Starting phenix.real_space_refine on Sat Jul 27 11:03:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5nv3_3699/07_2024/5nv3_3699_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5nv3_3699/07_2024/5nv3_3699.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.39 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5nv3_3699/07_2024/5nv3_3699.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5nv3_3699/07_2024/5nv3_3699.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5nv3_3699/07_2024/5nv3_3699_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5nv3_3699/07_2024/5nv3_3699_neut.cif" } resolution = 3.39 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= 0.002 sd= 0.273 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 16 5.49 5 Mg 8 5.21 5 S 240 5.16 5 C 23960 2.51 5 N 6544 2.21 5 O 7048 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 88": "NH1" <-> "NH2" Residue "A TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 112": "OE1" <-> "OE2" Residue "A ASP 371": "OD1" <-> "OD2" Residue "A TYR 470": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 477": "OD1" <-> "OD2" Residue "I GLU 36": "OE1" <-> "OE2" Residue "I ARG 102": "NH1" <-> "NH2" Residue "B ARG 88": "NH1" <-> "NH2" Residue "B TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 112": "OE1" <-> "OE2" Residue "B ASP 371": "OD1" <-> "OD2" Residue "B TYR 470": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 477": "OD1" <-> "OD2" Residue "J GLU 36": "OE1" <-> "OE2" Residue "J ARG 102": "NH1" <-> "NH2" Residue "C ARG 88": "NH1" <-> "NH2" Residue "C TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 112": "OE1" <-> "OE2" Residue "C ASP 371": "OD1" <-> "OD2" Residue "C TYR 470": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 477": "OD1" <-> "OD2" Residue "K GLU 36": "OE1" <-> "OE2" Residue "K ARG 102": "NH1" <-> "NH2" Residue "D ARG 88": "NH1" <-> "NH2" Residue "D TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 112": "OE1" <-> "OE2" Residue "D ASP 371": "OD1" <-> "OD2" Residue "D TYR 470": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 477": "OD1" <-> "OD2" Residue "L GLU 36": "OE1" <-> "OE2" Residue "L ARG 102": "NH1" <-> "NH2" Residue "E ARG 88": "NH1" <-> "NH2" Residue "E TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 112": "OE1" <-> "OE2" Residue "E ASP 371": "OD1" <-> "OD2" Residue "E TYR 470": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 477": "OD1" <-> "OD2" Residue "M GLU 36": "OE1" <-> "OE2" Residue "M ARG 102": "NH1" <-> "NH2" Residue "M TYR 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 88": "NH1" <-> "NH2" Residue "F TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 112": "OE1" <-> "OE2" Residue "F ASP 371": "OD1" <-> "OD2" Residue "F TYR 470": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 477": "OD1" <-> "OD2" Residue "N GLU 36": "OE1" <-> "OE2" Residue "N ARG 102": "NH1" <-> "NH2" Residue "G ARG 88": "NH1" <-> "NH2" Residue "G TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 112": "OE1" <-> "OE2" Residue "G ASP 371": "OD1" <-> "OD2" Residue "G TYR 470": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 477": "OD1" <-> "OD2" Residue "O GLU 36": "OE1" <-> "OE2" Residue "O ARG 102": "NH1" <-> "NH2" Residue "O TYR 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 88": "NH1" <-> "NH2" Residue "H TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 112": "OE1" <-> "OE2" Residue "H ASP 371": "OD1" <-> "OD2" Residue "H TYR 470": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 477": "OD1" <-> "OD2" Residue "P GLU 36": "OE1" <-> "OE2" Residue "P ARG 102": "NH1" <-> "NH2" Residue "P TYR 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 37816 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 3642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 467, 3642 Classifications: {'peptide': 467} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 446} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "I" Number of atoms: 1063 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1063 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 120} Chain: "B" Number of atoms: 3642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 467, 3642 Classifications: {'peptide': 467} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 446} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "J" Number of atoms: 1063 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1063 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 120} Chain: "C" Number of atoms: 3642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 467, 3642 Classifications: {'peptide': 467} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 446} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "K" Number of atoms: 1063 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1063 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 120} Chain: "D" Number of atoms: 3642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 467, 3642 Classifications: {'peptide': 467} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 446} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "L" Number of atoms: 1063 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1063 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 120} Chain: "E" Number of atoms: 3642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 467, 3642 Classifications: {'peptide': 467} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 446} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "M" Number of atoms: 1063 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1063 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 120} Chain: "F" Number of atoms: 3642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 467, 3642 Classifications: {'peptide': 467} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 446} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "N" Number of atoms: 1063 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1063 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 120} Chain: "G" Number of atoms: 3642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 467, 3642 Classifications: {'peptide': 467} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 446} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "O" Number of atoms: 1063 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1063 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 120} Chain: "H" Number of atoms: 3642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 467, 3642 Classifications: {'peptide': 467} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 446} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "P" Number of atoms: 1063 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1063 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 120} Chain: "A" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {' MG': 1, 'CAP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {' MG': 1, 'CAP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {' MG': 1, 'CAP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {' MG': 1, 'CAP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {' MG': 1, 'CAP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {' MG': 1, 'CAP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {' MG': 1, 'CAP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {' MG': 1, 'CAP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 128 residue: pdb=" N GLY A 464 " occ=0.40 ... (2 atoms not shown) pdb=" O GLY A 464 " occ=0.40 residue: pdb=" N ASN A 465 " occ=0.40 ... (6 atoms not shown) pdb=" ND2 ASN A 465 " occ=0.40 residue: pdb=" N ILE A 466 " occ=0.40 ... (6 atoms not shown) pdb=" CD1 ILE A 466 " occ=0.40 residue: pdb=" N THR A 467 " occ=0.40 ... (5 atoms not shown) pdb=" CG2 THR A 467 " occ=0.40 residue: pdb=" N PHE A 468 " occ=0.40 ... (9 atoms not shown) pdb=" CZ PHE A 468 " occ=0.40 residue: pdb=" N ASN A 469 " occ=0.40 ... (6 atoms not shown) pdb=" ND2 ASN A 469 " occ=0.40 residue: pdb=" N TYR A 470 " occ=0.40 ... (10 atoms not shown) pdb=" OH TYR A 470 " occ=0.40 residue: pdb=" N THR A 471 " occ=0.40 ... (5 atoms not shown) pdb=" CG2 THR A 471 " occ=0.40 residue: pdb=" N SER A 472 " occ=0.40 ... (4 atoms not shown) pdb=" OG SER A 472 " occ=0.40 residue: pdb=" N THR A 473 " occ=0.40 ... (5 atoms not shown) pdb=" CG2 THR A 473 " occ=0.40 residue: pdb=" N ASP A 474 " occ=0.40 ... (6 atoms not shown) pdb=" OD2 ASP A 474 " occ=0.40 residue: pdb=" N THR A 475 " occ=0.40 ... (5 atoms not shown) pdb=" CG2 THR A 475 " occ=0.40 ... (remaining 116 not shown) Time building chain proxies: 19.70, per 1000 atoms: 0.52 Number of scatterers: 37816 At special positions: 0 Unit cell: (132.08, 132.08, 127.92, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 240 16.00 P 16 15.00 Mg 8 11.99 O 7048 8.00 N 6544 7.00 C 23960 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: 13.17 Conformation dependent library (CDL) restraints added in 6.2 seconds 9424 Ramachandran restraints generated. 4712 Oldfield, 0 Emsley, 4712 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8656 Finding SS restraints... Secondary structure from input PDB file: 176 helices and 34 sheets defined 41.6% alpha, 16.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.34 Creating SS restraints... Processing helix chain 'A' and resid 20 through 25 Processing helix chain 'A' and resid 51 through 63 removed outlier: 3.551A pdb=" N SER A 63 " --> pdb=" O VAL A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 76 removed outlier: 3.564A pdb=" N ASP A 74 " --> pdb=" O VAL A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 83 removed outlier: 3.808A pdb=" N TYR A 82 " --> pdb=" O ALA A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 110 No H-bonds generated for 'chain 'A' and resid 108 through 110' Processing helix chain 'A' and resid 114 through 123 removed outlier: 3.682A pdb=" N LEU A 118 " --> pdb=" O SER A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 148 removed outlier: 3.537A pdb=" N LYS A 148 " --> pdb=" O VAL A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 165 removed outlier: 3.659A pdb=" N GLY A 159 " --> pdb=" O THR A 155 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ARG A 163 " --> pdb=" O GLY A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 198 removed outlier: 3.608A pdb=" N GLY A 188 " --> pdb=" O GLY A 184 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ARG A 189 " --> pdb=" O LYS A 185 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLY A 198 " --> pdb=" O GLY A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 235 removed outlier: 3.582A pdb=" N LEU A 221 " --> pdb=" O ARG A 217 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N MET A 224 " --> pdb=" O PHE A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 263 removed outlier: 3.502A pdb=" N ARG A 254 " --> pdb=" O GLU A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 287 removed outlier: 3.604A pdb=" N SER A 280 " --> pdb=" O THR A 276 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ILE A 281 " --> pdb=" O ALA A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 323 removed outlier: 3.607A pdb=" N ILE A 315 " --> pdb=" O SER A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 352 removed outlier: 3.549A pdb=" N TYR A 346 " --> pdb=" O THR A 342 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N CYS A 350 " --> pdb=" O TYR A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 386 No H-bonds generated for 'chain 'A' and resid 384 through 386' Processing helix chain 'A' and resid 387 through 395 removed outlier: 3.504A pdb=" N SER A 393 " --> pdb=" O HIS A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 409 removed outlier: 4.027A pdb=" N ILE A 408 " --> pdb=" O GLY A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 435 Processing helix chain 'A' and resid 441 through 450 Processing helix chain 'A' and resid 453 through 463 removed outlier: 3.683A pdb=" N GLU A 457 " --> pdb=" O CYS A 453 " (cutoff:3.500A) Processing helix chain 'I' and resid 15 through 30 Processing helix chain 'I' and resid 60 through 75 removed outlier: 4.173A pdb=" N VAL I 64 " --> pdb=" O ASP I 60 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N MET I 65 " --> pdb=" O PRO I 61 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLU I 67 " --> pdb=" O GLY I 63 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 25 Processing helix chain 'B' and resid 51 through 63 removed outlier: 3.546A pdb=" N SER B 63 " --> pdb=" O VAL B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 76 removed outlier: 3.601A pdb=" N ASP B 74 " --> pdb=" O VAL B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 83 removed outlier: 3.800A pdb=" N TYR B 82 " --> pdb=" O ALA B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 110 No H-bonds generated for 'chain 'B' and resid 108 through 110' Processing helix chain 'B' and resid 114 through 123 removed outlier: 3.699A pdb=" N LEU B 118 " --> pdb=" O SER B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 148 removed outlier: 3.535A pdb=" N LYS B 148 " --> pdb=" O VAL B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 165 removed outlier: 3.655A pdb=" N GLY B 159 " --> pdb=" O THR B 155 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ARG B 163 " --> pdb=" O GLY B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 198 removed outlier: 3.592A pdb=" N GLY B 188 " --> pdb=" O GLY B 184 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ARG B 189 " --> pdb=" O LYS B 185 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLY B 198 " --> pdb=" O GLY B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 215 through 235 removed outlier: 3.599A pdb=" N LEU B 221 " --> pdb=" O ARG B 217 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N MET B 224 " --> pdb=" O PHE B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 263 removed outlier: 3.503A pdb=" N ARG B 254 " --> pdb=" O GLU B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 287 removed outlier: 3.599A pdb=" N SER B 280 " --> pdb=" O THR B 276 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE B 281 " --> pdb=" O ALA B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 311 through 323 removed outlier: 3.621A pdb=" N ILE B 315 " --> pdb=" O SER B 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 352 removed outlier: 3.535A pdb=" N TYR B 346 " --> pdb=" O THR B 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 386 No H-bonds generated for 'chain 'B' and resid 384 through 386' Processing helix chain 'B' and resid 387 through 395 removed outlier: 3.503A pdb=" N SER B 393 " --> pdb=" O HIS B 389 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 409 removed outlier: 4.045A pdb=" N ILE B 408 " --> pdb=" O GLY B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 435 Processing helix chain 'B' and resid 441 through 450 Processing helix chain 'B' and resid 453 through 463 removed outlier: 3.700A pdb=" N GLU B 457 " --> pdb=" O CYS B 453 " (cutoff:3.500A) Processing helix chain 'J' and resid 15 through 30 Processing helix chain 'J' and resid 60 through 75 removed outlier: 4.169A pdb=" N VAL J 64 " --> pdb=" O ASP J 60 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N MET J 65 " --> pdb=" O PRO J 61 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLU J 67 " --> pdb=" O GLY J 63 " (cutoff:3.500A) Processing helix chain 'C' and resid 20 through 25 Processing helix chain 'C' and resid 51 through 63 removed outlier: 3.541A pdb=" N SER C 63 " --> pdb=" O VAL C 59 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 76 removed outlier: 3.563A pdb=" N ASP C 74 " --> pdb=" O VAL C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 78 through 83 removed outlier: 3.802A pdb=" N TYR C 82 " --> pdb=" O ALA C 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 108 through 110 No H-bonds generated for 'chain 'C' and resid 108 through 110' Processing helix chain 'C' and resid 114 through 123 removed outlier: 3.698A pdb=" N LEU C 118 " --> pdb=" O SER C 114 " (cutoff:3.500A) Processing helix chain 'C' and resid 143 through 148 removed outlier: 3.542A pdb=" N LYS C 148 " --> pdb=" O VAL C 144 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 165 removed outlier: 3.653A pdb=" N GLY C 159 " --> pdb=" O THR C 155 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ARG C 163 " --> pdb=" O GLY C 159 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 198 removed outlier: 3.599A pdb=" N GLY C 188 " --> pdb=" O GLY C 184 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ARG C 189 " --> pdb=" O LYS C 185 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLY C 198 " --> pdb=" O GLY C 194 " (cutoff:3.500A) Processing helix chain 'C' and resid 215 through 235 removed outlier: 3.599A pdb=" N LEU C 221 " --> pdb=" O ARG C 217 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N MET C 224 " --> pdb=" O PHE C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 248 through 263 Processing helix chain 'C' and resid 274 through 287 removed outlier: 3.603A pdb=" N SER C 280 " --> pdb=" O THR C 276 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE C 281 " --> pdb=" O ALA C 277 " (cutoff:3.500A) Processing helix chain 'C' and resid 311 through 323 removed outlier: 3.622A pdb=" N ILE C 315 " --> pdb=" O SER C 311 " (cutoff:3.500A) Processing helix chain 'C' and resid 339 through 352 removed outlier: 3.549A pdb=" N TYR C 346 " --> pdb=" O THR C 342 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 386 No H-bonds generated for 'chain 'C' and resid 384 through 386' Processing helix chain 'C' and resid 387 through 395 Processing helix chain 'C' and resid 404 through 409 removed outlier: 4.035A pdb=" N ILE C 408 " --> pdb=" O GLY C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 414 through 435 Processing helix chain 'C' and resid 441 through 450 Processing helix chain 'C' and resid 453 through 463 removed outlier: 3.693A pdb=" N GLU C 457 " --> pdb=" O CYS C 453 " (cutoff:3.500A) Processing helix chain 'K' and resid 15 through 30 Processing helix chain 'K' and resid 60 through 75 removed outlier: 4.174A pdb=" N VAL K 64 " --> pdb=" O ASP K 60 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N MET K 65 " --> pdb=" O PRO K 61 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLU K 67 " --> pdb=" O GLY K 63 " (cutoff:3.500A) Processing helix chain 'D' and resid 20 through 25 Processing helix chain 'D' and resid 51 through 63 removed outlier: 3.540A pdb=" N SER D 63 " --> pdb=" O VAL D 59 " (cutoff:3.500A) Processing helix chain 'D' and resid 71 through 76 removed outlier: 3.607A pdb=" N ASP D 74 " --> pdb=" O VAL D 71 " (cutoff:3.500A) Processing helix chain 'D' and resid 78 through 83 removed outlier: 3.795A pdb=" N TYR D 82 " --> pdb=" O ALA D 78 " (cutoff:3.500A) Processing helix chain 'D' and resid 108 through 110 No H-bonds generated for 'chain 'D' and resid 108 through 110' Processing helix chain 'D' and resid 114 through 123 removed outlier: 3.692A pdb=" N LEU D 118 " --> pdb=" O SER D 114 " (cutoff:3.500A) Processing helix chain 'D' and resid 143 through 148 removed outlier: 3.541A pdb=" N LYS D 148 " --> pdb=" O VAL D 144 " (cutoff:3.500A) Processing helix chain 'D' and resid 155 through 165 removed outlier: 3.659A pdb=" N GLY D 159 " --> pdb=" O THR D 155 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ARG D 163 " --> pdb=" O GLY D 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 198 removed outlier: 3.596A pdb=" N GLY D 188 " --> pdb=" O GLY D 184 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ARG D 189 " --> pdb=" O LYS D 185 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLY D 198 " --> pdb=" O GLY D 194 " (cutoff:3.500A) Processing helix chain 'D' and resid 215 through 235 removed outlier: 3.603A pdb=" N LEU D 221 " --> pdb=" O ARG D 217 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N MET D 224 " --> pdb=" O PHE D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 248 through 263 Processing helix chain 'D' and resid 274 through 287 removed outlier: 3.598A pdb=" N SER D 280 " --> pdb=" O THR D 276 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE D 281 " --> pdb=" O ALA D 277 " (cutoff:3.500A) Processing helix chain 'D' and resid 311 through 323 removed outlier: 3.609A pdb=" N ILE D 315 " --> pdb=" O SER D 311 " (cutoff:3.500A) Processing helix chain 'D' and resid 339 through 352 removed outlier: 3.546A pdb=" N TYR D 346 " --> pdb=" O THR D 342 " (cutoff:3.500A) Processing helix chain 'D' and resid 384 through 386 No H-bonds generated for 'chain 'D' and resid 384 through 386' Processing helix chain 'D' and resid 387 through 395 removed outlier: 3.513A pdb=" N SER D 393 " --> pdb=" O HIS D 389 " (cutoff:3.500A) Processing helix chain 'D' and resid 404 through 409 removed outlier: 4.030A pdb=" N ILE D 408 " --> pdb=" O GLY D 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 435 Processing helix chain 'D' and resid 441 through 450 Processing helix chain 'D' and resid 453 through 463 removed outlier: 3.692A pdb=" N GLU D 457 " --> pdb=" O CYS D 453 " (cutoff:3.500A) Processing helix chain 'L' and resid 15 through 30 Processing helix chain 'L' and resid 61 through 75 removed outlier: 3.646A pdb=" N MET L 65 " --> pdb=" O PRO L 61 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLU L 67 " --> pdb=" O GLY L 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 20 through 25 Processing helix chain 'E' and resid 51 through 63 removed outlier: 3.534A pdb=" N SER E 63 " --> pdb=" O VAL E 59 " (cutoff:3.500A) Processing helix chain 'E' and resid 71 through 76 removed outlier: 3.589A pdb=" N ASP E 74 " --> pdb=" O VAL E 71 " (cutoff:3.500A) Processing helix chain 'E' and resid 78 through 83 removed outlier: 3.801A pdb=" N TYR E 82 " --> pdb=" O ALA E 78 " (cutoff:3.500A) Processing helix chain 'E' and resid 108 through 110 No H-bonds generated for 'chain 'E' and resid 108 through 110' Processing helix chain 'E' and resid 114 through 123 removed outlier: 3.696A pdb=" N LEU E 118 " --> pdb=" O SER E 114 " (cutoff:3.500A) Processing helix chain 'E' and resid 143 through 148 removed outlier: 3.541A pdb=" N LYS E 148 " --> pdb=" O VAL E 144 " (cutoff:3.500A) Processing helix chain 'E' and resid 155 through 165 removed outlier: 3.671A pdb=" N GLY E 159 " --> pdb=" O THR E 155 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ARG E 163 " --> pdb=" O GLY E 159 " (cutoff:3.500A) Processing helix chain 'E' and resid 183 through 198 removed outlier: 3.591A pdb=" N GLY E 188 " --> pdb=" O GLY E 184 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ARG E 189 " --> pdb=" O LYS E 185 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLY E 198 " --> pdb=" O GLY E 194 " (cutoff:3.500A) Processing helix chain 'E' and resid 215 through 235 removed outlier: 3.618A pdb=" N LEU E 221 " --> pdb=" O ARG E 217 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N MET E 224 " --> pdb=" O PHE E 220 " (cutoff:3.500A) Processing helix chain 'E' and resid 248 through 263 Processing helix chain 'E' and resid 274 through 287 removed outlier: 3.591A pdb=" N SER E 280 " --> pdb=" O THR E 276 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE E 281 " --> pdb=" O ALA E 277 " (cutoff:3.500A) Processing helix chain 'E' and resid 311 through 323 removed outlier: 3.626A pdb=" N ILE E 315 " --> pdb=" O SER E 311 " (cutoff:3.500A) Processing helix chain 'E' and resid 339 through 352 removed outlier: 3.533A pdb=" N TYR E 346 " --> pdb=" O THR E 342 " (cutoff:3.500A) Processing helix chain 'E' and resid 384 through 386 No H-bonds generated for 'chain 'E' and resid 384 through 386' Processing helix chain 'E' and resid 387 through 395 removed outlier: 3.506A pdb=" N SER E 393 " --> pdb=" O HIS E 389 " (cutoff:3.500A) Processing helix chain 'E' and resid 404 through 409 removed outlier: 4.026A pdb=" N ILE E 408 " --> pdb=" O GLY E 404 " (cutoff:3.500A) Processing helix chain 'E' and resid 414 through 435 removed outlier: 3.502A pdb=" N GLY E 435 " --> pdb=" O ALA E 431 " (cutoff:3.500A) Processing helix chain 'E' and resid 441 through 450 Processing helix chain 'E' and resid 453 through 463 removed outlier: 3.705A pdb=" N GLU E 457 " --> pdb=" O CYS E 453 " (cutoff:3.500A) Processing helix chain 'M' and resid 15 through 30 Processing helix chain 'M' and resid 60 through 75 removed outlier: 4.170A pdb=" N VAL M 64 " --> pdb=" O ASP M 60 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N MET M 65 " --> pdb=" O PRO M 61 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLU M 67 " --> pdb=" O GLY M 63 " (cutoff:3.500A) Processing helix chain 'F' and resid 20 through 25 Processing helix chain 'F' and resid 51 through 63 removed outlier: 3.545A pdb=" N SER F 63 " --> pdb=" O VAL F 59 " (cutoff:3.500A) Processing helix chain 'F' and resid 71 through 76 removed outlier: 3.593A pdb=" N ASP F 74 " --> pdb=" O VAL F 71 " (cutoff:3.500A) Processing helix chain 'F' and resid 78 through 83 removed outlier: 3.803A pdb=" N TYR F 82 " --> pdb=" O ALA F 78 " (cutoff:3.500A) Processing helix chain 'F' and resid 108 through 110 No H-bonds generated for 'chain 'F' and resid 108 through 110' Processing helix chain 'F' and resid 114 through 123 removed outlier: 3.691A pdb=" N LEU F 118 " --> pdb=" O SER F 114 " (cutoff:3.500A) Processing helix chain 'F' and resid 143 through 148 removed outlier: 3.520A pdb=" N LYS F 148 " --> pdb=" O VAL F 144 " (cutoff:3.500A) Processing helix chain 'F' and resid 155 through 165 removed outlier: 3.657A pdb=" N GLY F 159 " --> pdb=" O THR F 155 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ARG F 163 " --> pdb=" O GLY F 159 " (cutoff:3.500A) Processing helix chain 'F' and resid 183 through 198 removed outlier: 3.596A pdb=" N GLY F 188 " --> pdb=" O GLY F 184 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ARG F 189 " --> pdb=" O LYS F 185 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLY F 198 " --> pdb=" O GLY F 194 " (cutoff:3.500A) Processing helix chain 'F' and resid 215 through 235 removed outlier: 3.599A pdb=" N LEU F 221 " --> pdb=" O ARG F 217 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N MET F 224 " --> pdb=" O PHE F 220 " (cutoff:3.500A) Processing helix chain 'F' and resid 248 through 263 Processing helix chain 'F' and resid 274 through 287 removed outlier: 3.587A pdb=" N SER F 280 " --> pdb=" O THR F 276 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE F 281 " --> pdb=" O ALA F 277 " (cutoff:3.500A) Processing helix chain 'F' and resid 311 through 323 removed outlier: 3.618A pdb=" N ILE F 315 " --> pdb=" O SER F 311 " (cutoff:3.500A) Processing helix chain 'F' and resid 339 through 352 removed outlier: 3.532A pdb=" N TYR F 346 " --> pdb=" O THR F 342 " (cutoff:3.500A) Processing helix chain 'F' and resid 384 through 386 No H-bonds generated for 'chain 'F' and resid 384 through 386' Processing helix chain 'F' and resid 387 through 395 removed outlier: 3.501A pdb=" N SER F 393 " --> pdb=" O HIS F 389 " (cutoff:3.500A) Processing helix chain 'F' and resid 404 through 409 removed outlier: 4.036A pdb=" N ILE F 408 " --> pdb=" O GLY F 404 " (cutoff:3.500A) Processing helix chain 'F' and resid 414 through 435 Processing helix chain 'F' and resid 441 through 450 Processing helix chain 'F' and resid 453 through 463 removed outlier: 3.688A pdb=" N GLU F 457 " --> pdb=" O CYS F 453 " (cutoff:3.500A) Processing helix chain 'N' and resid 15 through 30 Processing helix chain 'N' and resid 60 through 75 removed outlier: 4.165A pdb=" N VAL N 64 " --> pdb=" O ASP N 60 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N MET N 65 " --> pdb=" O PRO N 61 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N GLU N 67 " --> pdb=" O GLY N 63 " (cutoff:3.500A) Processing helix chain 'G' and resid 20 through 25 Processing helix chain 'G' and resid 51 through 63 removed outlier: 3.548A pdb=" N SER G 63 " --> pdb=" O VAL G 59 " (cutoff:3.500A) Processing helix chain 'G' and resid 71 through 76 removed outlier: 3.599A pdb=" N ASP G 74 " --> pdb=" O VAL G 71 " (cutoff:3.500A) Processing helix chain 'G' and resid 78 through 83 removed outlier: 3.805A pdb=" N TYR G 82 " --> pdb=" O ALA G 78 " (cutoff:3.500A) Processing helix chain 'G' and resid 108 through 110 No H-bonds generated for 'chain 'G' and resid 108 through 110' Processing helix chain 'G' and resid 114 through 123 removed outlier: 3.677A pdb=" N LEU G 118 " --> pdb=" O SER G 114 " (cutoff:3.500A) Processing helix chain 'G' and resid 143 through 148 removed outlier: 3.536A pdb=" N LYS G 148 " --> pdb=" O VAL G 144 " (cutoff:3.500A) Processing helix chain 'G' and resid 155 through 165 removed outlier: 3.673A pdb=" N GLY G 159 " --> pdb=" O THR G 155 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ARG G 163 " --> pdb=" O GLY G 159 " (cutoff:3.500A) Processing helix chain 'G' and resid 183 through 198 removed outlier: 3.599A pdb=" N GLY G 188 " --> pdb=" O GLY G 184 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ARG G 189 " --> pdb=" O LYS G 185 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLY G 198 " --> pdb=" O GLY G 194 " (cutoff:3.500A) Processing helix chain 'G' and resid 215 through 235 removed outlier: 3.600A pdb=" N LEU G 221 " --> pdb=" O ARG G 217 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N MET G 224 " --> pdb=" O PHE G 220 " (cutoff:3.500A) Processing helix chain 'G' and resid 248 through 263 removed outlier: 3.507A pdb=" N ARG G 254 " --> pdb=" O GLU G 250 " (cutoff:3.500A) Processing helix chain 'G' and resid 274 through 287 removed outlier: 3.586A pdb=" N SER G 280 " --> pdb=" O THR G 276 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE G 281 " --> pdb=" O ALA G 277 " (cutoff:3.500A) Processing helix chain 'G' and resid 311 through 323 removed outlier: 3.609A pdb=" N ILE G 315 " --> pdb=" O SER G 311 " (cutoff:3.500A) Processing helix chain 'G' and resid 339 through 352 removed outlier: 3.530A pdb=" N TYR G 346 " --> pdb=" O THR G 342 " (cutoff:3.500A) Processing helix chain 'G' and resid 384 through 386 No H-bonds generated for 'chain 'G' and resid 384 through 386' Processing helix chain 'G' and resid 387 through 395 removed outlier: 3.512A pdb=" N SER G 393 " --> pdb=" O HIS G 389 " (cutoff:3.500A) Processing helix chain 'G' and resid 404 through 409 removed outlier: 4.019A pdb=" N ILE G 408 " --> pdb=" O GLY G 404 " (cutoff:3.500A) Processing helix chain 'G' and resid 414 through 435 Processing helix chain 'G' and resid 441 through 450 Processing helix chain 'G' and resid 453 through 463 removed outlier: 3.693A pdb=" N GLU G 457 " --> pdb=" O CYS G 453 " (cutoff:3.500A) Processing helix chain 'O' and resid 15 through 30 Processing helix chain 'O' and resid 60 through 75 removed outlier: 4.168A pdb=" N VAL O 64 " --> pdb=" O ASP O 60 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N MET O 65 " --> pdb=" O PRO O 61 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLU O 67 " --> pdb=" O GLY O 63 " (cutoff:3.500A) Processing helix chain 'H' and resid 20 through 25 Processing helix chain 'H' and resid 51 through 63 removed outlier: 3.541A pdb=" N SER H 63 " --> pdb=" O VAL H 59 " (cutoff:3.500A) Processing helix chain 'H' and resid 71 through 76 removed outlier: 3.600A pdb=" N ASP H 74 " --> pdb=" O VAL H 71 " (cutoff:3.500A) Processing helix chain 'H' and resid 78 through 83 removed outlier: 3.799A pdb=" N TYR H 82 " --> pdb=" O ALA H 78 " (cutoff:3.500A) Processing helix chain 'H' and resid 108 through 110 No H-bonds generated for 'chain 'H' and resid 108 through 110' Processing helix chain 'H' and resid 114 through 123 removed outlier: 3.686A pdb=" N LEU H 118 " --> pdb=" O SER H 114 " (cutoff:3.500A) Processing helix chain 'H' and resid 143 through 148 removed outlier: 3.528A pdb=" N LYS H 148 " --> pdb=" O VAL H 144 " (cutoff:3.500A) Processing helix chain 'H' and resid 155 through 165 removed outlier: 3.660A pdb=" N GLY H 159 " --> pdb=" O THR H 155 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ARG H 163 " --> pdb=" O GLY H 159 " (cutoff:3.500A) Processing helix chain 'H' and resid 183 through 198 removed outlier: 3.599A pdb=" N GLY H 188 " --> pdb=" O GLY H 184 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ARG H 189 " --> pdb=" O LYS H 185 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLY H 198 " --> pdb=" O GLY H 194 " (cutoff:3.500A) Processing helix chain 'H' and resid 215 through 235 removed outlier: 3.605A pdb=" N LEU H 221 " --> pdb=" O ARG H 217 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N MET H 224 " --> pdb=" O PHE H 220 " (cutoff:3.500A) Processing helix chain 'H' and resid 248 through 263 Processing helix chain 'H' and resid 274 through 287 removed outlier: 3.585A pdb=" N SER H 280 " --> pdb=" O THR H 276 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE H 281 " --> pdb=" O ALA H 277 " (cutoff:3.500A) Processing helix chain 'H' and resid 311 through 323 removed outlier: 3.608A pdb=" N ILE H 315 " --> pdb=" O SER H 311 " (cutoff:3.500A) Processing helix chain 'H' and resid 339 through 352 removed outlier: 3.543A pdb=" N TYR H 346 " --> pdb=" O THR H 342 " (cutoff:3.500A) Processing helix chain 'H' and resid 384 through 386 No H-bonds generated for 'chain 'H' and resid 384 through 386' Processing helix chain 'H' and resid 387 through 395 removed outlier: 3.509A pdb=" N SER H 393 " --> pdb=" O HIS H 389 " (cutoff:3.500A) Processing helix chain 'H' and resid 404 through 409 removed outlier: 4.022A pdb=" N ILE H 408 " --> pdb=" O GLY H 404 " (cutoff:3.500A) Processing helix chain 'H' and resid 414 through 435 Processing helix chain 'H' and resid 441 through 450 Processing helix chain 'H' and resid 453 through 463 removed outlier: 3.683A pdb=" N GLU H 457 " --> pdb=" O CYS H 453 " (cutoff:3.500A) Processing helix chain 'P' and resid 15 through 30 Processing helix chain 'P' and resid 61 through 75 removed outlier: 3.649A pdb=" N MET P 65 " --> pdb=" O PRO P 61 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLU P 67 " --> pdb=" O GLY P 63 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 85 through 91 removed outlier: 5.492A pdb=" N ALA A 86 " --> pdb=" O ALA A 104 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N ALA A 104 " --> pdb=" O ALA A 86 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ARG A 88 " --> pdb=" O TYR A 102 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N LEU A 39 " --> pdb=" O MET A 140 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N MET A 140 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N LEU A 41 " --> pdb=" O GLU A 138 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 171 through 175 removed outlier: 6.692A pdb=" N LEU A 172 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 8.192A pdb=" N KCX A 203 " --> pdb=" O LEU A 172 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N ALA A 174 " --> pdb=" O KCX A 203 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N MET A 202 " --> pdb=" O TYR A 241 " (cutoff:3.500A) removed outlier: 8.400A pdb=" N ASN A 243 " --> pdb=" O MET A 202 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N HIS A 240 " --> pdb=" O ILE A 266 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N MET A 268 " --> pdb=" O HIS A 240 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N LEU A 242 " --> pdb=" O MET A 268 " (cutoff:3.500A) removed outlier: 8.029A pdb=" N ASP A 270 " --> pdb=" O LEU A 242 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N VAL A 267 " --> pdb=" O HIS A 293 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N HIS A 295 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N VAL A 269 " --> pdb=" O HIS A 295 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N LEU A 292 " --> pdb=" O HIS A 326 " (cutoff:3.500A) removed outlier: 8.732A pdb=" N HIS A 328 " --> pdb=" O LEU A 292 " (cutoff:3.500A) removed outlier: 8.287A pdb=" N MET A 294 " --> pdb=" O HIS A 328 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N LEU A 327 " --> pdb=" O VAL A 378 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N SER A 380 " --> pdb=" O LEU A 327 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 354 through 355 Processing sheet with id=AA4, first strand: chain 'I' and resid 49 through 50 removed outlier: 7.189A pdb=" N ILE I 80 " --> pdb=" O ILE I 99 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N ILE I 99 " --> pdb=" O ILE I 80 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ILE I 82 " --> pdb=" O SER I 97 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N SER I 97 " --> pdb=" O ILE I 82 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N ALA I 84 " --> pdb=" O THR I 95 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'I' and resid 109 through 115 removed outlier: 4.348A pdb=" N TYR I 123 " --> pdb=" O GLU J 115 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N HIS I 125 " --> pdb=" O ARG J 113 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N ARG J 113 " --> pdb=" O HIS I 125 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ILE I 127 " --> pdb=" O MET J 111 " (cutoff:3.500A) removed outlier: 8.513A pdb=" N MET J 111 " --> pdb=" O ILE I 127 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N TYR J 123 " --> pdb=" O GLU K 115 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N HIS J 125 " --> pdb=" O ARG K 113 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N ARG K 113 " --> pdb=" O HIS J 125 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N ILE J 127 " --> pdb=" O MET K 111 " (cutoff:3.500A) removed outlier: 8.503A pdb=" N MET K 111 " --> pdb=" O ILE J 127 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N TYR K 123 " --> pdb=" O GLU L 115 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N HIS K 125 " --> pdb=" O ARG L 113 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N ARG L 113 " --> pdb=" O HIS K 125 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ILE K 127 " --> pdb=" O MET L 111 " (cutoff:3.500A) removed outlier: 8.510A pdb=" N MET L 111 " --> pdb=" O ILE K 127 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N TYR L 123 " --> pdb=" O GLU I 115 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N HIS L 125 " --> pdb=" O ARG I 113 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N ARG I 113 " --> pdb=" O HIS L 125 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ILE L 127 " --> pdb=" O MET I 111 " (cutoff:3.500A) removed outlier: 8.520A pdb=" N MET I 111 " --> pdb=" O ILE L 127 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 85 through 91 removed outlier: 5.491A pdb=" N ALA B 86 " --> pdb=" O ALA B 104 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N ALA B 104 " --> pdb=" O ALA B 86 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ARG B 88 " --> pdb=" O TYR B 102 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N LEU B 39 " --> pdb=" O MET B 140 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N MET B 140 " --> pdb=" O LEU B 39 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N LEU B 41 " --> pdb=" O GLU B 138 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 171 through 175 removed outlier: 6.684A pdb=" N LEU B 172 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 8.183A pdb=" N KCX B 203 " --> pdb=" O LEU B 172 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N ALA B 174 " --> pdb=" O KCX B 203 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N MET B 202 " --> pdb=" O TYR B 241 " (cutoff:3.500A) removed outlier: 8.397A pdb=" N ASN B 243 " --> pdb=" O MET B 202 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N HIS B 240 " --> pdb=" O ILE B 266 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N MET B 268 " --> pdb=" O HIS B 240 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N LEU B 242 " --> pdb=" O MET B 268 " (cutoff:3.500A) removed outlier: 8.029A pdb=" N ASP B 270 " --> pdb=" O LEU B 242 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N VAL B 267 " --> pdb=" O HIS B 293 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N HIS B 295 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N VAL B 269 " --> pdb=" O HIS B 295 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N LEU B 292 " --> pdb=" O HIS B 326 " (cutoff:3.500A) removed outlier: 8.746A pdb=" N HIS B 328 " --> pdb=" O LEU B 292 " (cutoff:3.500A) removed outlier: 8.283A pdb=" N MET B 294 " --> pdb=" O HIS B 328 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N LEU B 327 " --> pdb=" O VAL B 378 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N SER B 380 " --> pdb=" O LEU B 327 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 354 through 355 Processing sheet with id=AA9, first strand: chain 'J' and resid 49 through 50 removed outlier: 7.191A pdb=" N ILE J 80 " --> pdb=" O ILE J 99 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N ILE J 99 " --> pdb=" O ILE J 80 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ILE J 82 " --> pdb=" O SER J 97 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N SER J 97 " --> pdb=" O ILE J 82 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ALA J 84 " --> pdb=" O THR J 95 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 85 through 91 removed outlier: 5.494A pdb=" N ALA C 86 " --> pdb=" O ALA C 104 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ALA C 104 " --> pdb=" O ALA C 86 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ARG C 88 " --> pdb=" O TYR C 102 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N LEU C 39 " --> pdb=" O MET C 140 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N MET C 140 " --> pdb=" O LEU C 39 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N LEU C 41 " --> pdb=" O GLU C 138 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 171 through 175 removed outlier: 6.693A pdb=" N LEU C 172 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 8.202A pdb=" N KCX C 203 " --> pdb=" O LEU C 172 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N ALA C 174 " --> pdb=" O KCX C 203 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N MET C 202 " --> pdb=" O TYR C 241 " (cutoff:3.500A) removed outlier: 8.405A pdb=" N ASN C 243 " --> pdb=" O MET C 202 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N HIS C 240 " --> pdb=" O ILE C 266 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N MET C 268 " --> pdb=" O HIS C 240 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N LEU C 242 " --> pdb=" O MET C 268 " (cutoff:3.500A) removed outlier: 8.040A pdb=" N ASP C 270 " --> pdb=" O LEU C 242 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N VAL C 267 " --> pdb=" O HIS C 293 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N HIS C 295 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N VAL C 269 " --> pdb=" O HIS C 295 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N LEU C 292 " --> pdb=" O HIS C 326 " (cutoff:3.500A) removed outlier: 8.745A pdb=" N HIS C 328 " --> pdb=" O LEU C 292 " (cutoff:3.500A) removed outlier: 8.301A pdb=" N MET C 294 " --> pdb=" O HIS C 328 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N LEU C 327 " --> pdb=" O VAL C 378 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N SER C 380 " --> pdb=" O LEU C 327 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 354 through 355 Processing sheet with id=AB4, first strand: chain 'K' and resid 49 through 50 removed outlier: 7.198A pdb=" N ILE K 80 " --> pdb=" O ILE K 99 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N ILE K 99 " --> pdb=" O ILE K 80 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ILE K 82 " --> pdb=" O SER K 97 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N SER K 97 " --> pdb=" O ILE K 82 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ALA K 84 " --> pdb=" O THR K 95 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 85 through 91 removed outlier: 5.485A pdb=" N ALA D 86 " --> pdb=" O ALA D 104 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N ALA D 104 " --> pdb=" O ALA D 86 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ARG D 88 " --> pdb=" O TYR D 102 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N LEU D 39 " --> pdb=" O MET D 140 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N MET D 140 " --> pdb=" O LEU D 39 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N LEU D 41 " --> pdb=" O GLU D 138 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 171 through 175 removed outlier: 6.690A pdb=" N LEU D 172 " --> pdb=" O PHE D 201 " (cutoff:3.500A) removed outlier: 8.182A pdb=" N KCX D 203 " --> pdb=" O LEU D 172 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N ALA D 174 " --> pdb=" O KCX D 203 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N MET D 202 " --> pdb=" O TYR D 241 " (cutoff:3.500A) removed outlier: 8.405A pdb=" N ASN D 243 " --> pdb=" O MET D 202 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N HIS D 240 " --> pdb=" O ILE D 266 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N MET D 268 " --> pdb=" O HIS D 240 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N LEU D 242 " --> pdb=" O MET D 268 " (cutoff:3.500A) removed outlier: 8.024A pdb=" N ASP D 270 " --> pdb=" O LEU D 242 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N VAL D 267 " --> pdb=" O HIS D 293 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N HIS D 295 " --> pdb=" O VAL D 267 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N VAL D 269 " --> pdb=" O HIS D 295 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N LEU D 292 " --> pdb=" O HIS D 326 " (cutoff:3.500A) removed outlier: 8.746A pdb=" N HIS D 328 " --> pdb=" O LEU D 292 " (cutoff:3.500A) removed outlier: 8.296A pdb=" N MET D 294 " --> pdb=" O HIS D 328 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N LEU D 327 " --> pdb=" O VAL D 378 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N SER D 380 " --> pdb=" O LEU D 327 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 354 through 355 Processing sheet with id=AB8, first strand: chain 'L' and resid 49 through 50 removed outlier: 7.183A pdb=" N ILE L 80 " --> pdb=" O ILE L 99 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N ILE L 99 " --> pdb=" O ILE L 80 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ILE L 82 " --> pdb=" O SER L 97 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N SER L 97 " --> pdb=" O ILE L 82 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ALA L 84 " --> pdb=" O THR L 95 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 85 through 91 removed outlier: 5.510A pdb=" N ALA E 86 " --> pdb=" O ALA E 104 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N ALA E 104 " --> pdb=" O ALA E 86 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ARG E 88 " --> pdb=" O TYR E 102 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N LEU E 39 " --> pdb=" O MET E 140 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N MET E 140 " --> pdb=" O LEU E 39 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N LEU E 41 " --> pdb=" O GLU E 138 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 171 through 175 removed outlier: 6.692A pdb=" N LEU E 172 " --> pdb=" O PHE E 201 " (cutoff:3.500A) removed outlier: 8.190A pdb=" N KCX E 203 " --> pdb=" O LEU E 172 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N ALA E 174 " --> pdb=" O KCX E 203 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N MET E 202 " --> pdb=" O TYR E 241 " (cutoff:3.500A) removed outlier: 8.418A pdb=" N ASN E 243 " --> pdb=" O MET E 202 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N HIS E 240 " --> pdb=" O ILE E 266 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N MET E 268 " --> pdb=" O HIS E 240 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N LEU E 242 " --> pdb=" O MET E 268 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N ASP E 270 " --> pdb=" O LEU E 242 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N VAL E 267 " --> pdb=" O HIS E 293 " (cutoff:3.500A) removed outlier: 7.898A pdb=" N HIS E 295 " --> pdb=" O VAL E 267 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N VAL E 269 " --> pdb=" O HIS E 295 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N LEU E 292 " --> pdb=" O HIS E 326 " (cutoff:3.500A) removed outlier: 8.734A pdb=" N HIS E 328 " --> pdb=" O LEU E 292 " (cutoff:3.500A) removed outlier: 8.287A pdb=" N MET E 294 " --> pdb=" O HIS E 328 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N LEU E 327 " --> pdb=" O VAL E 378 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N SER E 380 " --> pdb=" O LEU E 327 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 354 through 355 Processing sheet with id=AC3, first strand: chain 'M' and resid 49 through 50 removed outlier: 7.195A pdb=" N ILE M 80 " --> pdb=" O ILE M 99 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N ILE M 99 " --> pdb=" O ILE M 80 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N ILE M 82 " --> pdb=" O SER M 97 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N SER M 97 " --> pdb=" O ILE M 82 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ALA M 84 " --> pdb=" O THR M 95 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'M' and resid 109 through 115 removed outlier: 4.323A pdb=" N TYR M 123 " --> pdb=" O GLU P 115 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N HIS M 125 " --> pdb=" O ARG P 113 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N ARG P 113 " --> pdb=" O HIS M 125 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ILE M 127 " --> pdb=" O MET P 111 " (cutoff:3.500A) removed outlier: 8.509A pdb=" N MET P 111 " --> pdb=" O ILE M 127 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N TYR P 123 " --> pdb=" O GLU O 115 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N HIS P 125 " --> pdb=" O ARG O 113 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N ARG O 113 " --> pdb=" O HIS P 125 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N ILE P 127 " --> pdb=" O MET O 111 " (cutoff:3.500A) removed outlier: 8.520A pdb=" N MET O 111 " --> pdb=" O ILE P 127 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N TYR O 123 " --> pdb=" O GLU N 115 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N HIS O 125 " --> pdb=" O ARG N 113 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N ARG N 113 " --> pdb=" O HIS O 125 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ILE O 127 " --> pdb=" O MET N 111 " (cutoff:3.500A) removed outlier: 8.499A pdb=" N MET N 111 " --> pdb=" O ILE O 127 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N TYR N 123 " --> pdb=" O GLU M 115 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N HIS N 125 " --> pdb=" O ARG M 113 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N ARG M 113 " --> pdb=" O HIS N 125 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ILE N 127 " --> pdb=" O MET M 111 " (cutoff:3.500A) removed outlier: 8.511A pdb=" N MET M 111 " --> pdb=" O ILE N 127 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 85 through 91 removed outlier: 5.506A pdb=" N ALA F 86 " --> pdb=" O ALA F 104 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ALA F 104 " --> pdb=" O ALA F 86 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ARG F 88 " --> pdb=" O TYR F 102 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N LEU F 39 " --> pdb=" O MET F 140 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N MET F 140 " --> pdb=" O LEU F 39 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N LEU F 41 " --> pdb=" O GLU F 138 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 171 through 175 removed outlier: 6.685A pdb=" N LEU F 172 " --> pdb=" O PHE F 201 " (cutoff:3.500A) removed outlier: 8.177A pdb=" N KCX F 203 " --> pdb=" O LEU F 172 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N ALA F 174 " --> pdb=" O KCX F 203 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N MET F 202 " --> pdb=" O TYR F 241 " (cutoff:3.500A) removed outlier: 8.381A pdb=" N ASN F 243 " --> pdb=" O MET F 202 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N HIS F 240 " --> pdb=" O ILE F 266 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N MET F 268 " --> pdb=" O HIS F 240 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N LEU F 242 " --> pdb=" O MET F 268 " (cutoff:3.500A) removed outlier: 8.024A pdb=" N ASP F 270 " --> pdb=" O LEU F 242 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N VAL F 267 " --> pdb=" O HIS F 293 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N HIS F 295 " --> pdb=" O VAL F 267 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N VAL F 269 " --> pdb=" O HIS F 295 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N LEU F 292 " --> pdb=" O HIS F 326 " (cutoff:3.500A) removed outlier: 8.730A pdb=" N HIS F 328 " --> pdb=" O LEU F 292 " (cutoff:3.500A) removed outlier: 8.275A pdb=" N MET F 294 " --> pdb=" O HIS F 328 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N LEU F 327 " --> pdb=" O VAL F 378 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N SER F 380 " --> pdb=" O LEU F 327 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 354 through 355 Processing sheet with id=AC8, first strand: chain 'N' and resid 49 through 50 removed outlier: 7.193A pdb=" N ILE N 80 " --> pdb=" O ILE N 99 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N ILE N 99 " --> pdb=" O ILE N 80 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ILE N 82 " --> pdb=" O SER N 97 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N SER N 97 " --> pdb=" O ILE N 82 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N ALA N 84 " --> pdb=" O THR N 95 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 85 through 91 removed outlier: 5.509A pdb=" N ALA G 86 " --> pdb=" O ALA G 104 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N ALA G 104 " --> pdb=" O ALA G 86 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ARG G 88 " --> pdb=" O TYR G 102 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N LEU G 39 " --> pdb=" O MET G 140 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N MET G 140 " --> pdb=" O LEU G 39 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N LEU G 41 " --> pdb=" O GLU G 138 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 171 through 175 removed outlier: 6.690A pdb=" N LEU G 172 " --> pdb=" O PHE G 201 " (cutoff:3.500A) removed outlier: 8.180A pdb=" N KCX G 203 " --> pdb=" O LEU G 172 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N ALA G 174 " --> pdb=" O KCX G 203 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N MET G 202 " --> pdb=" O TYR G 241 " (cutoff:3.500A) removed outlier: 8.409A pdb=" N ASN G 243 " --> pdb=" O MET G 202 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N HIS G 240 " --> pdb=" O ILE G 266 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N MET G 268 " --> pdb=" O HIS G 240 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N LEU G 242 " --> pdb=" O MET G 268 " (cutoff:3.500A) removed outlier: 8.000A pdb=" N ASP G 270 " --> pdb=" O LEU G 242 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N VAL G 267 " --> pdb=" O HIS G 293 " (cutoff:3.500A) removed outlier: 7.899A pdb=" N HIS G 295 " --> pdb=" O VAL G 267 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N VAL G 269 " --> pdb=" O HIS G 295 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N LEU G 292 " --> pdb=" O HIS G 326 " (cutoff:3.500A) removed outlier: 8.722A pdb=" N HIS G 328 " --> pdb=" O LEU G 292 " (cutoff:3.500A) removed outlier: 8.269A pdb=" N MET G 294 " --> pdb=" O HIS G 328 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N LEU G 327 " --> pdb=" O VAL G 378 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N SER G 380 " --> pdb=" O LEU G 327 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 354 through 355 Processing sheet with id=AD3, first strand: chain 'O' and resid 49 through 50 removed outlier: 7.186A pdb=" N ILE O 80 " --> pdb=" O ILE O 99 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N ILE O 99 " --> pdb=" O ILE O 80 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N ILE O 82 " --> pdb=" O SER O 97 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N SER O 97 " --> pdb=" O ILE O 82 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ALA O 84 " --> pdb=" O THR O 95 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 85 through 91 removed outlier: 5.499A pdb=" N ALA H 86 " --> pdb=" O ALA H 104 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N ALA H 104 " --> pdb=" O ALA H 86 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ARG H 88 " --> pdb=" O TYR H 102 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N LEU H 39 " --> pdb=" O MET H 140 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N MET H 140 " --> pdb=" O LEU H 39 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N LEU H 41 " --> pdb=" O GLU H 138 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 171 through 175 removed outlier: 6.693A pdb=" N LEU H 172 " --> pdb=" O PHE H 201 " (cutoff:3.500A) removed outlier: 8.178A pdb=" N KCX H 203 " --> pdb=" O LEU H 172 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N ALA H 174 " --> pdb=" O KCX H 203 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N MET H 202 " --> pdb=" O TYR H 241 " (cutoff:3.500A) removed outlier: 8.388A pdb=" N ASN H 243 " --> pdb=" O MET H 202 " (cutoff:3.500A) removed outlier: 5.150A pdb=" N HIS H 240 " --> pdb=" O ILE H 266 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N MET H 268 " --> pdb=" O HIS H 240 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N LEU H 242 " --> pdb=" O MET H 268 " (cutoff:3.500A) removed outlier: 8.020A pdb=" N ASP H 270 " --> pdb=" O LEU H 242 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N VAL H 267 " --> pdb=" O HIS H 293 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N HIS H 295 " --> pdb=" O VAL H 267 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N VAL H 269 " --> pdb=" O HIS H 295 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N LEU H 292 " --> pdb=" O HIS H 326 " (cutoff:3.500A) removed outlier: 8.729A pdb=" N HIS H 328 " --> pdb=" O LEU H 292 " (cutoff:3.500A) removed outlier: 8.287A pdb=" N MET H 294 " --> pdb=" O HIS H 328 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N LEU H 327 " --> pdb=" O VAL H 378 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N SER H 380 " --> pdb=" O LEU H 327 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'H' and resid 354 through 355 Processing sheet with id=AD7, first strand: chain 'P' and resid 49 through 50 removed outlier: 7.187A pdb=" N ILE P 80 " --> pdb=" O ILE P 99 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N ILE P 99 " --> pdb=" O ILE P 80 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ILE P 82 " --> pdb=" O SER P 97 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N SER P 97 " --> pdb=" O ILE P 82 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ALA P 84 " --> pdb=" O THR P 95 " (cutoff:3.500A) 1468 hydrogen bonds defined for protein. 4188 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: 14.98 Time building geometry restraints manager: 14.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 12256 1.34 - 1.46: 4862 1.46 - 1.57: 21186 1.57 - 1.69: 16 1.69 - 1.81: 408 Bond restraints: 38728 Sorted by residual: bond pdb=" CX KCX G 203 " pdb=" OQ1 KCX G 203 " ideal model delta sigma weight residual 1.250 1.330 -0.080 2.00e-02 2.50e+03 1.61e+01 bond pdb=" CX KCX F 203 " pdb=" OQ1 KCX F 203 " ideal model delta sigma weight residual 1.250 1.330 -0.080 2.00e-02 2.50e+03 1.60e+01 bond pdb=" CX KCX E 203 " pdb=" OQ1 KCX E 203 " ideal model delta sigma weight residual 1.250 1.330 -0.080 2.00e-02 2.50e+03 1.59e+01 bond pdb=" CX KCX B 203 " pdb=" OQ2 KCX B 203 " ideal model delta sigma weight residual 1.251 1.331 -0.080 2.00e-02 2.50e+03 1.59e+01 bond pdb=" CX KCX H 203 " pdb=" OQ1 KCX H 203 " ideal model delta sigma weight residual 1.250 1.330 -0.080 2.00e-02 2.50e+03 1.59e+01 ... (remaining 38723 not shown) Histogram of bond angle deviations from ideal: 100.80 - 107.46: 1654 107.46 - 114.12: 20094 114.12 - 120.77: 16644 120.77 - 127.43: 13746 127.43 - 134.09: 406 Bond angle restraints: 52544 Sorted by residual: angle pdb=" C ASP C 339 " pdb=" N PRO C 340 " pdb=" CA PRO C 340 " ideal model delta sigma weight residual 119.84 125.45 -5.61 1.25e+00 6.40e-01 2.02e+01 angle pdb=" C ASP A 339 " pdb=" N PRO A 340 " pdb=" CA PRO A 340 " ideal model delta sigma weight residual 119.84 125.45 -5.61 1.25e+00 6.40e-01 2.02e+01 angle pdb=" C ASP G 339 " pdb=" N PRO G 340 " pdb=" CA PRO G 340 " ideal model delta sigma weight residual 119.84 125.42 -5.58 1.25e+00 6.40e-01 1.99e+01 angle pdb=" C ASP B 339 " pdb=" N PRO B 340 " pdb=" CA PRO B 340 " ideal model delta sigma weight residual 119.84 125.38 -5.54 1.25e+00 6.40e-01 1.97e+01 angle pdb=" C ASP H 339 " pdb=" N PRO H 340 " pdb=" CA PRO H 340 " ideal model delta sigma weight residual 119.84 125.34 -5.50 1.25e+00 6.40e-01 1.93e+01 ... (remaining 52539 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.40: 22336 35.40 - 70.79: 460 70.79 - 106.19: 4 106.19 - 141.58: 4 141.58 - 176.98: 4 Dihedral angle restraints: 22808 sinusoidal: 9200 harmonic: 13608 Sorted by residual: dihedral pdb=" C3 CAP A1001 " pdb=" C CAP A1001 " pdb=" C2 CAP A1001 " pdb=" O6 CAP A1001 " ideal model delta sinusoidal sigma weight residual 81.86 -101.16 -176.98 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C3 CAP C1001 " pdb=" C CAP C1001 " pdb=" C2 CAP C1001 " pdb=" O6 CAP C1001 " ideal model delta sinusoidal sigma weight residual 81.86 -101.18 -176.95 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C3 CAP B1001 " pdb=" C CAP B1001 " pdb=" C2 CAP B1001 " pdb=" O6 CAP B1001 " ideal model delta sinusoidal sigma weight residual 81.86 -101.57 -176.57 1 2.00e+01 2.50e-03 4.80e+01 ... (remaining 22805 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 4468 0.079 - 0.158: 981 0.158 - 0.237: 137 0.237 - 0.316: 14 0.316 - 0.394: 16 Chirality restraints: 5616 Sorted by residual: chirality pdb=" CA TYR G 87 " pdb=" N TYR G 87 " pdb=" C TYR G 87 " pdb=" CB TYR G 87 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.89e+00 chirality pdb=" CA TYR A 87 " pdb=" N TYR A 87 " pdb=" C TYR A 87 " pdb=" CB TYR A 87 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.84e+00 chirality pdb=" CA TYR F 87 " pdb=" N TYR F 87 " pdb=" C TYR F 87 " pdb=" CB TYR F 87 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.82e+00 ... (remaining 5613 not shown) Planarity restraints: 6800 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU C 359 " -0.022 5.00e-02 4.00e+02 3.34e-02 1.78e+00 pdb=" N PRO C 360 " 0.058 5.00e-02 4.00e+02 pdb=" CA PRO C 360 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO C 360 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 359 " 0.022 5.00e-02 4.00e+02 3.32e-02 1.76e+00 pdb=" N PRO A 360 " -0.057 5.00e-02 4.00e+02 pdb=" CA PRO A 360 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 360 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU D 359 " 0.021 5.00e-02 4.00e+02 3.16e-02 1.59e+00 pdb=" N PRO D 360 " -0.055 5.00e-02 4.00e+02 pdb=" CA PRO D 360 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO D 360 " 0.018 5.00e-02 4.00e+02 ... (remaining 6797 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 288 2.71 - 3.26: 33127 3.26 - 3.81: 59653 3.81 - 4.35: 85034 4.35 - 4.90: 136612 Nonbonded interactions: 314714 Sorted by model distance: nonbonded pdb=" OQ2 KCX A 203 " pdb="MG MG A1002 " model vdw 2.164 2.170 nonbonded pdb=" OQ2 KCX C 203 " pdb="MG MG C1002 " model vdw 2.169 2.170 nonbonded pdb=" OQ2 KCX D 203 " pdb="MG MG D1002 " model vdw 2.199 2.170 nonbonded pdb=" OQ1 KCX H 203 " pdb="MG MG H1002 " model vdw 2.202 2.170 nonbonded pdb=" OQ1 KCX G 203 " pdb="MG MG G1002 " model vdw 2.211 2.170 ... (remaining 314709 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' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' } 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=0.40 max=1.00 mean=0.98 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.180 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: 0.050 Extract box with map and model: 1.360 Check model and map are aligned: 0.270 Set scattering table: 0.340 Process input model: 94.090 Find NCS groups from input model: 3.160 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:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 104.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1481 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 : 0.007 0.080 38728 Z= 0.482 Angle : 1.218 9.597 52544 Z= 0.793 Chirality : 0.068 0.394 5616 Planarity : 0.004 0.033 6800 Dihedral : 14.589 176.981 14152 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.65 % Favored : 94.19 % Rotamer: Outliers : 0.94 % Allowed : 5.36 % Favored : 93.70 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.82 (0.10), residues: 4712 helix: -2.40 (0.08), residues: 1688 sheet: -0.28 (0.17), residues: 784 loop : -1.97 (0.11), residues: 2240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP K 48 HIS 0.005 0.001 HIS C 299 PHE 0.014 0.002 PHE A 213 TYR 0.015 0.001 TYR E 87 ARG 0.003 0.000 ARG I 119 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9424 Ramachandran restraints generated. 4712 Oldfield, 0 Emsley, 4712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9424 Ramachandran restraints generated. 4712 Oldfield, 0 Emsley, 4712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 685 residues out of total 3936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 648 time to evaluate : 3.556 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 THR cc_start: 0.3669 (p) cc_final: 0.3344 (p) REVERT: A 44 ILE cc_start: 0.2658 (mt) cc_final: 0.2416 (pt) REVERT: A 99 TYR cc_start: 0.3042 (m-80) cc_final: 0.2747 (m-80) REVERT: A 129 PHE cc_start: 0.1030 (m-80) cc_final: 0.0725 (m-80) REVERT: A 283 GLU cc_start: 0.2358 (tt0) cc_final: 0.2018 (mp0) REVERT: A 306 LYS cc_start: 0.3676 (ttpt) cc_final: 0.3265 (tptt) REVERT: I 50 MET cc_start: 0.4406 (mtt) cc_final: 0.3718 (mmt) REVERT: I 112 GLU cc_start: 0.2459 (mt-10) cc_final: 0.2081 (mp0) REVERT: B 36 THR cc_start: 0.3600 (p) cc_final: 0.3065 (p) REVERT: B 99 TYR cc_start: 0.2950 (m-80) cc_final: 0.2647 (m-80) REVERT: B 133 LYS cc_start: 0.3273 (tptp) cc_final: 0.3073 (mtmm) REVERT: B 283 GLU cc_start: 0.2370 (tt0) cc_final: 0.2023 (mp0) REVERT: B 306 LYS cc_start: 0.3622 (ttpt) cc_final: 0.3195 (tptt) REVERT: J 50 MET cc_start: 0.4543 (mtt) cc_final: 0.3812 (mmt) REVERT: J 112 GLU cc_start: 0.2467 (mt-10) cc_final: 0.2072 (mp0) REVERT: C 36 THR cc_start: 0.3589 (p) cc_final: 0.3026 (p) REVERT: C 44 ILE cc_start: 0.2675 (mt) cc_final: 0.2442 (pt) REVERT: C 99 TYR cc_start: 0.2972 (m-80) cc_final: 0.2683 (m-80) REVERT: C 129 PHE cc_start: 0.0985 (m-80) cc_final: 0.0678 (m-80) REVERT: C 133 LYS cc_start: 0.3270 (tptp) cc_final: 0.3068 (mtmm) REVERT: C 306 LYS cc_start: 0.3579 (ttpt) cc_final: 0.3185 (tptt) REVERT: C 457 GLU cc_start: 0.2482 (tt0) cc_final: 0.2277 (mt-10) REVERT: K 50 MET cc_start: 0.4560 (mtt) cc_final: 0.3851 (mmt) REVERT: K 112 GLU cc_start: 0.2461 (mt-10) cc_final: 0.2084 (mp0) REVERT: D 20 LYS cc_start: 0.1417 (mttt) cc_final: 0.1177 (ttpt) REVERT: D 36 THR cc_start: 0.3234 (p) cc_final: 0.2582 (p) REVERT: D 99 TYR cc_start: 0.2995 (m-80) cc_final: 0.2677 (m-80) REVERT: D 129 PHE cc_start: 0.1109 (m-80) cc_final: 0.0881 (m-80) REVERT: D 133 LYS cc_start: 0.3266 (tptp) cc_final: 0.3064 (mtmm) REVERT: D 283 GLU cc_start: 0.2389 (tt0) cc_final: 0.2040 (mp0) REVERT: D 306 LYS cc_start: 0.3616 (ttpt) cc_final: 0.3213 (tptt) REVERT: L 50 MET cc_start: 0.4508 (mtt) cc_final: 0.3803 (mmt) REVERT: L 112 GLU cc_start: 0.2467 (mt-10) cc_final: 0.2094 (mp0) REVERT: E 20 LYS cc_start: 0.1141 (mttt) cc_final: 0.0906 (ttpt) REVERT: E 36 THR cc_start: 0.3314 (p) cc_final: 0.2768 (p) REVERT: E 44 ILE cc_start: 0.2566 (mt) cc_final: 0.2364 (pt) REVERT: E 99 TYR cc_start: 0.2940 (m-80) cc_final: 0.2622 (m-80) REVERT: E 129 PHE cc_start: 0.0955 (m-80) cc_final: 0.0585 (m-80) REVERT: E 306 LYS cc_start: 0.3541 (ttpt) cc_final: 0.3125 (tptt) REVERT: E 457 GLU cc_start: 0.2702 (tt0) cc_final: 0.2486 (mt-10) REVERT: M 50 MET cc_start: 0.4404 (mtt) cc_final: 0.3698 (mmt) REVERT: M 112 GLU cc_start: 0.2454 (mt-10) cc_final: 0.2080 (mp0) REVERT: F 36 THR cc_start: 0.3452 (p) cc_final: 0.2922 (p) REVERT: F 99 TYR cc_start: 0.2944 (m-80) cc_final: 0.2640 (m-80) REVERT: F 129 PHE cc_start: 0.1039 (m-80) cc_final: 0.0668 (m-80) REVERT: F 306 LYS cc_start: 0.3576 (ttpt) cc_final: 0.3159 (tptt) REVERT: F 457 GLU cc_start: 0.2640 (tt0) cc_final: 0.2438 (mt-10) REVERT: N 50 MET cc_start: 0.4301 (mtt) cc_final: 0.3593 (mmt) REVERT: N 112 GLU cc_start: 0.2444 (mt-10) cc_final: 0.2072 (mp0) REVERT: G 36 THR cc_start: 0.3174 (p) cc_final: 0.2861 (p) REVERT: G 44 ILE cc_start: 0.2531 (mt) cc_final: 0.2322 (pt) REVERT: G 99 TYR cc_start: 0.2940 (m-80) cc_final: 0.2626 (m-80) REVERT: G 129 PHE cc_start: 0.1018 (m-80) cc_final: 0.0609 (m-80) REVERT: G 306 LYS cc_start: 0.3573 (ttpt) cc_final: 0.3157 (tptt) REVERT: G 457 GLU cc_start: 0.2884 (tt0) cc_final: 0.2637 (mt-10) REVERT: O 50 MET cc_start: 0.4314 (mtt) cc_final: 0.3611 (mmt) REVERT: O 112 GLU cc_start: 0.2415 (mt-10) cc_final: 0.2051 (mp0) REVERT: H 20 LYS cc_start: 0.1140 (mttt) cc_final: 0.0902 (ttpt) REVERT: H 36 THR cc_start: 0.3168 (p) cc_final: 0.2858 (p) REVERT: H 99 TYR cc_start: 0.3008 (m-80) cc_final: 0.2692 (m-80) REVERT: H 129 PHE cc_start: 0.1034 (m-80) cc_final: 0.0722 (m-80) REVERT: H 133 LYS cc_start: 0.3205 (tptp) cc_final: 0.2993 (mtmm) REVERT: H 306 LYS cc_start: 0.3555 (ttpt) cc_final: 0.3146 (tptt) REVERT: H 457 GLU cc_start: 0.2734 (tt0) cc_final: 0.2488 (mt-10) REVERT: P 50 MET cc_start: 0.4324 (mtt) cc_final: 0.3646 (mmt) REVERT: P 112 GLU cc_start: 0.2449 (mt-10) cc_final: 0.2055 (mp0) outliers start: 37 outliers final: 8 residues processed: 678 average time/residue: 0.5382 time to fit residues: 576.1513 Evaluate side-chains 441 residues out of total 3936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 433 time to evaluate : 3.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain C residue 281 ILE Chi-restraints excluded: chain D residue 281 ILE Chi-restraints excluded: chain E residue 281 ILE Chi-restraints excluded: chain F residue 281 ILE Chi-restraints excluded: chain G residue 281 ILE Chi-restraints excluded: chain H residue 281 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 391 optimal weight: 0.9990 chunk 351 optimal weight: 3.9990 chunk 195 optimal weight: 2.9990 chunk 120 optimal weight: 1.9990 chunk 237 optimal weight: 6.9990 chunk 187 optimal weight: 0.9990 chunk 363 optimal weight: 0.8980 chunk 140 optimal weight: 3.9990 chunk 221 optimal weight: 2.9990 chunk 270 optimal weight: 0.8980 chunk 421 optimal weight: 0.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 186 ASN A 215 HIS A 288 ASN A 295 HIS A 387 GLN A 415 GLN I 22 GLN I 37 HIS B 186 ASN B 215 HIS B 288 ASN B 387 GLN B 415 GLN J 22 GLN J 37 HIS C 186 ASN C 215 HIS C 288 ASN C 295 HIS C 387 GLN C 415 GLN K 22 GLN K 37 HIS D 186 ASN D 215 HIS D 288 ASN D 295 HIS D 387 GLN D 415 GLN L 22 GLN L 37 HIS E 186 ASN E 215 HIS E 288 ASN E 295 HIS E 387 GLN E 415 GLN E 421 ASN M 22 GLN M 37 HIS F 186 ASN F 215 HIS F 288 ASN F 387 GLN N 22 GLN N 37 HIS G 186 ASN G 215 HIS G 288 ASN G 387 GLN G 415 GLN O 22 GLN O 37 HIS H 186 ASN H 215 HIS H 288 ASN H 387 GLN H 415 GLN P 22 GLN P 37 HIS Total number of N/Q/H flips: 60 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1491 moved from start: 0.2337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 38728 Z= 0.205 Angle : 0.580 7.151 52544 Z= 0.300 Chirality : 0.042 0.157 5616 Planarity : 0.004 0.032 6800 Dihedral : 7.367 179.938 5408 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 0.89 % Allowed : 7.49 % Favored : 91.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.11), residues: 4712 helix: 0.12 (0.11), residues: 1760 sheet: 0.17 (0.17), residues: 912 loop : -1.47 (0.12), residues: 2040 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 318 HIS 0.005 0.001 HIS A 293 PHE 0.015 0.002 PHE H 213 TYR 0.017 0.002 TYR A 346 ARG 0.004 0.001 ARG D 88 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9424 Ramachandran restraints generated. 4712 Oldfield, 0 Emsley, 4712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9424 Ramachandran restraints generated. 4712 Oldfield, 0 Emsley, 4712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 551 residues out of total 3936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 516 time to evaluate : 3.909 Fit side-chains REVERT: A 283 GLU cc_start: 0.1907 (tt0) cc_final: 0.1618 (mp0) REVERT: A 286 ARG cc_start: 0.2211 (tpp80) cc_final: 0.1976 (tpm170) REVERT: A 306 LYS cc_start: 0.3395 (ttpt) cc_final: 0.2989 (tptt) REVERT: A 366 GLU cc_start: 0.4295 (mt-10) cc_final: 0.4070 (mt-10) REVERT: I 50 MET cc_start: 0.4464 (mtt) cc_final: 0.3810 (mmt) REVERT: I 112 GLU cc_start: 0.1381 (mt-10) cc_final: 0.1178 (mp0) REVERT: B 283 GLU cc_start: 0.1863 (tt0) cc_final: 0.1583 (mp0) REVERT: B 286 ARG cc_start: 0.2268 (tpp80) cc_final: 0.1924 (tpm170) REVERT: B 306 LYS cc_start: 0.3345 (ttpt) cc_final: 0.2931 (tptt) REVERT: B 366 GLU cc_start: 0.4284 (mt-10) cc_final: 0.4057 (mt-10) REVERT: B 447 ARG cc_start: 0.2369 (mtt90) cc_final: 0.2137 (mtp180) REVERT: J 50 MET cc_start: 0.4494 (mtt) cc_final: 0.3850 (mmt) REVERT: C 286 ARG cc_start: 0.2125 (tpp80) cc_final: 0.1815 (tpm170) REVERT: C 306 LYS cc_start: 0.3330 (ttpt) cc_final: 0.2928 (tptt) REVERT: C 366 GLU cc_start: 0.4276 (mt-10) cc_final: 0.4055 (mt-10) REVERT: C 447 ARG cc_start: 0.2408 (mtt90) cc_final: 0.2171 (mtp180) REVERT: K 50 MET cc_start: 0.4494 (mtt) cc_final: 0.3836 (mmt) REVERT: K 112 GLU cc_start: 0.1254 (mt-10) cc_final: 0.1042 (mp0) REVERT: D 283 GLU cc_start: 0.1949 (tt0) cc_final: 0.1649 (mp0) REVERT: D 286 ARG cc_start: 0.2155 (tpp80) cc_final: 0.1840 (tpm170) REVERT: D 306 LYS cc_start: 0.3357 (ttpt) cc_final: 0.2957 (tptt) REVERT: L 50 MET cc_start: 0.4491 (mtt) cc_final: 0.3840 (mmt) REVERT: L 112 GLU cc_start: 0.1284 (mt-10) cc_final: 0.1083 (mp0) REVERT: E 283 GLU cc_start: 0.1945 (tt0) cc_final: 0.1648 (mp0) REVERT: E 286 ARG cc_start: 0.2162 (tpp80) cc_final: 0.1809 (tpm170) REVERT: E 306 LYS cc_start: 0.3309 (ttpt) cc_final: 0.2946 (tptt) REVERT: E 366 GLU cc_start: 0.4305 (mt-10) cc_final: 0.4089 (mt-10) REVERT: M 50 MET cc_start: 0.4483 (mtt) cc_final: 0.3819 (mmt) REVERT: F 283 GLU cc_start: 0.1872 (tt0) cc_final: 0.1590 (mp0) REVERT: F 286 ARG cc_start: 0.2286 (tpp80) cc_final: 0.1929 (tpm170) REVERT: F 306 LYS cc_start: 0.3361 (ttpt) cc_final: 0.2954 (tptt) REVERT: F 366 GLU cc_start: 0.4159 (mt-10) cc_final: 0.3893 (mt-10) REVERT: N 50 MET cc_start: 0.4469 (mtt) cc_final: 0.3811 (mmt) REVERT: G 283 GLU cc_start: 0.1892 (tt0) cc_final: 0.1649 (mp0) REVERT: G 286 ARG cc_start: 0.2146 (tpp80) cc_final: 0.1833 (tpm170) REVERT: G 306 LYS cc_start: 0.3424 (ttpt) cc_final: 0.3039 (tptt) REVERT: G 366 GLU cc_start: 0.4281 (mt-10) cc_final: 0.4080 (mt-10) REVERT: O 50 MET cc_start: 0.4464 (mtt) cc_final: 0.3807 (mmt) REVERT: H 283 GLU cc_start: 0.1955 (tt0) cc_final: 0.1656 (mp0) REVERT: H 286 ARG cc_start: 0.2151 (tpp80) cc_final: 0.1833 (tpm170) REVERT: H 306 LYS cc_start: 0.3405 (ttpt) cc_final: 0.3012 (tptt) REVERT: P 50 MET cc_start: 0.4493 (mtt) cc_final: 0.3834 (mmt) outliers start: 35 outliers final: 25 residues processed: 551 average time/residue: 0.6382 time to fit residues: 528.1707 Evaluate side-chains 476 residues out of total 3936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 451 time to evaluate : 3.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain I residue 38 THR Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 342 THR Chi-restraints excluded: chain J residue 38 THR Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 342 THR Chi-restraints excluded: chain K residue 38 THR Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 342 THR Chi-restraints excluded: chain L residue 38 THR Chi-restraints excluded: chain E residue 264 SER Chi-restraints excluded: chain E residue 342 THR Chi-restraints excluded: chain M residue 38 THR Chi-restraints excluded: chain F residue 264 SER Chi-restraints excluded: chain F residue 342 THR Chi-restraints excluded: chain N residue 38 THR Chi-restraints excluded: chain G residue 264 SER Chi-restraints excluded: chain G residue 342 THR Chi-restraints excluded: chain O residue 38 THR Chi-restraints excluded: chain H residue 264 SER Chi-restraints excluded: chain H residue 342 THR Chi-restraints excluded: chain P residue 38 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 234 optimal weight: 2.9990 chunk 130 optimal weight: 5.9990 chunk 350 optimal weight: 2.9990 chunk 286 optimal weight: 0.9990 chunk 116 optimal weight: 9.9990 chunk 422 optimal weight: 0.8980 chunk 456 optimal weight: 0.9990 chunk 375 optimal weight: 0.6980 chunk 418 optimal weight: 5.9990 chunk 143 optimal weight: 4.9990 chunk 338 optimal weight: 6.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 421 ASN A 433 ASN I 18 GLN B 421 ASN B 433 ASN J 18 GLN C 415 GLN C 421 ASN C 433 ASN K 18 GLN D 415 GLN D 421 ASN D 433 ASN L 18 GLN E 433 ASN M 18 GLN F 415 GLN F 421 ASN N 18 GLN G 421 ASN G 433 ASN O 18 GLN H 421 ASN H 433 ASN P 18 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1502 moved from start: 0.3241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 38728 Z= 0.235 Angle : 0.591 6.282 52544 Z= 0.300 Chirality : 0.043 0.212 5616 Planarity : 0.005 0.039 6800 Dihedral : 7.272 175.965 5392 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 1.78 % Allowed : 8.97 % Favored : 89.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.12), residues: 4712 helix: 0.80 (0.12), residues: 1768 sheet: 0.25 (0.18), residues: 816 loop : -1.46 (0.12), residues: 2128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP I 75 HIS 0.004 0.001 HIS B 293 PHE 0.014 0.002 PHE E 201 TYR 0.020 0.002 TYR H 241 ARG 0.011 0.001 ARG G 361 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9424 Ramachandran restraints generated. 4712 Oldfield, 0 Emsley, 4712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9424 Ramachandran restraints generated. 4712 Oldfield, 0 Emsley, 4712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 609 residues out of total 3936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 539 time to evaluate : 3.955 Fit side-chains REVERT: A 283 GLU cc_start: 0.1785 (tt0) cc_final: 0.1534 (mp0) REVERT: A 286 ARG cc_start: 0.1863 (tpp80) cc_final: 0.1570 (tpm170) REVERT: A 306 LYS cc_start: 0.3419 (ttpt) cc_final: 0.3030 (tptt) REVERT: A 376 MET cc_start: 0.2508 (ttm) cc_final: 0.2290 (tpp) REVERT: I 111 MET cc_start: 0.2955 (ttp) cc_final: 0.2612 (ttm) REVERT: B 283 GLU cc_start: 0.1775 (tt0) cc_final: 0.1511 (mp0) REVERT: B 286 ARG cc_start: 0.1974 (tpp80) cc_final: 0.1670 (tpm170) REVERT: B 306 LYS cc_start: 0.3475 (ttpt) cc_final: 0.3054 (tptt) REVERT: C 286 ARG cc_start: 0.1891 (tpp80) cc_final: 0.1567 (tpm170) REVERT: C 306 LYS cc_start: 0.3388 (ttpt) cc_final: 0.2990 (tptt) REVERT: K 111 MET cc_start: 0.2937 (ttp) cc_final: 0.2603 (ttm) REVERT: D 283 GLU cc_start: 0.1777 (tt0) cc_final: 0.1510 (mp0) REVERT: D 286 ARG cc_start: 0.1948 (tpp80) cc_final: 0.1642 (tpm170) REVERT: D 306 LYS cc_start: 0.3479 (ttpt) cc_final: 0.3091 (tptt) REVERT: D 376 MET cc_start: 0.2447 (ttm) cc_final: 0.2239 (tpp) REVERT: L 111 MET cc_start: 0.2920 (ttp) cc_final: 0.2587 (ttm) REVERT: E 283 GLU cc_start: 0.1780 (tt0) cc_final: 0.1513 (mp0) REVERT: E 286 ARG cc_start: 0.1918 (tpp80) cc_final: 0.1593 (tpm170) REVERT: E 306 LYS cc_start: 0.3210 (ttpt) cc_final: 0.2831 (tptt) REVERT: F 283 GLU cc_start: 0.1826 (tt0) cc_final: 0.1559 (mp0) REVERT: F 286 ARG cc_start: 0.1954 (tpp80) cc_final: 0.1631 (tpm170) REVERT: F 306 LYS cc_start: 0.3505 (ttpt) cc_final: 0.3042 (tptt) REVERT: G 283 GLU cc_start: 0.1789 (tt0) cc_final: 0.1519 (mp0) REVERT: G 286 ARG cc_start: 0.1938 (tpp80) cc_final: 0.1621 (tpm170) REVERT: G 306 LYS cc_start: 0.3471 (ttpt) cc_final: 0.3074 (tptt) REVERT: H 283 GLU cc_start: 0.1788 (tt0) cc_final: 0.1517 (mp0) REVERT: H 286 ARG cc_start: 0.1948 (tpp80) cc_final: 0.1629 (tpm170) REVERT: H 306 LYS cc_start: 0.3493 (ttpt) cc_final: 0.3092 (tptt) outliers start: 70 outliers final: 46 residues processed: 597 average time/residue: 0.5836 time to fit residues: 546.6898 Evaluate side-chains 499 residues out of total 3936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 453 time to evaluate : 3.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain I residue 38 THR Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 342 THR Chi-restraints excluded: chain B residue 355 ASN Chi-restraints excluded: chain B residue 357 VAL Chi-restraints excluded: chain J residue 38 THR Chi-restraints excluded: chain J residue 117 ASP Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 342 THR Chi-restraints excluded: chain C residue 355 ASN Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain K residue 38 THR Chi-restraints excluded: chain K residue 117 ASP Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 342 THR Chi-restraints excluded: chain D residue 355 ASN Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain L residue 38 THR Chi-restraints excluded: chain E residue 265 VAL Chi-restraints excluded: chain E residue 342 THR Chi-restraints excluded: chain E residue 355 ASN Chi-restraints excluded: chain E residue 357 VAL Chi-restraints excluded: chain M residue 38 THR Chi-restraints excluded: chain M residue 117 ASP Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 265 VAL Chi-restraints excluded: chain F residue 342 THR Chi-restraints excluded: chain F residue 355 ASN Chi-restraints excluded: chain F residue 357 VAL Chi-restraints excluded: chain N residue 38 THR Chi-restraints excluded: chain N residue 117 ASP Chi-restraints excluded: chain G residue 265 VAL Chi-restraints excluded: chain G residue 342 THR Chi-restraints excluded: chain G residue 355 ASN Chi-restraints excluded: chain G residue 357 VAL Chi-restraints excluded: chain O residue 38 THR Chi-restraints excluded: chain H residue 265 VAL Chi-restraints excluded: chain H residue 342 THR Chi-restraints excluded: chain H residue 355 ASN Chi-restraints excluded: chain H residue 357 VAL Chi-restraints excluded: chain P residue 38 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 417 optimal weight: 0.9980 chunk 317 optimal weight: 1.9990 chunk 219 optimal weight: 9.9990 chunk 46 optimal weight: 8.9990 chunk 201 optimal weight: 5.9990 chunk 283 optimal weight: 0.0870 chunk 423 optimal weight: 4.9990 chunk 448 optimal weight: 0.8980 chunk 221 optimal weight: 3.9990 chunk 401 optimal weight: 0.0670 chunk 120 optimal weight: 1.9990 overall best weight: 0.8098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 415 GLN E 415 GLN F 415 GLN G 415 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1498 moved from start: 0.3525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 38728 Z= 0.167 Angle : 0.517 7.205 52544 Z= 0.261 Chirality : 0.041 0.136 5616 Planarity : 0.004 0.042 6800 Dihedral : 6.995 174.200 5392 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.82 % Allowed : 10.21 % Favored : 86.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.12), residues: 4712 helix: 1.22 (0.13), residues: 1760 sheet: 0.56 (0.18), residues: 800 loop : -1.36 (0.12), residues: 2152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP I 75 HIS 0.003 0.001 HIS B 293 PHE 0.010 0.001 PHE A 213 TYR 0.011 0.001 TYR N 47 ARG 0.010 0.000 ARG A 361 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9424 Ramachandran restraints generated. 4712 Oldfield, 0 Emsley, 4712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9424 Ramachandran restraints generated. 4712 Oldfield, 0 Emsley, 4712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 575 residues out of total 3936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 464 time to evaluate : 3.776 Fit side-chains REVERT: A 129 PHE cc_start: 0.1067 (OUTLIER) cc_final: 0.0768 (m-80) REVERT: A 286 ARG cc_start: 0.2053 (tpp80) cc_final: 0.1620 (tpm170) REVERT: A 306 LYS cc_start: 0.3526 (ttpt) cc_final: 0.3125 (tptt) REVERT: A 376 MET cc_start: 0.2514 (ttm) cc_final: 0.2303 (tpp) REVERT: B 129 PHE cc_start: 0.1402 (OUTLIER) cc_final: 0.1091 (m-80) REVERT: B 286 ARG cc_start: 0.1915 (tpp80) cc_final: 0.1603 (tpm170) REVERT: B 306 LYS cc_start: 0.3286 (ttpt) cc_final: 0.2820 (tptt) REVERT: C 129 PHE cc_start: 0.0894 (OUTLIER) cc_final: 0.0629 (m-80) REVERT: C 286 ARG cc_start: 0.2080 (tpp80) cc_final: 0.1610 (tpm170) REVERT: C 306 LYS cc_start: 0.3500 (ttpt) cc_final: 0.3096 (tptt) REVERT: D 129 PHE cc_start: 0.1024 (OUTLIER) cc_final: 0.0731 (m-80) REVERT: D 286 ARG cc_start: 0.1982 (tpp80) cc_final: 0.1629 (tpm170) REVERT: D 306 LYS cc_start: 0.3540 (ttpt) cc_final: 0.3088 (tptt) REVERT: D 376 MET cc_start: 0.2430 (ttm) cc_final: 0.2216 (tpp) REVERT: L 50 MET cc_start: 0.4425 (OUTLIER) cc_final: 0.3541 (mmt) REVERT: E 129 PHE cc_start: 0.0812 (OUTLIER) cc_final: 0.0542 (m-80) REVERT: E 286 ARG cc_start: 0.1951 (tpp80) cc_final: 0.1629 (tpm170) REVERT: E 306 LYS cc_start: 0.3500 (ttpt) cc_final: 0.3092 (tptt) REVERT: F 129 PHE cc_start: 0.1193 (OUTLIER) cc_final: 0.0880 (m-80) REVERT: F 286 ARG cc_start: 0.1958 (tpp80) cc_final: 0.1636 (tpm170) REVERT: F 306 LYS cc_start: 0.3504 (ttpt) cc_final: 0.3113 (tptt) REVERT: G 129 PHE cc_start: 0.0932 (OUTLIER) cc_final: 0.0636 (m-80) REVERT: G 286 ARG cc_start: 0.2061 (tpp80) cc_final: 0.1628 (tpm170) REVERT: G 306 LYS cc_start: 0.3518 (ttpt) cc_final: 0.3124 (tptt) REVERT: H 129 PHE cc_start: 0.1014 (OUTLIER) cc_final: 0.0720 (m-80) REVERT: H 286 ARG cc_start: 0.2024 (tpp80) cc_final: 0.1628 (tpm170) REVERT: H 306 LYS cc_start: 0.3545 (ttpt) cc_final: 0.3095 (tptt) outliers start: 111 outliers final: 77 residues processed: 529 average time/residue: 0.5482 time to fit residues: 459.2873 Evaluate side-chains 536 residues out of total 3936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 450 time to evaluate : 4.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 129 PHE Chi-restraints excluded: chain A residue 207 ASN Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain I residue 38 THR Chi-restraints excluded: chain I residue 50 MET Chi-restraints excluded: chain I residue 117 ASP Chi-restraints excluded: chain B residue 34 LYS Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 129 PHE Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 342 THR Chi-restraints excluded: chain B residue 355 ASN Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 357 VAL Chi-restraints excluded: chain J residue 38 THR Chi-restraints excluded: chain J residue 50 MET Chi-restraints excluded: chain J residue 117 ASP Chi-restraints excluded: chain C residue 34 LYS Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 129 PHE Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 342 THR Chi-restraints excluded: chain C residue 355 ASN Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain K residue 38 THR Chi-restraints excluded: chain K residue 50 MET Chi-restraints excluded: chain K residue 117 ASP Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain D residue 129 PHE Chi-restraints excluded: chain D residue 207 ASN Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 342 THR Chi-restraints excluded: chain D residue 356 THR Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain L residue 38 THR Chi-restraints excluded: chain L residue 50 MET Chi-restraints excluded: chain L residue 117 ASP Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 129 PHE Chi-restraints excluded: chain E residue 342 THR Chi-restraints excluded: chain E residue 355 ASN Chi-restraints excluded: chain E residue 357 VAL Chi-restraints excluded: chain M residue 38 THR Chi-restraints excluded: chain M residue 50 MET Chi-restraints excluded: chain M residue 105 VAL Chi-restraints excluded: chain M residue 117 ASP Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 129 PHE Chi-restraints excluded: chain F residue 342 THR Chi-restraints excluded: chain F residue 355 ASN Chi-restraints excluded: chain F residue 356 THR Chi-restraints excluded: chain N residue 38 THR Chi-restraints excluded: chain N residue 50 MET Chi-restraints excluded: chain N residue 117 ASP Chi-restraints excluded: chain G residue 126 VAL Chi-restraints excluded: chain G residue 129 PHE Chi-restraints excluded: chain G residue 207 ASN Chi-restraints excluded: chain G residue 269 VAL Chi-restraints excluded: chain G residue 271 LEU Chi-restraints excluded: chain G residue 276 THR Chi-restraints excluded: chain G residue 342 THR Chi-restraints excluded: chain G residue 355 ASN Chi-restraints excluded: chain G residue 356 THR Chi-restraints excluded: chain G residue 357 VAL Chi-restraints excluded: chain O residue 38 THR Chi-restraints excluded: chain O residue 50 MET Chi-restraints excluded: chain O residue 117 ASP Chi-restraints excluded: chain H residue 126 VAL Chi-restraints excluded: chain H residue 129 PHE Chi-restraints excluded: chain H residue 276 THR Chi-restraints excluded: chain H residue 342 THR Chi-restraints excluded: chain H residue 355 ASN Chi-restraints excluded: chain H residue 356 THR Chi-restraints excluded: chain P residue 38 THR Chi-restraints excluded: chain P residue 50 MET Chi-restraints excluded: chain P residue 117 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 373 optimal weight: 5.9990 chunk 254 optimal weight: 0.7980 chunk 6 optimal weight: 1.9990 chunk 333 optimal weight: 7.9990 chunk 185 optimal weight: 0.7980 chunk 382 optimal weight: 2.9990 chunk 310 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 229 optimal weight: 6.9990 chunk 402 optimal weight: 7.9990 chunk 113 optimal weight: 0.9980 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 415 GLN F 326 HIS H 415 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1500 moved from start: 0.3872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 38728 Z= 0.253 Angle : 0.593 8.116 52544 Z= 0.298 Chirality : 0.043 0.138 5616 Planarity : 0.005 0.036 6800 Dihedral : 7.185 169.974 5392 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 3.35 % Allowed : 10.72 % Favored : 85.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.12), residues: 4712 helix: 1.08 (0.12), residues: 1760 sheet: 0.45 (0.18), residues: 800 loop : -1.39 (0.12), residues: 2152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 216 HIS 0.005 0.001 HIS G 293 PHE 0.014 0.002 PHE C 201 TYR 0.016 0.002 TYR J 47 ARG 0.006 0.001 ARG G 304 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9424 Ramachandran restraints generated. 4712 Oldfield, 0 Emsley, 4712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9424 Ramachandran restraints generated. 4712 Oldfield, 0 Emsley, 4712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 619 residues out of total 3936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 487 time to evaluate : 3.726 Fit side-chains REVERT: A 129 PHE cc_start: 0.1358 (OUTLIER) cc_final: 0.1085 (m-80) REVERT: A 205 ASP cc_start: 0.1914 (t70) cc_final: 0.1638 (t0) REVERT: A 283 GLU cc_start: 0.1640 (tt0) cc_final: 0.1408 (mp0) REVERT: A 286 ARG cc_start: 0.2022 (tpp80) cc_final: 0.1675 (tpm170) REVERT: A 306 LYS cc_start: 0.3408 (ttpt) cc_final: 0.3016 (tptt) REVERT: A 373 ARG cc_start: 0.1575 (mmt90) cc_final: 0.0926 (mtm-85) REVERT: B 129 PHE cc_start: 0.1551 (OUTLIER) cc_final: 0.1265 (m-80) REVERT: B 205 ASP cc_start: 0.1992 (t70) cc_final: 0.1727 (t0) REVERT: B 283 GLU cc_start: 0.1662 (tt0) cc_final: 0.1441 (mp0) REVERT: B 286 ARG cc_start: 0.1991 (tpp80) cc_final: 0.1688 (tpm170) REVERT: B 306 LYS cc_start: 0.3593 (ttpt) cc_final: 0.3155 (tptt) REVERT: B 373 ARG cc_start: 0.1676 (mmt90) cc_final: 0.1034 (mtm-85) REVERT: C 129 PHE cc_start: 0.1219 (OUTLIER) cc_final: 0.0943 (m-80) REVERT: C 205 ASP cc_start: 0.1975 (t70) cc_final: 0.1703 (t0) REVERT: C 286 ARG cc_start: 0.2010 (tpp80) cc_final: 0.1660 (tpm170) REVERT: C 306 LYS cc_start: 0.3585 (ttpt) cc_final: 0.3143 (tptt) REVERT: C 373 ARG cc_start: 0.1548 (mmt90) cc_final: 0.0899 (mtm-85) REVERT: D 129 PHE cc_start: 0.1299 (OUTLIER) cc_final: 0.1028 (m-80) REVERT: D 283 GLU cc_start: 0.1943 (tt0) cc_final: 0.1675 (mp0) REVERT: D 286 ARG cc_start: 0.2030 (tpp80) cc_final: 0.1687 (tpm170) REVERT: D 306 LYS cc_start: 0.3383 (ttpt) cc_final: 0.2995 (tptt) REVERT: D 373 ARG cc_start: 0.1536 (mmt90) cc_final: 0.0884 (mtm-85) REVERT: L 50 MET cc_start: 0.4296 (OUTLIER) cc_final: 0.3380 (mmt) REVERT: E 129 PHE cc_start: 0.1310 (OUTLIER) cc_final: 0.1042 (m-80) REVERT: E 283 GLU cc_start: 0.1974 (tt0) cc_final: 0.1688 (mp0) REVERT: E 286 ARG cc_start: 0.1940 (tpp80) cc_final: 0.1639 (tpm170) REVERT: E 306 LYS cc_start: 0.3578 (ttpt) cc_final: 0.3146 (tptt) REVERT: E 373 ARG cc_start: 0.1569 (mmt90) cc_final: 0.0893 (mtm-85) REVERT: M 50 MET cc_start: 0.4308 (OUTLIER) cc_final: 0.3375 (mmt) REVERT: F 129 PHE cc_start: 0.1391 (OUTLIER) cc_final: 0.1111 (m-80) REVERT: F 205 ASP cc_start: 0.2004 (t70) cc_final: 0.1737 (t0) REVERT: F 283 GLU cc_start: 0.1664 (tt0) cc_final: 0.1424 (mp0) REVERT: F 286 ARG cc_start: 0.1979 (tpp80) cc_final: 0.1642 (tpm170) REVERT: F 306 LYS cc_start: 0.3397 (ttpt) cc_final: 0.2988 (tptt) REVERT: F 373 ARG cc_start: 0.1621 (mmt90) cc_final: 0.0992 (mtm-85) REVERT: G 129 PHE cc_start: 0.1152 (OUTLIER) cc_final: 0.0871 (m-80) REVERT: G 205 ASP cc_start: 0.1989 (t70) cc_final: 0.1711 (t0) REVERT: G 283 GLU cc_start: 0.1653 (tt0) cc_final: 0.1439 (mp0) REVERT: G 286 ARG cc_start: 0.2035 (tpp80) cc_final: 0.1701 (tpm170) REVERT: G 306 LYS cc_start: 0.3324 (ttpt) cc_final: 0.2938 (tptt) REVERT: G 373 ARG cc_start: 0.1511 (mmt90) cc_final: 0.0811 (mtm180) REVERT: H 129 PHE cc_start: 0.1065 (OUTLIER) cc_final: 0.0771 (m-80) REVERT: H 286 ARG cc_start: 0.2031 (tpp80) cc_final: 0.1692 (tpm170) REVERT: H 306 LYS cc_start: 0.3382 (ttpt) cc_final: 0.2997 (tptt) REVERT: H 373 ARG cc_start: 0.1528 (mmt90) cc_final: 0.0888 (mtm-85) REVERT: P 50 MET cc_start: 0.4300 (OUTLIER) cc_final: 0.3369 (mmt) outliers start: 132 outliers final: 98 residues processed: 575 average time/residue: 0.5457 time to fit residues: 494.3718 Evaluate side-chains 586 residues out of total 3936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 477 time to evaluate : 3.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 129 PHE Chi-restraints excluded: chain A residue 207 ASN Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain I residue 38 THR Chi-restraints excluded: chain I residue 50 MET Chi-restraints excluded: chain I residue 88 THR Chi-restraints excluded: chain I residue 117 ASP Chi-restraints excluded: chain B residue 34 LYS Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 129 PHE Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 342 THR Chi-restraints excluded: chain B residue 355 ASN Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 357 VAL Chi-restraints excluded: chain J residue 38 THR Chi-restraints excluded: chain J residue 50 MET Chi-restraints excluded: chain J residue 88 THR Chi-restraints excluded: chain J residue 117 ASP Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 129 PHE Chi-restraints excluded: chain C residue 265 VAL Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 342 THR Chi-restraints excluded: chain C residue 355 ASN Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain K residue 38 THR Chi-restraints excluded: chain K residue 50 MET Chi-restraints excluded: chain K residue 88 THR Chi-restraints excluded: chain K residue 117 ASP Chi-restraints excluded: chain D residue 34 LYS Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain D residue 129 PHE Chi-restraints excluded: chain D residue 207 ASN Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 342 THR Chi-restraints excluded: chain D residue 355 ASN Chi-restraints excluded: chain D residue 356 THR Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain L residue 38 THR Chi-restraints excluded: chain L residue 50 MET Chi-restraints excluded: chain L residue 88 THR Chi-restraints excluded: chain L residue 117 ASP Chi-restraints excluded: chain E residue 34 LYS Chi-restraints excluded: chain E residue 44 ILE Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 129 PHE Chi-restraints excluded: chain E residue 265 VAL Chi-restraints excluded: chain E residue 342 THR Chi-restraints excluded: chain E residue 355 ASN Chi-restraints excluded: chain E residue 356 THR Chi-restraints excluded: chain E residue 357 VAL Chi-restraints excluded: chain M residue 38 THR Chi-restraints excluded: chain M residue 50 MET Chi-restraints excluded: chain M residue 88 THR Chi-restraints excluded: chain M residue 105 VAL Chi-restraints excluded: chain M residue 117 ASP Chi-restraints excluded: chain F residue 34 LYS Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 129 PHE Chi-restraints excluded: chain F residue 265 VAL Chi-restraints excluded: chain F residue 342 THR Chi-restraints excluded: chain F residue 355 ASN Chi-restraints excluded: chain F residue 356 THR Chi-restraints excluded: chain F residue 357 VAL Chi-restraints excluded: chain N residue 38 THR Chi-restraints excluded: chain N residue 50 MET Chi-restraints excluded: chain N residue 88 THR Chi-restraints excluded: chain N residue 117 ASP Chi-restraints excluded: chain G residue 44 ILE Chi-restraints excluded: chain G residue 81 SER Chi-restraints excluded: chain G residue 126 VAL Chi-restraints excluded: chain G residue 129 PHE Chi-restraints excluded: chain G residue 207 ASN Chi-restraints excluded: chain G residue 271 LEU Chi-restraints excluded: chain G residue 276 THR Chi-restraints excluded: chain G residue 342 THR Chi-restraints excluded: chain G residue 355 ASN Chi-restraints excluded: chain G residue 356 THR Chi-restraints excluded: chain G residue 357 VAL Chi-restraints excluded: chain O residue 38 THR Chi-restraints excluded: chain O residue 50 MET Chi-restraints excluded: chain O residue 88 THR Chi-restraints excluded: chain O residue 105 VAL Chi-restraints excluded: chain O residue 117 ASP Chi-restraints excluded: chain H residue 81 SER Chi-restraints excluded: chain H residue 126 VAL Chi-restraints excluded: chain H residue 129 PHE Chi-restraints excluded: chain H residue 265 VAL Chi-restraints excluded: chain H residue 276 THR Chi-restraints excluded: chain H residue 342 THR Chi-restraints excluded: chain H residue 355 ASN Chi-restraints excluded: chain H residue 356 THR Chi-restraints excluded: chain H residue 357 VAL Chi-restraints excluded: chain P residue 38 THR Chi-restraints excluded: chain P residue 50 MET Chi-restraints excluded: chain P residue 88 THR Chi-restraints excluded: chain P residue 117 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 150 optimal weight: 3.9990 chunk 403 optimal weight: 5.9990 chunk 88 optimal weight: 2.9990 chunk 263 optimal weight: 5.9990 chunk 110 optimal weight: 5.9990 chunk 448 optimal weight: 8.9990 chunk 372 optimal weight: 3.9990 chunk 207 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 148 optimal weight: 0.6980 chunk 235 optimal weight: 3.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 402 GLN I 83 ASN B 402 GLN C 402 GLN D 402 GLN E 402 GLN M 83 ASN G 402 GLN H 402 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1507 moved from start: 0.4383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 38728 Z= 0.400 Angle : 0.739 8.211 52544 Z= 0.370 Chirality : 0.049 0.162 5616 Planarity : 0.006 0.049 6800 Dihedral : 7.889 172.558 5392 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 3.79 % Allowed : 12.09 % Favored : 84.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.12), residues: 4712 helix: 0.37 (0.12), residues: 1808 sheet: -0.18 (0.17), residues: 848 loop : -1.37 (0.12), residues: 2056 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP E 216 HIS 0.006 0.002 HIS G 293 PHE 0.017 0.003 PHE P 8 TYR 0.020 0.002 TYR J 47 ARG 0.007 0.001 ARG B 373 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9424 Ramachandran restraints generated. 4712 Oldfield, 0 Emsley, 4712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9424 Ramachandran restraints generated. 4712 Oldfield, 0 Emsley, 4712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 643 residues out of total 3936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 494 time to evaluate : 4.039 Fit side-chains REVERT: A 129 PHE cc_start: 0.1416 (OUTLIER) cc_final: 0.1167 (m-80) REVERT: A 205 ASP cc_start: 0.2079 (OUTLIER) cc_final: 0.1638 (t0) REVERT: A 283 GLU cc_start: 0.2009 (tt0) cc_final: 0.1771 (mp0) REVERT: A 286 ARG cc_start: 0.1888 (tpp80) cc_final: 0.1481 (tpm170) REVERT: I 50 MET cc_start: 0.4329 (OUTLIER) cc_final: 0.3460 (mmt) REVERT: B 129 PHE cc_start: 0.1788 (OUTLIER) cc_final: 0.1497 (m-80) REVERT: B 205 ASP cc_start: 0.2074 (OUTLIER) cc_final: 0.1603 (t0) REVERT: B 283 GLU cc_start: 0.2041 (tt0) cc_final: 0.1810 (mp0) REVERT: B 286 ARG cc_start: 0.2100 (tpp80) cc_final: 0.1660 (tpm170) REVERT: J 50 MET cc_start: 0.4315 (OUTLIER) cc_final: 0.3430 (mmt) REVERT: C 129 PHE cc_start: 0.1399 (OUTLIER) cc_final: 0.1151 (m-80) REVERT: C 205 ASP cc_start: 0.2015 (OUTLIER) cc_final: 0.1554 (t0) REVERT: C 286 ARG cc_start: 0.2131 (tpp80) cc_final: 0.1676 (tpm170) REVERT: K 50 MET cc_start: 0.4256 (OUTLIER) cc_final: 0.3380 (mmt) REVERT: D 129 PHE cc_start: 0.1739 (OUTLIER) cc_final: 0.1438 (m-80) REVERT: D 283 GLU cc_start: 0.2001 (tt0) cc_final: 0.1769 (mp0) REVERT: D 286 ARG cc_start: 0.2100 (tpp80) cc_final: 0.1662 (tpm170) REVERT: L 50 MET cc_start: 0.4300 (OUTLIER) cc_final: 0.3419 (mmt) REVERT: E 129 PHE cc_start: 0.1563 (OUTLIER) cc_final: 0.1319 (m-80) REVERT: E 283 GLU cc_start: 0.2042 (tt0) cc_final: 0.1809 (mp0) REVERT: E 286 ARG cc_start: 0.2093 (tpp80) cc_final: 0.1687 (tpm170) REVERT: M 50 MET cc_start: 0.4336 (OUTLIER) cc_final: 0.3458 (mmt) REVERT: F 129 PHE cc_start: 0.1539 (OUTLIER) cc_final: 0.1276 (m-80) REVERT: F 205 ASP cc_start: 0.2145 (OUTLIER) cc_final: 0.1729 (t0) REVERT: F 283 GLU cc_start: 0.1998 (tt0) cc_final: 0.1763 (mp0) REVERT: F 286 ARG cc_start: 0.2099 (tpp80) cc_final: 0.1692 (tpm170) REVERT: N 50 MET cc_start: 0.4266 (OUTLIER) cc_final: 0.3382 (mmt) REVERT: G 129 PHE cc_start: 0.1565 (OUTLIER) cc_final: 0.1319 (m-80) REVERT: G 205 ASP cc_start: 0.2152 (OUTLIER) cc_final: 0.1707 (t0) REVERT: G 283 GLU cc_start: 0.2008 (tt0) cc_final: 0.1774 (mp0) REVERT: G 286 ARG cc_start: 0.2099 (tpp80) cc_final: 0.1690 (tpm170) REVERT: O 50 MET cc_start: 0.4254 (OUTLIER) cc_final: 0.3375 (mmt) REVERT: H 129 PHE cc_start: 0.1701 (OUTLIER) cc_final: 0.1406 (m-80) REVERT: H 286 ARG cc_start: 0.2110 (tpp80) cc_final: 0.1699 (tpm170) REVERT: P 50 MET cc_start: 0.4271 (OUTLIER) cc_final: 0.3403 (mmt) outliers start: 149 outliers final: 105 residues processed: 582 average time/residue: 0.5508 time to fit residues: 504.0836 Evaluate side-chains 587 residues out of total 3936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 461 time to evaluate : 3.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 129 PHE Chi-restraints excluded: chain A residue 205 ASP Chi-restraints excluded: chain A residue 207 ASN Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain I residue 38 THR Chi-restraints excluded: chain I residue 50 MET Chi-restraints excluded: chain I residue 88 THR Chi-restraints excluded: chain I residue 117 ASP Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 129 PHE Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 207 ASN Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 342 THR Chi-restraints excluded: chain B residue 355 ASN Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 357 VAL Chi-restraints excluded: chain J residue 38 THR Chi-restraints excluded: chain J residue 50 MET Chi-restraints excluded: chain J residue 88 THR Chi-restraints excluded: chain J residue 117 ASP Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 129 PHE Chi-restraints excluded: chain C residue 205 ASP Chi-restraints excluded: chain C residue 207 ASN Chi-restraints excluded: chain C residue 265 VAL Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 342 THR Chi-restraints excluded: chain C residue 355 ASN Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain K residue 38 THR Chi-restraints excluded: chain K residue 50 MET Chi-restraints excluded: chain K residue 88 THR Chi-restraints excluded: chain K residue 117 ASP Chi-restraints excluded: chain D residue 34 LYS Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain D residue 129 PHE Chi-restraints excluded: chain D residue 207 ASN Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 342 THR Chi-restraints excluded: chain D residue 355 ASN Chi-restraints excluded: chain D residue 356 THR Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain L residue 38 THR Chi-restraints excluded: chain L residue 50 MET Chi-restraints excluded: chain L residue 88 THR Chi-restraints excluded: chain L residue 117 ASP Chi-restraints excluded: chain E residue 34 LYS Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 129 PHE Chi-restraints excluded: chain E residue 207 ASN Chi-restraints excluded: chain E residue 265 VAL Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 342 THR Chi-restraints excluded: chain E residue 355 ASN Chi-restraints excluded: chain E residue 356 THR Chi-restraints excluded: chain E residue 357 VAL Chi-restraints excluded: chain M residue 38 THR Chi-restraints excluded: chain M residue 50 MET Chi-restraints excluded: chain M residue 88 THR Chi-restraints excluded: chain M residue 105 VAL Chi-restraints excluded: chain M residue 117 ASP Chi-restraints excluded: chain F residue 34 LYS Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 129 PHE Chi-restraints excluded: chain F residue 205 ASP Chi-restraints excluded: chain F residue 207 ASN Chi-restraints excluded: chain F residue 265 VAL Chi-restraints excluded: chain F residue 269 VAL Chi-restraints excluded: chain F residue 342 THR Chi-restraints excluded: chain F residue 355 ASN Chi-restraints excluded: chain F residue 356 THR Chi-restraints excluded: chain F residue 357 VAL Chi-restraints excluded: chain N residue 38 THR Chi-restraints excluded: chain N residue 50 MET Chi-restraints excluded: chain N residue 88 THR Chi-restraints excluded: chain N residue 105 VAL Chi-restraints excluded: chain N residue 117 ASP Chi-restraints excluded: chain G residue 81 SER Chi-restraints excluded: chain G residue 126 VAL Chi-restraints excluded: chain G residue 129 PHE Chi-restraints excluded: chain G residue 205 ASP Chi-restraints excluded: chain G residue 207 ASN Chi-restraints excluded: chain G residue 265 VAL Chi-restraints excluded: chain G residue 269 VAL Chi-restraints excluded: chain G residue 271 LEU Chi-restraints excluded: chain G residue 276 THR Chi-restraints excluded: chain G residue 342 THR Chi-restraints excluded: chain G residue 355 ASN Chi-restraints excluded: chain G residue 356 THR Chi-restraints excluded: chain G residue 357 VAL Chi-restraints excluded: chain O residue 38 THR Chi-restraints excluded: chain O residue 50 MET Chi-restraints excluded: chain O residue 88 THR Chi-restraints excluded: chain O residue 105 VAL Chi-restraints excluded: chain O residue 117 ASP Chi-restraints excluded: chain H residue 81 SER Chi-restraints excluded: chain H residue 126 VAL Chi-restraints excluded: chain H residue 129 PHE Chi-restraints excluded: chain H residue 207 ASN Chi-restraints excluded: chain H residue 265 VAL Chi-restraints excluded: chain H residue 269 VAL Chi-restraints excluded: chain H residue 276 THR Chi-restraints excluded: chain H residue 342 THR Chi-restraints excluded: chain H residue 355 ASN Chi-restraints excluded: chain H residue 356 THR Chi-restraints excluded: chain H residue 357 VAL Chi-restraints excluded: chain P residue 38 THR Chi-restraints excluded: chain P residue 50 MET Chi-restraints excluded: chain P residue 88 THR Chi-restraints excluded: chain P residue 105 VAL Chi-restraints excluded: chain P residue 117 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 432 optimal weight: 2.9990 chunk 50 optimal weight: 0.5980 chunk 255 optimal weight: 1.9990 chunk 327 optimal weight: 1.9990 chunk 254 optimal weight: 0.1980 chunk 377 optimal weight: 3.9990 chunk 250 optimal weight: 0.6980 chunk 447 optimal weight: 2.9990 chunk 279 optimal weight: 0.7980 chunk 272 optimal weight: 1.9990 chunk 206 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1498 moved from start: 0.4272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 38728 Z= 0.148 Angle : 0.517 7.984 52544 Z= 0.260 Chirality : 0.041 0.127 5616 Planarity : 0.004 0.032 6800 Dihedral : 7.057 174.652 5392 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 3.00 % Allowed : 13.34 % Favored : 83.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.12), residues: 4712 helix: 1.22 (0.13), residues: 1760 sheet: 0.16 (0.17), residues: 880 loop : -1.29 (0.12), residues: 2072 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 216 HIS 0.003 0.001 HIS F 293 PHE 0.010 0.001 PHE A 201 TYR 0.009 0.001 TYR E 26 ARG 0.004 0.000 ARG G 304 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9424 Ramachandran restraints generated. 4712 Oldfield, 0 Emsley, 4712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9424 Ramachandran restraints generated. 4712 Oldfield, 0 Emsley, 4712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 630 residues out of total 3936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 512 time to evaluate : 3.879 Fit side-chains REVERT: A 129 PHE cc_start: 0.1600 (OUTLIER) cc_final: 0.1321 (m-80) REVERT: A 286 ARG cc_start: 0.2002 (tpp80) cc_final: 0.1547 (tpm170) REVERT: I 50 MET cc_start: 0.4342 (OUTLIER) cc_final: 0.3514 (mmt) REVERT: B 129 PHE cc_start: 0.1709 (OUTLIER) cc_final: 0.1418 (m-80) REVERT: B 286 ARG cc_start: 0.1961 (tpp80) cc_final: 0.1523 (tpm170) REVERT: J 50 MET cc_start: 0.4349 (OUTLIER) cc_final: 0.3524 (mmt) REVERT: C 129 PHE cc_start: 0.1589 (OUTLIER) cc_final: 0.1311 (m-80) REVERT: C 286 ARG cc_start: 0.1977 (tpp80) cc_final: 0.1501 (tpm170) REVERT: K 50 MET cc_start: 0.4318 (OUTLIER) cc_final: 0.3499 (mmt) REVERT: D 129 PHE cc_start: 0.1718 (OUTLIER) cc_final: 0.1420 (m-80) REVERT: D 286 ARG cc_start: 0.2016 (tpp80) cc_final: 0.1564 (tpm170) REVERT: D 376 MET cc_start: 0.2737 (OUTLIER) cc_final: 0.2532 (tpp) REVERT: L 50 MET cc_start: 0.4332 (OUTLIER) cc_final: 0.3504 (mmt) REVERT: E 129 PHE cc_start: 0.1586 (OUTLIER) cc_final: 0.1309 (m-80) REVERT: E 286 ARG cc_start: 0.2011 (tpp80) cc_final: 0.1567 (tpm170) REVERT: M 50 MET cc_start: 0.4330 (OUTLIER) cc_final: 0.3493 (mmt) REVERT: F 129 PHE cc_start: 0.1716 (OUTLIER) cc_final: 0.1424 (m-80) REVERT: F 205 ASP cc_start: 0.2056 (t70) cc_final: 0.1611 (t0) REVERT: F 286 ARG cc_start: 0.2012 (tpp80) cc_final: 0.1569 (tpm170) REVERT: F 306 LYS cc_start: 0.2644 (ttpp) cc_final: 0.2359 (tttp) REVERT: F 444 GLU cc_start: 0.1892 (tp30) cc_final: 0.1631 (mp0) REVERT: N 50 MET cc_start: 0.4347 (OUTLIER) cc_final: 0.3500 (mmt) REVERT: G 129 PHE cc_start: 0.1528 (OUTLIER) cc_final: 0.1245 (m-80) REVERT: G 205 ASP cc_start: 0.1947 (t70) cc_final: 0.1468 (t0) REVERT: G 286 ARG cc_start: 0.2017 (tpp80) cc_final: 0.1554 (tpm170) REVERT: O 50 MET cc_start: 0.4337 (OUTLIER) cc_final: 0.3492 (mmt) REVERT: H 129 PHE cc_start: 0.1676 (OUTLIER) cc_final: 0.1380 (m-80) REVERT: H 286 ARG cc_start: 0.2026 (tpp80) cc_final: 0.1576 (tpm170) REVERT: P 50 MET cc_start: 0.4319 (OUTLIER) cc_final: 0.3486 (mmt) outliers start: 118 outliers final: 76 residues processed: 566 average time/residue: 0.5186 time to fit residues: 471.3515 Evaluate side-chains 570 residues out of total 3936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 477 time to evaluate : 4.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 129 PHE Chi-restraints excluded: chain A residue 207 ASN Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain I residue 38 THR Chi-restraints excluded: chain I residue 50 MET Chi-restraints excluded: chain I residue 88 THR Chi-restraints excluded: chain I residue 117 ASP Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 129 PHE Chi-restraints excluded: chain B residue 207 ASN Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 342 THR Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 357 VAL Chi-restraints excluded: chain J residue 38 THR Chi-restraints excluded: chain J residue 50 MET Chi-restraints excluded: chain J residue 88 THR Chi-restraints excluded: chain J residue 117 ASP Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 129 PHE Chi-restraints excluded: chain C residue 207 ASN Chi-restraints excluded: chain C residue 265 VAL Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 342 THR Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain K residue 38 THR Chi-restraints excluded: chain K residue 50 MET Chi-restraints excluded: chain K residue 88 THR Chi-restraints excluded: chain K residue 117 ASP Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain D residue 129 PHE Chi-restraints excluded: chain D residue 207 ASN Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 342 THR Chi-restraints excluded: chain D residue 356 THR Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 376 MET Chi-restraints excluded: chain L residue 38 THR Chi-restraints excluded: chain L residue 50 MET Chi-restraints excluded: chain L residue 88 THR Chi-restraints excluded: chain L residue 117 ASP Chi-restraints excluded: chain E residue 34 LYS Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 129 PHE Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 342 THR Chi-restraints excluded: chain E residue 356 THR Chi-restraints excluded: chain E residue 357 VAL Chi-restraints excluded: chain M residue 38 THR Chi-restraints excluded: chain M residue 50 MET Chi-restraints excluded: chain M residue 88 THR Chi-restraints excluded: chain M residue 117 ASP Chi-restraints excluded: chain F residue 34 LYS Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 129 PHE Chi-restraints excluded: chain F residue 269 VAL Chi-restraints excluded: chain F residue 342 THR Chi-restraints excluded: chain F residue 357 VAL Chi-restraints excluded: chain N residue 38 THR Chi-restraints excluded: chain N residue 50 MET Chi-restraints excluded: chain N residue 88 THR Chi-restraints excluded: chain N residue 117 ASP Chi-restraints excluded: chain G residue 126 VAL Chi-restraints excluded: chain G residue 129 PHE Chi-restraints excluded: chain G residue 207 ASN Chi-restraints excluded: chain G residue 269 VAL Chi-restraints excluded: chain G residue 276 THR Chi-restraints excluded: chain G residue 356 THR Chi-restraints excluded: chain G residue 357 VAL Chi-restraints excluded: chain O residue 38 THR Chi-restraints excluded: chain O residue 50 MET Chi-restraints excluded: chain O residue 88 THR Chi-restraints excluded: chain O residue 117 ASP Chi-restraints excluded: chain H residue 126 VAL Chi-restraints excluded: chain H residue 129 PHE Chi-restraints excluded: chain H residue 269 VAL Chi-restraints excluded: chain H residue 342 THR Chi-restraints excluded: chain H residue 356 THR Chi-restraints excluded: chain H residue 357 VAL Chi-restraints excluded: chain P residue 38 THR Chi-restraints excluded: chain P residue 50 MET Chi-restraints excluded: chain P residue 88 THR Chi-restraints excluded: chain P residue 117 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 276 optimal weight: 0.8980 chunk 178 optimal weight: 4.9990 chunk 267 optimal weight: 4.9990 chunk 134 optimal weight: 0.6980 chunk 87 optimal weight: 3.9990 chunk 86 optimal weight: 4.9990 chunk 284 optimal weight: 2.9990 chunk 304 optimal weight: 7.9990 chunk 221 optimal weight: 0.0670 chunk 41 optimal weight: 0.7980 chunk 351 optimal weight: 4.9990 overall best weight: 1.0920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1501 moved from start: 0.4349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 38728 Z= 0.201 Angle : 0.549 9.927 52544 Z= 0.274 Chirality : 0.042 0.136 5616 Planarity : 0.004 0.038 6800 Dihedral : 7.012 175.262 5392 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.82 % Allowed : 13.57 % Favored : 83.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.12), residues: 4712 helix: 1.26 (0.13), residues: 1760 sheet: 0.16 (0.17), residues: 880 loop : -1.25 (0.12), residues: 2072 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 216 HIS 0.004 0.001 HIS H 293 PHE 0.011 0.001 PHE C 201 TYR 0.012 0.001 TYR J 47 ARG 0.008 0.000 ARG G 361 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9424 Ramachandran restraints generated. 4712 Oldfield, 0 Emsley, 4712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9424 Ramachandran restraints generated. 4712 Oldfield, 0 Emsley, 4712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 607 residues out of total 3936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 496 time to evaluate : 4.178 Fit side-chains REVERT: A 129 PHE cc_start: 0.1503 (OUTLIER) cc_final: 0.1221 (m-80) REVERT: A 286 ARG cc_start: 0.2014 (tpp80) cc_final: 0.1486 (tpm170) REVERT: I 50 MET cc_start: 0.4356 (OUTLIER) cc_final: 0.3494 (mmt) REVERT: B 129 PHE cc_start: 0.1643 (OUTLIER) cc_final: 0.1356 (m-80) REVERT: B 286 ARG cc_start: 0.1962 (tpp80) cc_final: 0.1503 (tpm170) REVERT: B 444 GLU cc_start: 0.1794 (tp30) cc_final: 0.1566 (mp0) REVERT: J 50 MET cc_start: 0.4268 (OUTLIER) cc_final: 0.3414 (mmt) REVERT: C 129 PHE cc_start: 0.1594 (OUTLIER) cc_final: 0.1315 (m-80) REVERT: C 286 ARG cc_start: 0.2004 (tpp80) cc_final: 0.1503 (tpm170) REVERT: K 50 MET cc_start: 0.4293 (OUTLIER) cc_final: 0.3438 (mmt) REVERT: D 129 PHE cc_start: 0.1600 (OUTLIER) cc_final: 0.1305 (m-80) REVERT: D 286 ARG cc_start: 0.1966 (tpp80) cc_final: 0.1522 (tpm170) REVERT: L 50 MET cc_start: 0.4349 (OUTLIER) cc_final: 0.3484 (mmt) REVERT: E 129 PHE cc_start: 0.1605 (OUTLIER) cc_final: 0.1333 (m-80) REVERT: E 286 ARG cc_start: 0.2015 (tpp80) cc_final: 0.1544 (tpm170) REVERT: M 50 MET cc_start: 0.4355 (OUTLIER) cc_final: 0.3486 (mmt) REVERT: F 129 PHE cc_start: 0.1597 (OUTLIER) cc_final: 0.1311 (m-80) REVERT: F 205 ASP cc_start: 0.1955 (t70) cc_final: 0.1522 (t0) REVERT: F 286 ARG cc_start: 0.2037 (tpp80) cc_final: 0.1570 (tpm170) REVERT: F 444 GLU cc_start: 0.1795 (tp30) cc_final: 0.1537 (mp0) REVERT: N 50 MET cc_start: 0.4266 (OUTLIER) cc_final: 0.3408 (mmt) REVERT: G 129 PHE cc_start: 0.1565 (OUTLIER) cc_final: 0.1293 (m-80) REVERT: G 205 ASP cc_start: 0.1936 (t70) cc_final: 0.1494 (t0) REVERT: G 283 GLU cc_start: 0.1458 (tt0) cc_final: 0.1257 (mp0) REVERT: G 286 ARG cc_start: 0.2017 (tpp80) cc_final: 0.1544 (tpm170) REVERT: O 50 MET cc_start: 0.4254 (OUTLIER) cc_final: 0.3400 (mmt) REVERT: H 129 PHE cc_start: 0.1587 (OUTLIER) cc_final: 0.1298 (m-80) REVERT: H 286 ARG cc_start: 0.2025 (tpp80) cc_final: 0.1551 (tpm170) REVERT: H 444 GLU cc_start: 0.1864 (tp30) cc_final: 0.1578 (mp0) REVERT: P 50 MET cc_start: 0.4310 (OUTLIER) cc_final: 0.3438 (mmt) outliers start: 111 outliers final: 84 residues processed: 558 average time/residue: 0.5244 time to fit residues: 467.1177 Evaluate side-chains 588 residues out of total 3936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 488 time to evaluate : 3.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 129 PHE Chi-restraints excluded: chain A residue 207 ASN Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain I residue 38 THR Chi-restraints excluded: chain I residue 50 MET Chi-restraints excluded: chain I residue 88 THR Chi-restraints excluded: chain I residue 117 ASP Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 129 PHE Chi-restraints excluded: chain B residue 207 ASN Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 342 THR Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 357 VAL Chi-restraints excluded: chain J residue 38 THR Chi-restraints excluded: chain J residue 50 MET Chi-restraints excluded: chain J residue 88 THR Chi-restraints excluded: chain J residue 117 ASP Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 129 PHE Chi-restraints excluded: chain C residue 207 ASN Chi-restraints excluded: chain C residue 265 VAL Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 342 THR Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain K residue 38 THR Chi-restraints excluded: chain K residue 50 MET Chi-restraints excluded: chain K residue 88 THR Chi-restraints excluded: chain K residue 117 ASP Chi-restraints excluded: chain D residue 34 LYS Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain D residue 129 PHE Chi-restraints excluded: chain D residue 207 ASN Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 342 THR Chi-restraints excluded: chain D residue 356 THR Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain L residue 38 THR Chi-restraints excluded: chain L residue 50 MET Chi-restraints excluded: chain L residue 88 THR Chi-restraints excluded: chain L residue 117 ASP Chi-restraints excluded: chain E residue 34 LYS Chi-restraints excluded: chain E residue 44 ILE Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 129 PHE Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 342 THR Chi-restraints excluded: chain E residue 356 THR Chi-restraints excluded: chain E residue 357 VAL Chi-restraints excluded: chain M residue 38 THR Chi-restraints excluded: chain M residue 50 MET Chi-restraints excluded: chain M residue 88 THR Chi-restraints excluded: chain M residue 117 ASP Chi-restraints excluded: chain F residue 34 LYS Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 129 PHE Chi-restraints excluded: chain F residue 269 VAL Chi-restraints excluded: chain F residue 342 THR Chi-restraints excluded: chain F residue 355 ASN Chi-restraints excluded: chain F residue 356 THR Chi-restraints excluded: chain F residue 357 VAL Chi-restraints excluded: chain N residue 38 THR Chi-restraints excluded: chain N residue 50 MET Chi-restraints excluded: chain N residue 88 THR Chi-restraints excluded: chain N residue 117 ASP Chi-restraints excluded: chain G residue 44 ILE Chi-restraints excluded: chain G residue 126 VAL Chi-restraints excluded: chain G residue 129 PHE Chi-restraints excluded: chain G residue 207 ASN Chi-restraints excluded: chain G residue 269 VAL Chi-restraints excluded: chain G residue 276 THR Chi-restraints excluded: chain G residue 342 THR Chi-restraints excluded: chain G residue 356 THR Chi-restraints excluded: chain G residue 357 VAL Chi-restraints excluded: chain O residue 38 THR Chi-restraints excluded: chain O residue 50 MET Chi-restraints excluded: chain O residue 88 THR Chi-restraints excluded: chain O residue 117 ASP Chi-restraints excluded: chain H residue 126 VAL Chi-restraints excluded: chain H residue 129 PHE Chi-restraints excluded: chain H residue 269 VAL Chi-restraints excluded: chain H residue 276 THR Chi-restraints excluded: chain H residue 342 THR Chi-restraints excluded: chain H residue 356 THR Chi-restraints excluded: chain H residue 357 VAL Chi-restraints excluded: chain P residue 38 THR Chi-restraints excluded: chain P residue 50 MET Chi-restraints excluded: chain P residue 88 THR Chi-restraints excluded: chain P residue 117 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 406 optimal weight: 9.9990 chunk 428 optimal weight: 0.7980 chunk 390 optimal weight: 10.0000 chunk 416 optimal weight: 0.9980 chunk 250 optimal weight: 2.9990 chunk 181 optimal weight: 3.9990 chunk 327 optimal weight: 6.9990 chunk 127 optimal weight: 5.9990 chunk 376 optimal weight: 4.9990 chunk 394 optimal weight: 6.9990 chunk 415 optimal weight: 0.8980 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 83 ASN O 83 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1505 moved from start: 0.4520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 38728 Z= 0.301 Angle : 0.641 9.131 52544 Z= 0.319 Chirality : 0.045 0.148 5616 Planarity : 0.005 0.050 6800 Dihedral : 7.300 175.608 5392 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 3.12 % Allowed : 13.57 % Favored : 83.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.12), residues: 4712 helix: 0.96 (0.12), residues: 1760 sheet: -0.01 (0.18), residues: 832 loop : -1.24 (0.12), residues: 2120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 216 HIS 0.006 0.002 HIS F 293 PHE 0.014 0.002 PHE P 8 TYR 0.017 0.002 TYR I 47 ARG 0.009 0.001 ARG G 361 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9424 Ramachandran restraints generated. 4712 Oldfield, 0 Emsley, 4712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9424 Ramachandran restraints generated. 4712 Oldfield, 0 Emsley, 4712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 574 residues out of total 3936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 451 time to evaluate : 3.849 Fit side-chains REVERT: A 129 PHE cc_start: 0.1400 (OUTLIER) cc_final: 0.1120 (m-80) REVERT: A 286 ARG cc_start: 0.2165 (tpp80) cc_final: 0.1743 (tpm170) REVERT: I 50 MET cc_start: 0.4288 (OUTLIER) cc_final: 0.3442 (mmt) REVERT: B 129 PHE cc_start: 0.1618 (OUTLIER) cc_final: 0.1330 (m-80) REVERT: B 286 ARG cc_start: 0.2114 (tpp80) cc_final: 0.1694 (tpm170) REVERT: J 50 MET cc_start: 0.4317 (OUTLIER) cc_final: 0.3438 (mmt) REVERT: C 129 PHE cc_start: 0.1340 (OUTLIER) cc_final: 0.1066 (m-80) REVERT: C 286 ARG cc_start: 0.2093 (tpp80) cc_final: 0.1679 (tpm170) REVERT: K 50 MET cc_start: 0.4280 (OUTLIER) cc_final: 0.3418 (mmt) REVERT: D 129 PHE cc_start: 0.1596 (OUTLIER) cc_final: 0.1313 (m-80) REVERT: D 286 ARG cc_start: 0.2065 (tpp80) cc_final: 0.1678 (tpm170) REVERT: L 50 MET cc_start: 0.4285 (OUTLIER) cc_final: 0.3436 (mmt) REVERT: E 129 PHE cc_start: 0.1381 (OUTLIER) cc_final: 0.1110 (m-80) REVERT: E 286 ARG cc_start: 0.2102 (tpp80) cc_final: 0.1710 (tpm170) REVERT: M 50 MET cc_start: 0.4291 (OUTLIER) cc_final: 0.3429 (mmt) REVERT: F 129 PHE cc_start: 0.1571 (OUTLIER) cc_final: 0.1290 (m-80) REVERT: F 286 ARG cc_start: 0.2249 (tpp80) cc_final: 0.1695 (tpm170) REVERT: F 306 LYS cc_start: 0.2591 (ttpp) cc_final: 0.2266 (tttp) REVERT: F 444 GLU cc_start: 0.1795 (tp30) cc_final: 0.1514 (mp0) REVERT: N 50 MET cc_start: 0.4316 (OUTLIER) cc_final: 0.3432 (mmt) REVERT: G 129 PHE cc_start: 0.1496 (OUTLIER) cc_final: 0.1223 (m-80) REVERT: G 286 ARG cc_start: 0.1942 (tpp80) cc_final: 0.1575 (tpm170) REVERT: O 50 MET cc_start: 0.4298 (OUTLIER) cc_final: 0.3432 (mmt) REVERT: H 129 PHE cc_start: 0.1569 (OUTLIER) cc_final: 0.1284 (m-80) REVERT: H 286 ARG cc_start: 0.2113 (tpp80) cc_final: 0.1717 (tpm170) REVERT: P 50 MET cc_start: 0.4281 (OUTLIER) cc_final: 0.3428 (mmt) outliers start: 123 outliers final: 96 residues processed: 532 average time/residue: 0.5274 time to fit residues: 448.3228 Evaluate side-chains 555 residues out of total 3936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 443 time to evaluate : 3.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 129 PHE Chi-restraints excluded: chain A residue 207 ASN Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 475 THR Chi-restraints excluded: chain I residue 38 THR Chi-restraints excluded: chain I residue 50 MET Chi-restraints excluded: chain I residue 88 THR Chi-restraints excluded: chain I residue 117 ASP Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 129 PHE Chi-restraints excluded: chain B residue 207 ASN Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 342 THR Chi-restraints excluded: chain B residue 355 ASN Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 357 VAL Chi-restraints excluded: chain J residue 38 THR Chi-restraints excluded: chain J residue 50 MET Chi-restraints excluded: chain J residue 88 THR Chi-restraints excluded: chain J residue 105 VAL Chi-restraints excluded: chain J residue 117 ASP Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 129 PHE Chi-restraints excluded: chain C residue 207 ASN Chi-restraints excluded: chain C residue 265 VAL Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain C residue 342 THR Chi-restraints excluded: chain C residue 355 ASN Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain K residue 38 THR Chi-restraints excluded: chain K residue 50 MET Chi-restraints excluded: chain K residue 88 THR Chi-restraints excluded: chain K residue 117 ASP Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain D residue 129 PHE Chi-restraints excluded: chain D residue 207 ASN Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 336 LEU Chi-restraints excluded: chain D residue 342 THR Chi-restraints excluded: chain D residue 356 THR Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 475 THR Chi-restraints excluded: chain L residue 38 THR Chi-restraints excluded: chain L residue 50 MET Chi-restraints excluded: chain L residue 88 THR Chi-restraints excluded: chain L residue 105 VAL Chi-restraints excluded: chain L residue 117 ASP Chi-restraints excluded: chain E residue 34 LYS Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 129 PHE Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 342 THR Chi-restraints excluded: chain E residue 356 THR Chi-restraints excluded: chain E residue 357 VAL Chi-restraints excluded: chain M residue 38 THR Chi-restraints excluded: chain M residue 50 MET Chi-restraints excluded: chain M residue 88 THR Chi-restraints excluded: chain M residue 105 VAL Chi-restraints excluded: chain M residue 117 ASP Chi-restraints excluded: chain F residue 34 LYS Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 129 PHE Chi-restraints excluded: chain F residue 207 ASN Chi-restraints excluded: chain F residue 269 VAL Chi-restraints excluded: chain F residue 342 THR Chi-restraints excluded: chain F residue 355 ASN Chi-restraints excluded: chain F residue 356 THR Chi-restraints excluded: chain F residue 357 VAL Chi-restraints excluded: chain N residue 38 THR Chi-restraints excluded: chain N residue 50 MET Chi-restraints excluded: chain N residue 88 THR Chi-restraints excluded: chain N residue 117 ASP Chi-restraints excluded: chain G residue 126 VAL Chi-restraints excluded: chain G residue 129 PHE Chi-restraints excluded: chain G residue 207 ASN Chi-restraints excluded: chain G residue 269 VAL Chi-restraints excluded: chain G residue 276 THR Chi-restraints excluded: chain G residue 342 THR Chi-restraints excluded: chain G residue 355 ASN Chi-restraints excluded: chain G residue 356 THR Chi-restraints excluded: chain G residue 357 VAL Chi-restraints excluded: chain O residue 38 THR Chi-restraints excluded: chain O residue 50 MET Chi-restraints excluded: chain O residue 88 THR Chi-restraints excluded: chain O residue 105 VAL Chi-restraints excluded: chain O residue 117 ASP Chi-restraints excluded: chain H residue 126 VAL Chi-restraints excluded: chain H residue 129 PHE Chi-restraints excluded: chain H residue 269 VAL Chi-restraints excluded: chain H residue 276 THR Chi-restraints excluded: chain H residue 342 THR Chi-restraints excluded: chain H residue 356 THR Chi-restraints excluded: chain H residue 357 VAL Chi-restraints excluded: chain P residue 38 THR Chi-restraints excluded: chain P residue 50 MET Chi-restraints excluded: chain P residue 88 THR Chi-restraints excluded: chain P residue 105 VAL Chi-restraints excluded: chain P residue 117 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 273 optimal weight: 0.9990 chunk 440 optimal weight: 4.9990 chunk 268 optimal weight: 3.9990 chunk 209 optimal weight: 0.7980 chunk 306 optimal weight: 1.9990 chunk 462 optimal weight: 0.2980 chunk 425 optimal weight: 2.9990 chunk 368 optimal weight: 1.9990 chunk 38 optimal weight: 4.9990 chunk 284 optimal weight: 3.9990 chunk 225 optimal weight: 0.0370 overall best weight: 0.8262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1500 moved from start: 0.4483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 38728 Z= 0.172 Angle : 0.536 9.596 52544 Z= 0.268 Chirality : 0.042 0.132 5616 Planarity : 0.004 0.037 6800 Dihedral : 6.907 177.187 5392 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.87 % Allowed : 13.67 % Favored : 83.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.00 (0.12), residues: 4712 helix: 1.29 (0.13), residues: 1760 sheet: 0.12 (0.17), residues: 880 loop : -1.18 (0.13), residues: 2072 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 216 HIS 0.003 0.001 HIS F 293 PHE 0.010 0.001 PHE G 364 TYR 0.011 0.001 TYR F 241 ARG 0.007 0.000 ARG G 361 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9424 Ramachandran restraints generated. 4712 Oldfield, 0 Emsley, 4712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9424 Ramachandran restraints generated. 4712 Oldfield, 0 Emsley, 4712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 614 residues out of total 3936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 501 time to evaluate : 4.018 Fit side-chains REVERT: A 129 PHE cc_start: 0.1521 (OUTLIER) cc_final: 0.1245 (m-80) REVERT: A 286 ARG cc_start: 0.2058 (tpp80) cc_final: 0.1561 (tpm170) REVERT: I 50 MET cc_start: 0.4327 (OUTLIER) cc_final: 0.3490 (mmt) REVERT: B 129 PHE cc_start: 0.1578 (OUTLIER) cc_final: 0.1306 (m-80) REVERT: B 286 ARG cc_start: 0.2016 (tpp80) cc_final: 0.1534 (tpm170) REVERT: J 50 MET cc_start: 0.4256 (OUTLIER) cc_final: 0.3411 (mmt) REVERT: C 129 PHE cc_start: 0.1620 (OUTLIER) cc_final: 0.1349 (m-80) REVERT: C 286 ARG cc_start: 0.1985 (tpp80) cc_final: 0.1485 (tpm170) REVERT: K 50 MET cc_start: 0.4349 (OUTLIER) cc_final: 0.3489 (mmt) REVERT: D 129 PHE cc_start: 0.1590 (OUTLIER) cc_final: 0.1303 (m-80) REVERT: D 286 ARG cc_start: 0.1970 (tpp80) cc_final: 0.1511 (tpm170) REVERT: L 50 MET cc_start: 0.4328 (OUTLIER) cc_final: 0.3480 (mmt) REVERT: E 129 PHE cc_start: 0.1534 (OUTLIER) cc_final: 0.1268 (m-80) REVERT: E 286 ARG cc_start: 0.2026 (tpp80) cc_final: 0.1557 (tpm170) REVERT: M 50 MET cc_start: 0.4299 (OUTLIER) cc_final: 0.3439 (mmt) REVERT: F 129 PHE cc_start: 0.1615 (OUTLIER) cc_final: 0.1337 (m-80) REVERT: F 286 ARG cc_start: 0.2275 (tpp80) cc_final: 0.1742 (tpm170) REVERT: F 444 GLU cc_start: 0.1713 (tp30) cc_final: 0.1457 (mp0) REVERT: N 50 MET cc_start: 0.4318 (OUTLIER) cc_final: 0.3449 (mmt) REVERT: G 129 PHE cc_start: 0.1488 (OUTLIER) cc_final: 0.1219 (m-80) REVERT: G 286 ARG cc_start: 0.2085 (tpp80) cc_final: 0.1608 (tpm170) REVERT: G 444 GLU cc_start: 0.1781 (tp30) cc_final: 0.1536 (mp0) REVERT: O 50 MET cc_start: 0.4302 (OUTLIER) cc_final: 0.3440 (mmt) REVERT: H 129 PHE cc_start: 0.1578 (OUTLIER) cc_final: 0.1301 (m-80) REVERT: H 286 ARG cc_start: 0.2034 (tpp80) cc_final: 0.1560 (tpm170) REVERT: H 444 GLU cc_start: 0.1898 (tp30) cc_final: 0.1620 (mp0) REVERT: P 50 MET cc_start: 0.4285 (OUTLIER) cc_final: 0.3425 (mmt) outliers start: 113 outliers final: 91 residues processed: 558 average time/residue: 0.5410 time to fit residues: 486.2999 Evaluate side-chains 595 residues out of total 3936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 488 time to evaluate : 3.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 129 PHE Chi-restraints excluded: chain A residue 207 ASN Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain I residue 38 THR Chi-restraints excluded: chain I residue 50 MET Chi-restraints excluded: chain I residue 88 THR Chi-restraints excluded: chain I residue 117 ASP Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 129 PHE Chi-restraints excluded: chain B residue 207 ASN Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 342 THR Chi-restraints excluded: chain B residue 355 ASN Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 357 VAL Chi-restraints excluded: chain J residue 38 THR Chi-restraints excluded: chain J residue 50 MET Chi-restraints excluded: chain J residue 88 THR Chi-restraints excluded: chain J residue 117 ASP Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 129 PHE Chi-restraints excluded: chain C residue 207 ASN Chi-restraints excluded: chain C residue 265 VAL Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain C residue 342 THR Chi-restraints excluded: chain C residue 355 ASN Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain C residue 475 THR Chi-restraints excluded: chain K residue 38 THR Chi-restraints excluded: chain K residue 50 MET Chi-restraints excluded: chain K residue 88 THR Chi-restraints excluded: chain K residue 117 ASP Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain D residue 129 PHE Chi-restraints excluded: chain D residue 207 ASN Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 336 LEU Chi-restraints excluded: chain D residue 342 THR Chi-restraints excluded: chain D residue 356 THR Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain L residue 38 THR Chi-restraints excluded: chain L residue 50 MET Chi-restraints excluded: chain L residue 88 THR Chi-restraints excluded: chain L residue 117 ASP Chi-restraints excluded: chain E residue 34 LYS Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 129 PHE Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 342 THR Chi-restraints excluded: chain E residue 356 THR Chi-restraints excluded: chain E residue 357 VAL Chi-restraints excluded: chain M residue 38 THR Chi-restraints excluded: chain M residue 50 MET Chi-restraints excluded: chain M residue 88 THR Chi-restraints excluded: chain M residue 105 VAL Chi-restraints excluded: chain M residue 117 ASP Chi-restraints excluded: chain F residue 34 LYS Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 129 PHE Chi-restraints excluded: chain F residue 207 ASN Chi-restraints excluded: chain F residue 269 VAL Chi-restraints excluded: chain F residue 342 THR Chi-restraints excluded: chain F residue 355 ASN Chi-restraints excluded: chain F residue 356 THR Chi-restraints excluded: chain F residue 357 VAL Chi-restraints excluded: chain N residue 38 THR Chi-restraints excluded: chain N residue 50 MET Chi-restraints excluded: chain N residue 88 THR Chi-restraints excluded: chain N residue 117 ASP Chi-restraints excluded: chain G residue 126 VAL Chi-restraints excluded: chain G residue 129 PHE Chi-restraints excluded: chain G residue 207 ASN Chi-restraints excluded: chain G residue 269 VAL Chi-restraints excluded: chain G residue 342 THR Chi-restraints excluded: chain G residue 355 ASN Chi-restraints excluded: chain G residue 356 THR Chi-restraints excluded: chain G residue 357 VAL Chi-restraints excluded: chain O residue 38 THR Chi-restraints excluded: chain O residue 50 MET Chi-restraints excluded: chain O residue 88 THR Chi-restraints excluded: chain O residue 105 VAL Chi-restraints excluded: chain O residue 117 ASP Chi-restraints excluded: chain H residue 126 VAL Chi-restraints excluded: chain H residue 129 PHE Chi-restraints excluded: chain H residue 269 VAL Chi-restraints excluded: chain H residue 276 THR Chi-restraints excluded: chain H residue 342 THR Chi-restraints excluded: chain H residue 356 THR Chi-restraints excluded: chain H residue 357 VAL Chi-restraints excluded: chain P residue 38 THR Chi-restraints excluded: chain P residue 50 MET Chi-restraints excluded: chain P residue 88 THR Chi-restraints excluded: chain P residue 117 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 292 optimal weight: 0.9990 chunk 392 optimal weight: 1.9990 chunk 112 optimal weight: 5.9990 chunk 339 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 102 optimal weight: 0.8980 chunk 368 optimal weight: 0.9980 chunk 154 optimal weight: 0.6980 chunk 378 optimal weight: 3.9990 chunk 46 optimal weight: 5.9990 chunk 67 optimal weight: 4.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.161613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.126460 restraints weight = 269621.741| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 6.11 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3191 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3191 r_free = 0.3191 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3189 r_free = 0.3189 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 99 | |-----------------------------------------------------------------------------| r_final: 0.3189 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7227 moved from start: 0.4518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 38728 Z= 0.205 Angle : 0.555 9.230 52544 Z= 0.276 Chirality : 0.042 0.135 5616 Planarity : 0.004 0.044 6800 Dihedral : 6.874 178.256 5392 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.90 % Allowed : 13.57 % Favored : 83.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.12), residues: 4712 helix: 1.31 (0.13), residues: 1752 sheet: 0.15 (0.17), residues: 880 loop : -1.20 (0.13), residues: 2080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 216 HIS 0.004 0.001 HIS G 293 PHE 0.011 0.001 PHE A 312 TYR 0.012 0.001 TYR P 47 ARG 0.007 0.000 ARG A 361 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8741.37 seconds wall clock time: 157 minutes 2.89 seconds (9422.89 seconds total)