue "D ASP 68": "OD1" <-> "OD2" Residue "D GLU 101": "OE1" <-> "OE2" Residue "D ASP 108": "OD1" <-> "OD2" Residue "D ASP 112": "OD1" <-> "OD2" Residue "D PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 126": "OE1" <-> "OE2" Residue "D GLU 127": "OE1" <-> "OE2" Residue "D GLU 131": "OE1" <-> "OE2" Residue "D PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 178": "OE1" <-> "OE2" Residue "D PHE 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 190": "OD1" <-> "OD2" Residue "D ARG 191": "NH1" <-> "NH2" Residue "D ARG 193": "NH1" <-> "NH2" Residue "D ASP 204": "OD1" <-> "OD2" Residue "D PHE 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 263": "OE1" <-> "OE2" Residue "D GLU 290": "OE1" <-> "OE2" Residue "D ASP 315": "OD1" <-> "OD2" Residue "D GLU 332": "OE1" <-> "OE2" Residue "D ARG 333": "NH1" <-> "NH2" Residue "D ASP 345": "OD1" <-> "OD2" Residue "D GLU 357": "OE1" <-> "OE2" Residue "D GLU 361": "OE1" <-> "OE2" Residue "D GLU 362": "OE1" <-> "OE2" Residue "D TYR 364": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 382": "OD1" <-> "OD2" Residue "D ASP 390": "OD1" <-> "OD2" Residue "D GLU 391": "OE1" <-> "OE2" Residue "D PHE 408": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 418": "OE1" <-> "OE2" Residue "D TYR 427": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 432": "OE1" <-> "OE2" Residue "D ARG 435": "NH1" <-> "NH2" Residue "D GLU 439": "OE1" <-> "OE2" Residue "D GLU 450": "OE1" <-> "OE2" Residue "D PHE 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 454": "NH1" <-> "NH2" Residue "D GLU 460": "OE1" <-> "OE2" Residue "D GLU 461": "OE1" <-> "OE2" Residue "E ARG 3": "NH1" <-> "NH2" Residue "E ASP 15": "OD1" <-> "OD2" Residue "E PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 43": "OD1" <-> "OD2" Residue "E ARG 72": "NH1" <-> "NH2" Residue "E GLU 89": "OE1" <-> "OE2" Residue "E GLU 106": "OE1" <-> "OE2" Residue "E ASP 108": "OD1" <-> "OD2" Residue "E ASP 112": "OD1" <-> "OD2" Residue "E ARG 114": "NH1" <-> "NH2" Residue "E PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 127": "OE1" <-> "OE2" Residue "E GLU 133": "OE1" <-> "OE2" Residue "E PHE 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 190": "OD1" <-> "OD2" Residue "E ASP 197": "OD1" <-> "OD2" Residue "E GLU 220": "OE1" <-> "OE2" Residue "E ARG 240": "NH1" <-> "NH2" Residue "E ASP 252": "OD1" <-> "OD2" Residue "E PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 263": "OE1" <-> "OE2" Residue "E GLU 284": "OE1" <-> "OE2" Residue "E TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 326": "OD1" <-> "OD2" Residue "E GLU 361": "OE1" <-> "OE2" Residue "E GLU 391": "OE1" <-> "OE2" Residue "E ARG 402": "NH1" <-> "NH2" Residue "E ARG 404": "NH1" <-> "NH2" Residue "E GLU 418": "OE1" <-> "OE2" Residue "E TYR 427": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 450": "OE1" <-> "OE2" Residue "E ASP 451": "OD1" <-> "OD2" Residue "E PHE 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 5": "NH1" <-> "NH2" Residue "F PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 37": "NH1" <-> "NH2" Residue "F ASP 57": "OD1" <-> "OD2" Residue "F GLU 89": "OE1" <-> "OE2" Residue "F ARG 120": "NH1" <-> "NH2" Residue "F PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 191": "NH1" <-> "NH2" Residue "F GLU 194": "OE1" <-> "OE2" Residue "F ASP 197": "OD1" <-> "OD2" Residue "F GLU 220": "OE1" <-> "OE2" Residue "F ARG 240": "NH1" <-> "NH2" Residue "F GLU 242": "OE1" <-> "OE2" Residue "F PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 252": "OD1" <-> "OD2" Residue "F GLU 263": "OE1" <-> "OE2" Residue "F TYR 307": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 311": "OD1" <-> "OD2" Residue "F ASP 315": "OD1" <-> "OD2" Residue "F GLU 332": "OE1" <-> "OE2" Residue "F ARG 352": "NH1" <-> "NH2" Residue "F GLU 362": "OE1" <-> "OE2" Residue "F GLU 379": "OE1" <-> "OE2" Residue "F ASP 390": "OD1" <-> "OD2" Residue "F ASP 394": "OD1" <-> "OD2" Residue "F ARG 402": "NH1" <-> "NH2" Residue "F ARG 404": "NH1" <-> "NH2" Residue "F TYR 427": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 437": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 461": "OE1" <-> "OE2" Residue "F GLU 464": "OE1" <-> "OE2" Residue "G ARG 8": "NH1" <-> "NH2" Residue "G ASP 9": "OD1" <-> "OD2" Residue "G ARG 37": "NH1" <-> "NH2" Residue "G TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 50": "OE1" <-> "OE2" Residue "G GLU 54": "OE1" <-> "OE2" Residue "G ASP 87": "OD1" <-> "OD2" Residue "G ARG 88": "NH1" <-> "NH2" Residue "G TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 109": "NH1" <-> "NH2" Residue "G GLU 115": "OE1" <-> "OE2" Residue "G TYR 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 130": "NH1" <-> "NH2" Residue "G ARG 132": "NH1" <-> "NH2" Residue "G ASP 139": "OD1" <-> "OD2" Residue "G PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 154": "OE1" <-> "OE2" Residue "G ASP 169": "OD1" <-> "OD2" Residue "G TYR 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 185": "OE1" <-> "OE2" Residue "G GLU 225": "OE1" <-> "OE2" Residue "G GLU 276": "OE1" <-> "OE2" Time to flip residues: 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/chem_data/mon_lib" Total number of atoms: 24176 Number of models: 1 Model: "" Number of chains: 12 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: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 37 Unusual residues: {' MG': 1, 'ATP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "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: 10.79, per 1000 atoms: 0.45 Number of scatterers: 24176 At special positions: 0 Unit cell: (149.52, 121.8, 128.52, 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 16 15.00 Mg 5 11.99 O 4643 8.00 N 4209 7.00 C 15225 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 9.30 Conformation dependent library (CDL) restraints added in 3.8 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: 115 helices and 22 sheets defined 42.3% alpha, 12.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.54 Creating SS restraints... Processing helix chain 'A' and resid 101 through 103 No H-bonds generated for 'chain 'A' and resid 101 through 103' Processing helix chain 'A' and resid 151 through 156 Processing helix chain 'A' and resid 176 through 186 removed outlier: 3.776A pdb=" N THR A 182 " --> pdb=" O VAL A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 214 Processing helix chain 'A' and resid 217 through 220 Processing helix chain 'A' and resid 232 through 252 Proline residue: A 239 - end of helix removed outlier: 3.845A pdb=" N TYR A 248 " --> pdb=" O ALA A 244 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N PHE A 249 " --> pdb=" O MET A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 277 removed outlier: 4.267A pdb=" N LEU A 277 " --> pdb=" O LEU A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 300 removed outlier: 3.683A pdb=" N ARG A 300 " --> pdb=" O ARG A 296 " (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: 3.670A pdb=" N SER A 336 " --> pdb=" O THR A 332 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE A 337 " --> pdb=" O ASN A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 351 Processing helix chain 'A' and resid 373 through 396 removed outlier: 5.413A pdb=" N THR A 381 " --> pdb=" O LYS A 377 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N LEU A 382 " --> pdb=" O VAL A 378 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ARG A 383 " --> pdb=" O ALA A 379 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LEU A 384 " --> pdb=" O GLY A 380 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ALA A 394 " --> pdb=" O ARG A 390 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N PHE A 395 " --> pdb=" O GLU A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 420 removed outlier: 3.509A pdb=" N ARG A 412 " --> pdb=" O ALA A 408 " (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 451 through 466 removed outlier: 4.141A pdb=" N ARG A 454 " --> pdb=" O GLU A 451 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N PHE A 460 " --> pdb=" O GLU A 457 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 478 Processing helix chain 'A' and resid 484 through 497 Processing helix chain 'B' and resid 101 through 103 No H-bonds generated for 'chain 'B' and resid 101 through 103' Processing helix chain 'B' and resid 151 through 156 Processing helix chain 'B' and resid 175 through 187 removed outlier: 3.754A pdb=" N ALA B 179 " --> pdb=" O LYS B 175 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LYS B 187 " --> pdb=" O ILE B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 214 Processing helix chain 'B' and resid 217 through 220 Processing helix chain 'B' and resid 232 through 252 Proline residue: B 239 - end of helix removed outlier: 3.552A pdb=" N VAL B 243 " --> pdb=" O PRO B 239 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N TYR B 248 " --> pdb=" O ALA B 244 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N PHE B 249 " --> pdb=" O MET B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 277 Processing helix chain 'B' and resid 288 through 300 removed outlier: 3.835A pdb=" N PHE B 291 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N HIS B 294 " --> pdb=" O PHE B 291 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N SER B 295 " --> pdb=" O TYR B 292 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ARG B 296 " --> pdb=" O LEU B 293 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N GLU B 299 " --> pdb=" O ARG B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 324 No H-bonds generated for 'chain 'B' and resid 322 through 324' Processing helix chain 'B' and resid 329 through 337 removed outlier: 3.557A pdb=" N ILE B 337 " --> pdb=" O ASN B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 350 Processing helix chain 'B' and resid 373 through 379 Processing helix chain 'B' and resid 382 through 398 removed outlier: 3.516A pdb=" N GLU B 391 " --> pdb=" O ALA B 387 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ALA B 394 " --> pdb=" O ARG B 390 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N PHE B 395 " --> pdb=" O GLU B 391 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N PHE B 398 " --> pdb=" O ALA B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 420 Processing helix chain 'B' and resid 430 through 442 Processing helix chain 'B' and resid 445 through 447 No H-bonds generated for 'chain 'B' and resid 445 through 447' Processing helix chain 'B' and resid 450 through 466 removed outlier: 4.336A pdb=" N ARG B 454 " --> pdb=" O VAL B 450 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N ARG B 455 " --> pdb=" O GLU B 451 " (cutoff:3.500A) Processing helix chain 'B' and resid 469 through 478 removed outlier: 3.529A pdb=" N ARG B 476 " --> pdb=" O LEU B 472 " (cutoff:3.500A) Processing helix chain 'B' and resid 484 through 497 removed outlier: 3.607A pdb=" N THR B 497 " --> pdb=" O ALA B 493 " (cutoff:3.500A) Processing helix chain 'C' and resid 101 through 103 No H-bonds generated for 'chain 'C' and resid 101 through 103' Processing helix chain 'C' and resid 151 through 156 Processing helix chain 'C' and resid 175 through 186 removed outlier: 3.564A pdb=" N ALA C 179 " --> pdb=" O LYS C 175 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 214 Processing helix chain 'C' and resid 217 through 220 Processing helix chain 'C' and resid 232 through 252 Proline residue: C 239 - end of helix removed outlier: 3.846A pdb=" N TYR C 248 " --> pdb=" O ALA C 244 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N PHE C 249 " --> pdb=" O MET C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 277 Processing helix chain 'C' and resid 288 through 300 removed outlier: 3.969A pdb=" N PHE C 291 " --> pdb=" O GLY C 288 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N TYR C 292 " --> pdb=" O ASP C 289 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N HIS C 294 " --> pdb=" O PHE C 291 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU C 297 " --> pdb=" O HIS C 294 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N GLU C 299 " --> pdb=" O ARG C 296 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ARG C 300 " --> pdb=" O LEU C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 322 through 324 No H-bonds generated for 'chain 'C' and resid 322 through 324' Processing helix chain 'C' and resid 329 through 337 removed outlier: 3.523A pdb=" N ILE C 337 " --> pdb=" O ASN C 333 " (cutoff:3.500A) Processing helix chain 'C' and resid 346 through 351 Processing helix chain 'C' and resid 373 through 378 Processing helix chain 'C' and resid 382 through 398 removed outlier: 3.636A pdb=" N ALA C 387 " --> pdb=" O ARG C 383 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ARG C 390 " --> pdb=" O LEU C 386 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N PHE C 398 " --> pdb=" O ALA C 394 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 419 Processing helix chain 'C' and resid 430 through 442 Processing helix chain 'C' and resid 444 through 447 removed outlier: 4.011A pdb=" N ASP C 447 " --> pdb=" O PHE C 444 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 444 through 447' Processing helix chain 'C' and resid 450 through 466 removed outlier: 4.485A pdb=" N ARG C 454 " --> pdb=" O GLU C 451 " (cutoff:3.500A) Processing helix chain 'C' and resid 469 through 478 Processing helix chain 'C' and resid 484 through 497 Processing helix chain 'D' and resid 89 through 91 No H-bonds generated for 'chain 'D' and resid 89 through 91' Processing helix chain 'D' and resid 140 through 145 Processing helix chain 'D' and resid 164 through 178 removed outlier: 4.096A pdb=" N GLN D 177 " --> pdb=" O HIS D 173 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N GLU D 178 " --> pdb=" O ASN D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 192 through 205 removed outlier: 4.012A pdb=" N ASP D 197 " --> pdb=" O ARG D 193 " (cutoff:3.500A) Processing helix chain 'D' and resid 207 through 210 Processing helix chain 'D' and resid 222 through 241 removed outlier: 4.823A pdb=" N ALA D 229 " --> pdb=" O ARG D 225 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N LEU D 230 " --> pdb=" O MET D 226 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLY D 232 " --> pdb=" O VAL D 228 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N MET D 235 " --> pdb=" O THR D 231 " (cutoff:3.500A) Processing helix chain 'D' and resid 254 through 268 removed outlier: 3.576A pdb=" N GLN D 259 " --> pdb=" O ARG D 256 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N ALA D 266 " --> pdb=" O GLU D 263 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU D 267 " --> pdb=" O VAL D 264 " (cutoff:3.500A) Processing helix chain 'D' and resid 281 through 291 removed outlier: 3.821A pdb=" N ARG D 291 " --> pdb=" O GLN D 287 " (cutoff:3.500A) Processing helix chain 'D' and resid 316 through 324 removed outlier: 3.916A pdb=" N SER D 323 " --> pdb=" O ALA D 319 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N HIS D 324 " --> pdb=" O THR D 320 " (cutoff:3.500A) Processing helix chain 'D' and resid 333 through 338 Processing helix chain 'D' and resid 356 through 359 No H-bonds generated for 'chain 'D' and resid 356 through 359' Processing helix chain 'D' and resid 361 through 387 removed outlier: 4.149A pdb=" N ASP D 382 " --> pdb=" O LYS D 378 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ILE D 383 " --> pdb=" O GLU D 379 " (cutoff:3.500A) Processing helix chain 'D' and resid 389 through 391 No H-bonds generated for 'chain 'D' and resid 389 through 391' Processing helix chain 'D' and resid 394 through 409 removed outlier: 3.623A pdb=" N ARG D 405 " --> pdb=" O HIS D 401 " (cutoff:3.500A) Processing helix chain 'D' and resid 417 through 421 Processing helix chain 'D' and resid 430 through 442 Processing helix chain 'D' and resid 450 through 453 Processing helix chain 'D' and resid 459 through 469 removed outlier: 3.550A pdb=" N GLU D 464 " --> pdb=" O GLU D 460 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N MET D 469 " --> pdb=" O LYS D 465 " (cutoff:3.500A) Processing helix chain 'E' and resid 89 through 91 No H-bonds generated for 'chain 'E' and resid 89 through 91' Processing helix chain 'E' and resid 140 through 145 Processing helix chain 'E' and resid 164 through 177 Processing helix chain 'E' and resid 192 through 204 Processing helix chain 'E' and resid 207 through 210 Processing helix chain 'E' and resid 222 through 241 removed outlier: 4.666A pdb=" N ALA E 229 " --> pdb=" O ARG E 225 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N LEU E 230 " --> pdb=" O MET E 226 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N TYR E 238 " --> pdb=" O THR E 234 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N PHE E 239 " --> pdb=" O MET E 235 " (cutoff:3.500A) Processing helix chain 'E' and resid 254 through 268 Processing helix chain 'E' and resid 274 through 276 No H-bonds generated for 'chain 'E' and resid 274 through 276' Processing helix chain 'E' and resid 281 through 291 removed outlier: 3.646A pdb=" N GLN E 287 " --> pdb=" O THR E 283 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N ARG E 291 " --> pdb=" O GLN E 287 " (cutoff:3.500A) Processing helix chain 'E' and resid 316 through 322 removed outlier: 3.517A pdb=" N THR E 320 " --> pdb=" O PRO E 316 " (cutoff:3.500A) Processing helix chain 'E' and resid 335 through 338 No H-bonds generated for 'chain 'E' and resid 335 through 338' Processing helix chain 'E' and resid 356 through 359 No H-bonds generated for 'chain 'E' and resid 356 through 359' Processing helix chain 'E' and resid 361 through 386 removed outlier: 3.700A pdb=" N ASP E 382 " --> pdb=" O LYS E 378 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ILE E 383 " --> pdb=" O GLU E 379 " (cutoff:3.500A) Processing helix chain 'E' and resid 389 through 391 No H-bonds generated for 'chain 'E' and resid 389 through 391' Processing helix chain 'E' and resid 394 through 410 Processing helix chain 'E' and resid 430 through 442 Processing helix chain 'E' and resid 450 through 453 Processing helix chain 'E' and resid 459 through 469 removed outlier: 3.633A pdb=" N VAL E 463 " --> pdb=" O ILE E 459 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N MET E 469 " --> pdb=" O LYS E 465 " (cutoff:3.500A) Processing helix chain 'F' and resid 89 through 91 No H-bonds generated for 'chain 'F' and resid 89 through 91' Processing helix chain 'F' and resid 140 through 145 Processing helix chain 'F' and resid 164 through 178 removed outlier: 3.816A pdb=" N GLN F 177 " --> pdb=" O HIS F 173 " (cutoff:3.500A) Processing helix chain 'F' and resid 192 through 205 removed outlier: 3.536A pdb=" N HIS F 200 " --> pdb=" O ASN F 196 " (cutoff:3.500A) Processing helix chain 'F' and resid 207 through 210 Processing helix chain 'F' and resid 222 through 241 removed outlier: 3.620A pdb=" N ARG F 227 " --> pdb=" O GLY F 223 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ALA F 229 " --> pdb=" O ARG F 225 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N LEU F 230 " --> pdb=" O MET F 226 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N MET F 235 " --> pdb=" O THR F 231 " (cutoff:3.500A) Processing helix chain 'F' and resid 255 through 268 removed outlier: 3.503A pdb=" N LEU F 267 " --> pdb=" O GLU F 263 " (cutoff:3.500A) Processing helix chain 'F' and resid 281 through 291 removed outlier: 3.516A pdb=" N LEU F 288 " --> pdb=" O GLU F 284 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ARG F 291 " --> pdb=" O GLN F 287 " (cutoff:3.500A) Processing helix chain 'F' and resid 316 through 324 removed outlier: 4.462A pdb=" N SER F 323 " --> pdb=" O ALA F 319 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N HIS F 324 " --> pdb=" O THR F 320 " (cutoff:3.500A) Processing helix chain 'F' and resid 333 through 338 Processing helix chain 'F' and resid 356 through 359 No H-bonds generated for 'chain 'F' and resid 356 through 359' Processing helix chain 'F' and resid 362 through 387 removed outlier: 4.083A pdb=" N ASP F 382 " --> pdb=" O LYS F 378 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N ILE F 383 " --> pdb=" O GLU F 379 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N ILE F 386 " --> pdb=" O ASP F 382 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU F 387 " --> pdb=" O ILE F 383 " (cutoff:3.500A) Processing helix chain 'F' and resid 394 through 409 removed outlier: 3.532A pdb=" N VAL F 399 " --> pdb=" O ASP F 396 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N PHE F 408 " --> pdb=" O ARG F 405 " (cutoff:3.500A) Processing helix chain 'F' and resid 415 through 417 No H-bonds generated for 'chain 'F' and resid 415 through 417' Processing helix chain 'F' and resid 430 through 442 removed outlier: 3.537A pdb=" N LYS F 438 " --> pdb=" O VAL F 434 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLU F 439 " --> pdb=" O ARG F 435 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ILE F 440 " --> pdb=" O GLY F 436 " (cutoff:3.500A) Processing helix chain 'F' and resid 450 through 453 Processing helix chain 'F' and resid 459 through 469 removed outlier: 3.503A pdb=" N GLU F 464 " --> pdb=" O GLU F 461 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ALA F 468 " --> pdb=" O LYS F 465 " (cutoff:3.500A) Processing helix chain 'G' and resid 7 through 61 removed outlier: 3.630A pdb=" N ARG G 37 " --> pdb=" O SER G 33 " (cutoff:3.500A) Proline residue: G 47 - end of helix Processing helix chain 'G' and resid 94 through 109 removed outlier: 3.985A pdb=" N VAL G 98 " --> pdb=" O TYR G 94 " (cutoff:3.500A) Processing helix chain 'G' and resid 113 through 115 No H-bonds generated for 'chain 'G' and resid 113 through 115' Processing helix chain 'G' and resid 123 through 130 Processing helix chain 'G' and resid 149 through 164 removed outlier: 3.929A pdb=" N GLU G 154 " --> pdb=" O ALA G 150 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ILE G 155 " --> pdb=" O ASP G 151 " (cutoff:3.500A) Processing helix chain 'G' and resid 212 through 286 removed outlier: 3.596A pdb=" N VAL G 218 " --> pdb=" O GLU G 214 " (cutoff:3.500A) Proline residue: G 221 - end of helix removed outlier: 3.522A pdb=" N SER G 264 " --> pdb=" O THR G 260 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 28 through 30 removed outlier: 6.772A pdb=" N GLY A 72 " --> pdb=" O LEU A 64 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLN A 33 " --> pdb=" O ARG A 40 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N HIS A 42 " --> pdb=" O VAL A 31 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N VAL A 31 " --> pdb=" O HIS A 42 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 96 through 99 Processing sheet with id= C, first strand: chain 'A' and resid 341 through 343 removed outlier: 6.657A pdb=" N LEU A 166 " --> pdb=" O ILE A 342 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 221 through 226 removed outlier: 7.019A pdb=" N SER A 193 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 8.296A pdb=" N VAL A 224 " --> pdb=" O SER A 193 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N TYR A 195 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N ALA A 226 " --> pdb=" O TYR A 195 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N ALA A 197 " --> pdb=" O ALA A 226 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N SER A 312 " --> pdb=" O VAL A 256 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N VAL A 258 " --> pdb=" O SER A 312 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N THR A 314 " --> pdb=" O VAL A 258 " (cutoff:3.500A) removed outlier: 8.125A pdb=" N TYR A 260 " --> pdb=" O THR A 314 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N LEU A 316 " --> pdb=" O TYR A 260 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 28 through 30 removed outlier: 3.505A pdb=" N VAL B 88 " --> pdb=" O GLY B 29 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N GLY B 72 " --> pdb=" O LEU B 64 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N LEU B 66 " --> pdb=" O ASN B 70 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ASN B 70 " --> pdb=" O LEU B 66 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLN B 33 " --> pdb=" O ARG B 40 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N HIS B 42 " --> pdb=" O VAL B 31 " (cutoff:3.500A) removed outlier: 5.461A pdb=" N VAL B 31 " --> pdb=" O HIS B 42 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 96 through 99 Processing sheet with id= G, first strand: chain 'B' and resid 341 through 344 removed outlier: 6.312A pdb=" N LEU B 166 " --> pdb=" O ILE B 342 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N LEU B 344 " --> pdb=" O LEU B 166 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ILE B 168 " --> pdb=" O LEU B 344 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 221 through 226 removed outlier: 6.940A pdb=" N SER B 193 " --> pdb=" O ILE B 222 " (cutoff:3.500A) removed outlier: 8.199A pdb=" N VAL B 224 " --> pdb=" O SER B 193 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N TYR B 195 " --> pdb=" O VAL B 224 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N ALA B 226 " --> pdb=" O TYR B 195 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ALA B 197 " --> pdb=" O ALA B 226 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 28 through 30 removed outlier: 6.527A pdb=" N GLY C 72 " --> pdb=" O LEU C 64 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLN C 33 " --> pdb=" O ARG C 40 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N HIS C 42 " --> pdb=" O VAL C 31 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N VAL C 31 " --> pdb=" O HIS C 42 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 96 through 99 Processing sheet with id= K, first strand: chain 'C' and resid 107 through 109 removed outlier: 8.827A pdb=" N VAL C 108 " --> pdb=" O THR C 221 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N VAL C 223 " --> pdb=" O VAL C 108 " (cutoff:3.500A) removed outlier: 8.645A pdb=" N ILE C 222 " --> pdb=" O MET C 191 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N SER C 193 " --> pdb=" O ILE C 222 " (cutoff:3.500A) removed outlier: 7.944A pdb=" N VAL C 224 " --> pdb=" O SER C 193 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N TYR C 195 " --> pdb=" O VAL C 224 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N ALA C 226 " --> pdb=" O TYR C 195 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N ALA C 197 " --> pdb=" O ALA C 226 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N HIS C 255 " --> pdb=" O ILE C 192 " (cutoff:3.500A) removed outlier: 8.517A pdb=" N ILE C 194 " --> pdb=" O HIS C 255 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N LEU C 257 " --> pdb=" O ILE C 194 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N VAL C 196 " --> pdb=" O LEU C 257 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N VAL C 259 " --> pdb=" O VAL C 196 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N ILE C 198 " --> pdb=" O VAL C 259 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 318 through 320 removed outlier: 6.647A pdb=" N ILE C 167 " --> pdb=" O VAL C 319 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N ILE C 342 " --> pdb=" O ILE C 168 " (cutoff:3.500A) No H-bonds generated for sheet with id= L Processing sheet with id= M, first strand: chain 'D' and resid 5 through 10 removed outlier: 6.727A pdb=" N ASP D 15 " --> pdb=" O ILE D 7 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N VAL D 9 " --> pdb=" O VAL D 13 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N VAL D 13 " --> pdb=" O VAL D 9 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU D 52 " --> pdb=" O ARG D 60 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N ILE D 62 " --> pdb=" O VAL D 50 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N VAL D 50 " --> pdb=" O ILE D 62 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 84 through 86 Processing sheet with id= O, first strand: chain 'D' and resid 327 through 331 removed outlier: 7.660A pdb=" N ILE D 154 " --> pdb=" O ILE D 300 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N SER D 302 " --> pdb=" O ILE D 154 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N LEU D 156 " --> pdb=" O SER D 302 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N GLN D 304 " --> pdb=" O LEU D 156 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N GLY D 158 " --> pdb=" O GLN D 304 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N ILE D 306 " --> pdb=" O GLY D 158 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N VAL D 247 " --> pdb=" O THR D 301 " (cutoff:3.500A) removed outlier: 7.970A pdb=" N ILE D 303 " --> pdb=" O VAL D 247 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N LEU D 249 " --> pdb=" O ILE D 303 " (cutoff:3.500A) removed outlier: 8.083A pdb=" N ALA D 305 " --> pdb=" O LEU D 249 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N ILE D 251 " --> pdb=" O ALA D 305 " (cutoff:3.500A) removed outlier: 8.873A pdb=" N TYR D 307 " --> pdb=" O ILE D 251 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'E' and resid 75 through 77 removed outlier: 6.391A pdb=" N ASP E 15 " --> pdb=" O ILE E 7 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N VAL E 9 " --> pdb=" O VAL E 13 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N VAL E 13 " --> pdb=" O VAL E 9 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N ILE E 62 " --> pdb=" O VAL E 50 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N VAL E 50 " --> pdb=" O ILE E 62 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'E' and resid 84 through 86 Processing sheet with id= R, first strand: chain 'E' and resid 327 through 330 removed outlier: 8.518A pdb=" N ILE E 154 " --> pdb=" O ILE E 300 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N SER E 302 " --> pdb=" O ILE E 154 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N LEU E 156 " --> pdb=" O SER E 302 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N GLN E 304 " --> pdb=" O LEU E 156 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N VAL E 247 " --> pdb=" O THR E 301 " (cutoff:3.500A) removed outlier: 8.103A pdb=" N ILE E 303 " --> pdb=" O VAL E 247 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N LEU E 249 " --> pdb=" O ILE E 303 " (cutoff:3.500A) removed outlier: 7.904A pdb=" N ALA E 305 " --> pdb=" O LEU E 249 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N ILE E 251 " --> pdb=" O ALA E 305 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLY E 216 " --> pdb=" O GLY E 187 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'F' and resid 5 through 10 removed outlier: 6.709A pdb=" N ASP F 15 " --> pdb=" O ILE F 7 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N VAL F 9 " --> pdb=" O VAL F 13 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N VAL F 13 " --> pdb=" O VAL F 9 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N ILE F 62 " --> pdb=" O VAL F 50 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N VAL F 50 " --> pdb=" O ILE F 62 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'F' and resid 84 through 86 Processing sheet with id= U, first strand: chain 'F' and resid 327 through 330 removed outlier: 8.134A pdb=" N ILE F 154 " --> pdb=" O ILE F 300 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N SER F 302 " --> pdb=" O ILE F 154 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N LEU F 156 " --> pdb=" O SER F 302 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N GLN F 304 " --> pdb=" O LEU F 156 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N GLY F 158 " --> pdb=" O GLN F 304 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N ILE F 306 " --> pdb=" O GLY F 158 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N VAL F 247 " --> pdb=" O THR F 301 " (cutoff:3.500A) removed outlier: 8.074A pdb=" N ILE F 303 " --> pdb=" O VAL F 247 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N LEU F 249 " --> pdb=" O ILE F 303 " (cutoff:3.500A) removed outlier: 8.127A pdb=" N ALA F 305 " --> pdb=" O LEU F 249 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N ILE F 251 " --> pdb=" O ALA F 305 " (cutoff:3.500A) removed outlier: 8.720A pdb=" N TYR F 307 " --> pdb=" O ILE F 251 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N ILE F 182 " --> pdb=" O LEU F 248 " (cutoff:3.500A) removed outlier: 8.486A pdb=" N PHE F 250 " --> pdb=" O ILE F 182 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N VAL F 184 " --> pdb=" O PHE F 250 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'G' and resid 184 through 192 removed outlier: 7.098A pdb=" N LEU G 171 " --> pdb=" O LEU G 191 " (cutoff:3.500A) removed outlier: 5.306A pdb=" N ASN G 176 " --> pdb=" O ILE G 84 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N LEU G 138 " --> pdb=" O VAL G 120 " (cutoff:3.500A) 946 hydrogen bonds defined for protein. 2586 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.15 Time building geometry restraints manager: 10.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 4304 1.31 - 1.44: 5752 1.44 - 1.57: 14341 1.57 - 1.69: 28 1.69 - 1.82: 154 Bond restraints: 24579 Sorted by residual: bond pdb=" C PRO A 280 " pdb=" O PRO A 280 " ideal model delta sigma weight residual 1.243 1.198 0.045 8.50e-03 1.38e+04 2.81e+01 bond pdb=" C PRO C 280 " pdb=" O PRO C 280 " ideal model delta sigma weight residual 1.240 1.185 0.055 1.12e-02 7.97e+03 2.43e+01 bond pdb=" O5' ATP B 600 " pdb=" PA ATP B 600 " ideal model delta sigma weight residual 1.579 1.631 -0.052 1.10e-02 8.26e+03 2.21e+01 bond pdb=" O5' ATP F 500 " pdb=" PA ATP F 500 " ideal model delta sigma weight residual 1.579 1.626 -0.047 1.10e-02 8.26e+03 1.81e+01 bond pdb=" CZ ARG E 60 " pdb=" NH1 ARG E 60 " ideal model delta sigma weight residual 1.323 1.265 0.058 1.40e-02 5.10e+03 1.73e+01 ... (remaining 24574 not shown) Histogram of bond angle deviations from ideal: 95.40 - 102.87: 197 102.87 - 110.33: 5763 110.33 - 117.80: 12262 117.80 - 125.27: 14593 125.27 - 132.73: 510 Bond angle restraints: 33325 Sorted by residual: angle pdb=" PB ATP F 500 " pdb=" O3B ATP F 500 " pdb=" PG ATP F 500 " ideal model delta sigma weight residual 139.87 122.14 17.73 1.00e+00 1.00e+00 3.14e+02 angle pdb=" PB ATP B 600 " pdb=" O3B ATP B 600 " pdb=" PG ATP B 600 " ideal model delta sigma weight residual 139.87 122.99 16.88 1.00e+00 1.00e+00 2.85e+02 angle pdb=" PA ATP F 500 " pdb=" O3A ATP F 500 " pdb=" PB ATP F 500 " ideal model delta sigma weight residual 136.83 121.41 15.42 1.00e+00 1.00e+00 2.38e+02 angle pdb=" PA ATP B 600 " pdb=" O3A ATP B 600 " pdb=" PB ATP B 600 " ideal model delta sigma weight residual 136.83 123.61 13.22 1.00e+00 1.00e+00 1.75e+02 angle pdb=" PB ATP C 600 " pdb=" O3B ATP C 600 " pdb=" PG ATP C 600 " ideal model delta sigma weight residual 139.87 127.91 11.96 1.00e+00 1.00e+00 1.43e+02 ... (remaining 33320 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.94: 13374 16.94 - 33.89: 1146 33.89 - 50.83: 281 50.83 - 67.77: 59 67.77 - 84.72: 18 Dihedral angle restraints: 14878 sinusoidal: 5986 harmonic: 8892 Sorted by residual: dihedral pdb=" C ARG A 283 " pdb=" N ARG A 283 " pdb=" CA ARG A 283 " pdb=" CB ARG A 283 " ideal model delta harmonic sigma weight residual -122.60 -143.42 20.82 0 2.50e+00 1.60e-01 6.93e+01 dihedral pdb=" C GLN A 172 " pdb=" N GLN A 172 " pdb=" CA GLN A 172 " pdb=" CB GLN A 172 " ideal model delta harmonic sigma weight residual -122.60 -141.83 19.23 0 2.50e+00 1.60e-01 5.91e+01 dihedral pdb=" N ARG A 283 " pdb=" C ARG A 283 " pdb=" CA ARG A 283 " pdb=" CB ARG A 283 " ideal model delta harmonic sigma weight residual 122.80 141.99 -19.19 0 2.50e+00 1.60e-01 5.89e+01 ... (remaining 14875 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.160: 3267 0.160 - 0.320: 516 0.320 - 0.480: 47 0.480 - 0.640: 3 0.640 - 0.800: 3 Chirality restraints: 3836 Sorted by residual: chirality pdb=" CA ARG A 283 " pdb=" N ARG A 283 " pdb=" C ARG A 283 " pdb=" CB ARG A 283 " both_signs ideal model delta sigma weight residual False 2.51 1.71 0.80 2.00e-01 2.50e+01 1.60e+01 chirality pdb=" CA GLN A 172 " pdb=" N GLN A 172 " pdb=" C GLN A 172 " pdb=" CB GLN A 172 " both_signs ideal model delta sigma weight residual False 2.51 1.78 0.73 2.00e-01 2.50e+01 1.32e+01 chirality pdb=" CA HIS G 110 " pdb=" N HIS G 110 " pdb=" C HIS G 110 " pdb=" CB HIS G 110 " both_signs ideal model delta sigma weight residual False 2.51 1.79 0.72 2.00e-01 2.50e+01 1.28e+01 ... (remaining 3833 not shown) Planarity restraints: 4348 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' ATP F 500 " -0.202 2.00e-02 2.50e+03 8.15e-02 1.83e+02 pdb=" C2 ATP F 500 " 0.033 2.00e-02 2.50e+03 pdb=" C4 ATP F 500 " 0.071 2.00e-02 2.50e+03 pdb=" C5 ATP F 500 " 0.020 2.00e-02 2.50e+03 pdb=" C6 ATP F 500 " -0.031 2.00e-02 2.50e+03 pdb=" C8 ATP F 500 " 0.077 2.00e-02 2.50e+03 pdb=" N1 ATP F 500 " -0.013 2.00e-02 2.50e+03 pdb=" N3 ATP F 500 " 0.047 2.00e-02 2.50e+03 pdb=" N6 ATP F 500 " -0.097 2.00e-02 2.50e+03 pdb=" N7 ATP F 500 " 0.012 2.00e-02 2.50e+03 pdb=" N9 ATP F 500 " 0.083 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 220 " 0.101 2.00e-02 2.50e+03 6.29e-02 7.91e+01 pdb=" CG TYR A 220 " -0.001 2.00e-02 2.50e+03 pdb=" CD1 TYR A 220 " -0.041 2.00e-02 2.50e+03 pdb=" CD2 TYR A 220 " -0.073 2.00e-02 2.50e+03 pdb=" CE1 TYR A 220 " -0.052 2.00e-02 2.50e+03 pdb=" CE2 TYR A 220 " -0.030 2.00e-02 2.50e+03 pdb=" CZ TYR A 220 " -0.009 2.00e-02 2.50e+03 pdb=" OH TYR A 220 " 0.104 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS E 173 " -0.096 2.00e-02 2.50e+03 7.19e-02 7.75e+01 pdb=" CG HIS E 173 " 0.116 2.00e-02 2.50e+03 pdb=" ND1 HIS E 173 " 0.037 2.00e-02 2.50e+03 pdb=" CD2 HIS E 173 " 0.043 2.00e-02 2.50e+03 pdb=" CE1 HIS E 173 " -0.047 2.00e-02 2.50e+03 pdb=" NE2 HIS E 173 " -0.053 2.00e-02 2.50e+03 ... (remaining 4345 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 166 2.59 - 3.17: 20306 3.17 - 3.74: 34913 3.74 - 4.32: 50658 4.32 - 4.90: 82273 Nonbonded interactions: 188316 Sorted by model distance: nonbonded pdb=" O1A ATP A 601 " pdb="MG MG A 602 " model vdw 2.011 2.170 nonbonded pdb=" O2G ATP C 600 " pdb="MG MG C 601 " model vdw 2.043 2.170 nonbonded pdb=" OG1 THR C 176 " pdb="MG MG C 601 " model vdw 2.055 2.170 nonbonded pdb=" OG1 THR D 165 " pdb="MG MG D 501 " model vdw 2.068 2.170 nonbonded pdb=" O1G ATP D 500 " pdb="MG MG D 501 " model vdw 2.074 2.170 ... (remaining 188311 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 group one per residue 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: 0.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 6.580 Check model and map are aligned: 0.370 Set scattering table: 0.240 Process input model: 59.230 Find NCS groups from input model: 1.950 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6853 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.011 0.084 24579 Z= 0.755 Angle : 1.811 17.731 33325 Z= 1.258 Chirality : 0.117 0.800 3836 Planarity : 0.011 0.128 4348 Dihedral : 14.048 84.718 9188 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.29 % Favored : 96.55 % Rotamer Outliers : 4.07 % Cbeta Deviations : 1.30 % 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 (0.14), residues: 3104 helix: 0.11 (0.14), residues: 1210 sheet: 0.26 (0.23), residues: 469 loop : -0.72 (0.16), residues: 1425 *********************** 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 1301 residues out of total 2558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 1197 time to evaluate : 2.665 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 104 outliers final: 31 residues processed: 1253 average time/residue: 0.4202 time to fit residues: 775.7592 Evaluate side-chains 1180 residues out of total 2558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 1149 time to evaluate : 2.613 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 31 outliers final: 1 residues processed: 31 average time/residue: 0.2603 time to fit residues: 18.5899 ------------------------------------------------------------------------------- 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: 3.9990 chunk 234 optimal weight: 7.9990 chunk 130 optimal weight: 7.9990 chunk 80 optimal weight: 0.9980 chunk 158 optimal weight: 0.9980 chunk 125 optimal weight: 0.9980 chunk 242 optimal weight: 0.3980 chunk 94 optimal weight: 6.9990 chunk 147 optimal weight: 1.9990 chunk 180 optimal weight: 0.3980 chunk 281 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 GLN A 185 ASN A 186 GLN ** A 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 469 GLN A 488 ASN B 185 ASN B 186 GLN ** B 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 397 GLN B 488 ASN C 46 ASN ** C 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 255 HIS C 333 ASN ** C 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 397 GLN ** C 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 425 HIS ** C 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 466 GLN C 488 ASN D 8 GLN D 20 ASN D 33 GLN D 119 HIS D 217 GLN D 324 HIS D 365 GLN D 375 GLN D 419 GLN E 33 GLN E 324 HIS E 365 GLN E 375 GLN ** E 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 33 GLN F 173 HIS F 217 GLN F 324 HIS F 372 GLN F 423 GLN G 36 ASN ** G 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 183 GLN G 285 ASN Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6874 moved from start: 0.2742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 24579 Z= 0.209 Angle : 0.692 10.524 33325 Z= 0.375 Chirality : 0.047 0.224 3836 Planarity : 0.005 0.071 4348 Dihedral : 5.755 87.238 3406 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer Outliers : 3.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.15), residues: 3104 helix: 0.95 (0.14), residues: 1246 sheet: 0.25 (0.22), residues: 519 loop : -0.49 (0.17), residues: 1339 *********************** 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 1268 residues out of total 2558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 1168 time to evaluate : 2.660 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 outliers start: 100 outliers final: 47 residues processed: 1199 average time/residue: 0.4138 time to fit residues: 733.5187 Evaluate side-chains 1187 residues out of total 2558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 1140 time to evaluate : 2.873 Switching outliers to nearest non-outliers outliers start: 47 outliers final: 0 residues processed: 47 average time/residue: 0.2893 time to fit residues: 26.5863 ------------------------------------------------------------------------------- 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: 4.9990 chunk 234 optimal weight: 9.9990 chunk 191 optimal weight: 0.0010 chunk 77 optimal weight: 2.9990 chunk 282 optimal weight: 0.9990 chunk 304 optimal weight: 10.0000 chunk 251 optimal weight: 5.9990 chunk 279 optimal weight: 5.9990 chunk 96 optimal weight: 9.9990 chunk 226 optimal weight: 2.9990 overall best weight: 2.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 466 GLN ** B 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 469 GLN ** C 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 333 ASN ** C 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 469 GLN D 217 GLN E 372 GLN E 415 HIS F 174 ASN F 304 GLN ** G 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 110 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6974 moved from start: 0.3817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.073 24579 Z= 0.261 Angle : 0.701 10.670 33325 Z= 0.376 Chirality : 0.048 0.198 3836 Planarity : 0.005 0.059 4348 Dihedral : 5.640 86.936 3406 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer Outliers : 4.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.15), residues: 3104 helix: 0.78 (0.14), residues: 1254 sheet: 0.24 (0.22), residues: 549 loop : -0.49 (0.17), residues: 1301 *********************** 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 1333 residues out of total 2558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 1217 time to evaluate : 2.846 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: 116 outliers final: 64 residues processed: 1243 average time/residue: 0.4066 time to fit residues: 745.0856 Evaluate side-chains 1248 residues out of total 2558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 1184 time to evaluate : 2.690 Switching outliers to nearest non-outliers outliers start: 64 outliers final: 0 residues processed: 64 average time/residue: 0.2675 time to fit residues: 33.2140 ------------------------------------------------------------------------------- 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: 3.9990 chunk 212 optimal weight: 1.9990 chunk 146 optimal weight: 20.0000 chunk 31 optimal weight: 7.9990 chunk 134 optimal weight: 20.0000 chunk 189 optimal weight: 8.9990 chunk 283 optimal weight: 0.9980 chunk 299 optimal weight: 0.8980 chunk 147 optimal weight: 9.9990 chunk 268 optimal weight: 5.9990 chunk 80 optimal weight: 20.0000 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 ASN ** B 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 467 ASN C 215 HIS C 333 ASN ** C 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 467 ASN D 259 GLN E 169 GLN ** E 179 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 415 HIS ** G 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7002 moved from start: 0.4552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.068 24579 Z= 0.268 Angle : 0.682 10.746 33325 Z= 0.369 Chirality : 0.047 0.173 3836 Planarity : 0.005 0.060 4348 Dihedral : 5.696 86.596 3406 Min Nonbonded Distance : 1.734 Molprobity Statistics. All-atom Clashscore : 14.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer Outliers : 3.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.15), residues: 3104 helix: 0.75 (0.14), residues: 1242 sheet: 0.16 (0.22), residues: 529 loop : -0.65 (0.17), residues: 1333 *********************** 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 1275 residues out of total 2558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 1184 time to evaluate : 2.659 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 outliers start: 91 outliers final: 43 residues processed: 1211 average time/residue: 0.4207 time to fit residues: 752.0479 Evaluate side-chains 1221 residues out of total 2558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 1178 time to evaluate : 2.901 Switching outliers to nearest non-outliers outliers start: 43 outliers final: 0 residues processed: 43 average time/residue: 0.2926 time to fit residues: 25.1327 ------------------------------------------------------------------------------- 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: 0.2980 chunk 170 optimal weight: 0.5980 chunk 4 optimal weight: 4.9990 chunk 223 optimal weight: 7.9990 chunk 123 optimal weight: 10.0000 chunk 255 optimal weight: 3.9990 chunk 207 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 153 optimal weight: 5.9990 chunk 268 optimal weight: 0.6980 chunk 75 optimal weight: 6.9990 overall best weight: 2.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 294 HIS ** C 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 215 HIS ** C 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 169 GLN ** E 179 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 196 ASN E 415 HIS ** F 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6991 moved from start: 0.4992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.056 24579 Z= 0.223 Angle : 0.664 11.753 33325 Z= 0.352 Chirality : 0.046 0.199 3836 Planarity : 0.005 0.076 4348 Dihedral : 5.655 86.587 3406 Min Nonbonded Distance : 1.730 Molprobity Statistics. All-atom Clashscore : 14.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer Outliers : 3.17 % 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: 0.04 (0.15), residues: 3104 helix: 0.73 (0.14), residues: 1237 sheet: 0.16 (0.22), residues: 525 loop : -0.60 (0.17), residues: 1342 *********************** 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 1253 residues out of total 2558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 1172 time to evaluate : 2.731 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 81 outliers final: 47 residues processed: 1187 average time/residue: 0.4187 time to fit residues: 729.9992 Evaluate side-chains 1213 residues out of total 2558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 1166 time to evaluate : 2.935 Switching outliers to nearest non-outliers outliers start: 47 outliers final: 0 residues processed: 47 average time/residue: 0.3142 time to fit residues: 27.7788 ------------------------------------------------------------------------------- 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: 6.9990 chunk 269 optimal weight: 2.9990 chunk 59 optimal weight: 4.9990 chunk 175 optimal weight: 0.7980 chunk 73 optimal weight: 4.9990 chunk 299 optimal weight: 10.0000 chunk 248 optimal weight: 6.9990 chunk 138 optimal weight: 20.0000 chunk 24 optimal weight: 3.9990 chunk 99 optimal weight: 7.9990 chunk 157 optimal weight: 0.8980 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 469 GLN ** B 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 466 GLN ** C 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 186 GLN C 333 ASN ** C 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 119 HIS E 169 GLN E 179 HIS E 200 HIS E 415 HIS E 419 GLN F 173 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7016 moved from start: 0.5394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.067 24579 Z= 0.258 Angle : 0.689 10.904 33325 Z= 0.372 Chirality : 0.048 0.219 3836 Planarity : 0.005 0.078 4348 Dihedral : 5.738 88.158 3406 Min Nonbonded Distance : 1.693 Molprobity Statistics. All-atom Clashscore : 16.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer Outliers : 2.66 % 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: -0.14 (0.15), residues: 3104 helix: 0.51 (0.14), residues: 1231 sheet: 0.20 (0.22), residues: 533 loop : -0.68 (0.17), residues: 1340 *********************** 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 1242 residues out of total 2558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 1174 time to evaluate : 2.727 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: 68 outliers final: 34 residues processed: 1193 average time/residue: 0.4250 time to fit residues: 743.9575 Evaluate side-chains 1195 residues out of total 2558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 1161 time to evaluate : 2.688 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 34 outliers final: 1 residues processed: 34 average time/residue: 0.2871 time to fit residues: 20.3696 ------------------------------------------------------------------------------- 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: 50.0000 chunk 33 optimal weight: 0.0970 chunk 170 optimal weight: 5.9990 chunk 219 optimal weight: 4.9990 chunk 169 optimal weight: 0.8980 chunk 252 optimal weight: 6.9990 chunk 167 optimal weight: 1.9990 chunk 298 optimal weight: 8.9990 chunk 186 optimal weight: 10.0000 chunk 182 optimal weight: 2.9990 chunk 137 optimal weight: 1.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 GLN ** A 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 469 GLN B 266 GLN B 371 GLN ** B 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 333 ASN ** C 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 173 HIS E 415 HIS ** F 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6987 moved from start: 0.5640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.049 24579 Z= 0.205 Angle : 0.683 11.816 33325 Z= 0.359 Chirality : 0.046 0.207 3836 Planarity : 0.005 0.065 4348 Dihedral : 5.611 87.013 3406 Min Nonbonded Distance : 1.752 Molprobity Statistics. All-atom Clashscore : 16.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer Outliers : 2.03 % 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: 0.60 (0.14), residues: 1228 sheet: 0.32 (0.22), residues: 530 loop : -0.61 (0.17), residues: 1346 *********************** 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 1208 residues out of total 2558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 1156 time to evaluate : 2.815 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 outliers start: 52 outliers final: 31 residues processed: 1169 average time/residue: 0.4305 time to fit residues: 736.4631 Evaluate side-chains 1181 residues out of total 2558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 1150 time to evaluate : 2.872 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 0 residues processed: 31 average time/residue: 0.3428 time to fit residues: 21.1704 ------------------------------------------------------------------------------- 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: 0.9990 chunk 119 optimal weight: 0.8980 chunk 178 optimal weight: 0.8980 chunk 90 optimal weight: 9.9990 chunk 58 optimal weight: 1.9990 chunk 57 optimal weight: 6.9990 chunk 189 optimal weight: 0.9990 chunk 203 optimal weight: 10.0000 chunk 147 optimal weight: 4.9990 chunk 27 optimal weight: 5.9990 chunk 234 optimal weight: 7.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 333 ASN ** A 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 322 GLN C 333 ASN ** C 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 467 ASN E 22 HIS ** E 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 173 HIS E 415 HIS F 169 GLN ** F 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6968 moved from start: 0.5855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 24579 Z= 0.188 Angle : 0.682 17.275 33325 Z= 0.355 Chirality : 0.046 0.209 3836 Planarity : 0.005 0.068 4348 Dihedral : 5.441 85.113 3406 Min Nonbonded Distance : 1.831 Molprobity Statistics. All-atom Clashscore : 15.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer Outliers : 1.68 % 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: 0.62 (0.15), residues: 1235 sheet: 0.34 (0.23), residues: 525 loop : -0.46 (0.17), residues: 1344 *********************** 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 1183 residues out of total 2558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 1140 time to evaluate : 2.857 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 43 outliers final: 20 residues processed: 1146 average time/residue: 0.4213 time to fit residues: 705.9533 Evaluate side-chains 1149 residues out of total 2558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 1129 time to evaluate : 2.641 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.2829 time to fit residues: 13.4850 ------------------------------------------------------------------------------- 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: 9.9990 chunk 286 optimal weight: 10.0000 chunk 261 optimal weight: 9.9990 chunk 278 optimal weight: 10.0000 chunk 167 optimal weight: 7.9990 chunk 121 optimal weight: 4.9990 chunk 218 optimal weight: 4.9990 chunk 85 optimal weight: 6.9990 chunk 251 optimal weight: 4.9990 chunk 263 optimal weight: 6.9990 chunk 277 optimal weight: 3.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 ASN A 255 HIS ** A 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 333 ASN B 425 HIS C 109 ASN ** C 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 333 ASN ** C 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 173 HIS ** F 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7074 moved from start: 0.6353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.090 24579 Z= 0.429 Angle : 0.871 22.093 33325 Z= 0.477 Chirality : 0.053 0.247 3836 Planarity : 0.007 0.103 4348 Dihedral : 6.366 86.536 3406 Min Nonbonded Distance : 1.559 Molprobity Statistics. All-atom Clashscore : 22.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer Outliers : 1.99 % 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: -0.84 (0.15), residues: 3104 helix: -0.18 (0.14), residues: 1208 sheet: -0.03 (0.23), residues: 523 loop : -1.00 (0.17), residues: 1373 *********************** 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 1210 residues out of total 2558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 1159 time to evaluate : 2.809 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 outliers start: 51 outliers final: 40 residues processed: 1168 average time/residue: 0.4309 time to fit residues: 736.6490 Evaluate side-chains 1188 residues out of total 2558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 1148 time to evaluate : 2.705 Switching outliers to nearest non-outliers outliers start: 40 outliers final: 0 residues processed: 40 average time/residue: 0.2939 time to fit residues: 23.4145 ------------------------------------------------------------------------------- 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: 0.9980 chunk 294 optimal weight: 10.0000 chunk 179 optimal weight: 5.9990 chunk 139 optimal weight: 9.9990 chunk 204 optimal weight: 2.9990 chunk 308 optimal weight: 4.9990 chunk 284 optimal weight: 2.9990 chunk 245 optimal weight: 0.0270 chunk 25 optimal weight: 0.4980 chunk 189 optimal weight: 2.9990 chunk 150 optimal weight: 3.9990 overall best weight: 1.5042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 ASN A 200 GLN ** A 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 333 ASN ** C 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 119 HIS ** F 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6990 moved from start: 0.6417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 24579 Z= 0.224 Angle : 0.772 13.793 33325 Z= 0.399 Chirality : 0.049 0.254 3836 Planarity : 0.006 0.089 4348 Dihedral : 5.829 81.236 3406 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 19.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer Outliers : 0.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.15), residues: 3104 helix: 0.27 (0.14), residues: 1216 sheet: 0.22 (0.23), residues: 499 loop : -0.80 (0.17), residues: 1389 ********************** 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 1169 residues out of total 2558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 1150 time to evaluate : 2.680 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 outliers start: 19 outliers final: 10 residues processed: 1152 average time/residue: 0.4448 time to fit residues: 756.1821 Evaluate side-chains 1153 residues out of total 2558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 1143 time to evaluate : 2.708 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.3403 time to fit residues: 9.2541 ------------------------------------------------------------------------------- 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: 0.7980 chunk 261 optimal weight: 7.9990 chunk 75 optimal weight: 2.9990 chunk 226 optimal weight: 0.4980 chunk 36 optimal weight: 0.6980 chunk 68 optimal weight: 0.9980 chunk 246 optimal weight: 6.9990 chunk 103 optimal weight: 0.7980 chunk 252 optimal weight: 10.0000 chunk 31 optimal weight: 9.9990 chunk 45 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 467 ASN ** C 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 333 ASN ** C 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 97 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.155787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.133452 restraints weight = 44822.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.138390 restraints weight = 23679.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.141676 restraints weight = 14601.442| |-----------------------------------------------------------------------------| r_work (final): 0.3920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6991 moved from start: 0.6505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.055 24579 Z= 0.205 Angle : 0.760 24.240 33325 Z= 0.389 Chirality : 0.048 0.353 3836 Planarity : 0.005 0.069 4348 Dihedral : 5.556 77.582 3406 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 18.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer Outliers : 0.59 % 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: -0.16 (0.15), residues: 3104 helix: 0.42 (0.15), residues: 1216 sheet: 0.38 (0.23), residues: 490 loop : -0.67 (0.17), residues: 1398 =============================================================================== Job complete usr+sys time: 9917.56 seconds wall clock time: 175 minutes 43.34 seconds (10543.34 seconds total)