Starting phenix.real_space_refine on Tue Apr 16 16:00:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6smh_10235/04_2024/6smh_10235_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6smh_10235/04_2024/6smh_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_10235/04_2024/6smh_10235.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6smh_10235/04_2024/6smh_10235.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6smh_10235/04_2024/6smh_10235_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6smh_10235/04_2024/6smh_10235_neut.pdb" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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 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. 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: 0.19s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/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: 21.53, per 1000 atoms: 0.54 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: 16.17 Conformation dependent library (CDL) restraints added in 7.3 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: 4.42 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: 13.65 Time building geometry restraints manager: 17.39 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 Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.890 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: 5.610 Check model and map are aligned: 0.600 Set scattering table: 0.380 Process input model: 102.090 Find NCS groups from input model: 2.790 Set up NCS constraints: 0.240 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 115.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 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 : 54.32 Ramachandran Plot: Outliers : 2.20 % Allowed : 11.96 % Favored : 85.84 % Rotamer: Outliers : 14.61 % Allowed : 9.71 % Favored : 75.68 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP M 28 HIS 0.020 0.002 HIS B 295 PHE 0.034 0.003 PHE I 131 TYR 0.027 0.003 TYR J 69 ARG 0.015 0.001 ARG I 82 *********************** 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 : 4.269 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 REVERT: A 26 TYR cc_start: 0.7885 (t80) cc_final: 0.6973 (t80) REVERT: A 146 GLN cc_start: 0.8718 (tp40) cc_final: 0.8481 (tp-100) REVERT: A 155 GLU cc_start: 0.7930 (tt0) cc_final: 0.7695 (tt0) REVERT: A 184 ARG cc_start: 0.8302 (mtt180) cc_final: 0.8100 (mtp180) REVERT: A 250 ARG cc_start: 0.8400 (mtt180) cc_final: 0.8154 (mtm-85) REVERT: A 255 LYS cc_start: 0.9274 (tmtt) cc_final: 0.8531 (tptp) REVERT: A 321 ASP cc_start: 0.8143 (m-30) cc_final: 0.7740 (m-30) REVERT: A 336 LYS cc_start: 0.9182 (tttm) cc_final: 0.8941 (tptt) REVERT: B 122 PHE cc_start: 0.7928 (OUTLIER) cc_final: 0.7721 (m-80) REVERT: B 184 ARG cc_start: 0.8109 (mtt180) cc_final: 0.7773 (mtt180) REVERT: B 197 THR cc_start: 0.8943 (p) cc_final: 0.8740 (p) REVERT: B 229 THR cc_start: 0.8209 (p) cc_final: 0.7978 (t) REVERT: B 250 ARG cc_start: 0.8708 (mtt180) cc_final: 0.8253 (mtm-85) REVERT: B 255 LYS cc_start: 0.9265 (tmtt) cc_final: 0.8632 (tptp) REVERT: B 321 ASP cc_start: 0.8440 (m-30) cc_final: 0.8188 (m-30) REVERT: B 389 GLU cc_start: 0.8284 (OUTLIER) cc_final: 0.7772 (pt0) REVERT: B 390 ILE cc_start: 0.9296 (OUTLIER) cc_final: 0.9093 (mm) REVERT: C 26 TYR cc_start: 0.7763 (t80) cc_final: 0.7153 (t80) REVERT: C 75 ASP cc_start: 0.8187 (t0) cc_final: 0.7885 (t0) REVERT: C 76 ARG cc_start: 0.8507 (OUTLIER) cc_final: 0.8107 (ttp80) REVERT: C 91 GLU cc_start: 0.7110 (OUTLIER) cc_final: 0.6861 (tm-30) REVERT: C 180 LYS cc_start: 0.7977 (OUTLIER) cc_final: 0.7581 (tppp) REVERT: C 237 LEU cc_start: 0.6946 (OUTLIER) cc_final: 0.6528 (tt) REVERT: C 240 THR cc_start: 0.9065 (m) cc_final: 0.8766 (m) REVERT: C 259 MET cc_start: 0.9131 (mmp) cc_final: 0.8886 (mmp) REVERT: C 281 CYS cc_start: 0.8695 (m) cc_final: 0.8459 (m) REVERT: C 301 GLN cc_start: 0.8842 (mm-40) cc_final: 0.8494 (mm-40) REVERT: C 321 ASP cc_start: 0.8127 (m-30) cc_final: 0.7821 (m-30) REVERT: C 331 LYS cc_start: 0.7850 (OUTLIER) cc_final: 0.7313 (mmmt) REVERT: C 363 GLN cc_start: 0.8659 (OUTLIER) cc_final: 0.8236 (pm20) REVERT: C 380 HIS cc_start: 0.7240 (OUTLIER) cc_final: 0.6529 (p-80) REVERT: C 382 TRP cc_start: 0.7154 (OUTLIER) cc_final: 0.6189 (m100) REVERT: C 425 VAL cc_start: 0.8863 (t) cc_final: 0.8651 (t) REVERT: C 459 TRP cc_start: 0.7318 (m-90) cc_final: 0.7023 (m-90) REVERT: D 26 TYR cc_start: 0.7975 (t80) cc_final: 0.6986 (t80) REVERT: D 57 GLU cc_start: 0.8300 (tp30) cc_final: 0.7816 (mm-30) REVERT: D 67 TRP cc_start: 0.7786 (p-90) cc_final: 0.7485 (p-90) REVERT: D 146 GLN cc_start: 0.8706 (tp40) cc_final: 0.8447 (tp-100) REVERT: D 162 TYR cc_start: 0.7972 (m-10) cc_final: 0.6987 (m-10) REVERT: D 206 GLN cc_start: 0.8148 (OUTLIER) cc_final: 0.7848 (mt0) REVERT: D 249 LYS cc_start: 0.9464 (OUTLIER) cc_final: 0.9115 (ttpp) REVERT: D 259 MET cc_start: 0.8959 (mmp) cc_final: 0.8737 (mmm) REVERT: D 331 LYS cc_start: 0.7847 (OUTLIER) cc_final: 0.6691 (mmmt) REVERT: D 365 TRP cc_start: 0.9367 (m100) cc_final: 0.8730 (m100) REVERT: D 428 ARG cc_start: 0.8746 (OUTLIER) cc_final: 0.8544 (tmm-80) REVERT: E 26 TYR cc_start: 0.7815 (t80) cc_final: 0.6948 (t80) REVERT: E 67 TRP cc_start: 0.7907 (p-90) cc_final: 0.7669 (p-90) REVERT: E 76 ARG cc_start: 0.7985 (ttt-90) cc_final: 0.7500 (ttt90) REVERT: E 81 CYS cc_start: 0.7311 (t) cc_final: 0.7073 (t) REVERT: E 133 GLU cc_start: 0.8362 (tp30) cc_final: 0.7400 (tp30) REVERT: E 134 ASP cc_start: 0.7315 (m-30) cc_final: 0.6966 (m-30) REVERT: E 180 LYS cc_start: 0.8873 (mmmt) cc_final: 0.8408 (mmmt) REVERT: E 191 ARG cc_start: 0.8506 (OUTLIER) cc_final: 0.7908 (ttp-110) REVERT: E 205 SER cc_start: 0.8615 (t) cc_final: 0.8288 (t) REVERT: E 237 LEU cc_start: 0.8715 (OUTLIER) cc_final: 0.8198 (tt) REVERT: E 279 LYS cc_start: 0.9303 (OUTLIER) cc_final: 0.8929 (ttmm) REVERT: E 282 ARG cc_start: 0.8300 (OUTLIER) cc_final: 0.7773 (tpp80) REVERT: E 360 PHE cc_start: 0.7313 (m-80) cc_final: 0.6998 (m-80) REVERT: F 26 TYR cc_start: 0.7659 (t80) cc_final: 0.6858 (t80) REVERT: F 81 CYS cc_start: 0.7215 (t) cc_final: 0.6963 (t) REVERT: F 133 GLU cc_start: 0.8238 (tp30) cc_final: 0.7164 (tp30) REVERT: F 141 LEU cc_start: 0.8883 (tp) cc_final: 0.8673 (tt) REVERT: F 210 ARG cc_start: 0.7727 (OUTLIER) cc_final: 0.6568 (mmt-90) REVERT: F 248 MET cc_start: 0.6111 (OUTLIER) cc_final: 0.4717 (mtm) REVERT: F 277 LEU cc_start: 0.9456 (tp) cc_final: 0.9140 (mm) REVERT: F 321 ASP cc_start: 0.8528 (m-30) cc_final: 0.8107 (m-30) REVERT: F 354 ASP cc_start: 0.7921 (t0) cc_final: 0.6659 (t0) REVERT: F 360 PHE cc_start: 0.7671 (m-10) cc_final: 0.7470 (m-80) REVERT: F 368 MET cc_start: 0.8360 (ttt) cc_final: 0.8147 (ttt) REVERT: F 444 GLU cc_start: 0.9163 (OUTLIER) cc_final: 0.8658 (pp20) REVERT: G 30 ASP cc_start: 0.8270 (OUTLIER) cc_final: 0.7768 (t0) REVERT: G 57 GLU cc_start: 0.8365 (tp30) cc_final: 0.8030 (mm-30) REVERT: G 146 GLN cc_start: 0.8750 (tp40) cc_final: 0.8419 (tp-100) REVERT: G 197 THR cc_start: 0.8924 (p) cc_final: 0.8672 (p) REVERT: G 315 LEU cc_start: 0.9371 (tp) cc_final: 0.9062 (tt) REVERT: G 321 ASP cc_start: 0.8297 (m-30) cc_final: 0.7692 (m-30) REVERT: G 331 LYS cc_start: 0.7328 (OUTLIER) cc_final: 0.6858 (mmmt) REVERT: G 363 GLN cc_start: 0.8775 (OUTLIER) cc_final: 0.8322 (pm20) REVERT: G 434 LEU cc_start: 0.8423 (tt) cc_final: 0.7534 (mp) REVERT: G 441 ILE cc_start: 0.8780 (OUTLIER) cc_final: 0.8433 (mm) REVERT: G 443 ARG cc_start: 0.8592 (OUTLIER) cc_final: 0.7791 (ttt-90) REVERT: G 444 GLU cc_start: 0.9225 (OUTLIER) cc_final: 0.8984 (pp20) REVERT: H 106 GLU cc_start: 0.8433 (tt0) cc_final: 0.7916 (tt0) REVERT: H 146 GLN cc_start: 0.8610 (tp40) cc_final: 0.8320 (tp-100) REVERT: H 184 ARG cc_start: 0.8125 (mmt90) cc_final: 0.7387 (mpt180) REVERT: H 255 LYS cc_start: 0.9206 (tmtt) cc_final: 0.8413 (tptp) REVERT: H 259 MET cc_start: 0.8669 (mmp) cc_final: 0.8387 (mmm) REVERT: H 301 GLN cc_start: 0.8892 (mm-40) cc_final: 0.8638 (mm-40) REVERT: H 321 ASP cc_start: 0.8378 (m-30) cc_final: 0.8137 (m-30) REVERT: H 465 GLU cc_start: 0.7815 (OUTLIER) cc_final: 0.7369 (pm20) REVERT: I 110 LEU cc_start: 0.6806 (OUTLIER) cc_final: 0.6485 (mp) REVERT: J 58 GLN cc_start: 0.8299 (pm20) cc_final: 0.6902 (tt0) REVERT: J 60 ASN cc_start: 0.6852 (t160) cc_final: 0.6520 (t0) REVERT: J 112 LEU cc_start: 0.6042 (OUTLIER) cc_final: 0.5554 (mt) REVERT: J 113 GLU cc_start: 0.2851 (OUTLIER) cc_final: 0.1994 (mm-30) REVERT: J 114 ARG cc_start: 0.5584 (tpt90) cc_final: 0.4399 (mpt180) REVERT: J 163 LEU cc_start: 0.7890 (OUTLIER) cc_final: 0.7609 (mp) REVERT: K 28 TRP cc_start: 0.6897 (t60) cc_final: 0.6454 (t60) REVERT: K 66 MET cc_start: 0.7665 (tmm) cc_final: 0.7135 (tmm) REVERT: K 97 ARG cc_start: 0.6387 (mtm-85) cc_final: 0.5361 (mtm-85) REVERT: K 98 GLU cc_start: 0.6072 (OUTLIER) cc_final: 0.5545 (tt0) REVERT: K 114 ARG cc_start: 0.5908 (tpt170) cc_final: 0.4788 (mtt-85) REVERT: K 187 GLU cc_start: 0.7629 (OUTLIER) cc_final: 0.7038 (pm20) REVERT: K 191 LEU cc_start: 0.7158 (OUTLIER) cc_final: 0.6421 (mt) REVERT: L 27 ARG cc_start: 0.7930 (mpt-90) cc_final: 0.7637 (mpp80) REVERT: L 55 GLU cc_start: 0.6812 (OUTLIER) cc_final: 0.6358 (mt-10) REVERT: L 58 GLN cc_start: 0.8317 (OUTLIER) cc_final: 0.6750 (tt0) REVERT: L 59 GLN cc_start: 0.7124 (OUTLIER) cc_final: 0.6870 (tt0) REVERT: L 60 ASN cc_start: 0.7093 (OUTLIER) cc_final: 0.6675 (t0) REVERT: L 72 ILE cc_start: 0.8292 (pp) cc_final: 0.8057 (tt) REVERT: L 86 GLN cc_start: 0.6676 (OUTLIER) cc_final: 0.6466 (mm-40) REVERT: L 97 ARG cc_start: 0.6098 (mtm180) cc_final: 0.5298 (ptt90) REVERT: L 98 GLU cc_start: 0.6855 (OUTLIER) cc_final: 0.5735 (tp30) REVERT: L 102 GLU cc_start: 0.6854 (mt-10) cc_final: 0.6566 (tp30) REVERT: L 106 LEU cc_start: 0.8462 (mp) cc_final: 0.8081 (mt) REVERT: L 113 GLU cc_start: 0.7017 (pt0) cc_final: 0.6406 (tp30) REVERT: L 139 GLU cc_start: 0.7358 (tt0) cc_final: 0.7023 (pm20) REVERT: L 158 GLN cc_start: 0.5184 (OUTLIER) cc_final: 0.4546 (tp40) REVERT: L 168 ARG cc_start: 0.5480 (tpt170) cc_final: 0.5276 (tpp-160) REVERT: L 172 ARG cc_start: 0.5056 (OUTLIER) cc_final: 0.4495 (tpp-160) REVERT: M 27 ARG cc_start: 0.7861 (mpt-90) cc_final: 0.7238 (mpp80) REVERT: M 58 GLN cc_start: 0.8124 (OUTLIER) cc_final: 0.6866 (tt0) REVERT: M 87 GLU cc_start: 0.4943 (OUTLIER) cc_final: 0.4703 (tp30) REVERT: M 113 GLU cc_start: 0.6725 (pt0) cc_final: 0.6278 (tp30) REVERT: M 139 GLU cc_start: 0.7695 (tt0) cc_final: 0.6882 (pp20) REVERT: M 160 ARG cc_start: 0.7506 (mmt-90) cc_final: 0.6989 (ptt-90) REVERT: N 27 ARG cc_start: 0.8060 (mpt-90) cc_final: 0.7318 (mpp80) REVERT: N 49 PHE cc_start: 0.7456 (t80) cc_final: 0.6994 (t80) REVERT: N 60 ASN cc_start: 0.7258 (t160) cc_final: 0.6903 (t0) REVERT: N 66 MET cc_start: 0.8317 (tmm) cc_final: 0.8114 (tmm) REVERT: N 122 ARG cc_start: 0.6172 (ttp80) cc_final: 0.4223 (ttp80) REVERT: N 172 ARG cc_start: 0.8444 (OUTLIER) cc_final: 0.7493 (tpm170) REVERT: O 27 ARG cc_start: 0.8100 (mpt-90) cc_final: 0.7771 (mpt-90) REVERT: O 60 ASN cc_start: 0.7071 (t160) cc_final: 0.6623 (t0) REVERT: O 64 VAL cc_start: 0.9281 (p) cc_final: 0.8856 (t) REVERT: O 110 LEU cc_start: 0.6023 (OUTLIER) cc_final: 0.5503 (tm) REVERT: O 114 ARG cc_start: 0.5442 (OUTLIER) cc_final: 0.5191 (tpp-160) REVERT: P 13 GLU cc_start: 0.6989 (pp20) cc_final: 0.4217 (mp0) REVERT: P 14 ARG cc_start: 0.6028 (OUTLIER) cc_final: 0.4707 (tpt-90) REVERT: P 122 ARG cc_start: 0.5964 (ttp80) cc_final: 0.4483 (ttp80) REVERT: P 155 ARG cc_start: 0.4603 (OUTLIER) cc_final: 0.3923 (mtp85) REVERT: P 165 GLU cc_start: 0.6875 (mm-30) cc_final: 0.6412 (pt0) outliers start: 603 outliers final: 366 residues processed: 1898 average time/residue: 0.6380 time to fit residues: 1906.0706 Evaluate side-chains 1279 residues out of total 4128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 417 poor density : 862 time to evaluate : 4.528 ------------------------------------------------------------------------------- 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: 6.9990 chunk 373 optimal weight: 6.9990 chunk 207 optimal weight: 6.9990 chunk 127 optimal weight: 2.9990 chunk 252 optimal weight: 0.9980 chunk 199 optimal weight: 3.9990 chunk 386 optimal weight: 6.9990 chunk 149 optimal weight: 1.9990 chunk 234 optimal weight: 1.9990 chunk 287 optimal weight: 2.9990 chunk 447 optimal weight: 10.0000 overall best weight: 2.1988 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 417 ASN C 112 ASN C 146 GLN C 209 GLN ** C 235 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 324 HIS ** C 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 112 ASN D 146 GLN ** D 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 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** E 83 HIS E 112 ASN E 160 ASN E 202 ASN ** E 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 226 GLN ** E 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 417 ASN F 83 HIS F 112 ASN F 150 HIS F 160 ASN ** F 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 274 ASN F 324 HIS G 83 HIS G 112 ASN G 146 GLN ** G 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 202 ASN ** G 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 206 GLN ** G 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 426 GLN H 112 ASN H 146 GLN 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 75 GLN L 86 GLN L 175 GLN M 46 GLN M 86 GLN N 67 GLN ** O 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 152 GLN Total number of N/Q/H flips: 44 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.4026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.203 40657 Z= 0.295 Angle : 0.806 12.057 55071 Z= 0.412 Chirality : 0.048 0.377 5917 Planarity : 0.006 0.134 7264 Dihedral : 6.978 170.791 5490 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 22.80 Ramachandran Plot: Outliers : 0.34 % Allowed : 9.47 % Favored : 90.19 % Rotamer: Outliers : 0.29 % Allowed : 5.06 % Favored : 94.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.43 % Cis-general : 0.00 % Twisted Proline : 0.43 % Twisted General : 0.25 % 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: -3.47 (0.10), residues: 4993 helix: -1.38 (0.10), residues: 2118 sheet: -2.68 (0.22), residues: 392 loop : -3.13 (0.11), residues: 2483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP M 28 HIS 0.012 0.001 HIS J 144 PHE 0.035 0.003 PHE L 176 TYR 0.022 0.002 TYR G 236 ARG 0.019 0.001 ARG L 155 *********************** 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 1248 residues out of total 4128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 1236 time to evaluate : 4.763 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: A 22 TYR cc_start: 0.7331 (m-80) cc_final: 0.6589 (m-80) REVERT: A 26 TYR cc_start: 0.7502 (t80) cc_final: 0.6860 (t80) REVERT: A 67 TRP cc_start: 0.7320 (p-90) cc_final: 0.6515 (p-90) REVERT: A 106 GLU cc_start: 0.8262 (tt0) cc_final: 0.7597 (tt0) REVERT: A 130 LEU cc_start: 0.9282 (tp) cc_final: 0.9080 (tp) REVERT: A 157 ASP cc_start: 0.9046 (m-30) cc_final: 0.8670 (m-30) REVERT: A 228 GLU cc_start: 0.8762 (tm-30) cc_final: 0.8551 (tm-30) REVERT: A 246 GLU cc_start: 0.8494 (tp30) cc_final: 0.8118 (tp30) REVERT: A 248 MET cc_start: 0.8705 (mmp) cc_final: 0.8423 (mmt) REVERT: A 284 ASN cc_start: 0.8845 (t0) cc_final: 0.8571 (t0) REVERT: A 331 LYS cc_start: 0.7676 (mtpp) cc_final: 0.7397 (mmmt) REVERT: A 344 ASP cc_start: 0.8258 (t70) cc_final: 0.7991 (t0) REVERT: A 422 GLU cc_start: 0.8031 (pt0) cc_final: 0.7454 (mm-30) REVERT: A 424 CYS cc_start: 0.9105 (m) cc_final: 0.7936 (t) REVERT: A 432 ARG cc_start: 0.7141 (mtp180) cc_final: 0.6871 (ptp-170) REVERT: B 34 LEU cc_start: 0.7869 (tp) cc_final: 0.7219 (tp) REVERT: B 205 SER cc_start: 0.8227 (t) cc_final: 0.7982 (p) REVERT: B 248 MET cc_start: 0.6537 (mtt) cc_final: 0.6233 (mpp) REVERT: B 259 MET cc_start: 0.9021 (mmp) cc_final: 0.8473 (mmt) REVERT: B 321 ASP cc_start: 0.8233 (m-30) cc_final: 0.8007 (m-30) REVERT: B 331 LYS cc_start: 0.7303 (mtpp) cc_final: 0.7058 (mmmt) REVERT: C 67 TRP cc_start: 0.7900 (p-90) cc_final: 0.7669 (p-90) REVERT: C 106 GLU cc_start: 0.8095 (tt0) cc_final: 0.7784 (tt0) REVERT: C 125 LYS cc_start: 0.7675 (mmpt) cc_final: 0.6796 (pttm) REVERT: C 247 MET cc_start: 0.8591 (tpp) cc_final: 0.8048 (tpp) REVERT: C 291 HIS cc_start: 0.8954 (t-90) cc_final: 0.7967 (t-90) REVERT: C 344 ASP cc_start: 0.8608 (t0) cc_final: 0.8030 (t0) REVERT: C 408 TRP cc_start: 0.7971 (m100) cc_final: 0.7627 (t-100) REVERT: D 22 TYR cc_start: 0.7512 (m-80) cc_final: 0.7030 (m-80) REVERT: D 26 TYR cc_start: 0.7698 (t80) cc_final: 0.7256 (t80) REVERT: D 57 GLU cc_start: 0.8310 (tp30) cc_final: 0.7901 (mm-30) REVERT: D 157 ASP cc_start: 0.9152 (m-30) cc_final: 0.8935 (m-30) REVERT: D 162 TYR cc_start: 0.7939 (m-10) cc_final: 0.7486 (m-10) REVERT: D 197 THR cc_start: 0.8828 (p) cc_final: 0.8599 (p) REVERT: D 226 GLN cc_start: 0.9029 (tt0) cc_final: 0.8746 (tt0) REVERT: D 246 GLU cc_start: 0.8666 (tp30) cc_final: 0.7805 (tm-30) REVERT: D 247 MET cc_start: 0.8964 (ttm) cc_final: 0.8356 (tmm) REVERT: D 281 CYS cc_start: 0.9291 (m) cc_final: 0.8949 (m) REVERT: D 344 ASP cc_start: 0.7837 (t0) cc_final: 0.7605 (t0) REVERT: D 452 LEU cc_start: 0.9002 (tp) cc_final: 0.8761 (tp) REVERT: E 22 TYR cc_start: 0.7488 (m-80) cc_final: 0.6802 (m-80) REVERT: E 26 TYR cc_start: 0.7973 (t80) cc_final: 0.6957 (t80) REVERT: E 30 ASP cc_start: 0.8047 (p0) cc_final: 0.7786 (p0) REVERT: E 91 GLU cc_start: 0.7915 (tt0) cc_final: 0.7702 (tt0) REVERT: E 92 ASN cc_start: 0.6927 (p0) cc_final: 0.6711 (p0) REVERT: E 125 LYS cc_start: 0.7966 (mmpt) cc_final: 0.7012 (pttm) REVERT: E 146 GLN cc_start: 0.9090 (tt0) cc_final: 0.8774 (tp40) REVERT: E 184 ARG cc_start: 0.8280 (mtt90) cc_final: 0.7898 (mtt90) REVERT: E 205 SER cc_start: 0.8191 (t) cc_final: 0.7919 (t) REVERT: E 255 LYS cc_start: 0.9196 (tmtt) cc_final: 0.8976 (tptm) REVERT: E 284 ASN cc_start: 0.9059 (t0) cc_final: 0.8471 (t0) REVERT: E 328 VAL cc_start: 0.8868 (m) cc_final: 0.8656 (p) REVERT: E 422 GLU cc_start: 0.8034 (tp30) cc_final: 0.7806 (mm-30) REVERT: E 444 GLU cc_start: 0.9113 (OUTLIER) cc_final: 0.8612 (pm20) REVERT: F 22 TYR cc_start: 0.7289 (m-80) cc_final: 0.6647 (m-80) REVERT: F 26 TYR cc_start: 0.7919 (t80) cc_final: 0.6791 (t80) REVERT: F 30 ASP cc_start: 0.7845 (p0) cc_final: 0.7360 (p0) REVERT: F 81 CYS cc_start: 0.6288 (t) cc_final: 0.5954 (t) REVERT: F 133 GLU cc_start: 0.8081 (tp30) cc_final: 0.7432 (tp30) REVERT: F 177 LEU cc_start: 0.8754 (mm) cc_final: 0.8491 (mm) REVERT: F 291 HIS cc_start: 0.8423 (t-90) cc_final: 0.7690 (t-90) REVERT: F 344 ASP cc_start: 0.8259 (t0) cc_final: 0.7305 (t0) REVERT: F 351 ILE cc_start: 0.9640 (mp) cc_final: 0.9429 (mp) REVERT: G 22 TYR cc_start: 0.7648 (m-80) cc_final: 0.6934 (m-80) REVERT: G 34 LEU cc_start: 0.8554 (tp) cc_final: 0.7722 (tt) REVERT: G 57 GLU cc_start: 0.8366 (tp30) cc_final: 0.8051 (mm-30) REVERT: G 67 TRP cc_start: 0.6982 (p-90) cc_final: 0.6381 (p-90) REVERT: G 85 GLU cc_start: 0.7936 (tt0) cc_final: 0.7530 (mt-10) REVERT: G 106 GLU cc_start: 0.8330 (tt0) cc_final: 0.7978 (tt0) REVERT: G 133 GLU cc_start: 0.8237 (tp30) cc_final: 0.7957 (tp30) REVERT: G 203 ILE cc_start: 0.9192 (mm) cc_final: 0.8962 (mm) REVERT: G 246 GLU cc_start: 0.8527 (tp30) cc_final: 0.7695 (tm-30) REVERT: G 363 GLN cc_start: 0.8869 (pp30) cc_final: 0.8427 (pp30) REVERT: G 424 CYS cc_start: 0.9129 (m) cc_final: 0.7762 (t) REVERT: G 430 GLU cc_start: 0.7859 (mt-10) cc_final: 0.7568 (mt-10) REVERT: H 22 TYR cc_start: 0.7062 (m-80) cc_final: 0.6522 (m-80) REVERT: H 184 ARG cc_start: 0.8189 (mmt90) cc_final: 0.7872 (mmt90) REVERT: H 205 SER cc_start: 0.8462 (t) cc_final: 0.8255 (p) REVERT: H 247 MET cc_start: 0.8616 (ttm) cc_final: 0.8022 (mmm) REVERT: H 331 LYS cc_start: 0.7740 (mtpp) cc_final: 0.7344 (mmmt) REVERT: H 382 TRP cc_start: 0.8460 (m100) cc_final: 0.7896 (m100) REVERT: I 179 SER cc_start: 0.4402 (t) cc_final: 0.4000 (t) REVERT: J 66 MET cc_start: 0.8560 (tmm) cc_final: 0.7879 (tmm) REVERT: J 159 GLU cc_start: 0.7543 (mp0) cc_final: 0.6932 (mp0) REVERT: J 175 GLN cc_start: 0.5783 (pp30) cc_final: 0.4051 (mm110) REVERT: K 39 LEU cc_start: 0.8607 (tp) cc_final: 0.8295 (mt) REVERT: K 62 ILE cc_start: 0.8129 (mm) cc_final: 0.7577 (pt) REVERT: K 63 THR cc_start: 0.9189 (m) cc_final: 0.8882 (m) REVERT: K 67 GLN cc_start: 0.6759 (tt0) cc_final: 0.6236 (tt0) REVERT: K 97 ARG cc_start: 0.6405 (mtm-85) cc_final: 0.5451 (mtm-85) REVERT: K 114 ARG cc_start: 0.6594 (tpt170) cc_final: 0.5930 (mtt-85) REVERT: L 27 ARG cc_start: 0.8125 (mpt-90) cc_final: 0.7684 (mpp80) REVERT: L 58 GLN cc_start: 0.8068 (mp10) cc_final: 0.6969 (tt0) REVERT: L 60 ASN cc_start: 0.7010 (t0) cc_final: 0.6711 (t0) REVERT: L 159 GLU cc_start: 0.5252 (tt0) cc_final: 0.4942 (tt0) REVERT: M 27 ARG cc_start: 0.8212 (mpt-90) cc_final: 0.5328 (tpp-160) REVERT: M 66 MET cc_start: 0.6198 (ptm) cc_final: 0.5857 (ppp) REVERT: M 114 ARG cc_start: 0.4510 (tpp80) cc_final: 0.3970 (tpm170) REVERT: M 122 ARG cc_start: 0.7834 (ttp-170) cc_final: 0.7513 (ttm170) REVERT: N 67 GLN cc_start: 0.6896 (tt0) cc_final: 0.6349 (tm-30) REVERT: O 159 GLU cc_start: 0.5954 (tt0) cc_final: 0.5729 (mt-10) REVERT: P 113 GLU cc_start: 0.7113 (tp30) cc_final: 0.6027 (pt0) REVERT: P 159 GLU cc_start: 0.6720 (tt0) cc_final: 0.6459 (mt-10) outliers start: 12 outliers final: 2 residues processed: 1246 average time/residue: 0.5546 time to fit residues: 1106.9219 Evaluate side-chains 837 residues out of total 4128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 834 time to evaluate : 4.718 ------------------------------------------------------------------------------- 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: 8.9990 chunk 138 optimal weight: 8.9990 chunk 372 optimal weight: 0.0010 chunk 304 optimal weight: 8.9990 chunk 123 optimal weight: 2.9990 chunk 448 optimal weight: 8.9990 chunk 484 optimal weight: 9.9990 chunk 399 optimal weight: 9.9990 chunk 444 optimal weight: 30.0000 chunk 152 optimal weight: 1.9990 chunk 359 optimal weight: 8.9990 overall best weight: 4.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 150 HIS ** A 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 83 HIS B 160 ASN ** B 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 417 ASN C 112 ASN ** C 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 235 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 150 HIS D 160 ASN ** D 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 291 HIS D 324 HIS ** 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** E 112 ASN ** E 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 204 ASN E 209 GLN E 291 HIS E 324 HIS ** E 383 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 274 ASN F 301 GLN ** F 383 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 206 GLN H 291 HIS H 324 HIS ** I 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 46 GLN ** J 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 60 ASN ** M 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 152 GLN O 46 GLN O 60 ASN O 101 GLN ** P 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.4858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.166 40657 Z= 0.373 Angle : 0.805 12.760 55071 Z= 0.413 Chirality : 0.048 0.302 5917 Planarity : 0.005 0.068 7264 Dihedral : 6.717 172.570 5490 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 23.33 Ramachandran Plot: Outliers : 0.34 % Allowed : 10.59 % Favored : 89.06 % Rotamer: Outliers : 0.39 % Allowed : 5.43 % Favored : 94.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.43 % Cis-general : 0.00 % Twisted Proline : 0.43 % Twisted General : 0.19 % 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: -2.97 (0.11), residues: 4993 helix: -0.80 (0.11), residues: 2063 sheet: -2.68 (0.22), residues: 456 loop : -2.93 (0.11), residues: 2474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP E 280 HIS 0.014 0.001 HIS P 144 PHE 0.040 0.003 PHE H 464 TYR 0.027 0.002 TYR E 236 ARG 0.007 0.001 ARG G 300 *********************** 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 1037 residues out of total 4128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 1021 time to evaluate : 4.425 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: A 22 TYR cc_start: 0.7613 (m-80) cc_final: 0.6522 (m-80) REVERT: A 26 TYR cc_start: 0.7585 (t80) cc_final: 0.7065 (t80) REVERT: A 106 GLU cc_start: 0.8401 (tt0) cc_final: 0.7793 (tt0) REVERT: A 130 LEU cc_start: 0.9347 (tp) cc_final: 0.9136 (tp) REVERT: A 184 ARG cc_start: 0.8197 (mtp180) cc_final: 0.7821 (mtt180) REVERT: A 246 GLU cc_start: 0.8558 (tp30) cc_final: 0.8204 (tp30) REVERT: A 331 LYS cc_start: 0.7880 (mtpp) cc_final: 0.7376 (mmmt) REVERT: A 382 TRP cc_start: 0.8289 (m100) cc_final: 0.7968 (m-10) REVERT: A 432 ARG cc_start: 0.7726 (mtp180) cc_final: 0.7276 (ptp-170) REVERT: A 440 ASP cc_start: 0.8699 (t0) cc_final: 0.8462 (p0) REVERT: B 34 LEU cc_start: 0.8505 (tp) cc_final: 0.7532 (tp) REVERT: B 122 PHE cc_start: 0.8627 (m-80) cc_final: 0.8421 (m-10) REVERT: B 130 LEU cc_start: 0.9398 (tp) cc_final: 0.9012 (tp) REVERT: B 184 ARG cc_start: 0.8336 (mtp180) cc_final: 0.8054 (mtt-85) REVERT: B 205 SER cc_start: 0.8173 (t) cc_final: 0.7945 (p) REVERT: B 228 GLU cc_start: 0.8834 (tm-30) cc_final: 0.8534 (tm-30) REVERT: B 246 GLU cc_start: 0.8673 (tp30) cc_final: 0.8301 (tp30) REVERT: B 255 LYS cc_start: 0.9424 (tmmt) cc_final: 0.9143 (tptp) REVERT: B 259 MET cc_start: 0.8993 (mmp) cc_final: 0.8776 (mmm) REVERT: C 22 TYR cc_start: 0.7973 (m-80) cc_final: 0.7687 (m-80) REVERT: C 106 GLU cc_start: 0.8361 (tt0) cc_final: 0.7601 (tt0) REVERT: C 184 ARG cc_start: 0.8535 (mmt180) cc_final: 0.8210 (mmt180) REVERT: C 205 SER cc_start: 0.8411 (t) cc_final: 0.7990 (p) REVERT: C 247 MET cc_start: 0.8629 (tpp) cc_final: 0.8061 (tpp) REVERT: C 291 HIS cc_start: 0.8564 (t-90) cc_final: 0.8339 (t-90) REVERT: C 321 ASP cc_start: 0.8219 (m-30) cc_final: 0.7964 (m-30) REVERT: C 364 ASP cc_start: 0.9194 (t0) cc_final: 0.8993 (t0) REVERT: D 22 TYR cc_start: 0.7405 (m-80) cc_final: 0.6896 (m-80) REVERT: D 26 TYR cc_start: 0.7615 (t80) cc_final: 0.7151 (t80) REVERT: D 146 GLN cc_start: 0.8963 (tt0) cc_final: 0.8184 (tp-100) REVERT: D 154 VAL cc_start: 0.9524 (t) cc_final: 0.9290 (t) REVERT: D 157 ASP cc_start: 0.9268 (m-30) cc_final: 0.8903 (m-30) REVERT: D 203 ILE cc_start: 0.9175 (tp) cc_final: 0.8837 (tp) REVERT: D 209 GLN cc_start: 0.8881 (tm-30) cc_final: 0.8416 (tm-30) REVERT: D 228 GLU cc_start: 0.8889 (tm-30) cc_final: 0.8689 (tm-30) REVERT: D 255 LYS cc_start: 0.9287 (tmtt) cc_final: 0.8920 (tptt) REVERT: D 291 HIS cc_start: 0.8348 (t70) cc_final: 0.7916 (t-90) REVERT: D 321 ASP cc_start: 0.8396 (m-30) cc_final: 0.7976 (m-30) REVERT: D 444 GLU cc_start: 0.9029 (OUTLIER) cc_final: 0.8696 (pm20) REVERT: E 22 TYR cc_start: 0.7519 (m-80) cc_final: 0.6607 (m-80) REVERT: E 26 TYR cc_start: 0.7685 (t80) cc_final: 0.6860 (t80) REVERT: E 34 LEU cc_start: 0.8820 (tp) cc_final: 0.8470 (tp) REVERT: E 77 TYR cc_start: 0.8839 (m-10) cc_final: 0.8481 (m-10) REVERT: E 154 VAL cc_start: 0.9345 (t) cc_final: 0.9138 (t) REVERT: E 279 LYS cc_start: 0.9102 (mtpt) cc_final: 0.8867 (ttmm) REVERT: E 291 HIS cc_start: 0.8859 (t70) cc_final: 0.8212 (t-90) REVERT: E 364 ASP cc_start: 0.9274 (t70) cc_final: 0.8986 (t0) REVERT: E 440 ASP cc_start: 0.8815 (t0) cc_final: 0.8381 (t0) REVERT: F 22 TYR cc_start: 0.7486 (m-80) cc_final: 0.6710 (m-80) REVERT: F 26 TYR cc_start: 0.7542 (t80) cc_final: 0.6880 (t80) REVERT: F 85 GLU cc_start: 0.7924 (mt-10) cc_final: 0.7718 (mp0) REVERT: F 246 GLU cc_start: 0.8790 (tp30) cc_final: 0.8509 (tp30) REVERT: F 248 MET cc_start: 0.6466 (mtm) cc_final: 0.5996 (mtm) REVERT: F 294 MET cc_start: 0.8580 (ptt) cc_final: 0.7937 (ppp) REVERT: F 297 VAL cc_start: 0.9509 (m) cc_final: 0.9056 (m) REVERT: F 424 CYS cc_start: 0.9127 (m) cc_final: 0.7773 (t) REVERT: G 22 TYR cc_start: 0.7692 (m-80) cc_final: 0.6915 (m-80) REVERT: G 34 LEU cc_start: 0.8743 (tp) cc_final: 0.8452 (tp) REVERT: G 85 GLU cc_start: 0.8209 (tt0) cc_final: 0.7735 (mt-10) REVERT: G 106 GLU cc_start: 0.8431 (tt0) cc_final: 0.8026 (tt0) REVERT: G 171 ILE cc_start: 0.8903 (mp) cc_final: 0.8653 (tp) REVERT: G 180 LYS cc_start: 0.8532 (mmmm) cc_final: 0.8199 (mmmt) REVERT: G 204 ASN cc_start: 0.7918 (m-40) cc_final: 0.7483 (m-40) REVERT: G 281 CYS cc_start: 0.8886 (m) cc_final: 0.8584 (m) REVERT: G 291 HIS cc_start: 0.8178 (t-90) cc_final: 0.7958 (t-90) REVERT: G 321 ASP cc_start: 0.8223 (m-30) cc_final: 0.7876 (m-30) REVERT: G 346 MET cc_start: 0.9197 (mpp) cc_final: 0.8969 (mpp) REVERT: G 363 GLN cc_start: 0.9014 (pp30) cc_final: 0.8696 (pp30) REVERT: G 364 ASP cc_start: 0.8863 (t70) cc_final: 0.8648 (t0) REVERT: H 22 TYR cc_start: 0.7155 (m-80) cc_final: 0.6551 (m-80) REVERT: H 34 LEU cc_start: 0.8458 (tp) cc_final: 0.8201 (tp) REVERT: H 146 GLN cc_start: 0.8526 (tp-100) cc_final: 0.8218 (tp-100) REVERT: H 154 VAL cc_start: 0.9353 (t) cc_final: 0.9060 (t) REVERT: H 205 SER cc_start: 0.8379 (t) cc_final: 0.7860 (p) REVERT: H 259 MET cc_start: 0.9046 (mmm) cc_final: 0.8816 (mmt) REVERT: H 321 ASP cc_start: 0.8298 (m-30) cc_final: 0.8007 (m-30) REVERT: H 383 HIS cc_start: 0.9019 (m170) cc_final: 0.8312 (m-70) REVERT: I 33 ARG cc_start: 0.6978 (ttt180) cc_final: 0.6157 (tmm160) REVERT: I 60 ASN cc_start: 0.7545 (t0) cc_final: 0.6930 (t0) REVERT: I 179 SER cc_start: 0.4169 (t) cc_final: 0.3746 (t) REVERT: J 104 ARG cc_start: 0.8262 (tmm160) cc_final: 0.8040 (tmm160) REVERT: J 114 ARG cc_start: 0.4598 (mmm160) cc_final: 0.3382 (mmt180) REVERT: J 159 GLU cc_start: 0.7705 (mp0) cc_final: 0.7087 (mp0) REVERT: K 28 TRP cc_start: 0.6843 (t60) cc_final: 0.6364 (t60) REVERT: K 67 GLN cc_start: 0.6547 (tt0) cc_final: 0.6094 (tt0) REVERT: K 97 ARG cc_start: 0.6503 (mtm-85) cc_final: 0.5524 (mtm-85) REVERT: K 114 ARG cc_start: 0.6581 (tpt170) cc_final: 0.5608 (mtt-85) REVERT: K 174 LEU cc_start: 0.5873 (mp) cc_final: 0.5503 (mt) REVERT: K 191 LEU cc_start: 0.7431 (tt) cc_final: 0.7133 (mt) REVERT: L 27 ARG cc_start: 0.8027 (mpt-90) cc_final: 0.7404 (mpp80) REVERT: L 62 ILE cc_start: 0.7779 (mm) cc_final: 0.7422 (mm) REVERT: L 159 GLU cc_start: 0.5589 (mt-10) cc_final: 0.4713 (mp0) REVERT: L 175 GLN cc_start: 0.7735 (mm110) cc_final: 0.7176 (pp30) REVERT: M 28 TRP cc_start: 0.7127 (t60) cc_final: 0.6903 (t60) REVERT: M 114 ARG cc_start: 0.4592 (tpp80) cc_final: 0.3863 (tpm170) REVERT: N 97 ARG cc_start: 0.6126 (mtm-85) cc_final: 0.5332 (mtm-85) REVERT: P 25 GLU cc_start: 0.7635 (tt0) cc_final: 0.7305 (tt0) outliers start: 16 outliers final: 4 residues processed: 1036 average time/residue: 0.5247 time to fit residues: 887.6273 Evaluate side-chains 778 residues out of total 4128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 773 time to evaluate : 4.848 ------------------------------------------------------------------------------- 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: 20.0000 chunk 337 optimal weight: 0.5980 chunk 232 optimal weight: 7.9990 chunk 49 optimal weight: 20.0000 chunk 214 optimal weight: 9.9990 chunk 301 optimal weight: 5.9990 chunk 450 optimal weight: 9.9990 chunk 476 optimal weight: 7.9990 chunk 235 optimal weight: 1.9990 chunk 426 optimal weight: 5.9990 chunk 128 optimal weight: 3.9990 overall best weight: 3.7188 ------------------------------------------------------------------------------- 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 417 ASN ** B 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 204 ASN B 274 ASN ** B 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 83 HIS C 150 HIS C 209 GLN ** C 235 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 274 ASN ** C 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 274 ASN ** 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 ** D 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 209 GLN ** E 295 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 301 GLN ** F 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 383 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 417 ASN ** G 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 417 ASN H 206 GLN ** H 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 417 ASN I 58 GLN ** J 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 60 ASN ** L 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 175 GLN N 46 GLN N 86 GLN O 60 ASN O 86 GLN ** P 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.5240 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= 0.313 Angle : 0.732 10.171 55071 Z= 0.372 Chirality : 0.046 0.275 5917 Planarity : 0.005 0.083 7264 Dihedral : 6.504 176.720 5490 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 21.02 Ramachandran Plot: Outliers : 0.34 % Allowed : 10.23 % Favored : 89.43 % Rotamer: Outliers : 0.02 % Allowed : 5.21 % Favored : 94.77 % 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: -2.68 (0.11), residues: 4993 helix: -0.48 (0.11), residues: 2066 sheet: -2.59 (0.21), residues: 472 loop : -2.83 (0.12), residues: 2455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP I 28 HIS 0.010 0.001 HIS P 144 PHE 0.029 0.002 PHE I 49 TYR 0.020 0.002 TYR D 94 ARG 0.008 0.001 ARG I 122 *********************** 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 972 residues out of total 4128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 971 time to evaluate : 4.741 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 TYR cc_start: 0.7767 (m-80) cc_final: 0.6602 (m-80) REVERT: A 26 TYR cc_start: 0.7598 (t80) cc_final: 0.7149 (t80) REVERT: A 67 TRP cc_start: 0.7504 (p-90) cc_final: 0.6872 (p-90) REVERT: A 246 GLU cc_start: 0.8615 (tp30) cc_final: 0.8295 (tp30) REVERT: A 321 ASP cc_start: 0.8193 (m-30) cc_final: 0.7744 (m-30) REVERT: A 344 ASP cc_start: 0.8729 (t0) cc_final: 0.8463 (t0) REVERT: A 432 ARG cc_start: 0.7687 (mtp180) cc_final: 0.7440 (ptp-170) REVERT: A 440 ASP cc_start: 0.8705 (t0) cc_final: 0.8232 (t70) REVERT: B 34 LEU cc_start: 0.8579 (tp) cc_final: 0.7734 (tp) REVERT: B 130 LEU cc_start: 0.9398 (tp) cc_final: 0.9123 (tp) REVERT: B 157 ASP cc_start: 0.9149 (m-30) cc_final: 0.8945 (m-30) REVERT: B 205 SER cc_start: 0.8307 (t) cc_final: 0.7998 (p) REVERT: B 233 LYS cc_start: 0.8763 (mmmt) cc_final: 0.8523 (mmmt) REVERT: B 246 GLU cc_start: 0.8665 (tp30) cc_final: 0.8359 (tp30) REVERT: B 255 LYS cc_start: 0.9422 (tmmt) cc_final: 0.9190 (tttt) REVERT: B 321 ASP cc_start: 0.8276 (m-30) cc_final: 0.7967 (m-30) REVERT: C 22 TYR cc_start: 0.7893 (m-80) cc_final: 0.7471 (m-80) REVERT: C 85 GLU cc_start: 0.8875 (pp20) cc_final: 0.8613 (tm-30) REVERT: C 146 GLN cc_start: 0.9038 (tt0) cc_final: 0.8199 (tp-100) REVERT: C 205 SER cc_start: 0.8541 (t) cc_final: 0.8132 (p) REVERT: C 222 ILE cc_start: 0.9237 (mt) cc_final: 0.8919 (mt) REVERT: C 247 MET cc_start: 0.8480 (tpp) cc_final: 0.7943 (tpp) REVERT: C 259 MET cc_start: 0.9027 (mmp) cc_final: 0.8610 (mmt) REVERT: C 321 ASP cc_start: 0.8146 (m-30) cc_final: 0.7831 (m-30) REVERT: C 328 VAL cc_start: 0.8817 (m) cc_final: 0.8488 (p) REVERT: D 22 TYR cc_start: 0.7626 (m-80) cc_final: 0.7187 (m-80) REVERT: D 26 TYR cc_start: 0.7523 (t80) cc_final: 0.7150 (t80) REVERT: D 85 GLU cc_start: 0.7926 (mt-10) cc_final: 0.7050 (mt-10) REVERT: D 146 GLN cc_start: 0.8950 (tt0) cc_final: 0.8147 (tp40) REVERT: D 162 TYR cc_start: 0.7988 (m-10) cc_final: 0.7739 (m-10) REVERT: D 203 ILE cc_start: 0.9140 (tp) cc_final: 0.8864 (tp) REVERT: D 209 GLN cc_start: 0.8921 (tm-30) cc_final: 0.8463 (tm-30) REVERT: D 228 GLU cc_start: 0.8899 (tm-30) cc_final: 0.8691 (tm-30) REVERT: D 255 LYS cc_start: 0.9270 (tmtt) cc_final: 0.8912 (tptt) REVERT: D 343 VAL cc_start: 0.9439 (t) cc_final: 0.9192 (t) REVERT: D 364 ASP cc_start: 0.9147 (t70) cc_final: 0.8898 (t0) REVERT: E 22 TYR cc_start: 0.7401 (m-80) cc_final: 0.6633 (m-80) REVERT: E 26 TYR cc_start: 0.7660 (t80) cc_final: 0.7154 (t80) REVERT: E 34 LEU cc_start: 0.8774 (tp) cc_final: 0.8451 (tp) REVERT: E 106 GLU cc_start: 0.8044 (tt0) cc_final: 0.7705 (tt0) REVERT: E 125 LYS cc_start: 0.8229 (mmpt) cc_final: 0.7319 (pttm) REVERT: E 146 GLN cc_start: 0.8729 (tp-100) cc_final: 0.8525 (tp-100) REVERT: E 205 SER cc_start: 0.8735 (t) cc_final: 0.8316 (p) REVERT: E 321 ASP cc_start: 0.8172 (m-30) cc_final: 0.7706 (m-30) REVERT: E 364 ASP cc_start: 0.9272 (t70) cc_final: 0.9004 (t0) REVERT: F 22 TYR cc_start: 0.7347 (m-80) cc_final: 0.6601 (m-80) REVERT: F 26 TYR cc_start: 0.7590 (t80) cc_final: 0.6947 (t80) REVERT: F 30 ASP cc_start: 0.7518 (p0) cc_final: 0.7096 (p0) REVERT: F 81 CYS cc_start: 0.6601 (t) cc_final: 0.6396 (t) REVERT: F 106 GLU cc_start: 0.7955 (tt0) cc_final: 0.7619 (tt0) REVERT: F 244 CYS cc_start: 0.7631 (t) cc_final: 0.7330 (t) REVERT: F 291 HIS cc_start: 0.8711 (t-90) cc_final: 0.7870 (t-90) REVERT: F 294 MET cc_start: 0.8516 (ptt) cc_final: 0.8183 (ptt) REVERT: F 297 VAL cc_start: 0.9494 (m) cc_final: 0.9211 (m) REVERT: F 384 MET cc_start: 0.8971 (ttt) cc_final: 0.8710 (ttt) REVERT: G 22 TYR cc_start: 0.7836 (m-80) cc_final: 0.7137 (m-80) REVERT: G 105 PHE cc_start: 0.8992 (m-80) cc_final: 0.8489 (m-10) REVERT: G 106 GLU cc_start: 0.8402 (tt0) cc_final: 0.7998 (tt0) REVERT: G 171 ILE cc_start: 0.8950 (mp) cc_final: 0.8747 (tp) REVERT: G 177 LEU cc_start: 0.8822 (mm) cc_final: 0.8614 (mm) REVERT: G 204 ASN cc_start: 0.7986 (m-40) cc_final: 0.7774 (m-40) REVERT: G 228 GLU cc_start: 0.8738 (tm-30) cc_final: 0.8509 (tm-30) REVERT: G 255 LYS cc_start: 0.9263 (tmtt) cc_final: 0.9015 (tptt) REVERT: G 321 ASP cc_start: 0.8136 (m-30) cc_final: 0.7717 (m-30) REVERT: G 343 VAL cc_start: 0.9574 (t) cc_final: 0.9283 (t) REVERT: G 346 MET cc_start: 0.9268 (mpp) cc_final: 0.8979 (mpp) REVERT: G 408 TRP cc_start: 0.7586 (t-100) cc_final: 0.7312 (t-100) REVERT: H 22 TYR cc_start: 0.7285 (m-80) cc_final: 0.6614 (m-80) REVERT: H 146 GLN cc_start: 0.8556 (tp-100) cc_final: 0.8237 (tp-100) REVERT: H 162 TYR cc_start: 0.8045 (m-80) cc_final: 0.7215 (m-80) REVERT: H 184 ARG cc_start: 0.8184 (mmt-90) cc_final: 0.7529 (mmt90) REVERT: H 291 HIS cc_start: 0.8745 (t-90) cc_final: 0.8518 (t-90) REVERT: H 382 TRP cc_start: 0.8651 (m100) cc_final: 0.8109 (m100) REVERT: H 383 HIS cc_start: 0.8995 (m170) cc_final: 0.8490 (m-70) REVERT: I 121 ILE cc_start: 0.7864 (tp) cc_final: 0.7583 (tp) REVERT: I 123 GLU cc_start: 0.8466 (pt0) cc_final: 0.8170 (pt0) REVERT: I 179 SER cc_start: 0.4041 (t) cc_final: 0.3665 (t) REVERT: J 159 GLU cc_start: 0.7848 (mp0) cc_final: 0.7544 (mp0) REVERT: J 187 GLU cc_start: 0.6560 (tt0) cc_final: 0.6213 (mm-30) REVERT: K 28 TRP cc_start: 0.6745 (t60) cc_final: 0.6419 (t60) REVERT: K 97 ARG cc_start: 0.6574 (mtm-85) cc_final: 0.5571 (mtm-85) REVERT: K 114 ARG cc_start: 0.6800 (tpt170) cc_final: 0.5729 (mtt-85) REVERT: K 191 LEU cc_start: 0.7495 (tt) cc_final: 0.6955 (mt) REVERT: L 27 ARG cc_start: 0.8186 (mpt-90) cc_final: 0.7620 (mpp80) REVERT: L 62 ILE cc_start: 0.7645 (mm) cc_final: 0.7334 (mm) REVERT: L 159 GLU cc_start: 0.5805 (mt-10) cc_final: 0.4873 (mp0) REVERT: M 27 ARG cc_start: 0.7947 (mpt-90) cc_final: 0.7125 (mpp80) REVERT: M 28 TRP cc_start: 0.7067 (t60) cc_final: 0.6819 (t60) REVERT: N 97 ARG cc_start: 0.6141 (mtm-85) cc_final: 0.5196 (mtm-85) REVERT: N 113 GLU cc_start: 0.6064 (pm20) cc_final: 0.5451 (tp30) REVERT: P 25 GLU cc_start: 0.7694 (tt0) cc_final: 0.7406 (tt0) REVERT: P 28 TRP cc_start: 0.7510 (t60) cc_final: 0.6589 (t60) outliers start: 1 outliers final: 0 residues processed: 972 average time/residue: 0.5241 time to fit residues: 833.9894 Evaluate side-chains 740 residues out of total 4128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 740 time to evaluate : 4.613 ------------------------------------------------------------------------------- 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: 3.9990 chunk 6 optimal weight: 4.9990 chunk 354 optimal weight: 0.0050 chunk 196 optimal weight: 5.9990 chunk 406 optimal weight: 9.9990 chunk 329 optimal weight: 2.9990 chunk 0 optimal weight: 9.9990 chunk 243 optimal weight: 4.9990 chunk 427 optimal weight: 20.0000 chunk 120 optimal weight: 0.7980 overall best weight: 2.5600 ------------------------------------------------------------------------------- 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 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 235 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 291 HIS C 324 HIS ** 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 274 ASN ** D 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 295 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 83 HIS F 112 ASN F 181 ASN F 202 ASN ** F 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 274 ASN F 324 HIS ** G 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 274 ASN ** H 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 324 HIS I 58 GLN I 86 GLN ** J 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 60 ASN ** L 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 60 ASN ** P 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.5515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.092 40657 Z= 0.249 Angle : 0.698 9.798 55071 Z= 0.352 Chirality : 0.045 0.293 5917 Planarity : 0.004 0.074 7264 Dihedral : 6.281 176.747 5490 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 18.94 Ramachandran Plot: Outliers : 0.34 % Allowed : 10.25 % Favored : 89.41 % Rotamer: Outliers : 0.07 % Allowed : 3.66 % Favored : 96.27 % 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: -2.46 (0.11), residues: 4993 helix: -0.26 (0.11), residues: 2078 sheet: -2.56 (0.21), residues: 456 loop : -2.75 (0.12), residues: 2459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.001 TRP I 28 HIS 0.017 0.001 HIS P 144 PHE 0.034 0.002 PHE F 266 TYR 0.020 0.002 TYR D 94 ARG 0.005 0.000 ARG I 27 *********************** 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 989 residues out of total 4128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 986 time to evaluate : 5.861 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: A 22 TYR cc_start: 0.7692 (m-80) cc_final: 0.6630 (m-80) REVERT: A 26 TYR cc_start: 0.7529 (t80) cc_final: 0.7114 (t80) REVERT: A 67 TRP cc_start: 0.7487 (p-90) cc_final: 0.6941 (p-90) REVERT: A 106 GLU cc_start: 0.8311 (tt0) cc_final: 0.7927 (tt0) REVERT: A 157 ASP cc_start: 0.9168 (m-30) cc_final: 0.8928 (m-30) REVERT: A 233 LYS cc_start: 0.8507 (mmmt) cc_final: 0.8300 (mmmm) REVERT: A 246 GLU cc_start: 0.8573 (tp30) cc_final: 0.8241 (tp30) REVERT: A 248 MET cc_start: 0.8953 (mmp) cc_final: 0.8634 (mmt) REVERT: A 259 MET cc_start: 0.8567 (mmt) cc_final: 0.8367 (mmp) REVERT: A 321 ASP cc_start: 0.8124 (m-30) cc_final: 0.7727 (m-30) REVERT: A 344 ASP cc_start: 0.8707 (t0) cc_final: 0.8467 (t0) REVERT: A 361 PHE cc_start: 0.7631 (m-80) cc_final: 0.7427 (m-80) REVERT: A 440 ASP cc_start: 0.8648 (t0) cc_final: 0.8170 (t0) REVERT: B 130 LEU cc_start: 0.9339 (tp) cc_final: 0.9101 (tp) REVERT: B 146 GLN cc_start: 0.8901 (tt0) cc_final: 0.8095 (tm-30) REVERT: B 157 ASP cc_start: 0.9091 (m-30) cc_final: 0.8855 (m-30) REVERT: B 190 LEU cc_start: 0.9507 (tp) cc_final: 0.9304 (tt) REVERT: B 205 SER cc_start: 0.8414 (t) cc_final: 0.8050 (p) REVERT: B 246 GLU cc_start: 0.8661 (tp30) cc_final: 0.8363 (tp30) REVERT: B 255 LYS cc_start: 0.9435 (tmmt) cc_final: 0.9105 (tptp) REVERT: B 291 HIS cc_start: 0.7938 (t-90) cc_final: 0.7640 (t-90) REVERT: B 361 PHE cc_start: 0.7832 (m-80) cc_final: 0.7191 (m-80) REVERT: C 22 TYR cc_start: 0.7805 (m-80) cc_final: 0.7364 (m-80) REVERT: C 30 ASP cc_start: 0.7969 (p0) cc_final: 0.7679 (p0) REVERT: C 130 LEU cc_start: 0.9411 (tp) cc_final: 0.9143 (tp) REVERT: C 146 GLN cc_start: 0.9123 (tt0) cc_final: 0.8194 (tp-100) REVERT: C 204 ASN cc_start: 0.8303 (m-40) cc_final: 0.8031 (m-40) REVERT: C 205 SER cc_start: 0.8470 (t) cc_final: 0.8228 (p) REVERT: C 247 MET cc_start: 0.8535 (tpp) cc_final: 0.8300 (tpt) REVERT: D 22 TYR cc_start: 0.7534 (m-80) cc_final: 0.7176 (m-80) REVERT: D 85 GLU cc_start: 0.7783 (mt-10) cc_final: 0.6899 (mt-10) REVERT: D 146 GLN cc_start: 0.8965 (tt0) cc_final: 0.7983 (tp-100) REVERT: D 203 ILE cc_start: 0.8990 (tp) cc_final: 0.8771 (tp) REVERT: D 209 GLN cc_start: 0.8972 (tm-30) cc_final: 0.8450 (tm-30) REVERT: D 255 LYS cc_start: 0.9243 (tmtt) cc_final: 0.8872 (tptt) REVERT: D 343 VAL cc_start: 0.9468 (t) cc_final: 0.9112 (t) REVERT: D 440 ASP cc_start: 0.8704 (t0) cc_final: 0.8364 (p0) REVERT: D 452 LEU cc_start: 0.9376 (tp) cc_final: 0.9172 (tp) REVERT: E 22 TYR cc_start: 0.7457 (m-80) cc_final: 0.6605 (m-80) REVERT: E 26 TYR cc_start: 0.7493 (t80) cc_final: 0.6999 (t80) REVERT: E 34 LEU cc_start: 0.8689 (tp) cc_final: 0.8399 (tp) REVERT: E 106 GLU cc_start: 0.8009 (tt0) cc_final: 0.7779 (tt0) REVERT: E 125 LYS cc_start: 0.8145 (mmpt) cc_final: 0.7183 (pttm) REVERT: E 162 TYR cc_start: 0.8125 (m-80) cc_final: 0.7550 (m-80) REVERT: E 184 ARG cc_start: 0.8196 (mtt-85) cc_final: 0.7973 (mmt-90) REVERT: E 205 SER cc_start: 0.8771 (t) cc_final: 0.8427 (p) REVERT: F 22 TYR cc_start: 0.7312 (m-80) cc_final: 0.6439 (m-80) REVERT: F 26 TYR cc_start: 0.7443 (t80) cc_final: 0.6840 (t80) REVERT: F 30 ASP cc_start: 0.7328 (p0) cc_final: 0.6878 (p0) REVERT: F 106 GLU cc_start: 0.7838 (tt0) cc_final: 0.7435 (tt0) REVERT: F 209 GLN cc_start: 0.8753 (tm-30) cc_final: 0.8350 (tm-30) REVERT: F 236 TYR cc_start: 0.7760 (m-10) cc_final: 0.7481 (m-10) REVERT: F 291 HIS cc_start: 0.8647 (t-90) cc_final: 0.7805 (t-90) REVERT: F 321 ASP cc_start: 0.8268 (m-30) cc_final: 0.7967 (m-30) REVERT: F 383 HIS cc_start: 0.8683 (m90) cc_final: 0.8470 (m90) REVERT: G 22 TYR cc_start: 0.7760 (m-80) cc_final: 0.7082 (m-80) REVERT: G 34 LEU cc_start: 0.8642 (tp) cc_final: 0.8353 (tp) REVERT: G 106 GLU cc_start: 0.8326 (tt0) cc_final: 0.7857 (tt0) REVERT: G 171 ILE cc_start: 0.8867 (mp) cc_final: 0.8577 (tp) REVERT: G 228 GLU cc_start: 0.8817 (tm-30) cc_final: 0.8602 (tm-30) REVERT: G 321 ASP cc_start: 0.8209 (m-30) cc_final: 0.7922 (m-30) REVERT: G 343 VAL cc_start: 0.9571 (t) cc_final: 0.9231 (t) REVERT: G 346 MET cc_start: 0.9356 (mpp) cc_final: 0.8992 (mpp) REVERT: G 382 TRP cc_start: 0.8788 (m100) cc_final: 0.8466 (m100) REVERT: G 383 HIS cc_start: 0.8693 (m170) cc_final: 0.8464 (m-70) REVERT: H 22 TYR cc_start: 0.7471 (m-80) cc_final: 0.6873 (m-80) REVERT: H 130 LEU cc_start: 0.9264 (tp) cc_final: 0.8994 (tp) REVERT: H 146 GLN cc_start: 0.8504 (tp-100) cc_final: 0.8129 (tp-100) REVERT: H 205 SER cc_start: 0.8496 (t) cc_final: 0.8147 (p) REVERT: H 255 LYS cc_start: 0.9329 (tmmt) cc_final: 0.8931 (tptp) REVERT: H 383 HIS cc_start: 0.8857 (m170) cc_final: 0.8432 (m-70) REVERT: I 121 ILE cc_start: 0.7896 (tp) cc_final: 0.7610 (tp) REVERT: I 179 SER cc_start: 0.4536 (t) cc_final: 0.4080 (t) REVERT: J 58 GLN cc_start: 0.7673 (pm20) cc_final: 0.6867 (tt0) REVERT: J 159 GLU cc_start: 0.7791 (mp0) cc_final: 0.7485 (mp0) REVERT: J 187 GLU cc_start: 0.6493 (tt0) cc_final: 0.6249 (mm-30) REVERT: K 28 TRP cc_start: 0.6759 (t60) cc_final: 0.6399 (t60) REVERT: K 62 ILE cc_start: 0.8078 (mm) cc_final: 0.7791 (mm) REVERT: K 114 ARG cc_start: 0.6831 (tpt170) cc_final: 0.5501 (mtt-85) REVERT: K 191 LEU cc_start: 0.7473 (tt) cc_final: 0.6921 (mt) REVERT: L 159 GLU cc_start: 0.6010 (mt-10) cc_final: 0.5326 (mp0) REVERT: M 27 ARG cc_start: 0.7787 (mpt-90) cc_final: 0.4919 (tpp-160) REVERT: M 54 PHE cc_start: 0.8384 (m-80) cc_final: 0.8033 (m-80) REVERT: N 113 GLU cc_start: 0.6359 (pm20) cc_final: 0.5857 (tp30) REVERT: N 132 CYS cc_start: 0.6348 (m) cc_final: 0.5564 (p) REVERT: O 49 PHE cc_start: 0.7181 (t80) cc_final: 0.6748 (t80) REVERT: O 97 ARG cc_start: 0.8795 (tmm160) cc_final: 0.8537 (tmm-80) outliers start: 3 outliers final: 0 residues processed: 989 average time/residue: 0.5303 time to fit residues: 861.5900 Evaluate side-chains 726 residues out of total 4128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 726 time to evaluate : 4.822 ------------------------------------------------------------------------------- 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: 9.9990 chunk 429 optimal weight: 0.7980 chunk 94 optimal weight: 10.0000 chunk 279 optimal weight: 10.0000 chunk 117 optimal weight: 2.9990 chunk 476 optimal weight: 7.9990 chunk 395 optimal weight: 20.0000 chunk 220 optimal weight: 9.9990 chunk 39 optimal weight: 3.9990 chunk 157 optimal weight: 6.9990 chunk 250 optimal weight: 0.4980 overall best weight: 3.0586 ------------------------------------------------------------------------------- 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** B 112 ASN ** B 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 181 ASN ** C 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 235 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 274 ASN ** C 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 291 HIS ** C 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 417 ASN ** D 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 274 ASN ** D 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 209 GLN E 291 HIS E 324 HIS ** E 383 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 274 ASN G 209 GLN ** G 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 274 ASN ** H 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 67 GLN ** L 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 137 GLN O 60 ASN ** O 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.5740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.102 40657 Z= 0.274 Angle : 0.710 10.544 55071 Z= 0.357 Chirality : 0.045 0.223 5917 Planarity : 0.005 0.079 7264 Dihedral : 6.245 176.638 5490 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 19.73 Ramachandran Plot: Outliers : 0.32 % Allowed : 10.45 % Favored : 89.22 % Rotamer: Outliers : 0.10 % Allowed : 2.64 % Favored : 97.26 % 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: -2.39 (0.11), residues: 4993 helix: -0.25 (0.11), residues: 2133 sheet: -2.53 (0.21), residues: 464 loop : -2.71 (0.12), residues: 2396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP I 28 HIS 0.014 0.001 HIS P 144 PHE 0.026 0.002 PHE I 49 TYR 0.020 0.002 TYR E 236 ARG 0.007 0.000 ARG J 33 *********************** 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 946 residues out of total 4128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 942 time to evaluate : 4.989 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: A 22 TYR cc_start: 0.7647 (m-80) cc_final: 0.6493 (m-80) REVERT: A 26 TYR cc_start: 0.7525 (t80) cc_final: 0.7103 (t80) REVERT: A 67 TRP cc_start: 0.7403 (p-90) cc_final: 0.6912 (p-90) REVERT: A 106 GLU cc_start: 0.8446 (tt0) cc_final: 0.8088 (tt0) REVERT: A 184 ARG cc_start: 0.8570 (mtt-85) cc_final: 0.8172 (mtt-85) REVERT: A 246 GLU cc_start: 0.8605 (tp30) cc_final: 0.8314 (tp30) REVERT: A 248 MET cc_start: 0.8907 (mmp) cc_final: 0.8617 (mmt) REVERT: A 255 LYS cc_start: 0.9063 (tmtt) cc_final: 0.8681 (tptt) REVERT: A 344 ASP cc_start: 0.8722 (t0) cc_final: 0.8451 (t0) REVERT: A 440 ASP cc_start: 0.8632 (t0) cc_final: 0.8151 (t0) REVERT: B 130 LEU cc_start: 0.9402 (tp) cc_final: 0.9128 (tp) REVERT: B 146 GLN cc_start: 0.8894 (tt0) cc_final: 0.8419 (tp40) REVERT: B 157 ASP cc_start: 0.9095 (m-30) cc_final: 0.8883 (m-30) REVERT: B 205 SER cc_start: 0.8287 (t) cc_final: 0.8045 (p) REVERT: B 246 GLU cc_start: 0.8669 (tp30) cc_final: 0.8394 (tp30) REVERT: B 255 LYS cc_start: 0.9354 (tmmt) cc_final: 0.9088 (tptp) REVERT: B 291 HIS cc_start: 0.7907 (t-90) cc_final: 0.7700 (t-90) REVERT: B 321 ASP cc_start: 0.8350 (m-30) cc_final: 0.8064 (m-30) REVERT: B 361 PHE cc_start: 0.7888 (m-80) cc_final: 0.7286 (m-80) REVERT: B 384 MET cc_start: 0.9000 (ttm) cc_final: 0.8671 (ttp) REVERT: C 22 TYR cc_start: 0.7823 (m-80) cc_final: 0.7411 (m-80) REVERT: C 84 ILE cc_start: 0.9212 (pt) cc_final: 0.8918 (mp) REVERT: C 130 LEU cc_start: 0.9471 (tp) cc_final: 0.9248 (tp) REVERT: C 146 GLN cc_start: 0.9112 (tt0) cc_final: 0.8160 (tp-100) REVERT: C 205 SER cc_start: 0.8580 (t) cc_final: 0.8266 (p) REVERT: D 22 TYR cc_start: 0.7548 (m-80) cc_final: 0.7165 (m-80) REVERT: D 85 GLU cc_start: 0.7774 (mt-10) cc_final: 0.6930 (mt-10) REVERT: D 146 GLN cc_start: 0.8973 (tt0) cc_final: 0.7963 (tp-100) REVERT: D 203 ILE cc_start: 0.9111 (tp) cc_final: 0.8556 (mt) REVERT: D 209 GLN cc_start: 0.9078 (tm-30) cc_final: 0.8496 (tm-30) REVERT: D 255 LYS cc_start: 0.9234 (tmtt) cc_final: 0.8896 (tptt) REVERT: D 328 VAL cc_start: 0.8543 (m) cc_final: 0.8226 (m) REVERT: D 440 ASP cc_start: 0.8592 (t0) cc_final: 0.8204 (p0) REVERT: E 22 TYR cc_start: 0.7585 (m-80) cc_final: 0.6834 (m-80) REVERT: E 26 TYR cc_start: 0.7402 (t80) cc_final: 0.6919 (t80) REVERT: E 34 LEU cc_start: 0.8771 (tp) cc_final: 0.8425 (tp) REVERT: E 106 GLU cc_start: 0.8068 (tt0) cc_final: 0.7826 (tt0) REVERT: E 125 LYS cc_start: 0.8123 (mmpt) cc_final: 0.7261 (pttm) REVERT: E 184 ARG cc_start: 0.8296 (mtt-85) cc_final: 0.7831 (mmt-90) REVERT: E 205 SER cc_start: 0.8888 (t) cc_final: 0.8454 (p) REVERT: F 22 TYR cc_start: 0.7259 (m-80) cc_final: 0.6496 (m-80) REVERT: F 26 TYR cc_start: 0.7421 (t80) cc_final: 0.6844 (t80) REVERT: F 30 ASP cc_start: 0.7244 (p0) cc_final: 0.6750 (p0) REVERT: F 34 LEU cc_start: 0.8195 (tp) cc_final: 0.7948 (tp) REVERT: F 106 GLU cc_start: 0.7847 (tt0) cc_final: 0.7413 (tt0) REVERT: F 203 ILE cc_start: 0.8737 (mt) cc_final: 0.8412 (mt) REVERT: F 238 ASN cc_start: 0.9087 (t0) cc_final: 0.8741 (t0) REVERT: F 291 HIS cc_start: 0.8553 (t-90) cc_final: 0.7923 (t-90) REVERT: F 383 HIS cc_start: 0.8606 (m90) cc_final: 0.8252 (m-70) REVERT: G 22 TYR cc_start: 0.7856 (m-80) cc_final: 0.7150 (m-80) REVERT: G 34 LEU cc_start: 0.8672 (tp) cc_final: 0.8348 (tp) REVERT: G 39 PHE cc_start: 0.7887 (t80) cc_final: 0.7447 (t80) REVERT: G 106 GLU cc_start: 0.8302 (tt0) cc_final: 0.7945 (tt0) REVERT: G 130 LEU cc_start: 0.9339 (tp) cc_final: 0.9127 (tp) REVERT: G 171 ILE cc_start: 0.8929 (mp) cc_final: 0.8681 (tp) REVERT: G 228 GLU cc_start: 0.8879 (tm-30) cc_final: 0.8641 (tm-30) REVERT: G 343 VAL cc_start: 0.9488 (t) cc_final: 0.9225 (t) REVERT: G 346 MET cc_start: 0.9428 (mpp) cc_final: 0.9031 (mpp) REVERT: G 382 TRP cc_start: 0.8778 (m100) cc_final: 0.8532 (m100) REVERT: G 408 TRP cc_start: 0.7532 (t-100) cc_final: 0.7275 (t-100) REVERT: H 22 TYR cc_start: 0.7503 (m-80) cc_final: 0.6919 (m-80) REVERT: H 130 LEU cc_start: 0.9308 (tp) cc_final: 0.9063 (tp) REVERT: H 146 GLN cc_start: 0.8444 (tp-100) cc_final: 0.8123 (tp-100) REVERT: H 184 ARG cc_start: 0.8445 (mmt-90) cc_final: 0.8167 (mmt-90) REVERT: H 205 SER cc_start: 0.8504 (t) cc_final: 0.8096 (p) REVERT: H 383 HIS cc_start: 0.8760 (m170) cc_final: 0.8546 (m-70) REVERT: H 430 GLU cc_start: 0.8348 (mt-10) cc_final: 0.8016 (mt-10) REVERT: I 121 ILE cc_start: 0.7865 (tp) cc_final: 0.7630 (tp) REVERT: I 179 SER cc_start: 0.4615 (t) cc_final: 0.4170 (t) REVERT: J 58 GLN cc_start: 0.7688 (pm20) cc_final: 0.7012 (tt0) REVERT: J 66 MET cc_start: 0.7941 (ppp) cc_final: 0.7211 (ppp) REVERT: J 159 GLU cc_start: 0.7724 (mp0) cc_final: 0.7326 (mp0) REVERT: K 28 TRP cc_start: 0.6858 (t60) cc_final: 0.6439 (t60) REVERT: K 62 ILE cc_start: 0.8233 (mm) cc_final: 0.7995 (mm) REVERT: K 114 ARG cc_start: 0.6521 (tpt170) cc_final: 0.5230 (mtt-85) REVERT: K 191 LEU cc_start: 0.7570 (tt) cc_final: 0.6989 (mt) REVERT: L 67 GLN cc_start: 0.6529 (tt0) cc_final: 0.6177 (tt0) REVERT: L 159 GLU cc_start: 0.6046 (mt-10) cc_final: 0.5486 (mp0) REVERT: M 27 ARG cc_start: 0.7816 (mpt-90) cc_final: 0.4989 (tpp-160) REVERT: M 49 PHE cc_start: 0.6773 (t80) cc_final: 0.6507 (t80) REVERT: N 27 ARG cc_start: 0.8236 (mpt-90) cc_final: 0.7522 (mpp80) REVERT: N 67 GLN cc_start: 0.6780 (tt0) cc_final: 0.6359 (tm-30) REVERT: N 113 GLU cc_start: 0.6039 (OUTLIER) cc_final: 0.5429 (tp30) REVERT: N 132 CYS cc_start: 0.6263 (m) cc_final: 0.5564 (p) REVERT: O 97 ARG cc_start: 0.8839 (tmm160) cc_final: 0.8411 (tmm-80) REVERT: P 28 TRP cc_start: 0.6903 (t60) cc_final: 0.5840 (t60) outliers start: 4 outliers final: 0 residues processed: 945 average time/residue: 0.5506 time to fit residues: 863.3951 Evaluate side-chains 713 residues out of total 4128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 712 time to evaluate : 4.363 ------------------------------------------------------------------------------- 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: 5.9990 chunk 53 optimal weight: 0.0870 chunk 271 optimal weight: 5.9990 chunk 348 optimal weight: 5.9990 chunk 269 optimal weight: 20.0000 chunk 401 optimal weight: 2.9990 chunk 266 optimal weight: 20.0000 chunk 475 optimal weight: 30.0000 chunk 297 optimal weight: 10.0000 chunk 289 optimal weight: 3.9990 chunk 219 optimal weight: 5.9990 overall best weight: 3.8166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: