Starting phenix.real_space_refine (version: dev) on Tue Dec 20 18:26:33 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6smh_10235/12_2022/6smh_10235_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6smh_10235/12_2022/6smh_10235.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6smh_10235/12_2022/6smh_10235.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6smh_10235/12_2022/6smh_10235.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6smh_10235/12_2022/6smh_10235_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6smh_10235/12_2022/6smh_10235_neut.pdb" } resolution = 4.3 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= 0.000 sd= 0.004 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 131": "NH1" <-> "NH2" Residue "A ARG 164": "NH1" <-> "NH2" Residue "A ARG 191": "NH1" <-> "NH2" Residue "A ARG 210": "NH1" <-> "NH2" Residue "A ARG 212": "NH1" <-> "NH2" Residue "A ARG 282": "NH1" <-> "NH2" Residue "A ARG 300": "NH1" <-> "NH2" Residue "A ARG 302": "NH1" <-> "NH2" Residue "A ARG 347": "NH1" <-> "NH2" Residue "A ARG 355": "NH1" <-> "NH2" Residue "A ARG 428": "NH1" <-> "NH2" Residue "A ARG 443": "NH1" <-> "NH2" Residue "B TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 106": "OE1" <-> "OE2" Residue "B ARG 131": "NH1" <-> "NH2" Residue "B ARG 164": "NH1" <-> "NH2" Residue "B ARG 191": "NH1" <-> "NH2" Residue "B ARG 210": "NH1" <-> "NH2" Residue "B ARG 212": "NH1" <-> "NH2" Residue "B ARG 282": "NH1" <-> "NH2" Residue "B ARG 300": "NH1" <-> "NH2" Residue "B ARG 302": "NH1" <-> "NH2" Residue "B PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 347": "NH1" <-> "NH2" Residue "B ARG 355": "NH1" <-> "NH2" Residue "B ARG 428": "NH1" <-> "NH2" Residue "B ARG 443": "NH1" <-> "NH2" Residue "C TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 131": "NH1" <-> "NH2" Residue "C TYR 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 164": "NH1" <-> "NH2" Residue "C TYR 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 199": "OD1" <-> "OD2" Residue "C ARG 210": "NH1" <-> "NH2" Residue "C ARG 212": "NH1" <-> "NH2" Residue "C GLU 228": "OE1" <-> "OE2" Residue "C TYR 236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 245": "OE1" <-> "OE2" Residue "C PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 282": "NH1" <-> "NH2" Residue "C ARG 300": "NH1" <-> "NH2" Residue "C ARG 302": "NH1" <-> "NH2" Residue "C PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 347": "NH1" <-> "NH2" Residue "C ARG 355": "NH1" <-> "NH2" Residue "C PHE 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 428": "NH1" <-> "NH2" Residue "C ARG 443": "NH1" <-> "NH2" Residue "D ASP 78": "OD1" <-> "OD2" Residue "D PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 131": "NH1" <-> "NH2" Residue "D ARG 164": "NH1" <-> "NH2" Residue "D TYR 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 199": "OD1" <-> "OD2" Residue "D ARG 210": "NH1" <-> "NH2" Residue "D ARG 212": "NH1" <-> "NH2" Residue "D GLU 245": "OE1" <-> "OE2" Residue "D ARG 250": "NH1" <-> "NH2" Residue "D PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 282": "NH1" <-> "NH2" Residue "D ARG 300": "NH1" <-> "NH2" Residue "D ARG 302": "NH1" <-> "NH2" Residue "D ASP 335": "OD1" <-> "OD2" Residue "D PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 355": "NH1" <-> "NH2" Residue "D PHE 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 428": "NH1" <-> "NH2" Residue "D ARG 443": "NH1" <-> "NH2" Residue "E TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 131": "NH1" <-> "NH2" Residue "E ARG 164": "NH1" <-> "NH2" Residue "E TYR 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 191": "NH1" <-> "NH2" Residue "E ASP 199": "OD1" <-> "OD2" Residue "E ARG 210": "NH1" <-> "NH2" Residue "E ARG 212": "NH1" <-> "NH2" Residue "E GLU 245": "OE1" <-> "OE2" Residue "E ARG 250": "NH1" <-> "NH2" Residue "E PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 292": "NH1" <-> "NH2" Residue "E ARG 300": "NH1" <-> "NH2" Residue "E ARG 302": "NH1" <-> "NH2" Residue "E ARG 316": "NH1" <-> "NH2" Residue "E PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 347": "NH1" <-> "NH2" Residue "E ARG 355": "NH1" <-> "NH2" Residue "E PHE 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 428": "NH1" <-> "NH2" Residue "E GLU 430": "OE1" <-> "OE2" Residue "E ARG 443": "NH1" <-> "NH2" Residue "F ASP 73": "OD1" <-> "OD2" Residue "F TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 78": "OD1" <-> "OD2" Residue "F PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 131": "NH1" <-> "NH2" Residue "F ARG 164": "NH1" <-> "NH2" Residue "F TYR 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 191": "NH1" <-> "NH2" Residue "F ASP 199": "OD1" <-> "OD2" Residue "F ARG 210": "NH1" <-> "NH2" Residue "F ARG 212": "NH1" <-> "NH2" Residue "F PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 282": "NH1" <-> "NH2" Residue "F ASP 335": "OD1" <-> "OD2" Residue "F PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 355": "NH1" <-> "NH2" Residue "F ARG 428": "NH1" <-> "NH2" Residue "F ARG 443": "NH1" <-> "NH2" Residue "G TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 38": "NH1" <-> "NH2" Residue "G PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 131": "NH1" <-> "NH2" Residue "G ARG 164": "NH1" <-> "NH2" Residue "G ARG 210": "NH1" <-> "NH2" Residue "G ARG 212": "NH1" <-> "NH2" Residue "G GLU 245": "OE1" <-> "OE2" Residue "G ARG 250": "NH1" <-> "NH2" Residue "G PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 282": "NH1" <-> "NH2" Residue "G ARG 300": "NH1" <-> "NH2" Residue "G ARG 302": "NH1" <-> "NH2" Residue "G PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 355": "NH1" <-> "NH2" Residue "G PHE 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 428": "NH1" <-> "NH2" Residue "G ARG 443": "NH1" <-> "NH2" Residue "G ASP 457": "OD1" <-> "OD2" Residue "H TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 78": "OD1" <-> "OD2" Residue "H TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 131": "NH1" <-> "NH2" Residue "H ARG 164": "NH1" <-> "NH2" Residue "H TYR 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 191": "NH1" <-> "NH2" Residue "H ASP 199": "OD1" <-> "OD2" Residue "H ARG 210": "NH1" <-> "NH2" Residue "H ARG 212": "NH1" <-> "NH2" Residue "H ARG 282": "NH1" <-> "NH2" Residue "H ARG 300": "NH1" <-> "NH2" Residue "H ARG 302": "NH1" <-> "NH2" Residue "H PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 347": "NH1" <-> "NH2" Residue "H ARG 355": "NH1" <-> "NH2" Residue "H ARG 428": "NH1" <-> "NH2" Residue "H ARG 443": "NH1" <-> "NH2" Residue "I ARG 14": "NH1" <-> "NH2" Residue "I ARG 74": "NH1" <-> "NH2" Residue "I ARG 82": "NH1" <-> "NH2" Residue "I ARG 133": "NH1" <-> "NH2" Residue "I ARG 166": "NH1" <-> "NH2" Residue "I ARG 168": "NH1" <-> "NH2" Residue "I ARG 172": "NH1" <-> "NH2" Residue "I ARG 183": "NH1" <-> "NH2" Residue "J ARG 33": "NH1" <-> "NH2" Residue "J ARG 74": "NH1" <-> "NH2" Residue "J ARG 82": "NH1" <-> "NH2" Residue "J TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 104": "NH1" <-> "NH2" Residue "J GLU 113": "OE1" <-> "OE2" Residue "J ARG 122": "NH1" <-> "NH2" Residue "J ARG 133": "NH1" <-> "NH2" Residue "J ARG 168": "NH1" <-> "NH2" Residue "J ARG 172": "NH1" <-> "NH2" Residue "J ARG 183": "NH1" <-> "NH2" Residue "J ARG 199": "NH1" <-> "NH2" Residue "K ARG 14": "NH1" <-> "NH2" Residue "K ARG 27": "NH1" <-> "NH2" Residue "K ARG 33": "NH1" <-> "NH2" Residue "K ARG 74": "NH1" <-> "NH2" Residue "K ARG 82": "NH1" <-> "NH2" Residue "K GLU 95": "OE1" <-> "OE2" Residue "K GLU 102": "OE1" <-> "OE2" Residue "K GLU 113": "OE1" <-> "OE2" Residue "K ARG 114": "NH1" <-> "NH2" Residue "K ARG 122": "NH1" <-> "NH2" Residue "K ARG 133": "NH1" <-> "NH2" Residue "K ARG 166": "NH1" <-> "NH2" Residue "K ARG 168": "NH1" <-> "NH2" Residue "K ARG 172": "NH1" <-> "NH2" Residue "K ARG 183": "NH1" <-> "NH2" Residue "L ARG 14": "NH1" <-> "NH2" Residue "L ARG 27": "NH1" <-> "NH2" Residue "L PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 74": "NH1" <-> "NH2" Residue "L ARG 82": "NH1" <-> "NH2" Residue "L TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 122": "NH1" <-> "NH2" Residue "L ARG 133": "NH1" <-> "NH2" Residue "L ARG 166": "NH1" <-> "NH2" Residue "L ARG 183": "NH1" <-> "NH2" Residue "L GLU 187": "OE1" <-> "OE2" Residue "M ARG 27": "NH1" <-> "NH2" Residue "M ARG 74": "NH1" <-> "NH2" Residue "M ARG 82": "NH1" <-> "NH2" Residue "M TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 119": "OD1" <-> "OD2" Residue "M ARG 122": "NH1" <-> "NH2" Residue "M GLU 123": "OE1" <-> "OE2" Residue "M PHE 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 133": "NH1" <-> "NH2" Residue "M ARG 166": "NH1" <-> "NH2" Residue "M ARG 168": "NH1" <-> "NH2" Residue "M ARG 172": "NH1" <-> "NH2" Residue "M ARG 183": "NH1" <-> "NH2" Residue "N ARG 27": "NH1" <-> "NH2" Residue "N ARG 74": "NH1" <-> "NH2" Residue "N ARG 82": "NH1" <-> "NH2" Residue "N ARG 122": "NH1" <-> "NH2" Residue "N ARG 133": "NH1" <-> "NH2" Residue "N GLU 139": "OE1" <-> "OE2" Residue "N ARG 166": "NH1" <-> "NH2" Residue "N ARG 168": "NH1" <-> "NH2" Residue "N ARG 172": "NH1" <-> "NH2" Residue "N ARG 183": "NH1" <-> "NH2" Residue "O ARG 27": "NH1" <-> "NH2" Residue "O ARG 74": "NH1" <-> "NH2" Residue "O ARG 82": "NH1" <-> "NH2" Residue "O ARG 114": "NH1" <-> "NH2" Residue "O ARG 122": "NH1" <-> "NH2" Residue "O PHE 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 133": "NH1" <-> "NH2" Residue "O GLU 139": "OE1" <-> "OE2" Residue "O ARG 166": "NH1" <-> "NH2" Residue "O ARG 168": "NH1" <-> "NH2" Residue "O ARG 172": "NH1" <-> "NH2" Residue "O PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 183": "NH1" <-> "NH2" Residue "P ARG 27": "NH1" <-> "NH2" Residue "P ARG 74": "NH1" <-> "NH2" Residue "P ARG 82": "NH1" <-> "NH2" Residue "P ARG 122": "NH1" <-> "NH2" Residue "P ARG 133": "NH1" <-> "NH2" Residue "P ARG 166": "NH1" <-> "NH2" Residue "P ARG 168": "NH1" <-> "NH2" Residue "P ARG 172": "NH1" <-> "NH2" Residue "P ARG 183": "NH1" <-> "NH2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 39744 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 3495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 447, 3495 Classifications: {'peptide': 447} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 424} Chain: "B" Number of atoms: 3495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 447, 3495 Classifications: {'peptide': 447} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 424} Chain: "C" Number of atoms: 3495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 447, 3495 Classifications: {'peptide': 447} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 424} Chain: "D" Number of atoms: 3495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 447, 3495 Classifications: {'peptide': 447} Link IDs: {'PTRANS': 22, 'TRANS': 424} Chain: "E" Number of atoms: 3495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 447, 3495 Classifications: {'peptide': 447} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 424} Chain: "F" Number of atoms: 3495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 447, 3495 Classifications: {'peptide': 447} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 424} Chain: "G" Number of atoms: 3495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 447, 3495 Classifications: {'peptide': 447} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 424} Chain: "H" Number of atoms: 3495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 447, 3495 Classifications: {'peptide': 447} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 424} Chain: "I" Number of atoms: 1457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1457 Classifications: {'peptide': 179} Link IDs: {'PTRANS': 7, 'TRANS': 171} Chain: "J" Number of atoms: 1523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1523 Classifications: {'peptide': 188} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 179} Chain: "K" Number of atoms: 1457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1457 Classifications: {'peptide': 179} Link IDs: {'PTRANS': 7, 'TRANS': 171} Chain: "L" Number of atoms: 1457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1457 Classifications: {'peptide': 179} Link IDs: {'PTRANS': 7, 'TRANS': 171} Chain: "M" Number of atoms: 1465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1465 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 7, 'TRANS': 172} Chain: "N" Number of atoms: 1473 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1473 Classifications: {'peptide': 181} Link IDs: {'PTRANS': 7, 'TRANS': 173} Chain: "O" Number of atoms: 1473 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1473 Classifications: {'peptide': 181} Link IDs: {'PTRANS': 7, 'TRANS': 173} Chain: "P" Number of atoms: 1479 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1479 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 7, 'TRANS': 174} Time building chain proxies: 22.17, per 1000 atoms: 0.56 Number of scatterers: 39744 At special positions: 0 Unit cell: (167.5, 165, 132.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 176 16.00 O 7342 8.00 N 7133 7.00 C 25093 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: 16.00 Conformation dependent library (CDL) restraints added in 5.9 seconds 9986 Ramachandran restraints generated. 4993 Oldfield, 0 Emsley, 4993 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9232 Finding SS restraints... Secondary structure from input PDB file: 204 helices and 28 sheets defined 44.9% alpha, 5.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.89 Creating SS restraints... Processing helix chain 'A' and resid 46 through 59 removed outlier: 3.534A pdb=" N ALA A 50 " --> pdb=" O PRO A 46 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N SER A 59 " --> pdb=" O ALA A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 118 Processing helix chain 'A' and resid 138 through 143 Processing helix chain 'A' and resid 151 through 160 Processing helix chain 'A' and resid 178 through 192 Processing helix chain 'A' and resid 210 through 230 removed outlier: 3.842A pdb=" N ARG A 214 " --> pdb=" O ARG A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 257 Processing helix chain 'A' and resid 270 through 285 Processing helix chain 'A' and resid 307 through 318 removed outlier: 3.548A pdb=" N LEU A 311 " --> pdb=" O HIS A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 345 Processing helix chain 'A' and resid 380 through 382 No H-bonds generated for 'chain 'A' and resid 380 through 382' Processing helix chain 'A' and resid 383 through 391 removed outlier: 3.794A pdb=" N GLU A 389 " --> pdb=" O PRO A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 430 Processing helix chain 'A' and resid 433 through 446 removed outlier: 3.534A pdb=" N GLU A 437 " --> pdb=" O ASP A 433 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N GLY A 439 " --> pdb=" O TYR A 435 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N ASP A 440 " --> pdb=" O ARG A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 459 removed outlier: 3.797A pdb=" N TRP A 459 " --> pdb=" O ALA A 455 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 59 removed outlier: 3.535A pdb=" N ALA B 50 " --> pdb=" O PRO B 46 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N SER B 59 " --> pdb=" O ALA B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 118 Processing helix chain 'B' and resid 151 through 160 Processing helix chain 'B' and resid 178 through 192 Processing helix chain 'B' and resid 210 through 230 removed outlier: 3.842A pdb=" N ARG B 214 " --> pdb=" O ARG B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 257 Processing helix chain 'B' and resid 270 through 285 Processing helix chain 'B' and resid 307 through 318 removed outlier: 3.547A pdb=" N LEU B 311 " --> pdb=" O HIS B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 348 removed outlier: 4.167A pdb=" N MET B 346 " --> pdb=" O PHE B 342 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N ARG B 347 " --> pdb=" O VAL B 343 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N GLU B 348 " --> pdb=" O ASP B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 391 Processing helix chain 'B' and resid 409 through 430 Processing helix chain 'B' and resid 433 through 446 removed outlier: 3.503A pdb=" N GLU B 437 " --> pdb=" O ASP B 433 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N GLY B 439 " --> pdb=" O TYR B 435 " (cutoff:3.500A) removed outlier: 5.800A pdb=" N ASP B 440 " --> pdb=" O ARG B 436 " (cutoff:3.500A) Processing helix chain 'B' and resid 449 through 459 removed outlier: 3.796A pdb=" N TRP B 459 " --> pdb=" O ALA B 455 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 59 removed outlier: 3.535A pdb=" N ALA C 50 " --> pdb=" O PRO C 46 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N SER C 59 " --> pdb=" O ALA C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 110 through 118 Processing helix chain 'C' and resid 151 through 160 Processing helix chain 'C' and resid 178 through 193 removed outlier: 3.660A pdb=" N GLY C 193 " --> pdb=" O CYS C 189 " (cutoff:3.500A) Processing helix chain 'C' and resid 210 through 225 removed outlier: 3.842A pdb=" N ARG C 214 " --> pdb=" O ARG C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 243 through 257 Processing helix chain 'C' and resid 270 through 285 Processing helix chain 'C' and resid 307 through 318 removed outlier: 3.547A pdb=" N LEU C 311 " --> pdb=" O HIS C 307 " (cutoff:3.500A) Processing helix chain 'C' and resid 332 through 344 Processing helix chain 'C' and resid 345 through 347 No H-bonds generated for 'chain 'C' and resid 345 through 347' Processing helix chain 'C' and resid 383 through 392 Processing helix chain 'C' and resid 409 through 431 Processing helix chain 'C' and resid 438 through 446 Processing helix chain 'C' and resid 449 through 459 removed outlier: 3.797A pdb=" N TRP C 459 " --> pdb=" O ALA C 455 " (cutoff:3.500A) Processing helix chain 'D' and resid 46 through 59 removed outlier: 3.535A pdb=" N ALA D 50 " --> pdb=" O PRO D 46 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N SER D 59 " --> pdb=" O ALA D 55 " (cutoff:3.500A) Processing helix chain 'D' and resid 110 through 118 Processing helix chain 'D' and resid 151 through 160 Processing helix chain 'D' and resid 180 through 192 removed outlier: 3.603A pdb=" N ALA D 185 " --> pdb=" O ASN D 181 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N VAL D 186 " --> pdb=" O TYR D 182 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLU D 188 " --> pdb=" O ARG D 184 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N CYS D 189 " --> pdb=" O ALA D 185 " (cutoff:3.500A) Processing helix chain 'D' and resid 211 through 230 removed outlier: 4.044A pdb=" N PHE D 215 " --> pdb=" O TRP D 211 " (cutoff:3.500A) Processing helix chain 'D' and resid 243 through 258 Processing helix chain 'D' and resid 270 through 285 Processing helix chain 'D' and resid 307 through 318 removed outlier: 3.547A pdb=" N LEU D 311 " --> pdb=" O HIS D 307 " (cutoff:3.500A) Processing helix chain 'D' and resid 332 through 344 Processing helix chain 'D' and resid 383 through 392 Processing helix chain 'D' and resid 409 through 431 Processing helix chain 'D' and resid 433 through 446 removed outlier: 3.534A pdb=" N GLU D 437 " --> pdb=" O ASP D 433 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N GLY D 439 " --> pdb=" O TYR D 435 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N ASP D 440 " --> pdb=" O ARG D 436 " (cutoff:3.500A) Processing helix chain 'D' and resid 449 through 459 removed outlier: 3.796A pdb=" N TRP D 459 " --> pdb=" O ALA D 455 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 59 removed outlier: 3.535A pdb=" N ALA E 50 " --> pdb=" O PRO E 46 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N SER E 59 " --> pdb=" O ALA E 55 " (cutoff:3.500A) Processing helix chain 'E' and resid 60 through 64 Processing helix chain 'E' and resid 110 through 118 Processing helix chain 'E' and resid 151 through 160 Processing helix chain 'E' and resid 178 through 193 removed outlier: 3.546A pdb=" N CYS E 189 " --> pdb=" O ALA E 185 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLY E 193 " --> pdb=" O CYS E 189 " (cutoff:3.500A) Processing helix chain 'E' and resid 210 through 230 removed outlier: 3.842A pdb=" N ARG E 214 " --> pdb=" O ARG E 210 " (cutoff:3.500A) Processing helix chain 'E' and resid 243 through 257 removed outlier: 3.776A pdb=" N ALA E 254 " --> pdb=" O ARG E 250 " (cutoff:3.500A) Processing helix chain 'E' and resid 270 through 282 Processing helix chain 'E' and resid 307 through 319 Processing helix chain 'E' and resid 332 through 345 Processing helix chain 'E' and resid 380 through 382 No H-bonds generated for 'chain 'E' and resid 380 through 382' Processing helix chain 'E' and resid 383 through 391 removed outlier: 3.793A pdb=" N GLU E 389 " --> pdb=" O PRO E 385 " (cutoff:3.500A) Processing helix chain 'E' and resid 409 through 431 Processing helix chain 'E' and resid 433 through 446 removed outlier: 3.535A pdb=" N GLU E 437 " --> pdb=" O ASP E 433 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N GLY E 439 " --> pdb=" O TYR E 435 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N ASP E 440 " --> pdb=" O ARG E 436 " (cutoff:3.500A) Processing helix chain 'E' and resid 449 through 459 removed outlier: 3.797A pdb=" N TRP E 459 " --> pdb=" O ALA E 455 " (cutoff:3.500A) Processing helix chain 'F' and resid 46 through 59 removed outlier: 3.535A pdb=" N ALA F 50 " --> pdb=" O PRO F 46 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N SER F 59 " --> pdb=" O ALA F 55 " (cutoff:3.500A) Processing helix chain 'F' and resid 110 through 118 Processing helix chain 'F' and resid 151 through 160 Processing helix chain 'F' and resid 178 through 193 removed outlier: 3.922A pdb=" N GLY F 193 " --> pdb=" O CYS F 189 " (cutoff:3.500A) Processing helix chain 'F' and resid 211 through 230 removed outlier: 3.897A pdb=" N PHE F 215 " --> pdb=" O TRP F 211 " (cutoff:3.500A) Processing helix chain 'F' and resid 243 through 258 removed outlier: 4.286A pdb=" N GLU F 252 " --> pdb=" O MET F 248 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA F 254 " --> pdb=" O ARG F 250 " (cutoff:3.500A) Processing helix chain 'F' and resid 270 through 285 Processing helix chain 'F' and resid 307 through 318 Processing helix chain 'F' and resid 332 through 344 Processing helix chain 'F' and resid 380 through 382 No H-bonds generated for 'chain 'F' and resid 380 through 382' Processing helix chain 'F' and resid 383 through 391 Processing helix chain 'F' and resid 409 through 430 Processing helix chain 'F' and resid 438 through 446 Processing helix chain 'F' and resid 449 through 459 removed outlier: 3.796A pdb=" N TRP F 459 " --> pdb=" O ALA F 455 " (cutoff:3.500A) Processing helix chain 'G' and resid 46 through 59 removed outlier: 3.534A pdb=" N ALA G 50 " --> pdb=" O PRO G 46 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N SER G 59 " --> pdb=" O ALA G 55 " (cutoff:3.500A) Processing helix chain 'G' and resid 110 through 118 Processing helix chain 'G' and resid 138 through 143 Processing helix chain 'G' and resid 151 through 160 Processing helix chain 'G' and resid 178 through 192 removed outlier: 4.354A pdb=" N GLY G 192 " --> pdb=" O GLU G 188 " (cutoff:3.500A) Processing helix chain 'G' and resid 210 through 230 removed outlier: 3.842A pdb=" N ARG G 214 " --> pdb=" O ARG G 210 " (cutoff:3.500A) Processing helix chain 'G' and resid 243 through 257 removed outlier: 3.601A pdb=" N ALA G 254 " --> pdb=" O ARG G 250 " (cutoff:3.500A) Processing helix chain 'G' and resid 270 through 285 Processing helix chain 'G' and resid 307 through 318 removed outlier: 3.548A pdb=" N LEU G 311 " --> pdb=" O HIS G 307 " (cutoff:3.500A) Processing helix chain 'G' and resid 332 through 344 Processing helix chain 'G' and resid 380 through 382 No H-bonds generated for 'chain 'G' and resid 380 through 382' Processing helix chain 'G' and resid 383 through 391 removed outlier: 4.419A pdb=" N GLU G 389 " --> pdb=" O PRO G 385 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE G 390 " --> pdb=" O ALA G 386 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N PHE G 391 " --> pdb=" O LEU G 387 " (cutoff:3.500A) Processing helix chain 'G' and resid 409 through 430 Processing helix chain 'G' and resid 437 through 446 Processing helix chain 'G' and resid 449 through 457 Processing helix chain 'H' and resid 46 through 59 removed outlier: 3.534A pdb=" N ALA H 50 " --> pdb=" O PRO H 46 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N SER H 59 " --> pdb=" O ALA H 55 " (cutoff:3.500A) Processing helix chain 'H' and resid 110 through 118 Processing helix chain 'H' and resid 138 through 143 Processing helix chain 'H' and resid 151 through 160 Processing helix chain 'H' and resid 178 through 192 Processing helix chain 'H' and resid 210 through 230 removed outlier: 3.842A pdb=" N ARG H 214 " --> pdb=" O ARG H 210 " (cutoff:3.500A) Processing helix chain 'H' and resid 243 through 257 Processing helix chain 'H' and resid 270 through 285 Processing helix chain 'H' and resid 295 through 300 removed outlier: 3.733A pdb=" N ASP H 299 " --> pdb=" O HIS H 295 " (cutoff:3.500A) Processing helix chain 'H' and resid 307 through 318 removed outlier: 3.547A pdb=" N LEU H 311 " --> pdb=" O HIS H 307 " (cutoff:3.500A) Processing helix chain 'H' and resid 332 through 348 removed outlier: 4.220A pdb=" N MET H 346 " --> pdb=" O PHE H 342 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N ARG H 347 " --> pdb=" O VAL H 343 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLU H 348 " --> pdb=" O ASP H 344 " (cutoff:3.500A) Processing helix chain 'H' and resid 380 through 382 No H-bonds generated for 'chain 'H' and resid 380 through 382' Processing helix chain 'H' and resid 383 through 392 Processing helix chain 'H' and resid 409 through 430 Processing helix chain 'H' and resid 437 through 446 Processing helix chain 'H' and resid 449 through 459 removed outlier: 3.796A pdb=" N TRP H 459 " --> pdb=" O ALA H 455 " (cutoff:3.500A) Processing helix chain 'I' and resid 15 through 24 removed outlier: 4.536A pdb=" N LEU I 21 " --> pdb=" O LEU I 17 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ARG I 22 " --> pdb=" O LEU I 18 " (cutoff:3.500A) Processing helix chain 'I' and resid 27 through 34 removed outlier: 3.695A pdb=" N ALA I 32 " --> pdb=" O TRP I 28 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ARG I 33 " --> pdb=" O LEU I 29 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ALA I 34 " --> pdb=" O ALA I 30 " (cutoff:3.500A) Processing helix chain 'I' and resid 44 through 48 removed outlier: 3.675A pdb=" N LEU I 48 " --> pdb=" O PRO I 45 " (cutoff:3.500A) Processing helix chain 'I' and resid 55 through 60 Processing helix chain 'I' and resid 63 through 66 Processing helix chain 'I' and resid 67 through 75 removed outlier: 3.653A pdb=" N ILE I 72 " --> pdb=" O VAL I 68 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N LEU I 73 " --> pdb=" O TYR I 69 " (cutoff:3.500A) Processing helix chain 'I' and resid 103 through 109 Processing helix chain 'I' and resid 121 through 130 removed outlier: 4.319A pdb=" N ALA I 125 " --> pdb=" O ILE I 121 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N ASP I 130 " --> pdb=" O LYS I 126 " (cutoff:3.500A) Processing helix chain 'I' and resid 144 through 157 removed outlier: 3.530A pdb=" N CYS I 153 " --> pdb=" O VAL I 149 " (cutoff:3.500A) Processing helix chain 'I' and resid 162 through 168 Processing helix chain 'I' and resid 179 through 185 removed outlier: 3.733A pdb=" N LEU I 185 " --> pdb=" O GLY I 181 " (cutoff:3.500A) Processing helix chain 'J' and resid 18 through 24 Processing helix chain 'J' and resid 44 through 52 removed outlier: 3.773A pdb=" N LEU J 48 " --> pdb=" O ASN J 44 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N PHE J 49 " --> pdb=" O PRO J 45 " (cutoff:3.500A) removed outlier: 5.771A pdb=" N GLU J 50 " --> pdb=" O GLN J 46 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ALA J 51 " --> pdb=" O THR J 47 " (cutoff:3.500A) Processing helix chain 'J' and resid 60 through 72 removed outlier: 3.535A pdb=" N VAL J 64 " --> pdb=" O ASN J 60 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ALA J 65 " --> pdb=" O GLN J 61 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N MET J 66 " --> pdb=" O ILE J 62 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLN J 67 " --> pdb=" O THR J 63 " (cutoff:3.500A) Processing helix chain 'J' and resid 89 through 96 removed outlier: 3.527A pdb=" N LEU J 96 " --> pdb=" O LEU J 92 " (cutoff:3.500A) Processing helix chain 'J' and resid 103 through 108 removed outlier: 3.676A pdb=" N ALA J 108 " --> pdb=" O ARG J 104 " (cutoff:3.500A) Processing helix chain 'J' and resid 109 through 114 removed outlier: 3.792A pdb=" N GLU J 113 " --> pdb=" O GLN J 109 " (cutoff:3.500A) Processing helix chain 'J' and resid 121 through 132 removed outlier: 3.561A pdb=" N ALA J 127 " --> pdb=" O GLU J 123 " (cutoff:3.500A) Processing helix chain 'J' and resid 144 through 149 removed outlier: 3.902A pdb=" N VAL J 149 " --> pdb=" O PRO J 145 " (cutoff:3.500A) Processing helix chain 'J' and resid 150 through 153 removed outlier: 4.010A pdb=" N CYS J 153 " --> pdb=" O ALA J 150 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 150 through 153' Processing helix chain 'J' and resid 179 through 187 removed outlier: 3.766A pdb=" N ARG J 183 " --> pdb=" O SER J 179 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N GLU J 187 " --> pdb=" O ARG J 183 " (cutoff:3.500A) Processing helix chain 'J' and resid 190 through 195 removed outlier: 3.893A pdb=" N SER J 194 " --> pdb=" O LEU J 190 " (cutoff:3.500A) Processing helix chain 'K' and resid 17 through 24 removed outlier: 3.721A pdb=" N LEU K 21 " --> pdb=" O LEU K 17 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ARG K 22 " --> pdb=" O LEU K 18 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LYS K 24 " --> pdb=" O GLN K 20 " (cutoff:3.500A) Processing helix chain 'K' and resid 28 through 38 removed outlier: 3.723A pdb=" N ALA K 32 " --> pdb=" O TRP K 28 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ARG K 33 " --> pdb=" O LEU K 29 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ALA K 34 " --> pdb=" O ALA K 30 " (cutoff:3.500A) Processing helix chain 'K' and resid 39 through 41 No H-bonds generated for 'chain 'K' and resid 39 through 41' Processing helix chain 'K' and resid 44 through 52 removed outlier: 3.997A pdb=" N LEU K 48 " --> pdb=" O ASN K 44 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N PHE K 49 " --> pdb=" O PRO K 45 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N GLU K 50 " --> pdb=" O GLN K 46 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ALA K 51 " --> pdb=" O THR K 47 " (cutoff:3.500A) Processing helix chain 'K' and resid 60 through 72 removed outlier: 4.126A pdb=" N ALA K 65 " --> pdb=" O GLN K 61 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N MET K 66 " --> pdb=" O ILE K 62 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLN K 67 " --> pdb=" O THR K 63 " (cutoff:3.500A) Processing helix chain 'K' and resid 89 through 96 removed outlier: 3.614A pdb=" N LEU K 96 " --> pdb=" O LEU K 92 " (cutoff:3.500A) Processing helix chain 'K' and resid 101 through 109 removed outlier: 3.723A pdb=" N SER K 105 " --> pdb=" O GLN K 101 " (cutoff:3.500A) Processing helix chain 'K' and resid 110 through 112 No H-bonds generated for 'chain 'K' and resid 110 through 112' Processing helix chain 'K' and resid 121 through 132 Processing helix chain 'K' and resid 144 through 156 removed outlier: 4.114A pdb=" N CYS K 153 " --> pdb=" O VAL K 149 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N TRP K 154 " --> pdb=" O ALA K 150 " (cutoff:3.500A) Processing helix chain 'K' and resid 179 through 186 removed outlier: 3.506A pdb=" N ARG K 183 " --> pdb=" O SER K 179 " (cutoff:3.500A) Processing helix chain 'L' and resid 18 through 23 Processing helix chain 'L' and resid 28 through 39 removed outlier: 4.069A pdb=" N ALA L 34 " --> pdb=" O ALA L 30 " (cutoff:3.500A) Processing helix chain 'L' and resid 44 through 49 removed outlier: 3.985A pdb=" N LEU L 48 " --> pdb=" O ASN L 44 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N PHE L 49 " --> pdb=" O PRO L 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 44 through 49' Processing helix chain 'L' and resid 55 through 62 Processing helix chain 'L' and resid 64 through 72 Processing helix chain 'L' and resid 89 through 96 removed outlier: 3.794A pdb=" N LEU L 96 " --> pdb=" O LEU L 92 " (cutoff:3.500A) Processing helix chain 'L' and resid 100 through 115 removed outlier: 4.744A pdb=" N SER L 105 " --> pdb=" O GLN L 101 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N LEU L 106 " --> pdb=" O GLU L 102 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LYS L 115 " --> pdb=" O ALA L 111 " (cutoff:3.500A) Processing helix chain 'L' and resid 123 through 132 removed outlier: 3.595A pdb=" N ALA L 127 " --> pdb=" O GLU L 123 " (cutoff:3.500A) Processing helix chain 'L' and resid 144 through 153 removed outlier: 3.580A pdb=" N CYS L 153 " --> pdb=" O VAL L 149 " (cutoff:3.500A) Processing helix chain 'L' and resid 162 through 166 removed outlier: 3.995A pdb=" N ARG L 166 " --> pdb=" O LEU L 163 " (cutoff:3.500A) Processing helix chain 'L' and resid 179 through 186 removed outlier: 3.526A pdb=" N ARG L 183 " --> pdb=" O SER L 179 " (cutoff:3.500A) Processing helix chain 'M' and resid 18 through 23 Processing helix chain 'M' and resid 28 through 39 removed outlier: 4.023A pdb=" N ALA M 34 " --> pdb=" O ALA M 30 " (cutoff:3.500A) Processing helix chain 'M' and resid 44 through 49 removed outlier: 3.794A pdb=" N LEU M 48 " --> pdb=" O ASN M 44 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N PHE M 49 " --> pdb=" O PRO M 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 44 through 49' Processing helix chain 'M' and resid 55 through 72 removed outlier: 3.638A pdb=" N GLN M 61 " --> pdb=" O ILE M 57 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N THR M 63 " --> pdb=" O GLN M 59 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL M 64 " --> pdb=" O ASN M 60 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ALA M 65 " --> pdb=" O GLN M 61 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N MET M 66 " --> pdb=" O ILE M 62 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N GLN M 67 " --> pdb=" O THR M 63 " (cutoff:3.500A) Processing helix chain 'M' and resid 89 through 96 removed outlier: 3.914A pdb=" N LEU M 96 " --> pdb=" O LEU M 92 " (cutoff:3.500A) Processing helix chain 'M' and resid 101 through 115 removed outlier: 4.095A pdb=" N SER M 105 " --> pdb=" O GLN M 101 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N CYS M 107 " --> pdb=" O GLN M 103 " (cutoff:3.500A) Processing helix chain 'M' and resid 123 through 134 removed outlier: 3.776A pdb=" N LEU M 134 " --> pdb=" O ASP M 130 " (cutoff:3.500A) Processing helix chain 'M' and resid 144 through 151 Processing helix chain 'M' and resid 163 through 168 removed outlier: 3.784A pdb=" N SER M 167 " --> pdb=" O LEU M 163 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N ARG M 168 " --> pdb=" O THR M 164 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 163 through 168' Processing helix chain 'M' and resid 179 through 185 removed outlier: 3.940A pdb=" N ARG M 183 " --> pdb=" O SER M 179 " (cutoff:3.500A) Processing helix chain 'M' and resid 186 through 190 removed outlier: 3.544A pdb=" N LEU M 190 " --> pdb=" O GLU M 187 " (cutoff:3.500A) Processing helix chain 'N' and resid 17 through 24 removed outlier: 4.123A pdb=" N LEU N 21 " --> pdb=" O LEU N 17 " (cutoff:3.500A) Processing helix chain 'N' and resid 28 through 39 removed outlier: 4.064A pdb=" N ALA N 34 " --> pdb=" O ALA N 30 " (cutoff:3.500A) Processing helix chain 'N' and resid 44 through 52 removed outlier: 3.843A pdb=" N LEU N 48 " --> pdb=" O ASN N 44 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N PHE N 49 " --> pdb=" O PRO N 45 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N GLU N 50 " --> pdb=" O GLN N 46 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ALA N 51 " --> pdb=" O THR N 47 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N THR N 52 " --> pdb=" O LEU N 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 44 through 52' Processing helix chain 'N' and resid 60 through 72 removed outlier: 3.691A pdb=" N ALA N 65 " --> pdb=" O GLN N 61 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N MET N 66 " --> pdb=" O ILE N 62 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLN N 67 " --> pdb=" O THR N 63 " (cutoff:3.500A) Processing helix chain 'N' and resid 89 through 96 removed outlier: 3.572A pdb=" N LEU N 96 " --> pdb=" O LEU N 92 " (cutoff:3.500A) Processing helix chain 'N' and resid 105 through 114 Processing helix chain 'N' and resid 121 through 132 Processing helix chain 'N' and resid 144 through 156 removed outlier: 3.560A pdb=" N ALA N 148 " --> pdb=" O HIS N 144 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N VAL N 149 " --> pdb=" O PRO N 145 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N CYS N 153 " --> pdb=" O VAL N 149 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N TRP N 154 " --> pdb=" O ALA N 150 " (cutoff:3.500A) Processing helix chain 'N' and resid 162 through 167 removed outlier: 3.901A pdb=" N SER N 167 " --> pdb=" O LEU N 163 " (cutoff:3.500A) Processing helix chain 'N' and resid 179 through 186 Processing helix chain 'N' and resid 187 through 190 Processing helix chain 'O' and resid 18 through 23 Processing helix chain 'O' and resid 28 through 39 removed outlier: 4.001A pdb=" N ALA O 34 " --> pdb=" O ALA O 30 " (cutoff:3.500A) Processing helix chain 'O' and resid 44 through 49 removed outlier: 3.816A pdb=" N LEU O 48 " --> pdb=" O ASN O 44 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N PHE O 49 " --> pdb=" O PRO O 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 44 through 49' Processing helix chain 'O' and resid 60 through 72 removed outlier: 3.531A pdb=" N VAL O 64 " --> pdb=" O ASN O 60 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N ALA O 65 " --> pdb=" O GLN O 61 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N MET O 66 " --> pdb=" O ILE O 62 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLN O 67 " --> pdb=" O THR O 63 " (cutoff:3.500A) Processing helix chain 'O' and resid 82 through 86 removed outlier: 3.738A pdb=" N TYR O 85 " --> pdb=" O ARG O 82 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N GLN O 86 " --> pdb=" O GLU O 83 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 82 through 86' Processing helix chain 'O' and resid 89 through 96 removed outlier: 3.691A pdb=" N LEU O 96 " --> pdb=" O LEU O 92 " (cutoff:3.500A) Processing helix chain 'O' and resid 104 through 115 removed outlier: 3.687A pdb=" N LEU O 110 " --> pdb=" O LEU O 106 " (cutoff:3.500A) Processing helix chain 'O' and resid 121 through 128 Processing helix chain 'O' and resid 129 through 132 Processing helix chain 'O' and resid 144 through 151 Processing helix chain 'O' and resid 179 through 185 removed outlier: 3.810A pdb=" N ARG O 183 " --> pdb=" O SER O 179 " (cutoff:3.500A) Processing helix chain 'O' and resid 189 through 193 Processing helix chain 'P' and resid 18 through 24 Processing helix chain 'P' and resid 28 through 39 removed outlier: 4.016A pdb=" N ALA P 34 " --> pdb=" O ALA P 30 " (cutoff:3.500A) Processing helix chain 'P' and resid 44 through 52 removed outlier: 3.804A pdb=" N LEU P 48 " --> pdb=" O ASN P 44 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N PHE P 49 " --> pdb=" O PRO P 45 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N GLU P 50 " --> pdb=" O GLN P 46 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N ALA P 51 " --> pdb=" O THR P 47 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N THR P 52 " --> pdb=" O LEU P 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 44 through 52' Processing helix chain 'P' and resid 60 through 72 removed outlier: 4.237A pdb=" N ALA P 65 " --> pdb=" O GLN P 61 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N MET P 66 " --> pdb=" O ILE P 62 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLN P 67 " --> pdb=" O THR P 63 " (cutoff:3.500A) Processing helix chain 'P' and resid 89 through 96 Processing helix chain 'P' and resid 101 through 115 removed outlier: 3.892A pdb=" N SER P 105 " --> pdb=" O GLN P 101 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ALA P 108 " --> pdb=" O ARG P 104 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N GLN P 109 " --> pdb=" O SER P 105 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU P 110 " --> pdb=" O LEU P 106 " (cutoff:3.500A) Processing helix chain 'P' and resid 121 through 132 removed outlier: 3.573A pdb=" N ALA P 125 " --> pdb=" O ILE P 121 " (cutoff:3.500A) Processing helix chain 'P' and resid 144 through 151 Processing helix chain 'P' and resid 162 through 167 removed outlier: 3.636A pdb=" N SER P 167 " --> pdb=" O LEU P 163 " (cutoff:3.500A) Processing helix chain 'P' and resid 179 through 185 removed outlier: 3.574A pdb=" N ARG P 183 " --> pdb=" O SER P 179 " (cutoff:3.500A) Processing helix chain 'P' and resid 189 through 194 Processing sheet with id=AA1, first strand: chain 'A' and resid 85 through 86 removed outlier: 6.775A pdb=" N ALA A 36 " --> pdb=" O GLU A 133 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLU A 133 " --> pdb=" O ALA A 36 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 287 through 289 removed outlier: 6.293A pdb=" N ILE A 262 " --> pdb=" O HIS A 289 " (cutoff:3.500A) removed outlier: 5.520A pdb=" N HIS A 235 " --> pdb=" O ILE A 261 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N MET A 263 " --> pdb=" O HIS A 235 " (cutoff:3.500A) removed outlier: 5.514A pdb=" N LEU A 237 " --> pdb=" O MET A 263 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N THR A 197 " --> pdb=" O TYR A 236 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N ASN A 238 " --> pdb=" O THR A 197 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N LEU A 167 " --> pdb=" O PHE A 196 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N LYS A 198 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N CYS A 169 " --> pdb=" O LYS A 198 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N MET A 166 " --> pdb=" O LEU A 397 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N LEU A 323 " --> pdb=" O VAL A 374 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 350 through 351 Processing sheet with id=AA4, first strand: chain 'B' and resid 80 through 81 Processing sheet with id=AA5, first strand: chain 'B' and resid 80 through 81 removed outlier: 6.775A pdb=" N ALA B 36 " --> pdb=" O GLU B 133 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLU B 133 " --> pdb=" O ALA B 36 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 287 through 289 removed outlier: 6.292A pdb=" N ILE B 262 " --> pdb=" O HIS B 289 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N HIS B 235 " --> pdb=" O ILE B 261 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N MET B 263 " --> pdb=" O HIS B 235 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N LEU B 237 " --> pdb=" O MET B 263 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N THR B 197 " --> pdb=" O TYR B 236 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N ASN B 238 " --> pdb=" O THR B 197 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N LEU B 167 " --> pdb=" O PHE B 196 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N LYS B 198 " --> pdb=" O LEU B 167 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N CYS B 169 " --> pdb=" O LYS B 198 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N MET B 166 " --> pdb=" O LEU B 397 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N LEU B 323 " --> pdb=" O VAL B 374 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'B' and resid 350 through 351 Processing sheet with id=AA8, first strand: chain 'C' and resid 85 through 86 removed outlier: 3.987A pdb=" N ASP C 134 " --> pdb=" O ALA C 36 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N ARG C 38 " --> pdb=" O LEU C 132 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N LEU C 132 " --> pdb=" O ARG C 38 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N SER C 40 " --> pdb=" O LEU C 130 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N LEU C 130 " --> pdb=" O SER C 40 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 196 through 198 removed outlier: 6.499A pdb=" N LEU C 167 " --> pdb=" O PHE C 196 " (cutoff:3.500A) removed outlier: 8.194A pdb=" N LYS C 198 " --> pdb=" O LEU C 167 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N CYS C 169 " --> pdb=" O LYS C 198 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N MET C 166 " --> pdb=" O LEU C 397 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N LEU C 323 " --> pdb=" O VAL C 374 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'C' and resid 237 through 238 removed outlier: 6.206A pdb=" N LEU C 237 " --> pdb=" O MET C 263 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N ILE C 262 " --> pdb=" O HIS C 289 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'D' and resid 81 through 86 removed outlier: 4.001A pdb=" N HIS D 83 " --> pdb=" O PHE D 97 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N PHE D 97 " --> pdb=" O HIS D 83 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N PHE D 39 " --> pdb=" O TYR D 94 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA D 35 " --> pdb=" O ILE D 98 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ALA D 36 " --> pdb=" O GLU D 133 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLU D 133 " --> pdb=" O ALA D 36 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 166 through 169 removed outlier: 6.354A pdb=" N MET D 166 " --> pdb=" O LEU D 397 " (cutoff:3.500A) removed outlier: 8.089A pdb=" N PHE D 399 " --> pdb=" O MET D 166 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N GLY D 168 " --> pdb=" O PHE D 399 " (cutoff:3.500A) removed outlier: 8.212A pdb=" N GLN D 398 " --> pdb=" O PRO D 373 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N ALA D 375 " --> pdb=" O GLN D 398 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N LEU D 323 " --> pdb=" O VAL D 374 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'D' and resid 196 through 198 removed outlier: 6.919A pdb=" N THR D 197 " --> pdb=" O TYR D 236 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N ASN D 238 " --> pdb=" O THR D 197 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N HIS D 235 " --> pdb=" O ILE D 261 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N MET D 263 " --> pdb=" O HIS D 235 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N LEU D 237 " --> pdb=" O MET D 263 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N ILE D 262 " --> pdb=" O HIS D 289 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'D' and resid 350 through 351 Processing sheet with id=AB6, first strand: chain 'E' and resid 85 through 86 removed outlier: 6.775A pdb=" N ALA E 36 " --> pdb=" O GLU E 133 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLU E 133 " --> pdb=" O ALA E 36 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 166 through 167 removed outlier: 6.353A pdb=" N MET E 166 " --> pdb=" O LEU E 397 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N LEU E 323 " --> pdb=" O VAL E 374 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 350 through 351 Processing sheet with id=AB9, first strand: chain 'F' and resid 85 through 86 removed outlier: 3.666A pdb=" N GLU F 85 " --> pdb=" O PHE F 95 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ALA F 36 " --> pdb=" O GLU F 133 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLU F 133 " --> pdb=" O ALA F 36 " (cutoff:3.500A) removed outlier: 9.016A pdb=" N GLY F 305 " --> pdb=" O ARG F 128 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N LEU F 130 " --> pdb=" O GLY F 305 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 166 through 167 removed outlier: 6.353A pdb=" N MET F 166 " --> pdb=" O LEU F 397 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N LEU F 323 " --> pdb=" O VAL F 374 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'F' and resid 237 through 238 removed outlier: 5.759A pdb=" N LEU F 237 " --> pdb=" O MET F 263 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'F' and resid 350 through 351 Processing sheet with id=AC4, first strand: chain 'G' and resid 36 through 39 Processing sheet with id=AC5, first strand: chain 'G' and resid 131 through 132 Processing sheet with id=AC6, first strand: chain 'G' and resid 234 through 235 removed outlier: 3.670A pdb=" N THR G 197 " --> pdb=" O GLY G 234 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N LEU G 167 " --> pdb=" O PHE G 196 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N LYS G 198 " --> pdb=" O LEU G 167 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N CYS G 169 " --> pdb=" O LYS G 198 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N MET G 166 " --> pdb=" O LEU G 397 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N LEU G 323 " --> pdb=" O VAL G 374 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'G' and resid 261 through 263 removed outlier: 6.319A pdb=" N ILE G 262 " --> pdb=" O HIS G 289 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'H' and resid 85 through 86 removed outlier: 3.865A pdb=" N PHE H 39 " --> pdb=" O TYR H 94 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N ALA H 36 " --> pdb=" O GLU H 133 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLU H 133 " --> pdb=" O ALA H 36 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'H' and resid 287 through 289 removed outlier: 6.292A pdb=" N ILE H 262 " --> pdb=" O HIS H 289 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N HIS H 235 " --> pdb=" O ILE H 261 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N MET H 263 " --> pdb=" O HIS H 235 " (cutoff:3.500A) removed outlier: 5.514A pdb=" N LEU H 237 " --> pdb=" O MET H 263 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N THR H 197 " --> pdb=" O TYR H 236 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N ASN H 238 " --> pdb=" O THR H 197 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N LEU H 167 " --> pdb=" O PHE H 196 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N LYS H 198 " --> pdb=" O LEU H 167 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N CYS H 169 " --> pdb=" O LYS H 198 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N MET H 166 " --> pdb=" O LEU H 397 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N LEU H 323 " --> pdb=" O VAL H 374 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'H' and resid 350 through 351 1366 hydrogen bonds defined for protein. 3972 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: 12.37 Time building geometry restraints manager: 17.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 11298 1.33 - 1.45: 7612 1.45 - 1.57: 21483 1.57 - 1.69: 0 1.69 - 1.81: 264 Bond restraints: 40657 Sorted by residual: bond pdb=" C GLN I 137 " pdb=" N PRO I 138 " ideal model delta sigma weight residual 1.333 1.367 -0.034 7.80e-03 1.64e+04 1.94e+01 bond pdb=" N GLN D 206 " pdb=" CA GLN D 206 " ideal model delta sigma weight residual 1.453 1.487 -0.034 8.30e-03 1.45e+04 1.68e+01 bond pdb=" N VAL E 239 " pdb=" CA VAL E 239 " ideal model delta sigma weight residual 1.455 1.494 -0.038 1.04e-02 9.25e+03 1.35e+01 bond pdb=" N ILE C 379 " pdb=" CA ILE C 379 " ideal model delta sigma weight residual 1.457 1.494 -0.037 1.15e-02 7.56e+03 1.04e+01 bond pdb=" N HIS O 144 " pdb=" CA HIS O 144 " ideal model delta sigma weight residual 1.456 1.489 -0.033 1.04e-02 9.25e+03 1.02e+01 ... (remaining 40652 not shown) Histogram of bond angle deviations from ideal: 98.77 - 105.89: 959 105.89 - 113.00: 20718 113.00 - 120.11: 16265 120.11 - 127.23: 16580 127.23 - 134.34: 549 Bond angle restraints: 55071 Sorted by residual: angle pdb=" N ILE P 170 " pdb=" CA ILE P 170 " pdb=" C ILE P 170 " ideal model delta sigma weight residual 113.71 107.30 6.41 9.50e-01 1.11e+00 4.55e+01 angle pdb=" N ILE M 170 " pdb=" CA ILE M 170 " pdb=" C ILE M 170 " ideal model delta sigma weight residual 113.22 104.94 8.28 1.23e+00 6.61e-01 4.53e+01 angle pdb=" N ILE K 170 " pdb=" CA ILE K 170 " pdb=" C ILE K 170 " ideal model delta sigma weight residual 113.53 107.13 6.40 9.80e-01 1.04e+00 4.26e+01 angle pdb=" C SER E 367 " pdb=" N MET E 368 " pdb=" CA MET E 368 " ideal model delta sigma weight residual 121.61 113.22 8.39 1.39e+00 5.18e-01 3.64e+01 angle pdb=" C SER B 367 " pdb=" N MET B 368 " pdb=" CA MET B 368 " ideal model delta sigma weight residual 121.61 113.23 8.38 1.39e+00 5.18e-01 3.63e+01 ... (remaining 55066 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.44: 22451 26.44 - 52.87: 1473 52.87 - 79.31: 288 79.31 - 105.74: 30 105.74 - 132.18: 1 Dihedral angle restraints: 24243 sinusoidal: 9890 harmonic: 14353 Sorted by residual: dihedral pdb=" CA LYS D 172 " pdb=" C LYS D 172 " pdb=" N PRO D 173 " pdb=" CA PRO D 173 " ideal model delta harmonic sigma weight residual 180.00 47.82 132.18 0 5.00e+00 4.00e-02 6.99e+02 dihedral pdb=" CD ARG J 27 " pdb=" NE ARG J 27 " pdb=" CZ ARG J 27 " pdb=" NH1 ARG J 27 " ideal model delta sinusoidal sigma weight residual 0.00 89.93 -89.93 1 1.00e+01 1.00e-02 9.59e+01 dihedral pdb=" CD ARG H 191 " pdb=" NE ARG H 191 " pdb=" CZ ARG H 191 " pdb=" NH1 ARG H 191 " ideal model delta sinusoidal sigma weight residual 0.00 -89.10 89.10 1 1.00e+01 1.00e-02 9.45e+01 ... (remaining 24240 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 3767 0.062 - 0.125: 1665 0.125 - 0.187: 433 0.187 - 0.250: 35 0.250 - 0.312: 17 Chirality restraints: 5917 Sorted by residual: chirality pdb=" CB VAL I 81 " pdb=" CA VAL I 81 " pdb=" CG1 VAL I 81 " pdb=" CG2 VAL I 81 " both_signs ideal model delta sigma weight residual False -2.63 -2.32 -0.31 2.00e-01 2.50e+01 2.44e+00 chirality pdb=" CB ILE B 203 " pdb=" CA ILE B 203 " pdb=" CG1 ILE B 203 " pdb=" CG2 ILE B 203 " both_signs ideal model delta sigma weight residual False 2.64 2.95 -0.30 2.00e-01 2.50e+01 2.32e+00 chirality pdb=" CB ILE H 203 " pdb=" CA ILE H 203 " pdb=" CG1 ILE H 203 " pdb=" CG2 ILE H 203 " both_signs ideal model delta sigma weight residual False 2.64 2.95 -0.30 2.00e-01 2.50e+01 2.30e+00 ... (remaining 5914 not shown) Planarity restraints: 7264 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG J 27 " -1.103 9.50e-02 1.11e+02 4.94e-01 1.47e+02 pdb=" NE ARG J 27 " 0.066 2.00e-02 2.50e+03 pdb=" CZ ARG J 27 " 0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG J 27 " -0.015 2.00e-02 2.50e+03 pdb=" NH2 ARG J 27 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG H 191 " -1.101 9.50e-02 1.11e+02 4.94e-01 1.47e+02 pdb=" NE ARG H 191 " 0.066 2.00e-02 2.50e+03 pdb=" CZ ARG H 191 " 0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG H 191 " -0.015 2.00e-02 2.50e+03 pdb=" NH2 ARG H 191 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG E 428 " 1.100 9.50e-02 1.11e+02 4.93e-01 1.46e+02 pdb=" NE ARG E 428 " -0.066 2.00e-02 2.50e+03 pdb=" CZ ARG E 428 " -0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG E 428 " 0.014 2.00e-02 2.50e+03 pdb=" NH2 ARG E 428 " 0.016 2.00e-02 2.50e+03 ... (remaining 7261 not shown) Histogram of nonbonded interaction distances: 0.29 - 1.21: 60 1.21 - 2.14: 519 2.14 - 3.06: 26676 3.06 - 3.98: 105877 3.98 - 4.90: 185538 Warning: very small nonbonded interaction distances. Nonbonded interactions: 318670 Sorted by model distance: nonbonded pdb=" C ILE C 351 " pdb=" CG2 THR C 362 " model vdw 0.292 3.690 nonbonded pdb=" O HIS F 295 " pdb=" CG ASP F 299 " model vdw 0.375 3.270 nonbonded pdb=" CG2 VAL F 328 " pdb=" NZ LYS F 336 " model vdw 0.483 3.540 nonbonded pdb=" NH2 ARG D 212 " pdb=" CE2 PHE D 253 " model vdw 0.501 3.420 nonbonded pdb=" CE2 TYR E 236 " pdb=" CE1 HIS E 289 " model vdw 0.502 3.560 ... (remaining 318665 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'I' selection = (chain 'J' and resid 13 through 191) selection = chain 'K' selection = chain 'L' selection = (chain 'M' and resid 13 through 191) selection = (chain 'N' and resid 13 through 191) selection = (chain 'O' and resid 13 through 191) selection = (chain 'P' and resid 13 through 191) } 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: 4 Type Number sf(0) Gaussians S 176 5.16 5 C 25093 2.51 5 N 7133 2.21 5 O 7342 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.220 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: 0.040 Extract box with map and model: 7.740 Check model and map are aligned: 0.560 Convert atoms to be neutral: 0.340 Process input model: 95.320 Find NCS groups from input model: 2.580 Set up NCS constraints: 0.220 Set refine NCS operators: 0.000 Set scattering table: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 111.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 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 : 0.009 0.059 40657 Z= 0.571 Angle : 1.334 14.129 55071 Z= 0.867 Chirality : 0.072 0.312 5917 Planarity : 0.039 0.494 7264 Dihedral : 17.186 132.177 15011 Min Nonbonded Distance : 0.292 Molprobity Statistics. All-atom Clashscore : 54.51 Ramachandran Plot: Outliers : 2.20 % Allowed : 11.96 % Favored : 85.84 % Rotamer Outliers : 14.61 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 3.43 % Cis-general : 0.00 % Twisted Proline : 0.43 % Twisted General : 0.34 % 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: -4.97 (0.09), residues: 4993 helix: -2.91 (0.08), residues: 2050 sheet: -3.44 (0.19), residues: 440 loop : -3.67 (0.10), residues: 2503 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9986 Ramachandran restraints generated. 4993 Oldfield, 0 Emsley, 4993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9986 Ramachandran restraints generated. 4993 Oldfield, 0 Emsley, 4993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2047 residues out of total 4128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 603 poor density : 1444 time to evaluate : 4.765 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 603 outliers final: 366 residues processed: 1898 average time/residue: 0.5543 time to fit residues: 1647.6908 Evaluate side-chains 1199 residues out of total 4128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 366 poor density : 833 time to evaluate : 4.558 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 366 outliers final: 42 residues processed: 366 average time/residue: 0.4916 time to fit residues: 298.0244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 493 random chunks: chunk 416 optimal weight: 0.9990 chunk 373 optimal weight: 9.9990 chunk 207 optimal weight: 7.9990 chunk 127 optimal weight: 2.9990 chunk 252 optimal weight: 0.9990 chunk 199 optimal weight: 7.9990 chunk 386 optimal weight: 9.9990 chunk 149 optimal weight: 1.9990 chunk 234 optimal weight: 7.9990 chunk 287 optimal weight: 3.9990 chunk 447 optimal weight: 10.0000 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 HIS A 112 ASN ** A 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 383 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 146 GLN B 160 ASN B 209 GLN ** B 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 146 GLN ** C 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 209 GLN ** C 235 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 324 HIS ** C 380 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 112 ASN D 160 ASN D 202 ASN ** D 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 284 ASN ** D 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 380 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 83 HIS E 112 ASN E 160 ASN ** E 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 226 GLN ** E 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 417 ASN F 83 HIS F 112 ASN ** F 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 274 ASN ** F 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 83 HIS G 112 ASN ** G 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 202 ASN G 206 GLN G 324 HIS G 426 GLN H 112 ASN H 160 ASN ** H 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 144 HIS J 86 GLN K 67 GLN K 86 GLN K 109 GLN ** K 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 58 GLN ** L 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 75 GLN M 46 GLN M 59 GLN M 140 ASN N 67 GLN O 46 GLN ** P 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 152 GLN Total number of N/Q/H flips: 41 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.3967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.100 40657 Z= 0.283 Angle : 0.802 11.793 55071 Z= 0.411 Chirality : 0.048 0.302 5917 Planarity : 0.006 0.095 7264 Dihedral : 6.492 63.022 5490 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 21.85 Ramachandran Plot: Outliers : 0.40 % Allowed : 9.61 % Favored : 89.99 % Rotamer Outliers : 0.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.43 % Cis-general : 0.00 % Twisted Proline : 0.43 % Twisted General : 0.15 % 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: -3.41 (0.10), residues: 4993 helix: -1.28 (0.10), residues: 2127 sheet: -2.69 (0.22), residues: 392 loop : -3.15 (0.11), residues: 2474 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9986 Ramachandran restraints generated. 4993 Oldfield, 0 Emsley, 4993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9986 Ramachandran restraints generated. 4993 Oldfield, 0 Emsley, 4993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1190 residues out of total 4128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 1167 time to evaluate : 4.655 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 3 residues processed: 1185 average time/residue: 0.5064 time to fit residues: 971.5401 Evaluate side-chains 795 residues out of total 4128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 792 time to evaluate : 4.376 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.3817 time to fit residues: 7.8394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 493 random chunks: chunk 248 optimal weight: 10.0000 chunk 138 optimal weight: 20.0000 chunk 372 optimal weight: 10.0000 chunk 304 optimal weight: 2.9990 chunk 123 optimal weight: 10.0000 chunk 448 optimal weight: 6.9990 chunk 484 optimal weight: 10.0000 chunk 399 optimal weight: 6.9990 chunk 444 optimal weight: 8.9990 chunk 152 optimal weight: 9.9990 chunk 359 optimal weight: 4.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 383 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 83 HIS ** B 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 112 ASN C 160 ASN ** C 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 235 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 324 HIS C 380 HIS ** D 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 226 GLN ** D 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 380 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 429 ASN E 112 ASN E 202 ASN E 204 ASN E 209 GLN E 324 HIS ** E 383 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 112 ASN F 150 HIS F 181 ASN ** F 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 274 ASN F 301 GLN F 324 HIS G 83 HIS ** G 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 324 HIS ** H 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 291 HIS H 324 HIS I 86 GLN J 46 GLN J 58 GLN ** K 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 75 GLN ** L 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 175 GLN M 58 GLN ** N 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 152 GLN ** O 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 101 GLN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.4854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.163 40657 Z= 0.451 Angle : 0.847 13.166 55071 Z= 0.438 Chirality : 0.049 0.303 5917 Planarity : 0.005 0.070 7264 Dihedral : 6.486 46.600 5490 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 25.27 Ramachandran Plot: Outliers : 0.36 % Allowed : 10.98 % Favored : 88.66 % Rotamer Outliers : 0.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.43 % Cis-general : 0.00 % Twisted Proline : 0.43 % Twisted General : 0.17 % 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: -3.03 (0.11), residues: 4993 helix: -0.85 (0.11), residues: 2076 sheet: -2.78 (0.21), residues: 472 loop : -2.95 (0.11), residues: 2445 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9986 Ramachandran restraints generated. 4993 Oldfield, 0 Emsley, 4993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9986 Ramachandran restraints generated. 4993 Oldfield, 0 Emsley, 4993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 985 residues out of total 4128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 969 time to evaluate : 4.703 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 8 residues processed: 982 average time/residue: 0.4992 time to fit residues: 800.3055 Evaluate side-chains 728 residues out of total 4128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 720 time to evaluate : 4.411 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.3439 time to fit residues: 11.4681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 493 random chunks: chunk 443 optimal weight: 7.9990 chunk 337 optimal weight: 2.9990 chunk 232 optimal weight: 2.9990 chunk 49 optimal weight: 20.0000 chunk 214 optimal weight: 5.9990 chunk 301 optimal weight: 8.9990 chunk 450 optimal weight: 9.9990 chunk 476 optimal weight: 20.0000 chunk 235 optimal weight: 5.9990 chunk 426 optimal weight: 8.9990 chunk 128 optimal weight: 6.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 ASN ** A 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 204 ASN B 274 ASN ** B 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 417 ASN C 83 HIS C 150 HIS C 160 ASN C 209 GLN ** C 235 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 209 GLN ** D 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 380 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 383 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 274 ASN F 301 GLN ** F 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 417 ASN H 206 GLN ** H 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 75 GLN L 175 GLN M 86 GLN ** N 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 86 GLN O 86 GLN ** O 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.5294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.146 40657 Z= 0.380 Angle : 0.787 11.306 55071 Z= 0.404 Chirality : 0.047 0.304 5917 Planarity : 0.005 0.082 7264 Dihedral : 6.335 47.467 5490 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 23.36 Ramachandran Plot: Outliers : 0.34 % Allowed : 10.55 % Favored : 89.10 % Rotamer Outliers : 0.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.43 % Cis-general : 0.00 % Twisted Proline : 0.43 % Twisted General : 0.17 % 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: -2.82 (0.11), residues: 4993 helix: -0.62 (0.11), residues: 2062 sheet: -2.68 (0.21), residues: 472 loop : -2.87 (0.12), residues: 2459 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9986 Ramachandran restraints generated. 4993 Oldfield, 0 Emsley, 4993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9986 Ramachandran restraints generated. 4993 Oldfield, 0 Emsley, 4993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 952 residues out of total 4128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 947 time to evaluate : 4.755 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 1 residues processed: 950 average time/residue: 0.4946 time to fit residues: 774.1880 Evaluate side-chains 713 residues out of total 4128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 712 time to evaluate : 4.588 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.4127 time to fit residues: 6.9367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 493 random chunks: chunk 396 optimal weight: 20.0000 chunk 270 optimal weight: 2.9990 chunk 6 optimal weight: 6.9990 chunk 354 optimal weight: 6.9990 chunk 196 optimal weight: 2.9990 chunk 406 optimal weight: 7.9990 chunk 329 optimal weight: 1.9990 chunk 0 optimal weight: 9.9990 chunk 243 optimal weight: 7.9990 chunk 427 optimal weight: 20.0000 chunk 120 optimal weight: 7.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 ASN ** A 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 383 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 417 ASN ** B 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 160 ASN ** C 235 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 291 HIS ** C 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 417 ASN ** D 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 380 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 209 GLN ** E 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 383 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 204 ASN ** F 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 274 ASN ** F 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 83 HIS ** G 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 209 GLN G 274 ASN H 206 GLN ** H 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 291 HIS H 324 HIS H 417 ASN K 101 GLN ** L 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 75 GLN N 46 GLN ** N 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.5653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.128 40657 Z= 0.338 Angle : 0.768 10.436 55071 Z= 0.391 Chirality : 0.047 0.419 5917 Planarity : 0.005 0.077 7264 Dihedral : 6.218 44.993 5490 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 22.13 Ramachandran Plot: Outliers : 0.34 % Allowed : 11.02 % Favored : 88.64 % Rotamer Outliers : 0.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.43 % Cis-general : 0.00 % Twisted Proline : 0.43 % Twisted General : 0.17 % 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: -2.64 (0.11), residues: 4993 helix: -0.51 (0.11), residues: 2095 sheet: -2.61 (0.21), residues: 456 loop : -2.76 (0.12), residues: 2442 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9986 Ramachandran restraints generated. 4993 Oldfield, 0 Emsley, 4993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9986 Ramachandran restraints generated. 4993 Oldfield, 0 Emsley, 4993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 902 residues out of total 4128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 896 time to evaluate : 4.955 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 1 residues processed: 901 average time/residue: 0.5104 time to fit residues: 756.9644 Evaluate side-chains 688 residues out of total 4128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 687 time to evaluate : 4.734 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.4302 time to fit residues: 7.6733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 493 random chunks: chunk 160 optimal weight: 4.9990 chunk 429 optimal weight: 10.0000 chunk 94 optimal weight: 7.9990 chunk 279 optimal weight: 1.9990 chunk 117 optimal weight: 0.8980 chunk 476 optimal weight: 8.9990 chunk 395 optimal weight: 20.0000 chunk 220 optimal weight: 9.9990 chunk 39 optimal weight: 0.8980 chunk 157 optimal weight: 0.9990 chunk 250 optimal weight: 10.0000 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 274 ASN ** B 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 417 ASN C 181 ASN ** C 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 209 GLN C 235 HIS C 291 HIS ** C 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 380 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 383 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 202 ASN F 204 ASN ** F 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 274 ASN ** F 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 274 ASN ** H 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 60 ASN L 75 GLN ** M 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 46 GLN ** P 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.5903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.086 40657 Z= 0.221 Angle : 0.709 10.705 55071 Z= 0.354 Chirality : 0.045 0.233 5917 Planarity : 0.005 0.078 7264 Dihedral : 5.899 43.560 5490 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 19.24 Ramachandran Plot: Outliers : 0.34 % Allowed : 9.79 % Favored : 89.87 % Rotamer Outliers : 0.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.43 % Cis-general : 0.00 % Twisted Proline : 0.43 % Twisted General : 0.06 % 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: -2.36 (0.12), residues: 4993 helix: -0.28 (0.11), residues: 2096 sheet: -2.41 (0.22), residues: 424 loop : -2.63 (0.12), residues: 2473 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9986 Ramachandran restraints generated. 4993 Oldfield, 0 Emsley, 4993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9986 Ramachandran restraints generated. 4993 Oldfield, 0 Emsley, 4993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 962 residues out of total 4128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 958 time to evaluate : 4.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 960 average time/residue: 0.5028 time to fit residues: 799.5589 Evaluate side-chains 703 residues out of total 4128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 702 time to evaluate : 4.575 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.4151 time to fit residues: 7.0518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 493 random chunks: chunk 459 optimal weight: 4.9990 chunk 53 optimal weight: 0.9990 chunk 271 optimal weight: 4.9990 chunk 348 optimal weight: 5.9990 chunk 269 optimal weight: 20.0000 chunk 401 optimal weight: 2.9990 chunk 266 optimal weight: 9.9990 chunk 475 optimal weight: 5.9990 chunk 297 optimal weight: 8.9990 chunk 289 optimal weight: 6.9990 chunk 219 optimal weight: 0.8980 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 274 ASN ** A 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 383 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 274 ASN ** B 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 417 ASN ** C 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 274 ASN ** C 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 150 HIS ** D 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 274 ASN ** D 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 380 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 209 GLN ** E 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 383 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 274 ASN ** F 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 274 ASN H 291 HIS ** I 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 60 ASN L 60 ASN L 75 GLN M 137 GLN N 46 GLN ** N 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.6102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.109 40657 Z= 0.268 Angle : 0.723 10.998 55071 Z= 0.362 Chirality : 0.045 0.224 5917 Planarity : 0.005 0.084 7264 Dihedral : 5.824 42.706 5490 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 20.77 Ramachandran Plot: Outliers : 0.34 % Allowed : 10.57 % Favored : 89.08 % Rotamer Outliers : 0.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.43 % Cis-general : 0.00 % Twisted Proline : 0.43 % Twisted General : 0.10 % 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: -2.26 (0.12), residues: 4993 helix: -0.26 (0.11), residues: 2142 sheet: -2.39 (0.22), residues: 408 loop : -2.54 (0.12), residues: 2443 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9986 Ramachandran restraints generated. 4993 Oldfield, 0 Emsley, 4993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9986 Ramachandran restraints generated. 4993 Oldfield, 0 Emsley, 4993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 890 residues out of total 4128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 883 time to evaluate : 4.698 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 1 residues processed: 888 average time/residue: 0.5068 time to fit residues: 741.6146 Evaluate side-chains 663 residues out of total 4128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 662 time to evaluate : 4.443 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.3965 time to fit residues: 6.7933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 493 random chunks: chunk 293 optimal weight: 0.9980 chunk 189 optimal weight: 5.9990 chunk 283 optimal weight: 6.9990 chunk 143 optimal weight: 0.9990 chunk 93 optimal weight: 4.9990 chunk 92 optimal weight: 9.9990 chunk 302 optimal weight: 1.9990 chunk 323 optimal weight: 9.9990 chunk 234 optimal weight: 0.5980 chunk 44 optimal weight: 10.0000 chunk 373 optimal weight: 7.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 274 ASN ** A 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 383 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 274 ASN ** B 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 181 ASN ** C 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 274 ASN ** C 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 380 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 383 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 83 HIS ** F 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 209 GLN ** G 383 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 274 ASN ** H 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 383 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 60 ASN L 60 ASN ** N 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.6253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.097 40657 Z= 0.227 Angle : 0.711 10.691 55071 Z= 0.354 Chirality : 0.045 0.226 5917 Planarity : 0.004 0.085 7264 Dihedral : 5.689 41.411 5490 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 19.66 Ramachandran Plot: Outliers : 0.32 % Allowed : 10.07 % Favored : 89.61 % Rotamer Outliers : 0.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.43 % Cis-general : 0.00 % Twisted Proline : 0.43 % Twisted General : 0.04 % 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: -2.10 (0.12), residues: 4993 helix: -0.19 (0.11), residues: 2127 sheet: -1.86 (0.28), residues: 264 loop : -2.47 (0.12), residues: 2602 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9986 Ramachandran restraints generated. 4993 Oldfield, 0 Emsley, 4993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9986 Ramachandran restraints generated. 4993 Oldfield, 0 Emsley, 4993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 927 residues out of total 4128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 923 time to evaluate : 4.983 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 0 residues processed: 927 average time/residue: 0.4997 time to fit residues: 770.4542 Evaluate side-chains 700 residues out of total 4128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 700 time to evaluate : 4.902 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 6.4248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 493 random chunks: chunk 432 optimal weight: 10.0000 chunk 455 optimal weight: 9.9990 chunk 415 optimal weight: 9.9990 chunk 442 optimal weight: 0.0770 chunk 266 optimal weight: 9.9990 chunk 192 optimal weight: 8.9990 chunk 347 optimal weight: 8.9990 chunk 135 optimal weight: 7.9990 chunk 400 optimal weight: 5.9990 chunk 418 optimal weight: 0.5980 chunk 441 optimal weight: 7.9990 overall best weight: 4.5344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 274 ASN ** A 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 383 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 274 ASN ** B 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 274 ASN ** C 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 83 HIS ** D 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 274 ASN ** D 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 380 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 426 GLN ** D 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 146 GLN E 209 GLN E 291 HIS E 324 HIS ** E 383 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 274 ASN ** F 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 83 HIS ** G 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 274 ASN ** H 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 291 HIS ** H 383 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 60 ASN L 60 ASN M 58 GLN ** N 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 137 GLN ** O 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 178 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.6336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.128 40657 Z= 0.348 Angle : 0.783 10.849 55071 Z= 0.395 Chirality : 0.047 0.219 5917 Planarity : 0.005 0.088 7264 Dihedral : 5.931 40.912 5490 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 22.78 Ramachandran Plot: Outliers : 0.32 % Allowed : 11.42 % Favored : 88.26 % Rotamer Outliers : 0.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.43 % Cis-general : 0.00 % Twisted Proline : 0.43 % Twisted General : 0.15 % 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: -2.28 (0.12), residues: 4993 helix: -0.31 (0.11), residues: 2122 sheet: -2.35 (0.22), residues: 408 loop : -2.50 (0.12), residues: 2463 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9986 Ramachandran restraints generated. 4993 Oldfield, 0 Emsley, 4993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9986 Ramachandran restraints generated. 4993 Oldfield, 0 Emsley, 4993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 837 residues out of total 4128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 831 time to evaluate : 4.691 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 0 residues processed: 836 average time/residue: 0.4988 time to fit residues: 686.6415 Evaluate side-chains 635 residues out of total 4128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 635 time to evaluate : 4.942 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 6.4923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 493 random chunks: chunk 290 optimal weight: 0.8980 chunk 468 optimal weight: 2.9990 chunk 285 optimal weight: 0.9990 chunk 222 optimal weight: 6.9990 chunk 325 optimal weight: 4.9990 chunk 491 optimal weight: 20.0000 chunk 452 optimal weight: 6.9990 chunk 391 optimal weight: 8.9990 chunk 40 optimal weight: 6.9990 chunk 302 optimal weight: 7.9990 chunk 239 optimal weight: 0.7980 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 274 ASN ** A 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 383 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 274 ASN B 284 ASN ** B 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 181 ASN C 274 ASN ** C 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 380 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 383 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 274 ASN ** F 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 383 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 274 ASN ** H 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 291 HIS ** H 383 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 60 ASN L 137 GLN M 58 GLN ** N 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 152 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.6481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.097 40657 Z= 0.237 Angle : 0.727 10.834 55071 Z= 0.362 Chirality : 0.045 0.213 5917 Planarity : 0.005 0.091 7264 Dihedral : 5.753 39.820 5490 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 20.10 Ramachandran Plot: Outliers : 0.32 % Allowed : 10.25 % Favored : 89.43 % Rotamer Outliers : 0.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.43 % Cis-general : 0.00 % Twisted Proline : 0.43 % Twisted General : 0.04 % 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: -2.08 (0.12), residues: 4993 helix: -0.13 (0.11), residues: 2096 sheet: -2.14 (0.23), residues: 376 loop : -2.41 (0.12), residues: 2521 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9986 Ramachandran restraints generated. 4993 Oldfield, 0 Emsley, 4993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9986 Ramachandran restraints generated. 4993 Oldfield, 0 Emsley, 4993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 868 residues out of total 4128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 862 time to evaluate : 4.322 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 0 residues processed: 865 average time/residue: 0.5042 time to fit residues: 727.4811 Evaluate side-chains 663 residues out of total 4128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 663 time to evaluate : 5.041 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 6.4948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 493 random chunks: chunk 310 optimal weight: 8.9990 chunk 416 optimal weight: 9.9990 chunk 119 optimal weight: 8.9990 chunk 360 optimal weight: 20.0000 chunk 57 optimal weight: 5.9990 chunk 108 optimal weight: 9.9990 chunk 391 optimal weight: 6.9990 chunk 163 optimal weight: 3.9990 chunk 402 optimal weight: 20.0000 chunk 49 optimal weight: 4.9990 chunk 72 optimal weight: 10.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 150 HIS A 274 ASN ** A 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 383 HIS ** A 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 274 ASN ** B 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 417 ASN ** B 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 146 GLN C 274 ASN ** C 383 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 274 ASN ** D 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 146 GLN ** E 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 209 GLN ** E 383 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 274 ASN ** F 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 150 HIS ** H 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 274 ASN ** H 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 291 HIS ** H 383 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 60 ASN L 60 ASN M 86 GLN ** N 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 152 GLN ** O 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 59 GLN P 67 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.145376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.111136 restraints weight = 85749.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.113841 restraints weight = 49472.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.115571 restraints weight = 34212.853| |-----------------------------------------------------------------------------| r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.6549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.149 40657 Z= 0.453 Angle : 0.852 12.499 55071 Z= 0.436 Chirality : 0.050 0.234 5917 Planarity : 0.005 0.089 7264 Dihedral : 6.214 39.731 5490 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 24.35 Ramachandran Plot: Outliers : 0.38 % Allowed : 12.54 % Favored : 87.08 % Rotamer Outliers : 0.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.43 % Cis-general : 0.00 % Twisted Proline : 0.43 % Twisted General : 0.13 % 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: -2.46 (0.11), residues: 4993 helix: -0.59 (0.11), residues: 2105 sheet: -2.35 (0.22), residues: 424 loop : -2.47 (0.12), residues: 2464 =============================================================================== Job complete usr+sys time: 12100.98 seconds wall clock time: 218 minutes 12.53 seconds (13092.53 seconds total)