Starting phenix.real_space_refine on Tue Apr 16 05:17:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5nv3_3699/04_2024/5nv3_3699_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5nv3_3699/04_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_3699/04_2024/5nv3_3699.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5nv3_3699/04_2024/5nv3_3699.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5nv3_3699/04_2024/5nv3_3699_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5nv3_3699/04_2024/5nv3_3699_updated.pdb" } 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: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/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: 19.41, per 1000 atoms: 0.51 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: 13.60 Conformation dependent library (CDL) restraints added in 7.2 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... running ksdssp... Secondary structure from input PDB file: 176 helices and 40 sheets defined 35.8% alpha, 12.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.08 Creating SS restraints... Processing helix chain 'A' and resid 21 through 24 No H-bonds generated for 'chain 'A' and resid 21 through 24' Processing helix chain 'A' and resid 52 through 62 Processing helix chain 'A' and resid 72 through 75 Processing helix chain 'A' and resid 79 through 82 No H-bonds generated for 'chain 'A' and resid 79 through 82' Processing helix chain 'A' and resid 107 through 109 No H-bonds generated for 'chain 'A' and resid 107 through 109' Processing helix chain 'A' and resid 115 through 122 Processing helix chain 'A' and resid 144 through 149 removed outlier: 3.537A pdb=" N LYS A 148 " --> pdb=" O VAL A 144 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N THR A 149 " --> pdb=" O ALA A 145 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 144 through 149' Processing helix chain 'A' and resid 156 through 164 removed outlier: 3.613A pdb=" N ARG A 163 " --> pdb=" O GLY A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 197 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) Processing helix chain 'A' and resid 216 through 234 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 249 through 262 removed outlier: 3.502A pdb=" N ARG A 254 " --> pdb=" O GLU A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 273 No H-bonds generated for 'chain 'A' and resid 271 through 273' Processing helix chain 'A' and resid 275 through 286 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 312 through 322 Processing helix chain 'A' and resid 340 through 351 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 385 through 394 removed outlier: 3.506A pdb=" N MET A 388 " --> pdb=" O ALA A 385 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N HIS A 389 " --> pdb=" O GLY A 386 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU A 391 " --> pdb=" O MET A 388 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N LEU A 392 " --> pdb=" O HIS A 389 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N SER A 393 " --> pdb=" O GLN A 390 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU A 394 " --> pdb=" O LEU A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 408 No H-bonds generated for 'chain 'A' and resid 405 through 408' Processing helix chain 'A' and resid 415 through 434 Processing helix chain 'A' and resid 442 through 449 Processing helix chain 'A' and resid 454 through 462 Processing helix chain 'I' and resid 16 through 29 Processing helix chain 'I' and resid 61 through 74 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 21 through 24 No H-bonds generated for 'chain 'B' and resid 21 through 24' Processing helix chain 'B' and resid 52 through 62 Processing helix chain 'B' and resid 72 through 75 Processing helix chain 'B' and resid 79 through 82 No H-bonds generated for 'chain 'B' and resid 79 through 82' Processing helix chain 'B' and resid 107 through 109 No H-bonds generated for 'chain 'B' and resid 107 through 109' Processing helix chain 'B' and resid 115 through 122 Processing helix chain 'B' and resid 144 through 149 removed outlier: 3.535A pdb=" N LYS B 148 " --> pdb=" O VAL B 144 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N THR B 149 " --> pdb=" O ALA B 145 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 144 through 149' Processing helix chain 'B' and resid 156 through 164 removed outlier: 3.613A pdb=" N ARG B 163 " --> pdb=" O GLY B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 184 through 197 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) Processing helix chain 'B' and resid 216 through 234 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 249 through 262 removed outlier: 3.503A pdb=" N ARG B 254 " --> pdb=" O GLU B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 273 No H-bonds generated for 'chain 'B' and resid 271 through 273' Processing helix chain 'B' and resid 275 through 286 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 312 through 322 Processing helix chain 'B' and resid 340 through 351 removed outlier: 3.535A pdb=" N TYR B 346 " --> pdb=" O THR B 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 394 removed outlier: 3.508A pdb=" N MET B 388 " --> pdb=" O ALA B 385 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N HIS B 389 " --> pdb=" O GLY B 386 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU B 391 " --> pdb=" O MET B 388 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LEU B 392 " --> pdb=" O HIS B 389 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N SER B 393 " --> pdb=" O GLN B 390 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU B 394 " --> pdb=" O LEU B 391 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 408 No H-bonds generated for 'chain 'B' and resid 405 through 408' Processing helix chain 'B' and resid 415 through 434 Processing helix chain 'B' and resid 442 through 451 removed outlier: 3.829A pdb=" N LYS B 451 " --> pdb=" O ARG B 447 " (cutoff:3.500A) Processing helix chain 'B' and resid 454 through 462 Processing helix chain 'J' and resid 16 through 29 Processing helix chain 'J' and resid 61 through 74 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 