Starting phenix.real_space_refine (version: dev) on Sat Feb 25 02:20:04 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l1r_23116/02_2023/7l1r_23116_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l1r_23116/02_2023/7l1r_23116.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l1r_23116/02_2023/7l1r_23116.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l1r_23116/02_2023/7l1r_23116.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l1r_23116/02_2023/7l1r_23116_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l1r_23116/02_2023/7l1r_23116_updated.pdb" } resolution = 3.1 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= 0.050 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Process input model Symmetric amino acids flipped Residue "A ASP 27": "OD1" <-> "OD2" Residue "A ASP 45": "OD1" <-> "OD2" Residue "A GLU 68": "OE1" <-> "OE2" Residue "A GLU 84": "OE1" <-> "OE2" Residue "A ASP 86": "OD1" <-> "OD2" Residue "A GLU 130": "OE1" <-> "OE2" Residue "A ARG 140": "NH1" <-> "NH2" Residue "A ASP 181": "OD1" <-> "OD2" Residue "A ARG 206": "NH1" <-> "NH2" Residue "A TYR 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 271": "NH1" <-> "NH2" Residue "A GLU 272": "OE1" <-> "OE2" Residue "A GLU 284": "OE1" <-> "OE2" Residue "A GLU 299": "OE1" <-> "OE2" Residue "A GLU 320": "OE1" <-> "OE2" Residue "A ASP 325": "OD1" <-> "OD2" Residue "A ASP 339": "OD1" <-> "OD2" Residue "A ASP 347": "OD1" <-> "OD2" Residue "A ARG 365": "NH1" <-> "NH2" Residue "A TYR 389": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 393": "OE1" <-> "OE2" Residue "A PHE 395": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 403": "OD1" <-> "OD2" Residue "A ARG 412": "NH1" <-> "NH2" Residue "A TYR 438": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 442": "NH1" <-> "NH2" Residue "A ASP 447": "OD1" <-> "OD2" Residue "A ASP 452": "OD1" <-> "OD2" Residue "A ARG 454": "NH1" <-> "NH2" Residue "A PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 463": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 484": "OE1" <-> "OE2" Residue "A ASP 485": "OD1" <-> "OD2" Residue "A ASP 486": "OD1" <-> "OD2" Residue "B ASP 27": "OD1" <-> "OD2" Residue "B ASP 45": "OD1" <-> "OD2" Residue "B GLU 68": "OE1" <-> "OE2" Residue "B GLU 84": "OE1" <-> "OE2" Residue "B ASP 86": "OD1" <-> "OD2" Residue "B GLU 87": "OE1" <-> "OE2" Residue "B GLU 130": "OE1" <-> "OE2" Residue "B ARG 140": "NH1" <-> "NH2" Residue "B ASP 181": "OD1" <-> "OD2" Residue "B ARG 206": "NH1" <-> "NH2" Residue "B TYR 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 271": "NH1" <-> "NH2" Residue "B GLU 272": "OE1" <-> "OE2" Residue "B GLU 299": "OE1" <-> "OE2" Residue "B GLU 320": "OE1" <-> "OE2" Residue "B ASP 339": "OD1" <-> "OD2" Residue "B ASP 347": "OD1" <-> "OD2" Residue "B PHE 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 365": "NH1" <-> "NH2" Residue "B GLU 393": "OE1" <-> "OE2" Residue "B ASP 401": "OD1" <-> "OD2" Residue "B ASP 403": "OD1" <-> "OD2" Residue "B ARG 412": "NH1" <-> "NH2" Residue "B TYR 438": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 442": "NH1" <-> "NH2" Residue "B PHE 444": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 447": "OD1" <-> "OD2" Residue "B ASP 452": "OD1" <-> "OD2" Residue "B ARG 454": "NH1" <-> "NH2" Residue "B PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 463": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 484": "OE1" <-> "OE2" Residue "B ASP 485": "OD1" <-> "OD2" Residue "B ASP 486": "OD1" <-> "OD2" Residue "C ASP 27": "OD1" <-> "OD2" Residue "C ASP 45": "OD1" <-> "OD2" Residue "C GLU 68": "OE1" <-> "OE2" Residue "C GLU 84": "OE1" <-> "OE2" Residue "C ASP 86": "OD1" <-> "OD2" Residue "C GLU 130": "OE1" <-> "OE2" Residue "C ARG 140": "NH1" <-> "NH2" Residue "C ASP 181": "OD1" <-> "OD2" Residue "C TYR 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 206": "NH1" <-> "NH2" Residue "C TYR 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 271": "NH1" <-> "NH2" Residue "C GLU 299": "OE1" <-> "OE2" Residue "C GLU 320": "OE1" <-> "OE2" Residue "C ASP 339": "OD1" <-> "OD2" Residue "C ASP 347": "OD1" <-> "OD2" Residue "C ARG 365": "NH1" <-> "NH2" Residue "C GLU 393": "OE1" <-> "OE2" Residue "C PHE 395": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 403": "OD1" <-> "OD2" Residue "C ARG 412": "NH1" <-> "NH2" Residue "C TYR 438": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 442": "NH1" <-> "NH2" Residue "C ASP 447": "OD1" <-> "OD2" Residue "C ASP 452": "OD1" <-> "OD2" Residue "C ARG 454": "NH1" <-> "NH2" Residue "C PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 463": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 484": "OE1" <-> "OE2" Residue "C ASP 485": "OD1" <-> "OD2" Residue "C ASP 486": "OD1" <-> "OD2" Residue "D ARG 5": "NH1" <-> "NH2" Residue "D ASP 15": "OD1" <-> "OD2" Residue "D ARG 37": "NH1" <-> "NH2" Residue "D ASP 43": "OD1" <-> "OD2" Residue "D ASP 68": "OD1" <-> "OD2" Residue "D PHE 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 101": "OE1" <-> "OE2" Residue "D ASP 108": "OD1" <-> "OD2" Residue "D ASP 112": "OD1" <-> "OD2" Residue "D PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 126": "OE1" <-> "OE2" Residue "D GLU 127": "OE1" <-> "OE2" Residue "D GLU 131": "OE1" <-> "OE2" Residue "D PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 178": "OE1" <-> "OE2" Residue "D PHE 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 190": "OD1" <-> "OD2" Residue "D ARG 191": "NH1" <-> "NH2" Residue "D ARG 193": "NH1" <-> "NH2" Residue "D ASP 204": "OD1" <-> "OD2" Residue "D PHE 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 263": "OE1" <-> "OE2" Residue "D GLU 290": "OE1" <-> "OE2" Residue "D TYR 307": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 315": "OD1" <-> "OD2" Residue "D GLU 332": "OE1" <-> "OE2" Residue "D ARG 333": "NH1" <-> "NH2" Residue "D ASP 345": "OD1" <-> "OD2" Residue "D GLU 357": "OE1" <-> "OE2" Residue "D GLU 361": "OE1" <-> "OE2" Residue "D GLU 362": "OE1" <-> "OE2" Residue "D TYR 364": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 382": "OD1" <-> "OD2" Residue "D ASP 390": "OD1" <-> "OD2" Residue "D GLU 391": "OE1" <-> "OE2" Residue "D PHE 408": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 418": "OE1" <-> "OE2" Residue "D TYR 427": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 432": "OE1" <-> "OE2" Residue "D ARG 435": "NH1" <-> "NH2" Residue "D GLU 439": "OE1" <-> "OE2" Residue "D GLU 450": "OE1" <-> "OE2" Residue "D PHE 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 454": "NH1" <-> "NH2" Residue "D GLU 460": "OE1" <-> "OE2" Residue "D GLU 461": "OE1" <-> "OE2" Residue "E ARG 3": "NH1" <-> "NH2" Residue "E ASP 15": "OD1" <-> "OD2" Residue "E PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 43": "OD1" <-> "OD2" Residue "E ARG 72": "NH1" <-> "NH2" Residue "E GLU 89": "OE1" <-> "OE2" Residue "E PHE 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 106": "OE1" <-> "OE2" Residue "E ASP 108": "OD1" <-> "OD2" Residue "E ASP 112": "OD1" <-> "OD2" Residue "E ARG 114": "NH1" <-> "NH2" Residue "E PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 127": "OE1" <-> "OE2" Residue "E GLU 133": "OE1" <-> "OE2" Residue "E PHE 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 190": "OD1" <-> "OD2" Residue "E ASP 197": "OD1" <-> "OD2" Residue "E GLU 220": "OE1" <-> "OE2" Residue "E ARG 240": "NH1" <-> "NH2" Residue "E ASP 252": "OD1" <-> "OD2" Residue "E PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 263": "OE1" <-> "OE2" Residue "E GLU 284": "OE1" <-> "OE2" Residue "E GLU 290": "OE1" <-> "OE2" Residue "E TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 315": "OD1" <-> "OD2" Residue "E ASP 326": "OD1" <-> "OD2" Residue "E GLU 361": "OE1" <-> "OE2" Residue "E ARG 402": "NH1" <-> "NH2" Residue "E ARG 404": "NH1" <-> "NH2" Residue "E GLU 418": "OE1" <-> "OE2" Residue "E TYR 427": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 450": "OE1" <-> "OE2" Residue "E ASP 451": "OD1" <-> "OD2" Residue "E PHE 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 5": "NH1" <-> "NH2" Residue "F PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 37": "NH1" <-> "NH2" Residue "F ASP 57": "OD1" <-> "OD2" Residue "F GLU 89": "OE1" <-> "OE2" Residue "F ARG 120": "NH1" <-> "NH2" Residue "F PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 191": "NH1" <-> "NH2" Residue "F GLU 194": "OE1" <-> "OE2" Residue "F ASP 197": "OD1" <-> "OD2" Residue "F GLU 220": "OE1" <-> "OE2" Residue "F ARG 240": "NH1" <-> "NH2" Residue "F GLU 242": "OE1" <-> "OE2" Residue "F PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 252": "OD1" <-> "OD2" Residue "F GLU 263": "OE1" <-> "OE2" Residue "F ASP 311": "OD1" <-> "OD2" Residue "F TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 315": "OD1" <-> "OD2" Residue "F GLU 332": "OE1" <-> "OE2" Residue "F ARG 352": "NH1" <-> "NH2" Residue "F GLU 362": "OE1" <-> "OE2" Residue "F GLU 379": "OE1" <-> "OE2" Residue "F ASP 382": "OD1" <-> "OD2" Residue "F ASP 390": "OD1" <-> "OD2" Residue "F ASP 394": "OD1" <-> "OD2" Residue "F ARG 402": "NH1" <-> "NH2" Residue "F ARG 404": "NH1" <-> "NH2" Residue "F TYR 427": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 461": "OE1" <-> "OE2" Residue "F GLU 464": "OE1" <-> "OE2" Residue "G ARG 8": "NH1" <-> "NH2" Residue "G ASP 9": "OD1" <-> "OD2" Residue "G ARG 37": "NH1" <-> "NH2" Residue "G GLU 39": "OE1" <-> "OE2" Residue "G TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 50": "OE1" <-> "OE2" Residue "G GLU 54": "OE1" <-> "OE2" Residue "G ASP 87": "OD1" <-> "OD2" Residue "G ARG 88": "NH1" <-> "NH2" Residue "G TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 109": "NH1" <-> "NH2" Residue "G GLU 115": "OE1" <-> "OE2" Residue "G TYR 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 130": "NH1" <-> "NH2" Residue "G ARG 132": "NH1" <-> "NH2" Residue "G ASP 139": "OD1" <-> "OD2" Residue "G PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 154": "OE1" <-> "OE2" Residue "G ASP 169": "OD1" <-> "OD2" Residue "G TYR 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 185": "OE1" <-> "OE2" Residue "G GLU 188": "OE1" <-> "OE2" Residue "G GLU 225": "OE1" <-> "OE2" Residue "G GLU 276": "OE1" <-> "OE2" Time to flip residues: 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 24199 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 3636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 474, 3636 Classifications: {'peptide': 474} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 451} Chain: "B" Number of atoms: 3643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 475, 3643 Classifications: {'peptide': 475} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 452} Chain: "C" Number of atoms: 3649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 476, 3649 Classifications: {'peptide': 476} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 453} Chain: "D" Number of atoms: 3621 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3621 Classifications: {'peptide': 470} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 446} Chain: "E" Number of atoms: 3622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3622 Classifications: {'peptide': 470} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 446} Chain: "F" Number of atoms: 3629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3629 Classifications: {'peptide': 471} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 447} Chain: "G" Number of atoms: 2211 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 2211 Classifications: {'peptide': 282} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 271} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 14.09, per 1000 atoms: 0.58 Number of scatterers: 24199 At special positions: 0 Unit cell: (152.88, 123.48, 126, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 78 16.00 P 17 15.00 Mg 6 11.99 O 4649 8.00 N 4214 7.00 C 15235 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 9.82 Conformation dependent library (CDL) restraints added in 3.7 seconds 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5690 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 114 helices and 22 sheets defined 42.0% alpha, 12.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.61 Creating SS restraints... Processing helix chain 'A' and resid 101 through 103 No H-bonds generated for 'chain 'A' and resid 101 through 103' Processing helix chain 'A' and resid 151 through 156 Processing helix chain 'A' and resid 176 through 186 Processing helix chain 'A' and resid 202 through 214 Processing helix chain 'A' and resid 217 through 220 Processing helix chain 'A' and resid 232 through 252 Proline residue: A 239 - end of helix removed outlier: 3.845A pdb=" N TYR A 248 " --> pdb=" O ALA A 244 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N PHE A 249 " --> pdb=" O MET A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 276 Processing helix chain 'A' and resid 290 through 298 Processing helix chain 'A' and resid 322 through 324 No H-bonds generated for 'chain 'A' and resid 322 through 324' Processing helix chain 'A' and resid 329 through 337 removed outlier: 3.671A pdb=" N SER A 336 " --> pdb=" O THR A 332 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE A 337 " --> pdb=" O ASN A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 351 Processing helix chain 'A' and resid 373 through 396 removed outlier: 3.931A pdb=" N LYS A 377 " --> pdb=" O LYS A 373 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N VAL A 378 " --> pdb=" O ALA A 374 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N THR A 381 " --> pdb=" O LYS A 377 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N LEU A 382 " --> pdb=" O VAL A 378 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LEU A 384 " --> pdb=" O GLY A 380 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LEU A 392 " --> pdb=" O ALA A 388 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N PHE A 395 " --> pdb=" O GLU A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 419 Processing helix chain 'A' and resid 430 through 441 Processing helix chain 'A' and resid 450 through 466 removed outlier: 3.988A pdb=" N ARG A 454 " --> pdb=" O GLU A 451 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N PHE A 456 " --> pdb=" O VAL A 453 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N GLU A 457 " --> pdb=" O ARG A 454 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLU A 459 " --> pdb=" O PHE A 456 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 478 removed outlier: 3.565A pdb=" N HIS A 474 " --> pdb=" O HIS A 470 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ILE A 475 " --> pdb=" O LEU A 471 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ARG A 476 " --> pdb=" O LEU A 472 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N THR A 477 " --> pdb=" O GLU A 473 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 497 Processing helix chain 'B' and resid 101 through 103 No H-bonds generated for 'chain 'B' and resid 101 through 103' Processing helix chain 'B' and resid 151 through 156 Processing helix chain 'B' and resid 175 through 187 removed outlier: 3.516A pdb=" N ALA B 179 " --> pdb=" O LYS B 175 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LYS B 187 " --> pdb=" O ILE B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 214 Processing helix chain 'B' and resid 217 through 220 Processing helix chain 'B' and resid 232 through 252 Proline residue: B 239 - end of helix removed outlier: 3.845A pdb=" N TYR B 248 " --> pdb=" O ALA B 244 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N PHE B 249 " --> pdb=" O MET B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 275 Processing helix chain 'B' and resid 288 through 300 removed outlier: 3.923A pdb=" N PHE B 291 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N TYR B 292 " --> pdb=" O ASP B 289 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N HIS B 294 " --> pdb=" O PHE B 291 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER B 295 " --> pdb=" O TYR B 292 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N GLU B 299 " --> pdb=" O ARG B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 324 No H-bonds generated for 'chain 'B' and resid 322 through 324' Processing helix chain 'B' and resid 329 through 337 removed outlier: 3.510A pdb=" N ILE B 337 " --> pdb=" O ASN B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 351 Processing helix chain 'B' and resid 373 through 379 Processing helix chain 'B' and resid 382 through 398 removed outlier: 3.519A pdb=" N ALA B 387 " --> pdb=" O ARG B 383 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA B 388 " --> pdb=" O LEU B 384 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLU B 391 " --> pdb=" O ALA B 387 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N PHE B 398 " --> pdb=" O ALA B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 419 removed outlier: 3.516A pdb=" N LYS B 409 " --> pdb=" O ALA B 405 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ALA B 414 " --> pdb=" O LEU B 410 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ARG B 415 " --> pdb=" O ALA B 411 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 442 Processing helix chain 'B' and resid 444 through 446 No H-bonds generated for 'chain 'B' and resid 444 through 446' Processing helix chain 'B' and resid 450 through 466 removed outlier: 3.833A pdb=" N ARG B 454 " --> pdb=" O GLU B 451 " (cutoff:3.500A) Processing helix chain 'B' and resid 469 through 478 removed outlier: 3.813A pdb=" N ARG B 476 " --> pdb=" O LEU B 472 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N THR B 477 " --> pdb=" O GLU B 473 " (cutoff:3.500A) Processing helix chain 'B' and resid 484 through 497 removed outlier: 3.607A pdb=" N THR B 497 " --> pdb=" O ALA B 493 " (cutoff:3.500A) Processing helix chain 'C' and resid 101 through 103 No H-bonds generated for 'chain 'C' and resid 101 through 103' Processing helix chain 'C' and resid 151 through 156 Processing helix chain 'C' and resid 175 through 186 Processing helix chain 'C' and resid 202 through 214 Processing helix chain 'C' and resid 217 through 220 Processing helix chain 'C' and resid 232 through 252 Proline residue: C 239 - end of helix removed outlier: 3.845A pdb=" N TYR C 248 " --> pdb=" O ALA C 244 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N PHE C 249 " --> pdb=" O MET C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 276 Processing helix chain 'C' and resid 288 through 300 removed outlier: 3.930A pdb=" N PHE C 291 " --> pdb=" O GLY C 288 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N TYR C 292 " --> pdb=" O ASP C 289 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N HIS C 294 " --> pdb=" O PHE C 291 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N GLU C 299 " --> pdb=" O ARG C 296 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ARG C 300 " --> pdb=" O LEU C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 322 through 324 No H-bonds generated for 'chain 'C' and resid 322 through 324' Processing helix chain 'C' and resid 329 through 337 Processing helix chain 'C' and resid 346 through 351 Processing helix chain 'C' and resid 373 through 378 Processing helix chain 'C' and resid 382 through 398 removed outlier: 4.003A pdb=" N PHE C 398 " --> pdb=" O ALA C 394 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 419 Processing helix chain 'C' and resid 430 through 442 Processing helix chain 'C' and resid 450 through 466 removed outlier: 4.364A pdb=" N ARG C 454 " --> pdb=" O GLU C 451 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLU C 459 " --> pdb=" O PHE C 456 " (cutoff:3.500A) Processing helix chain 'C' and resid 469 through 478 Processing helix chain 'C' and resid 484 through 497 Processing helix chain 'D' and resid 89 through 91 No H-bonds generated for 'chain 'D' and resid 89 through 91' Processing helix chain 'D' and resid 140 through 145 Processing helix chain 'D' and resid 165 through 178 removed outlier: 3.867A pdb=" N GLU D 170 " --> pdb=" O VAL D 166 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N GLN D 177 " --> pdb=" O HIS D 173 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N GLU D 178 " --> pdb=" O ASN D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 192 through 205 removed outlier: 3.801A pdb=" N ASN D 196 " --> pdb=" O THR D 192 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ASP D 197 " --> pdb=" O ARG D 193 " (cutoff:3.500A) Processing helix chain 'D' and resid 207 through 210 Processing helix chain 'D' and resid 222 through 241 removed outlier: 4.662A pdb=" N ALA D 229 " --> pdb=" O ARG D 225 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N LEU D 230 " --> pdb=" O MET D 226 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N THR D 231 " --> pdb=" O ARG D 227 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLY D 232 " --> pdb=" O VAL D 228 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N MET D 235 " --> pdb=" O THR D 231 " (cutoff:3.500A) Processing helix chain 'D' and resid 254 through 268 removed outlier: 3.611A pdb=" N THR D 258 " --> pdb=" O ILE D 254 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLY D 261 " --> pdb=" O PHE D 257 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N SER D 262 " --> pdb=" O THR D 258 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLU D 263 " --> pdb=" O GLN D 259 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ALA D 266 " --> pdb=" O SER D 262 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N LEU D 267 " --> pdb=" O GLU D 263 " (cutoff:3.500A) Processing helix chain 'D' and resid 281 through 291 removed outlier: 3.897A pdb=" N ARG D 291 " --> pdb=" O GLN D 287 " (cutoff:3.500A) Processing helix chain 'D' and resid 316 through 324 removed outlier: 4.003A pdb=" N SER D 323 " --> pdb=" O ALA D 319 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N HIS D 324 " --> pdb=" O THR D 320 " (cutoff:3.500A) Processing helix chain 'D' and resid 333 through 338 Processing helix chain 'D' and resid 356 through 359 No H-bonds generated for 'chain 'D' and resid 356 through 359' Processing helix chain 'D' and resid 361 through 387 removed outlier: 4.149A pdb=" N ASP D 382 " --> pdb=" O LYS D 378 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ILE D 383 " --> pdb=" O GLU D 379 " (cutoff:3.500A) Processing helix chain 'D' and resid 389 through 391 No H-bonds generated for 'chain 'D' and resid 389 through 391' Processing helix chain 'D' and resid 394 through 409 removed outlier: 3.622A pdb=" N ARG D 405 " --> pdb=" O HIS D 401 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 421 removed outlier: 3.838A pdb=" N GLN D 419 " --> pdb=" O VAL D 416 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N THR D 421 " --> pdb=" O GLU D 418 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 442 Processing helix chain 'D' and resid 450 through 453 Processing helix chain 'D' and resid 459 through 469 removed outlier: 3.550A pdb=" N GLU D 464 " --> pdb=" O GLU D 460 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N MET D 469 " --> pdb=" O LYS D 465 " (cutoff:3.500A) Processing helix chain 'E' and resid 89 through 91 No H-bonds generated for 'chain 'E' and resid 89 through 91' Processing helix chain 'E' and resid 140 through 145 Processing helix chain 'E' and resid 164 through 177 Processing helix chain 'E' and resid 192 through 204 removed outlier: 3.797A pdb=" N ASN E 196 " --> pdb=" O THR E 192 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ASP E 197 " --> pdb=" O ARG E 193 " (cutoff:3.500A) Processing helix chain 'E' and resid 207 through 210 Processing helix chain 'E' and resid 222 through 241 removed outlier: 4.960A pdb=" N ALA E 229 " --> pdb=" O ARG E 225 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N LEU E 230 " --> pdb=" O MET E 226 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N TYR E 238 " --> pdb=" O THR E 234 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N PHE E 239 " --> pdb=" O MET E 235 " (cutoff:3.500A) Processing helix chain 'E' and resid 254 through 268 Processing helix chain 'E' and resid 274 through 276 No H-bonds generated for 'chain 'E' and resid 274 through 276' Processing helix chain 'E' and resid 281 through 291 removed outlier: 4.728A pdb=" N ARG E 291 " --> pdb=" O GLN E 287 " (cutoff:3.500A) Processing helix chain 'E' and resid 316 through 324 removed outlier: 3.586A pdb=" N THR E 320 " --> pdb=" O PRO E 316 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N HIS E 324 " --> pdb=" O THR E 320 " (cutoff:3.500A) Processing helix chain 'E' and resid 333 through 338 Processing helix chain 'E' and resid 356 through 359 No H-bonds generated for 'chain 'E' and resid 356 through 359' Processing helix chain 'E' and resid 361 through 386 removed outlier: 4.098A pdb=" N ASP E 382 " --> pdb=" O LYS E 378 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ILE E 383 " --> pdb=" O GLU E 379 " (cutoff:3.500A) Processing helix chain 'E' and resid 389 through 391 No H-bonds generated for 'chain 'E' and resid 389 through 391' Processing helix chain 'E' and resid 394 through 410 removed outlier: 3.962A pdb=" N ARG E 402 " --> pdb=" O LEU E 398 " (cutoff:3.500A) Processing helix chain 'E' and resid 416 through 419 removed outlier: 3.766A pdb=" N GLN E 419 " --> pdb=" O VAL E 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 416 through 419' Processing helix chain 'E' and resid 430 through 442 Processing helix chain 'E' and resid 450 through 453 Processing helix chain 'E' and resid 459 through 469 removed outlier: 3.632A pdb=" N VAL E 463 " --> pdb=" O ILE E 459 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N MET E 469 " --> pdb=" O LYS E 465 " (cutoff:3.500A) Processing helix chain 'F' and resid 89 through 91 No H-bonds generated for 'chain 'F' and resid 89 through 91' Processing helix chain 'F' and resid 140 through 145 Processing helix chain 'F' and resid 164 through 178 removed outlier: 3.816A pdb=" N GLN F 177 " --> pdb=" O HIS F 173 " (cutoff:3.500A) Processing helix chain 'F' and resid 194 through 205 Processing helix chain 'F' and resid 207 through 210 Processing helix chain 'F' and resid 222 through 241 removed outlier: 3.531A pdb=" N MET F 226 " --> pdb=" O PRO F 222 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ARG F 227 " --> pdb=" O GLY F 223 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ALA F 229 " --> pdb=" O ARG F 225 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N LEU F 230 " --> pdb=" O MET F 226 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N MET F 235 " --> pdb=" O THR F 231 " (cutoff:3.500A) Processing helix chain 'F' and resid 255 through 268 removed outlier: 3.788A pdb=" N ALA F 266 " --> pdb=" O SER F 262 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N LEU F 267 " --> pdb=" O GLU F 263 " (cutoff:3.500A) Processing helix chain 'F' and resid 281 through 291 removed outlier: 3.614A pdb=" N LEU F 288 " --> pdb=" O GLU F 284 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ARG F 291 " --> pdb=" O GLN F 287 " (cutoff:3.500A) Processing helix chain 'F' and resid 316 through 324 removed outlier: 3.549A pdb=" N THR F 320 " --> pdb=" O PRO F 316 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N SER F 323 " --> pdb=" O ALA F 319 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N HIS F 324 " --> pdb=" O THR F 320 " (cutoff:3.500A) Processing helix chain 'F' and resid 333 through 338 Processing helix chain 'F' and resid 356 through 359 No H-bonds generated for 'chain 'F' and resid 356 through 359' Processing helix chain 'F' and resid 361 through 384 removed outlier: 4.986A pdb=" N ASP F 382 " --> pdb=" O LYS F 378 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N ILE F 383 " --> pdb=" O GLU F 379 " (cutoff:3.500A) Processing helix chain 'F' and resid 394 through 409 removed outlier: 3.530A pdb=" N VAL F 399 " --> pdb=" O ASP F 396 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N PHE F 408 " --> pdb=" O ARG F 405 " (cutoff:3.500A) Processing helix chain 'F' and resid 415 through 417 No H-bonds generated for 'chain 'F' and resid 415 through 417' Processing helix chain 'F' and resid 430 through 442 Processing helix chain 'F' and resid 450 through 453 Processing helix chain 'F' and resid 459 through 469 removed outlier: 3.550A pdb=" N MET F 469 " --> pdb=" O LYS F 465 " (cutoff:3.500A) Processing helix chain 'G' and resid 7 through 61 Proline residue: G 47 - end of helix Processing helix chain 'G' and resid 94 through 109 removed outlier: 3.569A pdb=" N VAL G 98 " --> pdb=" O TYR G 94 " (cutoff:3.500A) Processing helix chain 'G' and resid 113 through 115 No H-bonds generated for 'chain 'G' and resid 113 through 115' Processing helix chain 'G' and resid 123 through 130 Processing helix chain 'G' and resid 149 through 164 removed outlier: 3.930A pdb=" N GLU G 154 " --> pdb=" O ALA G 150 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ILE G 155 " --> pdb=" O ASP G 151 " (cutoff:3.500A) Processing helix chain 'G' and resid 212 through 286 removed outlier: 3.596A pdb=" N VAL G 218 " --> pdb=" O GLU G 214 " (cutoff:3.500A) Proline residue: G 221 - end of helix removed outlier: 3.523A pdb=" N SER G 264 " --> pdb=" O THR G 260 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ILE G 277 " --> pdb=" O ILE G 273 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 28 through 30 removed outlier: 6.853A pdb=" N GLY A 72 " --> pdb=" O LEU A 64 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N LEU A 66 " --> pdb=" O ASN A 70 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N ASN A 70 " --> pdb=" O LEU A 66 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLN A 33 " --> pdb=" O ARG A 40 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N HIS A 42 " --> pdb=" O VAL A 31 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N VAL A 31 " --> pdb=" O HIS A 42 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 96 through 99 Processing sheet with id= C, first strand: chain 'A' and resid 341 through 344 removed outlier: 6.656A pdb=" N LEU A 166 " --> pdb=" O ILE A 342 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N LEU A 344 " --> pdb=" O LEU A 166 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N ILE A 168 " --> pdb=" O LEU A 344 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 221 through 226 removed outlier: 7.020A pdb=" N SER A 193 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 8.297A pdb=" N VAL A 224 " --> pdb=" O SER A 193 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N TYR A 195 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N ALA A 226 " --> pdb=" O TYR A 195 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ALA A 197 " --> pdb=" O ALA A 226 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N SER A 312 " --> pdb=" O VAL A 256 " (cutoff:3.500A) removed outlier: 7.784A pdb=" N VAL A 258 " --> pdb=" O SER A 312 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N THR A 314 " --> pdb=" O VAL A 258 " (cutoff:3.500A) removed outlier: 8.125A pdb=" N TYR A 260 " --> pdb=" O THR A 314 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N LEU A 316 " --> pdb=" O TYR A 260 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 38 through 41 removed outlier: 3.604A pdb=" N ILE B 73 " --> pdb=" O ALA B 39 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N VAL B 74 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N ALA B 63 " --> pdb=" O VAL B 74 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 96 through 99 Processing sheet with id= G, first strand: chain 'B' and resid 341 through 343 removed outlier: 6.573A pdb=" N LEU B 166 " --> pdb=" O ILE B 342 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 221 through 226 removed outlier: 6.939A pdb=" N SER B 193 " --> pdb=" O ILE B 222 " (cutoff:3.500A) removed outlier: 8.200A pdb=" N VAL B 224 " --> pdb=" O SER B 193 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N TYR B 195 " --> pdb=" O VAL B 224 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N ALA B 226 " --> pdb=" O TYR B 195 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ALA B 197 " --> pdb=" O ALA B 226 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N TYR B 260 " --> pdb=" O LEU B 316 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 28 through 30 removed outlier: 6.873A pdb=" N GLY C 72 " --> pdb=" O LEU C 64 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N LEU C 66 " --> pdb=" O ASN C 70 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N ASN C 70 " --> pdb=" O LEU C 66 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLN C 33 " --> pdb=" O ARG C 40 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N HIS C 42 " --> pdb=" O VAL C 31 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N VAL C 31 " --> pdb=" O HIS C 42 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 96 through 99 Processing sheet with id= K, first strand: chain 'C' and resid 107 through 109 removed outlier: 8.827A pdb=" N VAL C 108 " --> pdb=" O THR C 221 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N VAL C 223 " --> pdb=" O VAL C 108 " (cutoff:3.500A) removed outlier: 8.646A pdb=" N ILE C 222 " --> pdb=" O MET C 191 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N SER C 193 " --> pdb=" O ILE C 222 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N VAL C 224 " --> pdb=" O SER C 193 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N TYR C 195 " --> pdb=" O VAL C 224 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N ALA C 226 " --> pdb=" O TYR C 195 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N ALA C 197 " --> pdb=" O ALA C 226 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N HIS C 255 " --> pdb=" O ILE C 192 " (cutoff:3.500A) removed outlier: 8.479A pdb=" N ILE C 194 " --> pdb=" O HIS C 255 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N LEU C 257 " --> pdb=" O ILE C 194 " (cutoff:3.500A) removed outlier: 7.899A pdb=" N VAL C 196 " --> pdb=" O LEU C 257 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N VAL C 259 " --> pdb=" O VAL C 196 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N ILE C 198 " --> pdb=" O VAL C 259 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 318 through 320 removed outlier: 6.578A pdb=" N ILE C 167 " --> pdb=" O VAL C 319 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N ILE C 342 " --> pdb=" O ILE C 168 " (cutoff:3.500A) No H-bonds generated for sheet with id= L Processing sheet with id= M, first strand: chain 'D' and resid 5 through 10 removed outlier: 6.728A pdb=" N ASP D 15 " --> pdb=" O ILE D 7 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N VAL D 9 " --> pdb=" O VAL D 13 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N VAL D 13 " --> pdb=" O VAL D 9 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU D 52 " --> pdb=" O ARG D 60 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ILE D 62 " --> pdb=" O VAL D 50 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N VAL D 50 " --> pdb=" O ILE D 62 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 84 through 86 Processing sheet with id= O, first strand: chain 'D' and resid 327 through 331 removed outlier: 7.687A pdb=" N ILE D 154 " --> pdb=" O ILE D 300 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N SER D 302 " --> pdb=" O ILE D 154 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N LEU D 156 " --> pdb=" O SER D 302 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N GLN D 304 " --> pdb=" O LEU D 156 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N GLY D 158 " --> pdb=" O GLN D 304 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N ILE D 306 " --> pdb=" O GLY D 158 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N VAL D 247 " --> pdb=" O THR D 301 " (cutoff:3.500A) removed outlier: 8.117A pdb=" N ILE D 303 " --> pdb=" O VAL D 247 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N LEU D 249 " --> pdb=" O ILE D 303 " (cutoff:3.500A) removed outlier: 8.095A pdb=" N ALA D 305 " --> pdb=" O LEU D 249 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N ILE D 251 " --> pdb=" O ALA D 305 " (cutoff:3.500A) removed outlier: 8.552A pdb=" N TYR D 307 " --> pdb=" O ILE D 251 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'E' and resid 5 through 10 removed outlier: 6.426A pdb=" N ASP E 15 " --> pdb=" O ILE E 7 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N VAL E 9 " --> pdb=" O VAL E 13 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N VAL E 13 " --> pdb=" O VAL E 9 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N ILE E 62 " --> pdb=" O VAL E 50 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N VAL E 50 " --> pdb=" O ILE E 62 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'E' and resid 84 through 86 Processing sheet with id= R, first strand: chain 'E' and resid 327 through 331 removed outlier: 3.524A pdb=" N ALA E 327 " --> pdb=" O LYS E 153 " (cutoff:3.500A) removed outlier: 8.516A pdb=" N ILE E 154 " --> pdb=" O ILE E 300 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N SER E 302 " --> pdb=" O ILE E 154 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N LEU E 156 " --> pdb=" O SER E 302 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N GLN E 304 " --> pdb=" O LEU E 156 " (cutoff:3.500A) removed outlier: 8.342A pdb=" N GLY E 158 " --> pdb=" O GLN E 304 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N VAL E 247 " --> pdb=" O THR E 301 " (cutoff:3.500A) removed outlier: 8.082A pdb=" N ILE E 303 " --> pdb=" O VAL E 247 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N LEU E 249 " --> pdb=" O ILE E 303 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N ALA E 305 " --> pdb=" O LEU E 249 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N ILE E 251 " --> pdb=" O ALA E 305 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'F' and resid 5 through 10 removed outlier: 6.621A pdb=" N ASP F 15 " --> pdb=" O ILE F 7 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N VAL F 9 " --> pdb=" O VAL F 13 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N VAL F 13 " --> pdb=" O VAL F 9 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N ILE F 62 " --> pdb=" O VAL F 50 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N VAL F 50 " --> pdb=" O ILE F 62 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'F' and resid 84 through 86 Processing sheet with id= U, first strand: chain 'F' and resid 327 through 330 removed outlier: 8.098A pdb=" N ILE F 154 " --> pdb=" O ILE F 300 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N SER F 302 " --> pdb=" O ILE F 154 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N LEU F 156 " --> pdb=" O SER F 302 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N GLN F 304 " --> pdb=" O LEU F 156 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N GLY F 158 " --> pdb=" O GLN F 304 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N ILE F 306 " --> pdb=" O GLY F 158 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N VAL F 247 " --> pdb=" O THR F 301 " (cutoff:3.500A) removed outlier: 8.038A pdb=" N ILE F 303 " --> pdb=" O VAL F 247 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N LEU F 249 " --> pdb=" O ILE F 303 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N ALA F 305 " --> pdb=" O LEU F 249 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N ILE F 251 " --> pdb=" O ALA F 305 " (cutoff:3.500A) removed outlier: 8.547A pdb=" N TYR F 307 " --> pdb=" O ILE F 251 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N ILE F 182 " --> pdb=" O LEU F 248 " (cutoff:3.500A) removed outlier: 8.460A pdb=" N PHE F 250 " --> pdb=" O ILE F 182 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N VAL F 184 " --> pdb=" O PHE F 250 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'G' and resid 184 through 192 removed outlier: 7.301A pdb=" N LEU G 171 " --> pdb=" O LEU G 191 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N ASN G 176 " --> pdb=" O ILE G 84 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N LEU G 138 " --> pdb=" O VAL G 120 " (cutoff:3.500A) 927 hydrogen bonds defined for protein. 2538 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.06 Time building geometry restraints manager: 10.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 4272 1.31 - 1.44: 5802 1.44 - 1.57: 14343 1.57 - 1.69: 33 1.69 - 1.82: 154 Bond restraints: 24604 Sorted by residual: bond pdb=" C PRO B 280 " pdb=" O PRO B 280 " ideal model delta sigma weight residual 1.246 1.196 0.049 8.50e-03 1.38e+04 3.34e+01 bond pdb=" C4 ADP E 501 " pdb=" C5 ADP E 501 " ideal model delta sigma weight residual 1.490 1.379 0.111 2.00e-02 2.50e+03 3.10e+01 bond pdb=" CA SER A 295 " pdb=" CB SER A 295 " ideal model delta sigma weight residual 1.528 1.463 0.066 1.56e-02 4.11e+03 1.76e+01 bond pdb=" C5 ADP E 501 " pdb=" C6 ADP E 501 " ideal model delta sigma weight residual 1.490 1.407 0.083 2.00e-02 2.50e+03 1.72e+01 bond pdb=" C ARG B 40 " pdb=" O ARG B 40 " ideal model delta sigma weight residual 1.234 1.184 0.050 1.22e-02 6.72e+03 1.71e+01 ... (remaining 24599 not shown) Histogram of bond angle deviations from ideal: 98.12 - 105.06: 612 105.06 - 111.99: 9833 111.99 - 118.93: 10046 118.93 - 125.86: 12521 125.86 - 132.80: 352 Bond angle restraints: 33364 Sorted by residual: angle pdb=" PB ATP D 500 " pdb=" O3B ATP D 500 " pdb=" PG ATP D 500 " ideal model delta sigma weight residual 139.87 123.33 16.54 1.00e+00 1.00e+00 2.74e+02 angle pdb=" PB ATP C 600 " pdb=" O3B ATP C 600 " pdb=" PG ATP C 600 " ideal model delta sigma weight residual 139.87 125.52 14.35 1.00e+00 1.00e+00 2.06e+02 angle pdb=" PB ATP F 500 " pdb=" O3B ATP F 500 " pdb=" PG ATP F 500 " ideal model delta sigma weight residual 139.87 126.51 13.36 1.00e+00 1.00e+00 1.78e+02 angle pdb=" PA ATP D 500 " pdb=" O3A ATP D 500 " pdb=" PB ATP D 500 " ideal model delta sigma weight residual 136.83 123.69 13.14 1.00e+00 1.00e+00 1.73e+02 angle pdb=" PB ATP A 600 " pdb=" O3B ATP A 600 " pdb=" PG ATP A 600 " ideal model delta sigma weight residual 139.87 127.16 12.71 1.00e+00 1.00e+00 1.62e+02 ... (remaining 33359 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.03: 14421 30.03 - 60.07: 432 60.07 - 90.10: 34 90.10 - 120.13: 0 120.13 - 150.16: 2 Dihedral angle restraints: 14889 sinusoidal: 5997 harmonic: 8892 Sorted by residual: dihedral pdb=" C ARG A 283 " pdb=" N ARG A 283 " pdb=" CA ARG A 283 " pdb=" CB ARG A 283 " ideal model delta harmonic sigma weight residual -122.60 -140.28 17.68 0 2.50e+00 1.60e-01 5.00e+01 dihedral pdb=" C ASP C 261 " pdb=" N ASP C 261 " pdb=" CA ASP C 261 " pdb=" CB ASP C 261 " ideal model delta harmonic sigma weight residual -122.60 -139.55 16.95 0 2.50e+00 1.60e-01 4.60e+01 dihedral pdb=" O1B ADP E 501 " pdb=" O3A ADP E 501 " pdb=" PB ADP E 501 " pdb=" PA ADP E 501 " ideal model delta sinusoidal sigma weight residual 300.00 149.83 150.16 1 2.00e+01 2.50e-03 4.48e+01 ... (remaining 14886 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.133: 3061 0.133 - 0.266: 685 0.266 - 0.399: 76 0.399 - 0.531: 15 0.531 - 0.664: 3 Chirality restraints: 3840 Sorted by residual: chirality pdb=" CA ASP C 261 " pdb=" N ASP C 261 " pdb=" C ASP C 261 " pdb=" CB ASP C 261 " both_signs ideal model delta sigma weight residual False 2.51 1.85 0.66 2.00e-01 2.50e+01 1.10e+01 chirality pdb=" CA ARG A 283 " pdb=" N ARG A 283 " pdb=" C ARG A 283 " pdb=" CB ARG A 283 " both_signs ideal model delta sigma weight residual False 2.51 1.85 0.66 2.00e-01 2.50e+01 1.08e+01 chirality pdb=" CA TYR D 27 " pdb=" N TYR D 27 " pdb=" C TYR D 27 " pdb=" CB TYR D 27 " both_signs ideal model delta sigma weight residual False 2.51 1.96 0.55 2.00e-01 2.50e+01 7.58e+00 ... (remaining 3837 not shown) Planarity restraints: 4349 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 220 " -0.101 2.00e-02 2.50e+03 6.26e-02 7.84e+01 pdb=" CG TYR A 220 " 0.001 2.00e-02 2.50e+03 pdb=" CD1 TYR A 220 " 0.040 2.00e-02 2.50e+03 pdb=" CD2 TYR A 220 " 0.072 2.00e-02 2.50e+03 pdb=" CE1 TYR A 220 " 0.052 2.00e-02 2.50e+03 pdb=" CE2 TYR A 220 " 0.030 2.00e-02 2.50e+03 pdb=" CZ TYR A 220 " 0.008 2.00e-02 2.50e+03 pdb=" OH TYR A 220 " -0.103 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 199 " 0.110 2.00e-02 2.50e+03 6.02e-02 7.25e+01 pdb=" CG TYR D 199 " -0.040 2.00e-02 2.50e+03 pdb=" CD1 TYR D 199 " -0.044 2.00e-02 2.50e+03 pdb=" CD2 TYR D 199 " -0.042 2.00e-02 2.50e+03 pdb=" CE1 TYR D 199 " -0.034 2.00e-02 2.50e+03 pdb=" CE2 TYR D 199 " -0.039 2.00e-02 2.50e+03 pdb=" CZ TYR D 199 " -0.005 2.00e-02 2.50e+03 pdb=" OH TYR D 199 " 0.095 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 313 " 0.081 2.00e-02 2.50e+03 5.47e-02 5.97e+01 pdb=" CG TYR D 313 " -0.003 2.00e-02 2.50e+03 pdb=" CD1 TYR D 313 " -0.041 2.00e-02 2.50e+03 pdb=" CD2 TYR D 313 " -0.028 2.00e-02 2.50e+03 pdb=" CE1 TYR D 313 " -0.034 2.00e-02 2.50e+03 pdb=" CE2 TYR D 313 " -0.050 2.00e-02 2.50e+03 pdb=" CZ TYR D 313 " -0.026 2.00e-02 2.50e+03 pdb=" OH TYR D 313 " 0.102 2.00e-02 2.50e+03 ... (remaining 4346 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 99 2.55 - 3.14: 18833 3.14 - 3.73: 34567 3.73 - 4.31: 51288 4.31 - 4.90: 84644 Nonbonded interactions: 189431 Sorted by model distance: nonbonded pdb=" O2G ATP C 600 " pdb="MG MG C 601 " model vdw 1.965 2.170 nonbonded pdb=" O THR F 192 " pdb=" OG1 THR F 192 " model vdw 2.043 2.440 nonbonded pdb=" O1G ATP D 500 " pdb="MG MG D 501 " model vdw 2.098 2.170 nonbonded pdb=" O1G ATP F 500 " pdb="MG MG F 501 " model vdw 2.107 2.170 nonbonded pdb=" OG1 THR B 176 " pdb="MG MG B 601 " model vdw 2.201 2.170 ... (remaining 189426 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 499 or resid 600 through 601)) selection = (chain 'B' and (resid 27 through 499 or resid 600 through 601)) selection = (chain 'C' and (resid 27 through 499 or resid 600 through 601)) } ncs_group { reference = (chain 'D' and (resid 2 through 470 or resid 501)) selection = (chain 'E' and (resid 2 through 470 or resid 502)) selection = (chain 'F' and (resid 2 through 470 or resid 501)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 17 5.49 5 Mg 6 5.21 5 S 78 5.16 5 C 15235 2.51 5 N 4214 2.21 5 O 4649 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.680 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: 5.750 Check model and map are aligned: 0.370 Process input model: 62.370 Find NCS groups from input model: 1.780 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Set scattering table: 0.210 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 74.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7140 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.011 0.111 24604 Z= 0.749 Angle : 1.763 16.538 33364 Z= 1.202 Chirality : 0.111 0.664 3840 Planarity : 0.010 0.089 4349 Dihedral : 14.028 150.162 9199 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.25 % Favored : 96.71 % Rotamer Outliers : 3.32 % Cbeta Deviations : 0.98 % Peptide Plane: Cis-proline : 4.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.14), residues: 3104 helix: -0.08 (0.14), residues: 1225 sheet: 0.26 (0.24), residues: 461 loop : -0.79 (0.16), residues: 1418 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1295 residues out of total 2558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 1210 time to evaluate : 2.721 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 85 outliers final: 23 residues processed: 1252 average time/residue: 0.4659 time to fit residues: 841.0870 Evaluate side-chains 1106 residues out of total 2558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 1083 time to evaluate : 2.654 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.2668 time to fit residues: 14.2132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 261 optimal weight: 0.8980 chunk 234 optimal weight: 1.9990 chunk 130 optimal weight: 0.9980 chunk 80 optimal weight: 2.9990 chunk 158 optimal weight: 2.9990 chunk 125 optimal weight: 0.9980 chunk 242 optimal weight: 2.9990 chunk 94 optimal weight: 4.9990 chunk 147 optimal weight: 0.8980 chunk 180 optimal weight: 1.9990 chunk 281 optimal weight: 0.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 GLN A 186 GLN A 200 GLN A 266 GLN ** A 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 371 GLN A 425 HIS A 466 GLN ** A 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 488 ASN B 33 GLN B 163 GLN B 186 GLN B 230 GLN B 371 GLN B 397 GLN B 469 GLN B 488 ASN C 46 ASN C 147 GLN ** C 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 345 GLN C 397 GLN C 407 GLN C 422 GLN C 425 HIS C 466 GLN C 488 ASN D 8 GLN D 33 GLN D 169 GLN D 253 ASN D 304 GLN D 365 GLN E 33 GLN E 119 HIS E 169 GLN E 363 HIS E 365 GLN ** E 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 412 GLN E 423 GLN F 8 GLN F 33 GLN F 173 HIS F 217 GLN F 324 HIS F 371 GLN F 372 GLN F 423 GLN ** G 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 41 ASN ** G 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 183 GLN G 184 GLN G 240 HIS G 249 ASN G 253 ASN G 266 ASN G 285 ASN Total number of N/Q/H flips: 54 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7122 moved from start: 0.2794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 24604 Z= 0.215 Angle : 0.664 10.288 33364 Z= 0.356 Chirality : 0.047 0.180 3840 Planarity : 0.005 0.060 4349 Dihedral : 6.725 137.455 3417 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer Outliers : 3.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.15), residues: 3104 helix: 0.91 (0.14), residues: 1234 sheet: 0.33 (0.23), residues: 491 loop : -0.59 (0.16), residues: 1379 *********************** 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 1179 residues out of total 2558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 1089 time to evaluate : 2.930 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 outliers start: 90 outliers final: 48 residues processed: 1121 average time/residue: 0.4521 time to fit residues: 738.9130 Evaluate side-chains 1080 residues out of total 2558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 1032 time to evaluate : 3.277 Switching outliers to nearest non-outliers outliers start: 48 outliers final: 0 residues processed: 48 average time/residue: 0.2693 time to fit residues: 27.4975 ------------------------------------------------------------------------------- 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: 5.9990 chunk 87 optimal weight: 3.9990 chunk 234 optimal weight: 10.0000 chunk 191 optimal weight: 8.9990 chunk 77 optimal weight: 1.9990 chunk 282 optimal weight: 0.7980 chunk 304 optimal weight: 8.9990 chunk 251 optimal weight: 5.9990 chunk 279 optimal weight: 7.9990 chunk 96 optimal weight: 9.9990 chunk 226 optimal weight: 4.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 HIS A 163 GLN A 172 GLN A 294 HIS ** A 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 469 GLN B 345 GLN ** C 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 371 GLN C 470 HIS C 474 HIS D 119 HIS D 304 GLN E 169 GLN E 401 HIS E 412 GLN F 324 HIS ** G 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 95 ASN ** G 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7232 moved from start: 0.3669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.075 24604 Z= 0.417 Angle : 0.723 7.158 33364 Z= 0.389 Chirality : 0.051 0.179 3840 Planarity : 0.006 0.061 4349 Dihedral : 6.829 137.161 3417 Min Nonbonded Distance : 1.708 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer Outliers : 4.10 % 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: -0.23 (0.14), residues: 3104 helix: 0.60 (0.14), residues: 1232 sheet: 0.10 (0.23), residues: 518 loop : -0.88 (0.16), residues: 1354 *********************** 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 1224 residues out of total 2558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 1119 time to evaluate : 2.928 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 105 outliers final: 60 residues processed: 1148 average time/residue: 0.4541 time to fit residues: 761.7888 Evaluate side-chains 1148 residues out of total 2558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 1088 time to evaluate : 2.921 Switching outliers to nearest non-outliers outliers start: 60 outliers final: 0 residues processed: 60 average time/residue: 0.2976 time to fit residues: 34.1390 ------------------------------------------------------------------------------- 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: 0.8980 chunk 212 optimal weight: 5.9990 chunk 146 optimal weight: 4.9990 chunk 31 optimal weight: 0.9990 chunk 134 optimal weight: 4.9990 chunk 189 optimal weight: 2.9990 chunk 283 optimal weight: 0.9990 chunk 299 optimal weight: 0.0270 chunk 147 optimal weight: 0.9990 chunk 268 optimal weight: 5.9990 chunk 80 optimal weight: 0.7980 overall best weight: 0.7442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 GLN A 215 HIS C 172 GLN ** C 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 174 ASN D 219 ASN D 304 GLN E 375 GLN E 381 GLN ** F 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7192 moved from start: 0.4109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 24604 Z= 0.172 Angle : 0.574 7.546 33364 Z= 0.303 Chirality : 0.044 0.179 3840 Planarity : 0.005 0.051 4349 Dihedral : 6.128 121.830 3417 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer Outliers : 2.19 % 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: 0.19 (0.15), residues: 3104 helix: 0.99 (0.15), residues: 1239 sheet: 0.34 (0.22), residues: 520 loop : -0.72 (0.17), residues: 1345 *********************** 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 1117 residues out of total 2558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 1061 time to evaluate : 2.874 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 outliers start: 56 outliers final: 26 residues processed: 1077 average time/residue: 0.4481 time to fit residues: 703.3931 Evaluate side-chains 1070 residues out of total 2558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 1044 time to evaluate : 2.832 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 0 residues processed: 26 average time/residue: 0.2636 time to fit residues: 16.1068 ------------------------------------------------------------------------------- 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: 5.9990 chunk 170 optimal weight: 5.9990 chunk 4 optimal weight: 0.0970 chunk 223 optimal weight: 0.3980 chunk 123 optimal weight: 0.5980 chunk 255 optimal weight: 0.0870 chunk 207 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 153 optimal weight: 0.7980 chunk 268 optimal weight: 7.9990 chunk 75 optimal weight: 9.9990 overall best weight: 0.3956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 GLN A 172 GLN A 345 GLN A 422 GLN C 185 ASN C 371 GLN ** C 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 217 GLN F 423 GLN ** G 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 95 ASN ** G 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7176 moved from start: 0.4387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.033 24604 Z= 0.152 Angle : 0.549 7.320 33364 Z= 0.286 Chirality : 0.043 0.143 3840 Planarity : 0.005 0.048 4349 Dihedral : 5.621 106.614 3417 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % 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: 0.48 (0.15), residues: 3104 helix: 1.23 (0.15), residues: 1249 sheet: 0.51 (0.22), residues: 542 loop : -0.59 (0.17), residues: 1313 *********************** 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 1105 residues out of total 2558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 1053 time to evaluate : 3.053 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 outliers start: 52 outliers final: 28 residues processed: 1066 average time/residue: 0.4493 time to fit residues: 693.7997 Evaluate side-chains 1056 residues out of total 2558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 1028 time to evaluate : 2.949 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 0 residues processed: 28 average time/residue: 0.2858 time to fit residues: 17.4800 ------------------------------------------------------------------------------- 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: 9.9990 chunk 269 optimal weight: 6.9990 chunk 59 optimal weight: 6.9990 chunk 175 optimal weight: 0.9990 chunk 73 optimal weight: 2.9990 chunk 299 optimal weight: 6.9990 chunk 248 optimal weight: 9.9990 chunk 138 optimal weight: 9.9990 chunk 24 optimal weight: 3.9990 chunk 99 optimal weight: 5.9990 chunk 157 optimal weight: 3.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 172 GLN A 474 HIS ** B 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 371 GLN ** C 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 474 HIS ** F 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 217 GLN ** G 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7247 moved from start: 0.4496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.070 24604 Z= 0.428 Angle : 0.690 8.448 33364 Z= 0.364 Chirality : 0.050 0.193 3840 Planarity : 0.006 0.067 4349 Dihedral : 6.114 96.991 3417 Min Nonbonded Distance : 1.759 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer Outliers : 2.42 % 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: -0.00 (0.15), residues: 3104 helix: 0.81 (0.14), residues: 1235 sheet: 0.19 (0.22), residues: 525 loop : -0.78 (0.17), residues: 1344 *********************** 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 1155 residues out of total 2558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 1093 time to evaluate : 3.316 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 62 outliers final: 39 residues processed: 1114 average time/residue: 0.4543 time to fit residues: 732.3291 Evaluate side-chains 1130 residues out of total 2558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 1091 time to evaluate : 2.810 Switching outliers to nearest non-outliers outliers start: 39 outliers final: 0 residues processed: 39 average time/residue: 0.3050 time to fit residues: 24.4622 ------------------------------------------------------------------------------- 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: 0.8980 chunk 33 optimal weight: 5.9990 chunk 170 optimal weight: 0.8980 chunk 219 optimal weight: 4.9990 chunk 169 optimal weight: 0.8980 chunk 252 optimal weight: 1.9990 chunk 167 optimal weight: 3.9990 chunk 298 optimal weight: 9.9990 chunk 186 optimal weight: 3.9990 chunk 182 optimal weight: 0.9980 chunk 137 optimal weight: 4.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 172 GLN A 345 GLN A 358 ASN B 186 GLN C 163 GLN C 172 GLN ** C 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 371 GLN ** C 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 474 HIS D 119 HIS D 447 HIS E 169 GLN E 174 ASN ** E 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 401 HIS ** F 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 217 GLN F 259 GLN ** G 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 40 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7215 moved from start: 0.4734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 24604 Z= 0.192 Angle : 0.594 7.991 33364 Z= 0.307 Chirality : 0.044 0.166 3840 Planarity : 0.005 0.059 4349 Dihedral : 5.694 90.480 3417 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer Outliers : 1.92 % 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: 0.25 (0.15), residues: 3104 helix: 1.07 (0.15), residues: 1237 sheet: 0.39 (0.22), residues: 527 loop : -0.74 (0.17), residues: 1340 *********************** 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 1129 residues out of total 2558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 1080 time to evaluate : 2.714 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 49 outliers final: 35 residues processed: 1092 average time/residue: 0.4552 time to fit residues: 720.5939 Evaluate side-chains 1097 residues out of total 2558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 1062 time to evaluate : 2.908 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 0 residues processed: 35 average time/residue: 0.3086 time to fit residues: 22.2067 ------------------------------------------------------------------------------- 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: 4.9990 chunk 119 optimal weight: 1.9990 chunk 178 optimal weight: 4.9990 chunk 90 optimal weight: 6.9990 chunk 58 optimal weight: 3.9990 chunk 57 optimal weight: 5.9990 chunk 189 optimal weight: 0.9980 chunk 203 optimal weight: 7.9990 chunk 147 optimal weight: 7.9990 chunk 27 optimal weight: 9.9990 chunk 234 optimal weight: 7.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 GLN B 467 ASN C 172 GLN C 185 ASN C 371 GLN ** C 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 217 GLN F 423 GLN ** G 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 95 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7251 moved from start: 0.4788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.067 24604 Z= 0.404 Angle : 0.698 9.018 33364 Z= 0.364 Chirality : 0.049 0.176 3840 Planarity : 0.006 0.064 4349 Dihedral : 6.013 87.474 3417 Min Nonbonded Distance : 1.745 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer Outliers : 1.56 % 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: -0.17 (0.15), residues: 3104 helix: 0.70 (0.14), residues: 1238 sheet: 0.09 (0.22), residues: 528 loop : -0.91 (0.17), residues: 1338 *********************** 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 1141 residues out of total 2558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 1101 time to evaluate : 2.839 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 40 outliers final: 28 residues processed: 1116 average time/residue: 0.4494 time to fit residues: 729.9137 Evaluate side-chains 1111 residues out of total 2558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 1083 time to evaluate : 3.060 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 0 residues processed: 28 average time/residue: 0.2667 time to fit residues: 17.1615 ------------------------------------------------------------------------------- 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: 4.9990 chunk 286 optimal weight: 0.0570 chunk 261 optimal weight: 2.9990 chunk 278 optimal weight: 4.9990 chunk 167 optimal weight: 0.8980 chunk 121 optimal weight: 1.9990 chunk 218 optimal weight: 0.9990 chunk 85 optimal weight: 8.9990 chunk 251 optimal weight: 0.7980 chunk 263 optimal weight: 0.9990 chunk 277 optimal weight: 6.9990 overall best weight: 0.7502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 GLN B 46 ASN B 371 GLN ** B 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 147 GLN C 172 GLN C 185 ASN C 371 GLN ** C 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 169 GLN F 8 GLN ** F 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 217 GLN G 36 ASN G 95 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7211 moved from start: 0.5018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 24604 Z= 0.180 Angle : 0.603 8.655 33364 Z= 0.310 Chirality : 0.044 0.183 3840 Planarity : 0.005 0.059 4349 Dihedral : 5.520 83.152 3417 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer Outliers : 1.29 % 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: 0.99 (0.15), residues: 1241 sheet: 0.33 (0.22), residues: 527 loop : -0.80 (0.17), residues: 1336 *********************** 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 1100 residues out of total 2558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 1067 time to evaluate : 2.813 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 33 outliers final: 19 residues processed: 1076 average time/residue: 0.4719 time to fit residues: 744.4632 Evaluate side-chains 1074 residues out of total 2558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 1055 time to evaluate : 2.856 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.2397 time to fit residues: 12.3474 ------------------------------------------------------------------------------- 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: 0.0670 chunk 294 optimal weight: 0.5980 chunk 179 optimal weight: 9.9990 chunk 139 optimal weight: 4.9990 chunk 204 optimal weight: 4.9990 chunk 308 optimal weight: 3.9990 chunk 284 optimal weight: 5.9990 chunk 245 optimal weight: 5.9990 chunk 25 optimal weight: 0.0980 chunk 189 optimal weight: 3.9990 chunk 150 optimal weight: 5.9990 overall best weight: 1.7522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 371 GLN B 433 GLN C 70 ASN C 113 GLN C 185 ASN C 371 GLN ** C 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 169 GLN ** F 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 95 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7227 moved from start: 0.5041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.049 24604 Z= 0.245 Angle : 0.628 9.282 33364 Z= 0.324 Chirality : 0.045 0.185 3840 Planarity : 0.005 0.057 4349 Dihedral : 5.541 88.128 3417 Min Nonbonded Distance : 1.827 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer Outliers : 0.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.15), residues: 3104 helix: 0.95 (0.15), residues: 1250 sheet: 0.24 (0.22), residues: 538 loop : -0.81 (0.17), residues: 1316 ********************** 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 1093 residues out of total 2558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 1073 time to evaluate : 3.051 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 12 residues processed: 1073 average time/residue: 0.4540 time to fit residues: 707.6930 Evaluate side-chains 1077 residues out of total 2558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 1065 time to evaluate : 3.133 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.3120 time to fit residues: 10.3463 ------------------------------------------------------------------------------- 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: 5.9990 chunk 261 optimal weight: 7.9990 chunk 75 optimal weight: 9.9990 chunk 226 optimal weight: 5.9990 chunk 36 optimal weight: 7.9990 chunk 68 optimal weight: 1.9990 chunk 246 optimal weight: 0.3980 chunk 103 optimal weight: 3.9990 chunk 252 optimal weight: 0.8980 chunk 31 optimal weight: 4.9990 chunk 45 optimal weight: 0.8980 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 GLN A 345 GLN A 426 GLN ** A 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 371 GLN B 433 GLN C 185 ASN C 371 GLN ** C 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 474 HIS E 419 GLN ** F 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 107 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.129006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.114563 restraints weight = 35251.483| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 2.18 r_work: 0.3345 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3176 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.5128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.048 24604 Z= 0.237 Angle : 0.627 9.263 33364 Z= 0.322 Chirality : 0.045 0.178 3840 Planarity : 0.005 0.059 4349 Dihedral : 5.484 88.059 3417 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer Outliers : 1.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.15), residues: 3104 helix: 0.91 (0.15), residues: 1246 sheet: 0.31 (0.22), residues: 528 loop : -0.81 (0.17), residues: 1330 =============================================================================== Job complete usr+sys time: 10305.49 seconds wall clock time: 183 minutes 26.01 seconds (11006.01 seconds total)