21 through 24 No H-bonds generated for 'chain 'C' and resid 21 through 24' Processing helix chain 'C' and resid 52 through 62 Processing helix chain 'C' and resid 72 through 75 Processing helix chain 'C' and resid 79 through 82 No H-bonds generated for 'chain 'C' and resid 79 through 82' Processing helix chain 'C' and resid 107 through 109 No H-bonds generated for 'chain 'C' and resid 107 through 109' Processing helix chain 'C' and resid 115 through 122 Processing helix chain 'C' and resid 144 through 149 removed outlier: 3.542A pdb=" N LYS C 148 " --> pdb=" O VAL C 144 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N THR C 149 " --> pdb=" O ALA C 145 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 144 through 149' Processing helix chain 'C' and resid 156 through 164 removed outlier: 3.612A pdb=" N ARG C 163 " --> pdb=" O GLY C 159 " (cutoff:3.500A) Processing helix chain 'C' and resid 184 through 197 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) Processing helix chain 'C' and resid 216 through 234 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 249 through 262 Processing helix chain 'C' and resid 271 through 273 No H-bonds generated for 'chain 'C' and resid 271 through 273' Processing helix chain 'C' and resid 275 through 286 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 312 through 322 Processing helix chain 'C' and resid 340 through 351 removed outlier: 3.549A pdb=" N TYR C 346 " --> pdb=" O THR C 342 " (cutoff:3.500A) Processing helix chain 'C' and resid 385 through 394 removed outlier: 3.508A pdb=" N MET C 388 " --> pdb=" O ALA C 385 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N HIS C 389 " --> pdb=" O GLY C 386 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU C 391 " --> pdb=" O MET C 388 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LEU C 392 " --> pdb=" O HIS C 389 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N SER C 393 " --> pdb=" O GLN C 390 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU C 394 " --> pdb=" O LEU C 391 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 408 No H-bonds generated for 'chain 'C' and resid 405 through 408' Processing helix chain 'C' and resid 415 through 434 Processing helix chain 'C' and resid 442 through 449 Processing helix chain 'C' and resid 454 through 462 Processing helix chain 'K' and resid 16 through 29 Processing helix chain 'K' and resid 61 through 74 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 21 through 24 No H-bonds generated for 'chain 'D' and resid 21 through 24' Processing helix chain 'D' and resid 52 through 62 Processing helix chain 'D' and resid 72 through 75 Processing helix chain 'D' and resid 79 through 82 No H-bonds generated for 'chain 'D' and resid 79 through 82' Processing helix chain 'D' and resid 107 through 109 No H-bonds generated for 'chain 'D' and resid 107 through 109' Processing helix chain 'D' and resid 115 through 122 Processing helix chain 'D' and resid 144 through 149 removed outlier: 3.541A pdb=" N LYS D 148 " --> pdb=" O VAL D 144 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N THR D 149 " --> pdb=" O ALA D 145 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 144 through 149' Processing helix chain 'D' and resid 156 through 164 removed outlier: 3.607A pdb=" N ARG D 163 " --> pdb=" O GLY D 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 184 through 197 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) Processing helix chain 'D' and resid 216 through 234 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 249 through 262 Processing helix chain 'D' and resid 271 through 273 No H-bonds generated for 'chain 'D' and resid 271 through 273' Processing helix chain 'D' and resid 275 through 286 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 312 through 322 Processing helix chain 'D' and resid 340 through 351 removed outlier: 3.546A pdb=" N TYR D 346 " --> pdb=" O THR D 342 " (cutoff:3.500A) Processing helix chain 'D' and resid 385 through 394 removed outlier: 3.503A pdb=" N MET D 388 " --> pdb=" O ALA D 385 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N HIS D 389 " --> pdb=" O GLY D 386 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU D 391 " --> pdb=" O MET D 388 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LEU D 392 " --> pdb=" O HIS D 389 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N SER D 393 " --> pdb=" O GLN D 390 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LEU D 394 " --> pdb=" O LEU D 391 " (cutoff:3.500A) Processing helix chain 'D' and resid 405 through 408 No H-bonds generated for 'chain 'D' and resid 405 through 408' Processing helix chain 'D' and resid 415 through 434 Processing helix chain 'D' and resid 442 through 451 removed outlier: 3.828A pdb=" N LYS D 451 " --> pdb=" O ARG D 447 " (cutoff:3.500A) Processing helix chain 'D' and resid 454 through 462 Processing helix chain 'L' and resid 16 through 29 Processing helix chain 'L' and resid 61 through 74 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 21 through 24 No H-bonds generated for 'chain 'E' and resid 21 through 24' Processing helix chain 'E' and resid 52 through 62 Processing helix chain 'E' and resid 72 through 75 Processing helix chain 'E' and resid 79 through 82 No H-bonds generated for 'chain 'E' and resid 79 through 82' Processing helix chain 'E' and resid 107 through 109 No H-bonds generated for 'chain 'E' and resid 107 through 109' Processing helix chain 'E' and resid 115 through 122 Processing helix chain 'E' and resid 144 through 149 removed outlier: 3.541A pdb=" N LYS E 148 " --> pdb=" O VAL E 144 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N THR E 149 " --> pdb=" O ALA E 145 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 144 through 149' Processing helix chain 'E' and resid 156 through 164 removed outlier: 3.617A pdb=" N ARG E 163 " --> pdb=" O GLY E 159 " (cutoff:3.500A) Processing helix chain 'E' and resid 184 through 197 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) Processing helix chain 'E' and resid 216 through 234 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 249 through 262 Processing helix chain 'E' and resid 271 through 273 No H-bonds generated for 'chain 'E' and resid 271 through 273' Processing helix chain 'E' and resid 275 through 286 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 312 through 322 Processing helix chain 'E' and resid 340 through 351 removed outlier: 3.533A pdb=" N TYR E 346 " --> pdb=" O THR E 342 " (cutoff:3.500A) Processing helix chain 'E' and resid 385 through 394 removed outlier: 3.503A pdb=" N MET E 388 " --> pdb=" O ALA E 385 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N HIS E 389 " --> pdb=" O GLY E 386 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU E 391 " --> pdb=" O MET E 388 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LEU E 392 " --> pdb=" O HIS E 389 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N SER E 393 " --> pdb=" O GLN E 390 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU E 394 " --> pdb=" O LEU E 391 " (cutoff:3.500A) Processing helix chain 'E' and resid 405 through 408 No H-bonds generated for 'chain 'E' and resid 405 through 408' Processing helix chain 'E' and resid 415 through 434 Processing helix chain 'E' and resid 442 through 449 Processing helix chain 'E' and resid 454 through 462 Processing helix chain 'M' and resid 16 through 29 Processing helix chain 'M' and resid 61 through 74 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 21 through 24 No H-bonds generated for 'chain 'F' and resid 21 through 24' Processing helix chain 'F' and resid 52 through 62 Processing helix chain 'F' and resid 72 through 75 Processing helix chain 'F' and resid 79 through 82 No H-bonds generated for 'chain 'F' and resid 79 through 82' Processing helix chain 'F' and resid 107 through 109 No H-bonds generated for 'chain 'F' and resid 107 through 109' Processing helix chain 'F' and resid 115 through 122 Processing helix chain 'F' and resid 144 through 149 removed outlier: 3.520A pdb=" N LYS F 148 " --> pdb=" O VAL F 144 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N THR F 149 " --> pdb=" O ALA F 145 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 144 through 149' Processing helix chain 'F' and resid 156 through 164 removed outlier: 3.620A pdb=" N ARG F 163 " --> pdb=" O GLY F 159 " (cutoff:3.500A) Processing helix chain 'F' and resid 184 through 197 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) Processing helix chain 'F' and resid 216 through 234 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 249 through 262 Processing helix chain 'F' and resid 271 through 273 No H-bonds generated for 'chain 'F' and resid 271 through 273' Processing helix chain 'F' and resid 275 through 286 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 312 through 322 Processing helix chain 'F' and resid 340 through 351 removed outlier: 3.532A pdb=" N TYR F 346 " --> pdb=" O THR F 342 " (cutoff:3.500A) Processing helix chain 'F' and resid 385 through 394 removed outlier: 3.511A pdb=" N MET F 388 " --> pdb=" O ALA F 385 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N HIS F 389 " --> pdb=" O GLY F 386 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU F 391 " --> pdb=" O MET F 388 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LEU F 392 " --> pdb=" O HIS F 389 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N SER F 393 " --> pdb=" O GLN F 390 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU F 394 " --> pdb=" O LEU F 391 " (cutoff:3.500A) Processing helix chain 'F' and resid 405 through 408 No H-bonds generated for 'chain 'F' and resid 405 through 408' Processing helix chain 'F' and resid 415 through 434 Processing helix chain 'F' and resid 442 through 449 Processing helix chain 'F' and resid 454 through 462 Processing helix chain 'N' and resid 16 through 29 Processing helix chain 'N' and resid 61 through 74 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 21 through 24 No H-bonds generated for 'chain 'G' and resid 21 through 24' Processing helix chain 'G' and resid 52 through 62 Processing helix chain 'G' and resid 72 through 75 Processing helix chain 'G' and resid 79 through 82 No H-bonds generated for 'chain 'G' and resid 79 through 82' Processing helix chain 'G' and resid 107 through 109 No H-bonds generated for 'chain 'G' and resid 107 through 109' Processing helix chain 'G' and resid 115 through 122 Processing helix chain 'G' and resid 144 through 149 removed outlier: 3.536A pdb=" N LYS G 148 " --> pdb=" O VAL G 144 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N THR G 149 " --> pdb=" O ALA G 145 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 144 through 149' Processing helix chain 'G' and resid 156 through 164 removed outlier: 3.612A pdb=" N ARG G 163 " --> pdb=" O GLY G 159 " (cutoff:3.500A) Processing helix chain 'G' and resid 184 through 197 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) Processing helix chain 'G' and resid 216 through 234 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 249 through 262 removed outlier: 3.507A pdb=" N ARG G 254 " --> pdb=" O GLU G 250 " (cutoff:3.500A) Processing helix chain 'G' and resid 271 through 273 No H-bonds generated for 'chain 'G' and resid 271 through 273' Processing helix chain 'G' and resid 275 through 286 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 312 through 322 Processing helix chain 'G' and resid 340 through 351 removed outlier: 3.530A pdb=" N TYR G 346 " --> pdb=" O THR G 342 " (cutoff:3.500A) Processing helix chain 'G' and resid 385 through 394 removed outlier: 3.503A pdb=" N MET G 388 " --> pdb=" O ALA G 385 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N HIS G 389 " --> pdb=" O GLY G 386 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU G 391 " --> pdb=" O MET G 388 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N LEU G 392 " --> pdb=" O HIS G 389 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N SER G 393 " --> pdb=" O GLN G 390 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU G 394 " --> pdb=" O LEU G 391 " (cutoff:3.500A) Processing helix chain 'G' and resid 405 through 408 No H-bonds generated for 'chain 'G' and resid 405 through 408' Processing helix chain 'G' and resid 415 through 434 Processing helix chain 'G' and resid 442 through 449 Processing helix chain 'G' and resid 454 through 462 Processing helix chain 'O' and resid 16 through 29 Processing helix chain 'O' and resid 61 through 74 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 21 through 24 No H-bonds generated for 'chain 'H' and resid 21 through 24' Processing helix chain 'H' and resid 52 through 62 Processing helix chain 'H' and resid 72 through 75 Processing helix chain 'H' and resid 79 through 82 No H-bonds generated for 'chain 'H' and resid 79 through 82' Processing helix chain 'H' and resid 107 through 109 No H-bonds generated for 'chain 'H' and resid 107 through 109' Processing helix chain 'H' and resid 115 through 122 Processing helix chain 'H' and resid 144 through 149 removed outlier: 3.528A pdb=" N LYS H 148 " --> pdb=" O VAL H 144 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N THR H 149 " --> pdb=" O ALA H 145 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 144 through 149' Processing helix chain 'H' and resid 156 through 164 removed outlier: 3.616A pdb=" N ARG H 163 " --> pdb=" O GLY H 159 " (cutoff:3.500A) Processing helix chain 'H' and resid 184 through 197 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) Processing helix chain 'H' and resid 216 through 234 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 249 through 262 Processing helix chain 'H' and resid 271 through 273 No H-bonds generated for 'chain 'H' and resid 271 through 273' Processing helix chain 'H' and resid 275 through 286 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 312 through 322 Processing helix chain 'H' and resid 340 through 351 removed outlier: 3.543A pdb=" N TYR H 346 " --> pdb=" O THR H 342 " (cutoff:3.500A) Processing helix chain 'H' and resid 385 through 394 removed outlier: 3.504A pdb=" N MET H 388 " --> pdb=" O ALA H 385 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N HIS H 389 " --> pdb=" O GLY H 386 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU H 391 " --> pdb=" O MET H 388 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N LEU H 392 " --> pdb=" O HIS H 389 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N SER H 393 " --> pdb=" O GLN H 390 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU H 394 " --> pdb=" O LEU H 391 " (cutoff:3.500A) Processing helix chain 'H' and resid 405 through 408 No H-bonds generated for 'chain 'H' and resid 405 through 408' Processing helix chain 'H' and resid 415 through 434 Processing helix chain 'H' and resid 442 through 449 Processing helix chain 'H' and resid 454 through 462 Processing helix chain 'P' and resid 16 through 29 Processing helix chain 'P' and resid 61 through 74 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= A, first strand: chain 'A' and resid 132 through 137 removed outlier: 6.852A pdb=" N THR A 45 " --> pdb=" O LYS A 133 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ALA A 135 " --> pdb=" O ARG A 43 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N ARG A 43 " --> pdb=" O ALA A 135 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N LEU A 137 " --> pdb=" O LEU A 41 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N LEU A 41 " --> pdb=" O LEU A 137 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ARG A 88 " --> pdb=" O TYR A 102 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N ALA A 104 " --> pdb=" O ALA A 86 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N ALA A 86 " --> pdb=" O ALA A 104 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 171 through 173 removed outlier: 8.099A pdb=" N GLN A 402 " --> pdb=" O PRO A 377 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N ALA A 379 " --> pdb=" O GLN A 402 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 266 through 270 removed outlier: 6.216A pdb=" N ILE A 291 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N VAL A 269 " --> pdb=" O ILE A 291 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N HIS A 293 " --> pdb=" O VAL A 269 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'I' and resid 32 through 38 removed outlier: 6.742A pdb=" N ILE I 82 " --> pdb=" O ILE I 99 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N ILE I 99 " --> pdb=" O ILE I 82 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N ALA I 84 " --> pdb=" O SER I 97 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N SER I 97 " --> pdb=" O ALA I 84 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'I' and resid 109 through 115 Processing sheet with id= F, first strand: chain 'B' and resid 132 through 137 removed outlier: 6.861A pdb=" N THR B 45 " --> pdb=" O LYS B 133 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N ALA B 135 " --> pdb=" O ARG B 43 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N ARG B 43 " --> pdb=" O ALA B 135 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N LEU B 137 " --> pdb=" O LEU B 41 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N LEU B 41 " --> pdb=" O LEU B 137 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ARG B 88 " --> pdb=" O TYR B 102 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N ALA B 104 " --> pdb=" O ALA B 86 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N ALA B 86 " --> pdb=" O ALA B 104 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 171 through 173 removed outlier: 8.098A pdb=" N GLN B 402 " --> pdb=" O PRO B 377 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N ALA B 379 " --> pdb=" O GLN B 402 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 266 through 270 removed outlier: 6.204A pdb=" N ILE B 291 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N VAL B 269 " --> pdb=" O ILE B 291 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N HIS B 293 " --> pdb=" O VAL B 269 " (cutoff:3.500A) No H-bonds generated for sheet with id= H Processing sheet with id= I, first strand: chain 'J' and resid 32 through 38 removed outlier: 6.710A pdb=" N ILE J 82 " --> pdb=" O ILE J 99 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N ILE J 99 " --> pdb=" O ILE J 82 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N ALA J 84 " --> pdb=" O SER J 97 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N SER J 97 " --> pdb=" O ALA J 84 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'J' and resid 109 through 115 Processing sheet with id= K, first strand: chain 'C' and resid 132 through 137 removed outlier: 6.840A pdb=" N THR C 45 " --> pdb=" O LYS C 133 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N ALA C 135 " --> pdb=" O ARG C 43 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N ARG C 43 " --> pdb=" O ALA C 135 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N LEU C 137 " --> pdb=" O LEU C 41 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N LEU C 41 " --> pdb=" O LEU C 137 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ARG C 88 " --> pdb=" O TYR C 102 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ALA C 104 " --> pdb=" O ALA C 86 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N ALA C 86 " --> pdb=" O ALA C 104 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 171 through 173 removed outlier: 8.093A pdb=" N GLN C 402 " --> pdb=" O PRO C 377 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N ALA C 379 " --> pdb=" O GLN C 402 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 266 through 270 removed outlier: 6.224A pdb=" N ILE C 291 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N VAL C 269 " --> pdb=" O ILE C 291 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N HIS C 293 " --> pdb=" O VAL C 269 " (cutoff:3.500A) No H-bonds generated for sheet with id= M Processing sheet with id= N, first strand: chain 'K' and resid 32 through 38 removed outlier: 6.728A pdb=" N ILE K 82 " --> pdb=" O ILE K 99 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N ILE K 99 " --> pdb=" O ILE K 82 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N ALA K 84 " --> pdb=" O SER K 97 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N SER K 97 " --> pdb=" O ALA K 84 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'K' and resid 109 through 115 Processing sheet with id= P, first strand: chain 'D' and resid 132 through 137 removed outlier: 6.856A pdb=" N THR D 45 " --> pdb=" O LYS D 133 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N ALA D 135 " --> pdb=" O ARG D 43 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N ARG D 43 " --> pdb=" O ALA D 135 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N LEU D 137 " --> pdb=" O LEU D 41 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N LEU D 41 " --> pdb=" O LEU D 137 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ARG D 88 " --> pdb=" O TYR D 102 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N ALA D 104 " --> pdb=" O ALA D 86 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N ALA D 86 " --> pdb=" O ALA D 104 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'D' and resid 171 through 173 removed outlier: 8.099A pdb=" N GLN D 402 " --> pdb=" O PRO D 377 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N ALA D 379 " --> pdb=" O GLN D 402 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'D' and resid 266 through 270 removed outlier: 6.199A pdb=" N ILE D 291 " --> pdb=" O VAL D 267 " (cutoff:3.500A) removed outlier: 7.646A pdb=" N VAL D 269 " --> pdb=" O ILE D 291 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N HIS D 293 " --> pdb=" O VAL D 269 " (cutoff:3.500A) No H-bonds generated for sheet with id= R Processing sheet with id= S, first strand: chain 'L' and resid 32 through 38 removed outlier: 6.730A pdb=" N ILE L 82 " --> pdb=" O ILE L 99 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N ILE L 99 " --> pdb=" O ILE L 82 " (cutoff:3.500A) removed outlier: 7.838A pdb=" N ALA L 84 " --> pdb=" O SER L 97 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N SER L 97 " --> pdb=" O ALA L 84 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'L' and resid 109 through 115 Processing sheet with id= U, first strand: chain 'E' and resid 132 through 137 removed outlier: 6.854A pdb=" N THR E 45 " --> pdb=" O LYS E 133 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N ALA E 135 " --> pdb=" O ARG E 43 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N ARG E 43 " --> pdb=" O ALA E 135 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N LEU E 137 " --> pdb=" O LEU E 41 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N LEU E 41 " --> pdb=" O LEU E 137 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ARG E 88 " --> pdb=" O TYR E 102 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N ALA E 104 " --> pdb=" O ALA E 86 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N ALA E 86 " --> pdb=" O ALA E 104 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'E' and resid 171 through 173 removed outlier: 8.097A pdb=" N GLN E 402 " --> pdb=" O PRO E 377 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N ALA E 379 " --> pdb=" O GLN E 402 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'E' and resid 266 through 270 removed outlier: 6.221A pdb=" N ILE E 291 " --> pdb=" O VAL E 267 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N VAL E 269 " --> pdb=" O ILE E 291 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N HIS E 293 " --> pdb=" O VAL E 269 " (cutoff:3.500A) No H-bonds generated for sheet with id= W Processing sheet with id= X, first strand: chain 'M' and resid 32 through 38 removed outlier: 6.720A pdb=" N ILE M 82 " --> pdb=" O ILE M 99 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N ILE M 99 " --> pdb=" O ILE M 82 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N ALA M 84 " --> pdb=" O SER M 97 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N SER M 97 " --> pdb=" O ALA M 84 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'M' and resid 109 through 115 Processing sheet with id= Z, first strand: chain 'F' and resid 132 through 137 removed outlier: 6.861A pdb=" N THR F 45 " --> pdb=" O LYS F 133 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N ALA F 135 " --> pdb=" O ARG F 43 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N ARG F 43 " --> pdb=" O ALA F 135 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N LEU F 137 " --> pdb=" O LEU F 41 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N LEU F 41 " --> pdb=" O LEU F 137 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ARG F 88 " --> pdb=" O TYR F 102 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ALA F 104 " --> pdb=" O ALA F 86 " (cutoff:3.500A) removed outlier: 5.506A pdb=" N ALA F 86 " --> pdb=" O ALA F 104 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'F' and resid 171 through 173 removed outlier: 8.099A pdb=" N GLN F 402 " --> pdb=" O PRO F 377 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N ALA F 379 " --> pdb=" O GLN F 402 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'F' and resid 266 through 270 removed outlier: 6.217A pdb=" N ILE F 291 " --> pdb=" O VAL F 267 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N VAL F 269 " --> pdb=" O ILE F 291 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N HIS F 293 " --> pdb=" O VAL F 269 " (cutoff:3.500A) No H-bonds generated for sheet with id= AB Processing sheet with id= AC, first strand: chain 'N' and resid 32 through 38 removed outlier: 6.704A pdb=" N ILE N 82 " --> pdb=" O ILE N 99 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N ILE N 99 " --> pdb=" O ILE N 82 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N ALA N 84 " --> pdb=" O SER N 97 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N SER N 97 " --> pdb=" O ALA N 84 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'N' and resid 109 through 115 Processing sheet with id= AE, first strand: chain 'G' and resid 132 through 137 removed outlier: 6.867A pdb=" N THR G 45 " --> pdb=" O LYS G 133 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N ALA G 135 " --> pdb=" O ARG G 43 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N ARG G 43 " --> pdb=" O ALA G 135 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N LEU G 137 " --> pdb=" O LEU G 41 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N LEU G 41 " --> pdb=" O LEU G 137 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ARG G 88 " --> pdb=" O TYR G 102 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N ALA G 104 " --> pdb=" O ALA G 86 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N ALA G 86 " --> pdb=" O ALA G 104 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'G' and resid 171 through 173 removed outlier: 8.105A pdb=" N GLN G 402 " --> pdb=" O PRO G 377 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N ALA G 379 " --> pdb=" O GLN G 402 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'G' and resid 266 through 270 removed outlier: 6.210A pdb=" N ILE G 291 " --> pdb=" O VAL G 267 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N VAL G 269 " --> pdb=" O ILE G 291 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N HIS G 293 " --> pdb=" O VAL G 269 " (cutoff:3.500A) No H-bonds generated for sheet with id= AG Processing sheet with id= AH, first strand: chain 'O' and resid 32 through 38 removed outlier: 6.736A pdb=" N ILE O 82 " --> pdb=" O ILE O 99 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N ILE O 99 " --> pdb=" O ILE O 82 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N ALA O 84 " --> pdb=" O SER O 97 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N SER O 97 " --> pdb=" O ALA O 84 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'O' and resid 109 through 115 Processing sheet with id= AJ, first strand: chain 'H' and resid 132 through 137 removed outlier: 6.857A pdb=" N THR H 45 " --> pdb=" O LYS H 133 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N ALA H 135 " --> pdb=" O ARG H 43 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N ARG H 43 " --> pdb=" O ALA H 135 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N LEU H 137 " --> pdb=" O LEU H 41 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N LEU H 41 " --> pdb=" O LEU H 137 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ARG H 88 " --> pdb=" O TYR H 102 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N ALA H 104 " --> pdb=" O ALA H 86 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N ALA H 86 " --> pdb=" O ALA H 104 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'H' and resid 171 through 173 removed outlier: 8.099A pdb=" N GLN H 402 " --> pdb=" O PRO H 377 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N ALA H 379 " --> pdb=" O GLN H 402 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'H' and resid 266 through 270 removed outlier: 6.213A pdb=" N ILE H 291 " --> pdb=" O VAL H 267 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N VAL H 269 " --> pdb=" O ILE H 291 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N HIS H 293 " --> pdb=" O VAL H 269 " (cutoff:3.500A) No H-bonds generated for sheet with id= AL Processing sheet with id= AM, first strand: chain 'P' and resid 32 through 38 removed outlier: 6.727A pdb=" N ILE P 82 " --> pdb=" O ILE P 99 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N ILE P 99 " --> pdb=" O ILE P 82 " (cutoff:3.500A) removed outlier: 7.832A pdb=" N ALA P 84 " --> pdb=" O SER P 97 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N SER P 97 " --> pdb=" O ALA P 84 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'P' and resid 109 through 115 1150 hydrogen bonds defined for protein. 3306 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 13.10 Time building geometry restraints manager: 14.91 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: 295 2.71 - 3.26: 33330 3.26 - 3.81: 59974 3.81 - 4.35: 85638 4.35 - 4.90: 136749 Nonbonded interactions: 315986 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 315981 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: 2.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 8.480 Check model and map are aligned: 0.550 Set scattering table: 0.330 Process input model: 98.970 Find NCS groups from input model: 2.920 Set up NCS constraints: 0.420 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: 0.020 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 117.280 ------------------------------------------------------------------------------- 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= 0.481 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 : 4.109 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: 0.5905 time to fit residues: 636.2857 Evaluate side-chains 441 residues out of total 3936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 433 time to evaluate : 4.153 ------------------------------------------------------------------------------- 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: 0.5980 chunk 351 optimal weight: 2.9990 chunk 195 optimal weight: 2.9990 chunk 120 optimal weight: 4.9990 chunk 237 optimal weight: 7.9990 chunk 187 optimal weight: 0.0970 chunk 363 optimal weight: 0.8980 chunk 140 optimal weight: 3.9990 chunk 221 optimal weight: 0.9980 chunk 270 optimal weight: 0.6980 chunk 421 optimal weight: 1.9990 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 215 HIS A 288 ASN A 295 HIS I 22 GLN I 37 HIS B 215 HIS B 288 ASN B 387 GLN J 22 GLN J 37 HIS C 215 HIS C 288 ASN C 295 HIS K 22 GLN K 37 HIS D 215 HIS D 288 ASN D 295 HIS D 387 GLN L 22 GLN L 37 HIS E 215 HIS E 288 ASN E 295 HIS M 22 GLN M 37 HIS F 215 HIS F 288 ASN N 22 GLN N 37 HIS G 215 HIS G 288 ASN O 22 GLN O 37 HIS H 215 HIS H 288 ASN P 22 GLN P 37 HIS Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1491 moved from start: 0.1998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 38728 Z= 0.174 Angle : 0.538 6.456 52544 Z= 0.279 Chirality : 0.041 0.167 5616 Planarity : 0.004 0.033 6800 Dihedral : 7.148 176.878 5408 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 0.86 % Allowed : 7.55 % Favored : 91.59 % 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: -1.13 (0.11), residues: 4712 helix: -0.15 (0.11), residues: 1720 sheet: 0.27 (0.17), residues: 800 loop : -1.62 (0.12), residues: 2192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 318 HIS 0.004 0.001 HIS G 293 PHE 0.014 0.002 PHE H 213 TYR 0.014 0.001 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 518 residues out of total 3936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 484 time to evaluate : 3.870 Fit side-chains REVERT: A 283 GLU cc_start: 0.2227 (tt0) cc_final: 0.1918 (mp0) REVERT: A 286 ARG cc_start: 0.2192 (tpp80) cc_final: 0.1752 (tpm170) REVERT: A 306 LYS cc_start: 0.3381 (ttpt) cc_final: 0.3010 (tptt) REVERT: I 50 MET cc_start: 0.4516 (mtt) cc_final: 0.3850 (mmt) REVERT: I 112 GLU cc_start: 0.1490 (mt-10) cc_final: 0.1289 (mp0) REVERT: B 283 GLU cc_start: 0.2016 (tt0) cc_final: 0.1709 (mp0) REVERT: B 286 ARG cc_start: 0.2161 (tpp80) cc_final: 0.1788 (tpm170) REVERT: B 306 LYS cc_start: 0.3339 (ttpt) cc_final: 0.2946 (tptt) REVERT: B 447 ARG cc_start: 0.2388 (mtt90) cc_final: 0.2169 (mtp180) REVERT: J 50 MET cc_start: 0.4447 (mtt) cc_final: 0.3783 (mmt) REVERT: J 112 GLU cc_start: 0.1578 (mt-10) cc_final: 0.1361 (mp0) REVERT: C 283 GLU cc_start: 0.1920 (tt0) cc_final: 0.1643 (mp0) REVERT: C 286 ARG cc_start: 0.2165 (tpp80) cc_final: 0.1752 (tpm170) REVERT: C 306 LYS cc_start: 0.3346 (ttpt) cc_final: 0.2963 (tptt) REVERT: C 447 ARG cc_start: 0.2282 (mtt90) cc_final: 0.2065 (mtp180) REVERT: K 50 MET cc_start: 0.4518 (mtt) cc_final: 0.3850 (mmt) REVERT: K 112 GLU cc_start: 0.1544 (mt-10) cc_final: 0.1343 (mp0) REVERT: D 283 GLU cc_start: 0.1998 (tt0) cc_final: 0.1664 (mp0) REVERT: D 286 ARG cc_start: 0.2219 (tpp80) cc_final: 0.1785 (tpm170) REVERT: D 306 LYS cc_start: 0.3384 (ttpt) cc_final: 0.3008 (tptt) REVERT: L 50 MET cc_start: 0.4521 (mtt) cc_final: 0.3852 (mmt) REVERT: E 283 GLU cc_start: 0.2039 (tt0) cc_final: 0.1705 (mp0) REVERT: E 286 ARG cc_start: 0.2059 (tpp80) cc_final: 0.1660 (tpm170) REVERT: E 306 LYS cc_start: 0.3325 (ttpt) cc_final: 0.2942 (tptt) REVERT: E 447 ARG cc_start: 0.2266 (mtt90) cc_final: 0.2043 (mtp180) REVERT: M 50 MET cc_start: 0.4502 (mtt) cc_final: 0.3830 (mmt) REVERT: F 283 GLU cc_start: 0.2039 (tt0) cc_final: 0.1709 (mp0) REVERT: F 286 ARG cc_start: 0.2240 (tpp80) cc_final: 0.1773 (tpm170) REVERT: F 306 LYS cc_start: 0.3346 (ttpt) cc_final: 0.2963 (tptt) REVERT: F 447 ARG cc_start: 0.2700 (mtt90) cc_final: 0.2485 (mtp180) REVERT: N 50 MET cc_start: 0.4480 (mtt) cc_final: 0.3812 (mmt) REVERT: G 283 GLU cc_start: 0.2230 (tt0) cc_final: 0.1921 (mp0) REVERT: G 286 ARG cc_start: 0.2223 (tpp80) cc_final: 0.1764 (tpm170) REVERT: G 306 LYS cc_start: 0.3378 (ttpt) cc_final: 0.3014 (tptt) REVERT: O 50 MET cc_start: 0.4481 (mtt) cc_final: 0.3817 (mmt) REVERT: H 283 GLU cc_start: 0.1836 (tt0) cc_final: 0.1537 (mp0) REVERT: H 286 ARG cc_start: 0.2217 (tpp80) cc_final: 0.1783 (tpm170) REVERT: H 306 LYS cc_start: 0.3380 (ttpt) cc_final: 0.3000 (tptt) REVERT: P 50 MET cc_start: 0.4500 (mtt) cc_final: 0.3829 (mmt) outliers start: 34 outliers final: 19 residues processed: 513 average time/residue: 0.6667 time to fit residues: 510.5541 Evaluate side-chains 450 residues out of total 3936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 431 time to evaluate : 4.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain I residue 38 THR Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain J residue 38 THR Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain K residue 38 THR Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain L residue 38 THR Chi-restraints excluded: chain E residue 73 THR Chi-restraints excluded: chain M residue 38 THR Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain N residue 38 THR Chi-restraints excluded: chain G residue 73 THR Chi-restraints excluded: chain O residue 38 THR Chi-restraints excluded: chain H residue 73 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: 3.9990 chunk 130 optimal weight: 5.9990 chunk 350 optimal weight: 2.9990 chunk 286 optimal weight: 5.9990 chunk 116 optimal weight: 10.0000 chunk 422 optimal weight: 0.6980 chunk 456 optimal weight: 4.9990 chunk 375 optimal weight: 6.9990 chunk 418 optimal weight: 5.9990 chunk 143 optimal weight: 3.9990 chunk 338 optimal weight: 0.9980 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 186 ASN A 355 ASN A 387 GLN A 421 ASN A 433 ASN B 186 ASN B 355 ASN B 415 GLN B 421 ASN B 433 ASN C 186 ASN C 355 ASN C 387 GLN C 421 ASN C 433 ASN D 186 ASN D 355 ASN D 415 GLN D 421 ASN D 433 ASN E 186 ASN E 355 ASN E 387 GLN E 421 ASN E 433 ASN F 186 ASN F 326 HIS F 355 ASN F 387 GLN F 421 ASN F 433 ASN G 186 ASN G 355 ASN G 387 GLN G 421 ASN G 433 ASN H 186 ASN H 355 ASN H 387 GLN H 415 GLN H 421 ASN H 433 ASN Total number of N/Q/H flips: 42 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1503 moved from start: 0.3581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 38728 Z= 0.387 Angle : 0.733 7.244 52544 Z= 0.370 Chirality : 0.048 0.171 5616 Planarity : 0.006 0.065 6800 Dihedral : 7.808 166.431 5392 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 1.80 % Allowed : 9.53 % Favored : 88.67 % 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: -1.25 (0.11), residues: 4712 helix: -0.18 (0.12), residues: 1768 sheet: 0.00 (0.17), residues: 816 loop : -1.70 (0.11), residues: 2128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP K 75 HIS 0.007 0.002 HIS A 215 PHE 0.020 0.003 PHE C 201 TYR 0.026 0.003 TYR D 241 ARG 0.010 0.001 ARG H 320 *********************** 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 606 residues out of total 3936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 535 time to evaluate : 4.055 Fit side-chains REVERT: A 129 PHE cc_start: 0.1488 (OUTLIER) cc_final: 0.1223 (m-80) REVERT: A 283 GLU cc_start: 0.1898 (tt0) cc_final: 0.1619 (mp0) REVERT: A 306 LYS cc_start: 0.3323 (ttpt) cc_final: 0.2946 (tptt) REVERT: A 373 ARG cc_start: 0.1747 (mmt90) cc_final: 0.1050 (mtm180) REVERT: I 111 MET cc_start: 0.2773 (ttp) cc_final: 0.2471 (ttm) REVERT: B 129 PHE cc_start: 0.1742 (OUTLIER) cc_final: 0.1443 (m-80) REVERT: B 283 GLU cc_start: 0.1887 (tt0) cc_final: 0.1601 (mp0) REVERT: B 306 LYS cc_start: 0.3348 (ttpt) cc_final: 0.2963 (tptt) REVERT: B 373 ARG cc_start: 0.1748 (mmt90) cc_final: 0.1065 (mtm180) REVERT: C 129 PHE cc_start: 0.1399 (OUTLIER) cc_final: 0.1135 (m-80) REVERT: C 283 GLU cc_start: 0.1787 (tt0) cc_final: 0.1570 (mp0) REVERT: C 306 LYS cc_start: 0.3316 (ttpt) cc_final: 0.2942 (tptt) REVERT: C 373 ARG cc_start: 0.1753 (mmt90) cc_final: 0.1062 (mtm180) REVERT: K 111 MET cc_start: 0.2733 (ttp) cc_final: 0.2447 (ttm) REVERT: D 129 PHE cc_start: 0.1678 (OUTLIER) cc_final: 0.1388 (m-80) REVERT: D 283 GLU cc_start: 0.1889 (tt0) cc_final: 0.1598 (mp0) REVERT: D 286 ARG cc_start: 0.2335 (tpp80) cc_final: 0.2132 (tpm170) REVERT: D 306 LYS cc_start: 0.3328 (ttpt) cc_final: 0.2952 (tptt) REVERT: D 373 ARG cc_start: 0.1794 (mmt90) cc_final: 0.1092 (mtm180) REVERT: E 129 PHE cc_start: 0.1492 (OUTLIER) cc_final: 0.1192 (m-80) REVERT: E 283 GLU cc_start: 0.1941 (tt0) cc_final: 0.1654 (mp0) REVERT: E 306 LYS cc_start: 0.3325 (ttpt) cc_final: 0.2920 (tptt) REVERT: E 373 ARG cc_start: 0.1559 (mmt90) cc_final: 0.0843 (mtm180) REVERT: F 129 PHE cc_start: 0.1650 (OUTLIER) cc_final: 0.1346 (m-80) REVERT: F 283 GLU cc_start: 0.1888 (tt0) cc_final: 0.1604 (mp0) REVERT: F 306 LYS cc_start: 0.3346 (ttpt) cc_final: 0.2968 (tptt) REVERT: F 373 ARG cc_start: 0.1637 (mmt90) cc_final: 0.0928 (mtm180) REVERT: G 129 PHE cc_start: 0.1565 (OUTLIER) cc_final: 0.1268 (m-80) REVERT: G 283 GLU cc_start: 0.1949 (tt0) cc_final: 0.1664 (mp0) REVERT: G 286 ARG cc_start: 0.2350 (tpp80) cc_final: 0.2136 (tpm170) REVERT: G 306 LYS cc_start: 0.3311 (ttpt) cc_final: 0.2873 (tptt) REVERT: G 354 PHE cc_start: 0.2563 (t80) cc_final: 0.2208 (t80) REVERT: G 373 ARG cc_start: 0.1588 (mmt90) cc_final: 0.0880 (mtm180) REVERT: H 129 PHE cc_start: 0.1538 (OUTLIER) cc_final: 0.1238 (m-80) REVERT: H 283 GLU cc_start: 0.1957 (tt0) cc_final: 0.1663 (mp0) REVERT: H 306 LYS cc_start: 0.3332 (ttpt) cc_final: 0.2958 (tptt) REVERT: H 354 PHE cc_start: 0.2562 (t80) cc_final: 0.2213 (t80) REVERT: H 373 ARG cc_start: 0.1709 (mmt90) cc_final: 0.0989 (mtm180) outliers start: 71 outliers final: 55 residues processed: 589 average time/residue: 0.5294 time to fit residues: 490.7835 Evaluate side-chains 507 residues out of total 3936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 444 time to evaluate : 2.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 129 PHE 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 357 VAL Chi-restraints excluded: chain I residue 38 THR Chi-restraints excluded: chain I residue 117 ASP Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 129 PHE Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 342 THR 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 73 THR 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 357 VAL Chi-restraints excluded: chain K residue 38 THR Chi-restraints excluded: chain K residue 117 ASP Chi-restraints excluded: chain D residue 67 THR Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 129 PHE Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 342 THR Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain L residue 38 THR Chi-restraints excluded: chain L residue 117 ASP Chi-restraints excluded: chain E residue 67 THR Chi-restraints excluded: chain E residue 73 THR 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 357 VAL Chi-restraints excluded: chain M residue 38 THR Chi-restraints excluded: chain M residue 117 ASP Chi-restraints excluded: chain F residue 73 THR 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 357 VAL Chi-restraints excluded: chain N residue 38 THR Chi-restraints excluded: chain N residue 117 ASP Chi-restraints excluded: chain G residue 73 THR Chi-restraints excluded: chain G residue 129 PHE Chi-restraints excluded: chain G residue 265 VAL Chi-restraints excluded: chain G residue 276 THR Chi-restraints excluded: chain G residue 342 THR Chi-restraints excluded: chain G residue 357 VAL Chi-restraints excluded: chain O residue 38 THR Chi-restraints excluded: chain O residue 117 ASP Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 129 PHE Chi-restraints excluded: chain H residue 265 VAL Chi-restraints excluded: chain H residue 342 THR Chi-restraints excluded: chain H residue 357 VAL Chi-restraints excluded: chain P residue 38 THR Chi-restraints excluded: chain P residue 117 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 417 optimal weight: 0.3980 chunk 317 optimal weight: 5.9990 chunk 219 optimal weight: 4.9990 chunk 46 optimal weight: 0.7980 chunk 201 optimal weight: 5.9990 chunk 283 optimal weight: 0.0060 chunk 423 optimal weight: 3.9990 chunk 448 optimal weight: 9.9990 chunk 221 optimal weight: 2.9990 chunk 401 optimal weight: 5.9990 chunk 120 optimal weight: 5.9990 overall best weight: 1.6400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: