Starting phenix.real_space_refine on Mon Aug 5 21:20:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wcr_37447/08_2024/8wcr_37447.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wcr_37447/08_2024/8wcr_37447.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.74 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wcr_37447/08_2024/8wcr_37447.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wcr_37447/08_2024/8wcr_37447.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wcr_37447/08_2024/8wcr_37447.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wcr_37447/08_2024/8wcr_37447.cif" } resolution = 2.74 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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 40 5.49 5 S 20 5.16 5 Cl 5 4.86 5 C 9620 2.51 5 N 2070 2.21 5 O 2860 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "E PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 154": "OD1" <-> "OD2" Residue "E GLU 181": "OE1" <-> "OE2" Residue "A PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 154": "OD1" <-> "OD2" Residue "A GLU 181": "OE1" <-> "OE2" Residue "B PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 154": "OD1" <-> "OD2" Residue "B GLU 181": "OE1" <-> "OE2" Residue "C PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 154": "OD1" <-> "OD2" Residue "C GLU 181": "OE1" <-> "OE2" Residue "D PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 154": "OD1" <-> "OD2" Residue "D GLU 181": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 14615 Number of models: 1 Model: "" Number of chains: 15 Chain: "E" Number of atoms: 2537 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 312, 2529 Classifications: {'peptide': 312} Link IDs: {'PTRANS': 18, 'TRANS': 293} Conformer: "B" Number of residues, atoms: 312, 2529 Classifications: {'peptide': 312} Link IDs: {'PTRANS': 18, 'TRANS': 293} bond proxies already assigned to first conformer: 2588 Chain: "A" Number of atoms: 2537 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 312, 2529 Classifications: {'peptide': 312} Link IDs: {'PTRANS': 18, 'TRANS': 293} Conformer: "B" Number of residues, atoms: 312, 2529 Classifications: {'peptide': 312} Link IDs: {'PTRANS': 18, 'TRANS': 293} bond proxies already assigned to first conformer: 2588 Chain: "B" Number of atoms: 2537 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 312, 2529 Classifications: {'peptide': 312} Link IDs: {'PTRANS': 18, 'TRANS': 293} Conformer: "B" Number of residues, atoms: 312, 2529 Classifications: {'peptide': 312} Link IDs: {'PTRANS': 18, 'TRANS': 293} bond proxies already assigned to first conformer: 2588 Chain: "C" Number of atoms: 2537 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 312, 2529 Classifications: {'peptide': 312} Link IDs: {'PTRANS': 18, 'TRANS': 293} Conformer: "B" Number of residues, atoms: 312, 2529 Classifications: {'peptide': 312} Link IDs: {'PTRANS': 18, 'TRANS': 293} bond proxies already assigned to first conformer: 2588 Chain: "D" Number of atoms: 2537 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 312, 2529 Classifications: {'peptide': 312} Link IDs: {'PTRANS': 18, 'TRANS': 293} Conformer: "B" Number of residues, atoms: 312, 2529 Classifications: {'peptide': 312} Link IDs: {'PTRANS': 18, 'TRANS': 293} bond proxies already assigned to first conformer: 2588 Chain: "E" Number of atoms: 332 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 332 Unusual residues: {' CL': 1, 'PEE': 9} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 128 Unresolved non-hydrogen angles: 134 Unresolved non-hydrogen dihedrals: 130 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PEE:plan-1': 1, 'PEE:plan-2': 1} Unresolved non-hydrogen planarities: 6 Chain: "A" Number of atoms: 332 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 332 Unusual residues: {' CL': 1, 'PEE': 9} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 128 Unresolved non-hydrogen angles: 134 Unresolved non-hydrogen dihedrals: 130 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PEE:plan-1': 1, 'PEE:plan-2': 1} Unresolved non-hydrogen planarities: 6 Chain: "B" Number of atoms: 332 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 332 Unusual residues: {' CL': 1, 'PEE': 9} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 128 Unresolved non-hydrogen angles: 134 Unresolved non-hydrogen dihedrals: 130 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PEE:plan-1': 1, 'PEE:plan-2': 1} Unresolved non-hydrogen planarities: 6 Chain: "C" Number of atoms: 332 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 332 Unusual residues: {' CL': 1, 'PEE': 9} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 128 Unresolved non-hydrogen angles: 134 Unresolved non-hydrogen dihedrals: 130 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PEE:plan-1': 1, 'PEE:plan-2': 1} Unresolved non-hydrogen planarities: 6 Chain: "D" Number of atoms: 332 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 332 Unusual residues: {' CL': 1, 'PEE': 9} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 128 Unresolved non-hydrogen angles: 134 Unresolved non-hydrogen dihedrals: 130 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PEE:plan-1': 1, 'PEE:plan-2': 1} Unresolved non-hydrogen planarities: 6 Chain: "E" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 54 Classifications: {'water': 54} Link IDs: {None: 53} Chain: "A" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 54 Classifications: {'water': 54} Link IDs: {None: 53} Chain: "B" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 54 Classifications: {'water': 54} Link IDs: {None: 53} Chain: "C" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 54 Classifications: {'water': 54} Link IDs: {None: 53} Chain: "D" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 54 Classifications: {'water': 54} Link IDs: {None: 53} Time building chain proxies: 14.28, per 1000 atoms: 0.98 Number of scatterers: 14615 At special positions: 0 Unit cell: (91.2, 92.72, 128.44, 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) Cl 5 17.00 S 20 16.00 P 40 15.00 O 2860 8.00 N 2070 7.00 C 9620 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: 5.65 Conformation dependent library (CDL) restraints added in 4.3 seconds 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3060 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 15 sheets defined 41.3% alpha, 45.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.62 Creating SS restraints... Processing helix chain 'E' and resid 50 through 53 Processing helix chain 'E' and resid 55 through 60 Processing helix chain 'E' and resid 118 through 121 Processing helix chain 'E' and resid 146 through 149 removed outlier: 3.907A pdb=" N VAL E 149 " --> pdb=" O LEU E 146 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 146 through 149' Processing helix chain 'E' and resid 196 through 213 removed outlier: 5.265A pdb=" N LEU E 203 " --> pdb=" O PRO E 199 " (cutoff:3.500A) Proline residue: E 204 - end of helix Processing helix chain 'E' and resid 214 through 218 removed outlier: 3.651A pdb=" N SER E 218 " --> pdb=" O ALA E 215 " (cutoff:3.500A) Processing helix chain 'E' and resid 220 through 244 Processing helix chain 'E' and resid 253 through 282 Processing helix chain 'E' and resid 284 through 316 removed outlier: 3.553A pdb=" N ALA E 288 " --> pdb=" O GLN E 284 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ILE E 297 " --> pdb=" O ARG E 293 " (cutoff:3.500A) Proline residue: E 300 - end of helix Processing helix chain 'A' and resid 50 through 53 Processing helix chain 'A' and resid 55 through 60 Processing helix chain 'A' and resid 118 through 121 Processing helix chain 'A' and resid 146 through 149 removed outlier: 3.907A pdb=" N VAL A 149 " --> pdb=" O LEU A 146 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 146 through 149' Processing helix chain 'A' and resid 196 through 213 removed outlier: 5.266A pdb=" N LEU A 203 " --> pdb=" O PRO A 199 " (cutoff:3.500A) Proline residue: A 204 - end of helix Processing helix chain 'A' and resid 214 through 218 removed outlier: 3.652A pdb=" N SER A 218 " --> pdb=" O ALA A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 244 Processing helix chain 'A' and resid 253 through 282 Processing helix chain 'A' and resid 284 through 316 removed outlier: 3.553A pdb=" N ALA A 288 " --> pdb=" O GLN A 284 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ILE A 297 " --> pdb=" O ARG A 293 " (cutoff:3.500A) Proline residue: A 300 - end of helix Processing helix chain 'B' and resid 50 through 53 Processing helix chain 'B' and resid 55 through 60 Processing helix chain 'B' and resid 118 through 121 Processing helix chain 'B' and resid 146 through 149 removed outlier: 3.907A pdb=" N VAL B 149 " --> pdb=" O LEU B 146 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 146 through 149' Processing helix chain 'B' and resid 196 through 213 removed outlier: 5.266A pdb=" N LEU B 203 " --> pdb=" O PRO B 199 " (cutoff:3.500A) Proline residue: B 204 - end of helix Processing helix chain 'B' and resid 214 through 218 removed outlier: 3.651A pdb=" N SER B 218 " --> pdb=" O ALA B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 244 Processing helix chain 'B' and resid 253 through 282 Processing helix chain 'B' and resid 284 through 316 removed outlier: 3.553A pdb=" N ALA B 288 " --> pdb=" O GLN B 284 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ILE B 297 " --> pdb=" O ARG B 293 " (cutoff:3.500A) Proline residue: B 300 - end of helix Processing helix chain 'C' and resid 50 through 53 Processing helix chain 'C' and resid 55 through 60 Processing helix chain 'C' and resid 118 through 121 Processing helix chain 'C' and resid 146 through 149 removed outlier: 3.908A pdb=" N VAL C 149 " --> pdb=" O LEU C 146 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 146 through 149' Processing helix chain 'C' and resid 196 through 213 removed outlier: 5.266A pdb=" N LEU C 203 " --> pdb=" O PRO C 199 " (cutoff:3.500A) Proline residue: C 204 - end of helix Processing helix chain 'C' and resid 214 through 218 removed outlier: 3.651A pdb=" N SER C 218 " --> pdb=" O ALA C 215 " (cutoff:3.500A) Processing helix chain 'C' and resid 220 through 244 Processing helix chain 'C' and resid 253 through 282 Processing helix chain 'C' and resid 284 through 316 removed outlier: 3.553A pdb=" N ALA C 288 " --> pdb=" O GLN C 284 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ILE C 297 " --> pdb=" O ARG C 293 " (cutoff:3.500A) Proline residue: C 300 - end of helix Processing helix chain 'D' and resid 50 through 53 Processing helix chain 'D' and resid 55 through 60 Processing helix chain 'D' and resid 118 through 121 Processing helix chain 'D' and resid 146 through 149 removed outlier: 3.908A pdb=" N VAL D 149 " --> pdb=" O LEU D 146 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 146 through 149' Processing helix chain 'D' and resid 196 through 213 removed outlier: 5.266A pdb=" N LEU D 203 " --> pdb=" O PRO D 199 " (cutoff:3.500A) Proline residue: D 204 - end of helix Processing helix chain 'D' and resid 214 through 218 removed outlier: 3.651A pdb=" N SER D 218 " --> pdb=" O ALA D 215 " (cutoff:3.500A) Processing helix chain 'D' and resid 220 through 244 Processing helix chain 'D' and resid 253 through 282 Processing helix chain 'D' and resid 284 through 316 removed outlier: 3.554A pdb=" N ALA D 288 " --> pdb=" O GLN D 284 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ILE D 297 " --> pdb=" O ARG D 293 " (cutoff:3.500A) Proline residue: D 300 - end of helix Processing sheet with id=AA1, first strand: chain 'E' and resid 64 through 65 removed outlier: 5.670A pdb=" N ALA E 87 " --> pdb=" O SER E 107 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N SER E 107 " --> pdb=" O ALA E 87 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N VAL E 89 " --> pdb=" O ARG E 105 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ARG E 105 " --> pdb=" O VAL E 89 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASP E 91 " --> pdb=" O LEU E 103 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N THR E 36 " --> pdb=" O LEU E 30 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N LEU E 30 " --> pdb=" O THR E 36 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N PHE E 42 " --> pdb=" O LEU E 24 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N LEU E 24 " --> pdb=" O PHE E 42 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N SER E 44 " --> pdb=" O ILE E 22 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N ILE E 22 " --> pdb=" O SER E 44 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N SER E 46 " --> pdb=" O THR E 20 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N THR E 20 " --> pdb=" O SER E 46 " (cutoff:3.500A) removed outlier: 9.013A pdb=" N LYS E 48 " --> pdb=" O VAL E 18 " (cutoff:3.500A) removed outlier: 8.488A pdb=" N VAL E 18 " --> pdb=" O LYS E 48 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N LEU E 16 " --> pdb=" O VAL E 141 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N ALA E 143 " --> pdb=" O LEU E 16 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N VAL E 18 " --> pdb=" O ALA E 143 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 64 through 65 removed outlier: 5.670A pdb=" N ALA E 87 " --> pdb=" O SER E 107 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N SER E 107 " --> pdb=" O ALA E 87 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N VAL E 89 " --> pdb=" O ARG E 105 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ARG E 105 " --> pdb=" O VAL E 89 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASP E 91 " --> pdb=" O LEU E 103 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N THR E 36 " --> pdb=" O LEU E 30 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N LEU E 30 " --> pdb=" O THR E 36 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N PHE E 42 " --> pdb=" O LEU E 24 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N LEU E 24 " --> pdb=" O PHE E 42 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N SER E 44 " --> pdb=" O ILE E 22 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N ILE E 22 " --> pdb=" O SER E 44 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N SER E 46 " --> pdb=" O THR E 20 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N THR E 20 " --> pdb=" O SER E 46 " (cutoff:3.500A) removed outlier: 9.013A pdb=" N LYS E 48 " --> pdb=" O VAL E 18 " (cutoff:3.500A) removed outlier: 8.488A pdb=" N VAL E 18 " --> pdb=" O LYS E 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 76 through 78 removed outlier: 11.076A pdb=" N ARG E 179 " --> pdb=" O ASN E 173 " (cutoff:3.500A) removed outlier: 9.811A pdb=" N ASN E 173 " --> pdb=" O ARG E 179 " (cutoff:3.500A) removed outlier: 10.311A pdb=" N GLU E 181 " --> pdb=" O PRO E 171 " (cutoff:3.500A) removed outlier: 8.858A pdb=" N LYS E 183 " --> pdb=" O VAL E 169 " (cutoff:3.500A) removed outlier: 8.128A pdb=" N VAL E 169 " --> pdb=" O LYS E 183 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N ASP E 185 " --> pdb=" O ALA E 167 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N ALA E 167 " --> pdb=" O ASP E 185 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N GLN E 187 " --> pdb=" O PHE E 165 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N PHE E 165 " --> pdb=" O GLN E 187 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ARG E 189 " --> pdb=" O GLU E 163 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 64 through 65 removed outlier: 5.671A pdb=" N ALA A 87 " --> pdb=" O SER A 107 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N SER A 107 " --> pdb=" O ALA A 87 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N VAL A 89 " --> pdb=" O ARG A 105 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ARG A 105 " --> pdb=" O VAL A 89 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASP A 91 " --> pdb=" O LEU A 103 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N THR A 36 " --> pdb=" O LEU A 30 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N LEU A 30 " --> pdb=" O THR A 36 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N PHE A 42 " --> pdb=" O LEU A 24 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N LEU A 24 " --> pdb=" O PHE A 42 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N SER A 44 " --> pdb=" O ILE A 22 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N ILE A 22 " --> pdb=" O SER A 44 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N SER A 46 " --> pdb=" O THR A 20 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N THR A 20 " --> pdb=" O SER A 46 " (cutoff:3.500A) removed outlier: 9.013A pdb=" N LYS A 48 " --> pdb=" O VAL A 18 " (cutoff:3.500A) removed outlier: 8.488A pdb=" N VAL A 18 " --> pdb=" O LYS A 48 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N LEU A 16 " --> pdb=" O VAL A 141 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N ALA A 143 " --> pdb=" O LEU A 16 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N VAL A 18 " --> pdb=" O ALA A 143 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 64 through 65 removed outlier: 5.671A pdb=" N ALA A 87 " --> pdb=" O SER A 107 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N SER A 107 " --> pdb=" O ALA A 87 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N VAL A 89 " --> pdb=" O ARG A 105 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ARG A 105 " --> pdb=" O VAL A 89 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASP A 91 " --> pdb=" O LEU A 103 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N THR A 36 " --> pdb=" O LEU A 30 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N LEU A 30 " --> pdb=" O THR A 36 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N PHE A 42 " --> pdb=" O LEU A 24 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N LEU A 24 " --> pdb=" O PHE A 42 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N SER A 44 " --> pdb=" O ILE A 22 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N ILE A 22 " --> pdb=" O SER A 44 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N SER A 46 " --> pdb=" O THR A 20 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N THR A 20 " --> pdb=" O SER A 46 " (cutoff:3.500A) removed outlier: 9.013A pdb=" N LYS A 48 " --> pdb=" O VAL A 18 " (cutoff:3.500A) removed outlier: 8.488A pdb=" N VAL A 18 " --> pdb=" O LYS A 48 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 76 through 78 removed outlier: 11.077A pdb=" N ARG A 179 " --> pdb=" O ASN A 173 " (cutoff:3.500A) removed outlier: 9.812A pdb=" N ASN A 173 " --> pdb=" O ARG A 179 " (cutoff:3.500A) removed outlier: 10.310A pdb=" N GLU A 181 " --> pdb=" O PRO A 171 " (cutoff:3.500A) removed outlier: 8.859A pdb=" N LYS A 183 " --> pdb=" O VAL A 169 " (cutoff:3.500A) removed outlier: 8.129A pdb=" N VAL A 169 " --> pdb=" O LYS A 183 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N ASP A 185 " --> pdb=" O ALA A 167 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N ALA A 167 " --> pdb=" O ASP A 185 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N GLN A 187 " --> pdb=" O PHE A 165 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N PHE A 165 " --> pdb=" O GLN A 187 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N ARG A 189 " --> pdb=" O GLU A 163 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 64 through 65 removed outlier: 5.670A pdb=" N ALA B 87 " --> pdb=" O SER B 107 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N SER B 107 " --> pdb=" O ALA B 87 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N VAL B 89 " --> pdb=" O ARG B 105 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ARG B 105 " --> pdb=" O VAL B 89 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASP B 91 " --> pdb=" O LEU B 103 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N THR B 36 " --> pdb=" O LEU B 30 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N LEU B 30 " --> pdb=" O THR B 36 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N PHE B 42 " --> pdb=" O LEU B 24 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N LEU B 24 " --> pdb=" O PHE B 42 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N SER B 44 " --> pdb=" O ILE B 22 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N ILE B 22 " --> pdb=" O SER B 44 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N SER B 46 " --> pdb=" O THR B 20 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N THR B 20 " --> pdb=" O SER B 46 " (cutoff:3.500A) removed outlier: 9.013A pdb=" N LYS B 48 " --> pdb=" O VAL B 18 " (cutoff:3.500A) removed outlier: 8.489A pdb=" N VAL B 18 " --> pdb=" O LYS B 48 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N LEU B 16 " --> pdb=" O VAL B 141 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N ALA B 143 " --> pdb=" O LEU B 16 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N VAL B 18 " --> pdb=" O ALA B 143 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 64 through 65 removed outlier: 5.670A pdb=" N ALA B 87 " --> pdb=" O SER B 107 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N SER B 107 " --> pdb=" O ALA B 87 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N VAL B 89 " --> pdb=" O ARG B 105 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ARG B 105 " --> pdb=" O VAL B 89 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASP B 91 " --> pdb=" O LEU B 103 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N THR B 36 " --> pdb=" O LEU B 30 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N LEU B 30 " --> pdb=" O THR B 36 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N PHE B 42 " --> pdb=" O LEU B 24 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N LEU B 24 " --> pdb=" O PHE B 42 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N SER B 44 " --> pdb=" O ILE B 22 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N ILE B 22 " --> pdb=" O SER B 44 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N SER B 46 " --> pdb=" O THR B 20 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N THR B 20 " --> pdb=" O SER B 46 " (cutoff:3.500A) removed outlier: 9.013A pdb=" N LYS B 48 " --> pdb=" O VAL B 18 " (cutoff:3.500A) removed outlier: 8.489A pdb=" N VAL B 18 " --> pdb=" O LYS B 48 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 76 through 78 removed outlier: 11.077A pdb=" N ARG B 179 " --> pdb=" O ASN B 173 " (cutoff:3.500A) removed outlier: 9.811A pdb=" N ASN B 173 " --> pdb=" O ARG B 179 " (cutoff:3.500A) removed outlier: 10.311A pdb=" N GLU B 181 " --> pdb=" O PRO B 171 " (cutoff:3.500A) removed outlier: 8.859A pdb=" N LYS B 183 " --> pdb=" O VAL B 169 " (cutoff:3.500A) removed outlier: 8.128A pdb=" N VAL B 169 " --> pdb=" O LYS B 183 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N ASP B 185 " --> pdb=" O ALA B 167 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N ALA B 167 " --> pdb=" O ASP B 185 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N GLN B 187 " --> pdb=" O PHE B 165 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N PHE B 165 " --> pdb=" O GLN B 187 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N ARG B 189 " --> pdb=" O GLU B 163 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 64 through 65 removed outlier: 5.671A pdb=" N ALA C 87 " --> pdb=" O SER C 107 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N SER C 107 " --> pdb=" O ALA C 87 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N VAL C 89 " --> pdb=" O ARG C 105 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ARG C 105 " --> pdb=" O VAL C 89 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASP C 91 " --> pdb=" O LEU C 103 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N THR C 36 " --> pdb=" O LEU C 30 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N LEU C 30 " --> pdb=" O THR C 36 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N PHE C 42 " --> pdb=" O LEU C 24 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N LEU C 24 " --> pdb=" O PHE C 42 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N SER C 44 " --> pdb=" O ILE C 22 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N ILE C 22 " --> pdb=" O SER C 44 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N SER C 46 " --> pdb=" O THR C 20 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N THR C 20 " --> pdb=" O SER C 46 " (cutoff:3.500A) removed outlier: 9.013A pdb=" N LYS C 48 " --> pdb=" O VAL C 18 " (cutoff:3.500A) removed outlier: 8.488A pdb=" N VAL C 18 " --> pdb=" O LYS C 48 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N LEU C 16 " --> pdb=" O VAL C 141 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N ALA C 143 " --> pdb=" O LEU C 16 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N VAL C 18 " --> pdb=" O ALA C 143 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 64 through 65 removed outlier: 5.671A pdb=" N ALA C 87 " --> pdb=" O SER C 107 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N SER C 107 " --> pdb=" O ALA C 87 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N VAL C 89 " --> pdb=" O ARG C 105 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ARG C 105 " --> pdb=" O VAL C 89 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASP C 91 " --> pdb=" O LEU C 103 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N THR C 36 " --> pdb=" O LEU C 30 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N LEU C 30 " --> pdb=" O THR C 36 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N PHE C 42 " --> pdb=" O LEU C 24 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N LEU C 24 " --> pdb=" O PHE C 42 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N SER C 44 " --> pdb=" O ILE C 22 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N ILE C 22 " --> pdb=" O SER C 44 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N SER C 46 " --> pdb=" O THR C 20 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N THR C 20 " --> pdb=" O SER C 46 " (cutoff:3.500A) removed outlier: 9.013A pdb=" N LYS C 48 " --> pdb=" O VAL C 18 " (cutoff:3.500A) removed outlier: 8.488A pdb=" N VAL C 18 " --> pdb=" O LYS C 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 76 through 78 removed outlier: 11.077A pdb=" N ARG C 179 " --> pdb=" O ASN C 173 " (cutoff:3.500A) removed outlier: 9.812A pdb=" N ASN C 173 " --> pdb=" O ARG C 179 " (cutoff:3.500A) removed outlier: 10.311A pdb=" N GLU C 181 " --> pdb=" O PRO C 171 " (cutoff:3.500A) removed outlier: 8.859A pdb=" N LYS C 183 " --> pdb=" O VAL C 169 " (cutoff:3.500A) removed outlier: 8.127A pdb=" N VAL C 169 " --> pdb=" O LYS C 183 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N ASP C 185 " --> pdb=" O ALA C 167 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N ALA C 167 " --> pdb=" O ASP C 185 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N GLN C 187 " --> pdb=" O PHE C 165 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N PHE C 165 " --> pdb=" O GLN C 187 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N ARG C 189 " --> pdb=" O GLU C 163 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 64 through 65 removed outlier: 5.670A pdb=" N ALA D 87 " --> pdb=" O SER D 107 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N SER D 107 " --> pdb=" O ALA D 87 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N VAL D 89 " --> pdb=" O ARG D 105 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N ARG D 105 " --> pdb=" O VAL D 89 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASP D 91 " --> pdb=" O LEU D 103 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N THR D 36 " --> pdb=" O LEU D 30 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N LEU D 30 " --> pdb=" O THR D 36 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N PHE D 42 " --> pdb=" O LEU D 24 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N LEU D 24 " --> pdb=" O PHE D 42 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N SER D 44 " --> pdb=" O ILE D 22 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N ILE D 22 " --> pdb=" O SER D 44 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N SER D 46 " --> pdb=" O THR D 20 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N THR D 20 " --> pdb=" O SER D 46 " (cutoff:3.500A) removed outlier: 9.014A pdb=" N LYS D 48 " --> pdb=" O VAL D 18 " (cutoff:3.500A) removed outlier: 8.488A pdb=" N VAL D 18 " --> pdb=" O LYS D 48 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N LEU D 16 " --> pdb=" O VAL D 141 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N ALA D 143 " --> pdb=" O LEU D 16 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N VAL D 18 " --> pdb=" O ALA D 143 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 64 through 65 removed outlier: 5.670A pdb=" N ALA D 87 " --> pdb=" O SER D 107 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N SER D 107 " --> pdb=" O ALA D 87 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N VAL D 89 " --> pdb=" O ARG D 105 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N ARG D 105 " --> pdb=" O VAL D 89 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASP D 91 " --> pdb=" O LEU D 103 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N THR D 36 " --> pdb=" O LEU D 30 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N LEU D 30 " --> pdb=" O THR D 36 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N PHE D 42 " --> pdb=" O LEU D 24 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N LEU D 24 " --> pdb=" O PHE D 42 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N SER D 44 " --> pdb=" O ILE D 22 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N ILE D 22 " --> pdb=" O SER D 44 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N SER D 46 " --> pdb=" O THR D 20 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N THR D 20 " --> pdb=" O SER D 46 " (cutoff:3.500A) removed outlier: 9.014A pdb=" N LYS D 48 " --> pdb=" O VAL D 18 " (cutoff:3.500A) removed outlier: 8.488A pdb=" N VAL D 18 " --> pdb=" O LYS D 48 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 76 through 78 removed outlier: 11.077A pdb=" N ARG D 179 " --> pdb=" O ASN D 173 " (cutoff:3.500A) removed outlier: 9.811A pdb=" N ASN D 173 " --> pdb=" O ARG D 179 " (cutoff:3.500A) removed outlier: 10.310A pdb=" N GLU D 181 " --> pdb=" O PRO D 171 " (cutoff:3.500A) removed outlier: 8.859A pdb=" N LYS D 183 " --> pdb=" O VAL D 169 " (cutoff:3.500A) removed outlier: 8.129A pdb=" N VAL D 169 " --> pdb=" O LYS D 183 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N ASP D 185 " --> pdb=" O ALA D 167 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N ALA D 167 " --> pdb=" O ASP D 185 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N GLN D 187 " --> pdb=" O PHE D 165 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N PHE D 165 " --> pdb=" O GLN D 187 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N ARG D 189 " --> pdb=" O GLU D 163 " (cutoff:3.500A) 725 hydrogen bonds defined for protein. 2080 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: 4.31 Time building geometry restraints manager: 6.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2083 1.32 - 1.44: 3889 1.44 - 1.56: 8551 1.56 - 1.69: 82 1.69 - 1.81: 35 Bond restraints: 14640 Sorted by residual: bond pdb=" CB AARG B 293 " pdb=" CG AARG B 293 " ideal model delta sigma weight residual 1.520 1.635 -0.115 3.00e-02 1.11e+03 1.47e+01 bond pdb=" CB BARG B 293 " pdb=" CG BARG B 293 " ideal model delta sigma weight residual 1.520 1.609 -0.089 3.00e-02 1.11e+03 8.82e+00 bond pdb=" CE1 TYR D 251 " pdb=" CZ TYR D 251 " ideal model delta sigma weight residual 1.378 1.432 -0.054 2.40e-02 1.74e+03 5.03e+00 bond pdb=" CE1 TYR E 251 " pdb=" CZ TYR E 251 " ideal model delta sigma weight residual 1.378 1.432 -0.054 2.40e-02 1.74e+03 4.99e+00 bond pdb=" CE1 TYR C 251 " pdb=" CZ TYR C 251 " ideal model delta sigma weight residual 1.378 1.432 -0.054 2.40e-02 1.74e+03 4.98e+00 ... (remaining 14635 not shown) Histogram of bond angle deviations from ideal: 92.66 - 100.96: 61 100.96 - 109.26: 1354 109.26 - 117.56: 9715 117.56 - 125.86: 8290 125.86 - 134.16: 200 Bond angle restraints: 19620 Sorted by residual: angle pdb=" CB AARG B 293 " pdb=" CG AARG B 293 " pdb=" CD AARG B 293 " ideal model delta sigma weight residual 111.30 98.39 12.91 2.30e+00 1.89e-01 3.15e+01 angle pdb=" CD AARG B 293 " pdb=" NE AARG B 293 " pdb=" CZ AARG B 293 " ideal model delta sigma weight residual 124.40 117.71 6.69 1.40e+00 5.10e-01 2.28e+01 angle pdb=" C ARG B 293 " pdb=" CA BARG B 293 " pdb=" CB BARG B 293 " ideal model delta sigma weight residual 110.79 105.20 5.59 1.66e+00 3.63e-01 1.13e+01 angle pdb=" CA BARG B 293 " pdb=" CB BARG B 293 " pdb=" CG BARG B 293 " ideal model delta sigma weight residual 114.10 108.20 5.90 2.00e+00 2.50e-01 8.71e+00 angle pdb=" CB GLU C 163 " pdb=" CG GLU C 163 " pdb=" CD GLU C 163 " ideal model delta sigma weight residual 112.60 117.29 -4.69 1.70e+00 3.46e-01 7.62e+00 ... (remaining 19615 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.67: 8468 32.67 - 65.34: 557 65.34 - 98.01: 45 98.01 - 130.68: 75 130.68 - 163.34: 15 Dihedral angle restraints: 9160 sinusoidal: 4460 harmonic: 4700 Sorted by residual: dihedral pdb=" C3 PEE B 409 " pdb=" C1 PEE B 409 " pdb=" C2 PEE B 409 " pdb=" O3P PEE B 409 " ideal model delta sinusoidal sigma weight residual 62.73 -133.93 -163.34 1 3.00e+01 1.11e-03 2.09e+01 dihedral pdb=" C3 PEE C 409 " pdb=" C1 PEE C 409 " pdb=" C2 PEE C 409 " pdb=" O3P PEE C 409 " ideal model delta sinusoidal sigma weight residual 62.73 -133.98 -163.29 1 3.00e+01 1.11e-03 2.09e+01 dihedral pdb=" C3 PEE A 409 " pdb=" C1 PEE A 409 " pdb=" C2 PEE A 409 " pdb=" O3P PEE A 409 " ideal model delta sinusoidal sigma weight residual 62.73 -134.00 -163.27 1 3.00e+01 1.11e-03 2.09e+01 ... (remaining 9157 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.120: 2039 0.120 - 0.241: 66 0.241 - 0.361: 10 0.361 - 0.481: 0 0.481 - 0.602: 5 Chirality restraints: 2120 Sorted by residual: chirality pdb=" CG LEU E 209 " pdb=" CB LEU E 209 " pdb=" CD1 LEU E 209 " pdb=" CD2 LEU E 209 " both_signs ideal model delta sigma weight residual False -2.59 -1.99 -0.60 2.00e-01 2.50e+01 9.05e+00 chirality pdb=" CG LEU C 209 " pdb=" CB LEU C 209 " pdb=" CD1 LEU C 209 " pdb=" CD2 LEU C 209 " both_signs ideal model delta sigma weight residual False -2.59 -1.99 -0.60 2.00e-01 2.50e+01 8.96e+00 chirality pdb=" CG LEU A 209 " pdb=" CB LEU A 209 " pdb=" CD1 LEU A 209 " pdb=" CD2 LEU A 209 " both_signs ideal model delta sigma weight residual False -2.59 -1.99 -0.60 2.00e-01 2.50e+01 8.91e+00 ... (remaining 2117 not shown) Planarity restraints: 2315 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP D 213 " -0.011 2.00e-02 2.50e+03 2.73e-02 1.87e+01 pdb=" CG TRP D 213 " -0.027 2.00e-02 2.50e+03 pdb=" CD1 TRP D 213 " 0.003 2.00e-02 2.50e+03 pdb=" CD2 TRP D 213 " 0.024 2.00e-02 2.50e+03 pdb=" NE1 TRP D 213 " 0.009 2.00e-02 2.50e+03 pdb=" CE2 TRP D 213 " -0.016 2.00e-02 2.50e+03 pdb=" CE3 TRP D 213 " 0.059 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 213 " 0.010 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 213 " -0.046 2.00e-02 2.50e+03 pdb=" CH2 TRP D 213 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP E 213 " -0.011 2.00e-02 2.50e+03 2.72e-02 1.85e+01 pdb=" CG TRP E 213 " -0.027 2.00e-02 2.50e+03 pdb=" CD1 TRP E 213 " 0.003 2.00e-02 2.50e+03 pdb=" CD2 TRP E 213 " 0.024 2.00e-02 2.50e+03 pdb=" NE1 TRP E 213 " 0.009 2.00e-02 2.50e+03 pdb=" CE2 TRP E 213 " -0.016 2.00e-02 2.50e+03 pdb=" CE3 TRP E 213 " 0.058 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 213 " 0.010 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 213 " -0.046 2.00e-02 2.50e+03 pdb=" CH2 TRP E 213 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 213 " -0.011 2.00e-02 2.50e+03 2.71e-02 1.84e+01 pdb=" CG TRP C 213 " -0.027 2.00e-02 2.50e+03 pdb=" CD1 TRP C 213 " 0.003 2.00e-02 2.50e+03 pdb=" CD2 TRP C 213 " 0.024 2.00e-02 2.50e+03 pdb=" NE1 TRP C 213 " 0.009 2.00e-02 2.50e+03 pdb=" CE2 TRP C 213 " -0.015 2.00e-02 2.50e+03 pdb=" CE3 TRP C 213 " 0.058 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 213 " 0.010 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 213 " -0.046 2.00e-02 2.50e+03 pdb=" CH2 TRP C 213 " -0.005 2.00e-02 2.50e+03 ... (remaining 2312 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 3003 2.79 - 3.32: 11966 3.32 - 3.85: 22228 3.85 - 4.37: 29057 4.37 - 4.90: 50506 Nonbonded interactions: 116760 Sorted by model distance: nonbonded pdb=" O LEU B 241 " pdb=" OG1 THR B 244 " model vdw 2.265 3.040 nonbonded pdb=" O LEU D 241 " pdb=" OG1 THR D 244 " model vdw 2.265 3.040 nonbonded pdb=" O LEU C 241 " pdb=" OG1 THR C 244 " model vdw 2.266 3.040 nonbonded pdb=" O LEU A 241 " pdb=" OG1 THR A 244 " model vdw 2.266 3.040 nonbonded pdb=" O LEU E 241 " pdb=" OG1 THR E 244 " model vdw 2.266 3.040 ... (remaining 116755 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 5 through 292 or resid 294 through 316 or (resid 403 and ( \ name C1 or name C10 or name C11 or name C12 or name C13 or name C14 or name C15 \ or name C16 or name C17 or name C2 or name C3 or name C30 or name C31 or name C3 \ 2 or name C33 or name C34 or name C35 or name C36 or name C37 or name C38 or nam \ e O1P or name O2 or name O2P or name O3 or name O3P or name O4 or name O4P or na \ me O5 or name P )) or resid 404 or (resid 405 through 406 and (name N or name C1 \ or name C10 or name C11 or name C12 or name C13 or name C14 or name C15 or name \ C16 or name C17 or name C18 or name C19 or name C2 or name C3 or name C30 or na \ me C31 or name C32 or name C33 or name C4 or name C5 or name O1P or name O2 or n \ ame O2P or name O3 or name O3P or name O4 or name O4P or name O5 or name P )) or \ (resid 407 through 408 and (name N or name C1 or name C10 or name C11 or name C \ 12 or name C13 or name C14 or name C15 or name C16 or name C17 or name C18 or na \ me C19 or name C2 or name C20 or name C21 or name C3 or name C30 or name C31 or \ name C32 or name C33 or name C34 or name C35 or name C36 or name C37 or name C38 \ or name C39 or name C4 or name C40 or name C5 or name O1P or name O2 or name O2 \ P or name O3 or name O3P or name O4 or name O4P or name O5 or name P )) or (resi \ d 409 through 410 and (name C10 or name C11 or name C12 or name C13 or name C14 \ or name C15 or name C16 or name C17 or name C18 or name C19 or name C20 or name \ C21 or name C22)))) selection = (chain 'B' and (resid 5 through 292 or resid 294 through 316 or (resid 403 and ( \ name C1 or name C10 or name C11 or name C12 or name C13 or name C14 or name C15 \ or name C16 or name C17 or name C2 or name C3 or name C30 or name C31 or name C3 \ 2 or name C33 or name C34 or name C35 or name C36 or name C37 or name C38 or nam \ e O1P or name O2 or name O2P or name O3 or name O3P or name O4 or name O4P or na \ me O5 or name P )) or resid 404 or (resid 405 through 406 and (name N or name C1 \ or name C10 or name C11 or name C12 or name C13 or name C14 or name C15 or name \ C16 or name C17 or name C18 or name C19 or name C2 or name C3 or name C30 or na \ me C31 or name C32 or name C33 or name C4 or name C5 or name O1P or name O2 or n \ ame O2P or name O3 or name O3P or name O4 or name O4P or name O5 or name P )) or \ (resid 407 through 408 and (name N or name C1 or name C10 or name C11 or name C \ 12 or name C13 or name C14 or name C15 or name C16 or name C17 or name C18 or na \ me C19 or name C2 or name C20 or name C21 or name C3 or name C30 or name C31 or \ name C32 or name C33 or name C34 or name C35 or name C36 or name C37 or name C38 \ or name C39 or name C4 or name C40 or name C5 or name O1P or name O2 or name O2 \ P or name O3 or name O3P or name O4 or name O4P or name O5 or name P )) or (resi \ d 409 through 410 and (name C10 or name C11 or name C12 or name C13 or name C14 \ or name C15 or name C16 or name C17 or name C18 or name C19 or name C20 or name \ C21 or name C22)))) selection = (chain 'C' and (resid 5 through 292 or resid 294 through 316 or (resid 403 and ( \ name C1 or name C10 or name C11 or name C12 or name C13 or name C14 or name C15 \ or name C16 or name C17 or name C2 or name C3 or name C30 or name C31 or name C3 \ 2 or name C33 or name C34 or name C35 or name C36 or name C37 or name C38 or nam \ e O1P or name O2 or name O2P or name O3 or name O3P or name O4 or name O4P or na \ me O5 or name P )) or resid 404 or (resid 405 through 406 and (name N or name C1 \ or name C10 or name C11 or name C12 or name C13 or name C14 or name C15 or name \ C16 or name C17 or name C18 or name C19 or name C2 or name C3 or name C30 or na \ me C31 or name C32 or name C33 or name C4 or name C5 or name O1P or name O2 or n \ ame O2P or name O3 or name O3P or name O4 or name O4P or name O5 or name P )) or \ (resid 407 through 408 and (name N or name C1 or name C10 or name C11 or name C \ 12 or name C13 or name C14 or name C15 or name C16 or name C17 or name C18 or na \ me C19 or name C2 or name C20 or name C21 or name C3 or name C30 or name C31 or \ name C32 or name C33 or name C34 or name C35 or name C36 or name C37 or name C38 \ or name C39 or name C4 or name C40 or name C5 or name O1P or name O2 or name O2 \ P or name O3 or name O3P or name O4 or name O4P or name O5 or name P )) or (resi \ d 409 through 410 and (name C10 or name C11 or name C12 or name C13 or name C14 \ or name C15 or name C16 or name C17 or name C18 or name C19 or name C20 or name \ C21 or name C22)))) selection = (chain 'D' and (resid 5 through 292 or resid 294 through 316 or (resid 403 and ( \ name C1 or name C10 or name C11 or name C12 or name C13 or name C14 or name C15 \ or name C16 or name C17 or name C2 or name C3 or name C30 or name C31 or name C3 \ 2 or name C33 or name C34 or name C35 or name C36 or name C37 or name C38 or nam \ e O1P or name O2 or name O2P or name O3 or name O3P or name O4 or name O4P or na \ me O5 or name P )) or resid 404 or (resid 405 through 406 and (name N or name C1 \ or name C10 or name C11 or name C12 or name C13 or name C14 or name C15 or name \ C16 or name C17 or name C18 or name C19 or name C2 or name C3 or name C30 or na \ me C31 or name C32 or name C33 or name C4 or name C5 or name O1P or name O2 or n \ ame O2P or name O3 or name O3P or name O4 or name O4P or name O5 or name P )) or \ (resid 407 through 408 and (name N or name C1 or name C10 or name C11 or name C \ 12 or name C13 or name C14 or name C15 or name C16 or name C17 or name C18 or na \ me C19 or name C2 or name C20 or name C21 or name C3 or name C30 or name C31 or \ name C32 or name C33 or name C34 or name C35 or name C36 or name C37 or name C38 \ or name C39 or name C4 or name C40 or name C5 or name O1P or name O2 or name O2 \ P or name O3 or name O3P or name O4 or name O4P or name O5 or name P )) or (resi \ d 409 through 410 and (name C10 or name C11 or name C12 or name C13 or name C14 \ or name C15 or name C16 or name C17 or name C18 or name C19 or name C20 or name \ C21 or name C22)))) selection = (chain 'E' and (resid 5 through 292 or resid 294 through 316 or (resid 403 and ( \ name C1 or name C10 or name C11 or name C12 or name C13 or name C14 or name C15 \ or name C16 or name C17 or name C2 or name C3 or name C30 or name C31 or name C3 \ 2 or name C33 or name C34 or name C35 or name C36 or name C37 or name C38 or nam \ e O1P or name O2 or name O2P or name O3 or name O3P or name O4 or name O4P or na \ me O5 or name P )) or (resid 404 and (name C1 or name C10 or name C11 or name C1 \ 2 or name C13 or name C14 or name C15 or name C16 or name C17 or name C18 or nam \ e C2 or name C3 or name C30 or name C31 or name C32 or name C33 or name C34 or n \ ame C35 or name C36 or name C37 or name C38 or name O1P or name O2 or name O2P o \ r name O3 or name O3P or name O4 or name O4P or name O5 or name P )) or (resid 4 \ 05 through 406 and (name N or name C1 or name C10 or name C11 or name C12 or nam \ e C13 or name C14 or name C15 or name C16 or name C17 or name C18 or name C19 or \ name C2 or name C3 or name C30 or name C31 or name C32 or name C33 or name C4 o \ r name C5 or name O1P or name O2 or name O2P or name O3 or name O3P or name O4 o \ r name O4P or name O5 or name P )) or (resid 407 through 408 and (name N or name \ C1 or name C10 or name C11 or name C12 or name C13 or name C14 or name C15 or n \ ame C16 or name C17 or name C18 or name C19 or name C2 or name C20 or name C21 o \ r name C3 or name C30 or name C31 or name C32 or name C33 or name C34 or name C3 \ 5 or name C36 or name C37 or name C38 or name C39 or name C4 or name C40 or name \ C5 or name O1P or name O2 or name O2P or name O3 or name O3P or name O4 or name \ O4P or name O5 or name P )) or (resid 409 through 410 and (name C10 or name C11 \ or name C12 or name C13 or name C14 or name C15 or name C16 or name C17 or name \ C18 or name C19 or name C20 or name C21 or name C22)))) } 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=0.48 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.560 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: 0.010 Extract box with map and model: 0.650 Check model and map are aligned: 0.110 Set scattering table: 0.150 Process input model: 48.040 Find NCS groups from input model: 0.730 Set up NCS constraints: 0.100 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:14.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8804 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 : 0.005 0.115 14640 Z= 0.317 Angle : 0.813 12.909 19620 Z= 0.430 Chirality : 0.065 0.602 2120 Planarity : 0.010 0.051 2315 Dihedral : 24.232 163.344 6100 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.14 % Allowed : 17.37 % Favored : 81.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.16 (0.21), residues: 1555 helix: 2.73 (0.20), residues: 530 sheet: 0.73 (0.27), residues: 410 loop : -1.02 (0.23), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.012 TRP D 213 HIS 0.005 0.002 HIS E 127 PHE 0.047 0.007 PHE E 207 TYR 0.050 0.008 TYR C 263 ARG 0.028 0.004 ARG E 287 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 121 time to evaluate : 1.525 Fit side-chains REVERT: D 205 MET cc_start: 0.8031 (mmm) cc_final: 0.7809 (mmp) outliers start: 11 outliers final: 11 residues processed: 132 average time/residue: 1.5333 time to fit residues: 219.8304 Evaluate side-chains 116 residues out of total 1395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 105 time to evaluate : 1.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 91 ASP Chi-restraints excluded: chain E residue 191 SER Chi-restraints excluded: chain E residue 219 THR Chi-restraints excluded: chain A residue 191 SER Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain C residue 191 SER Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain D residue 191 SER Chi-restraints excluded: chain D residue 219 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 130 optimal weight: 4.9990 chunk 117 optimal weight: 2.9990 chunk 65 optimal weight: 7.9990 chunk 40 optimal weight: 1.9990 chunk 79 optimal weight: 6.9990 chunk 62 optimal weight: 10.0000 chunk 121 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 73 optimal weight: 0.5980 chunk 90 optimal weight: 2.9990 chunk 140 optimal weight: 4.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 101 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8842 moved from start: 0.0859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 14640 Z= 0.276 Angle : 0.610 5.441 19620 Z= 0.312 Chirality : 0.046 0.144 2120 Planarity : 0.005 0.041 2315 Dihedral : 25.551 160.641 3167 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.28 % Allowed : 15.94 % Favored : 81.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.32 (0.21), residues: 1555 helix: 3.21 (0.20), residues: 525 sheet: 0.71 (0.26), residues: 410 loop : -1.16 (0.23), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP B 213 HIS 0.002 0.001 HIS A 277 PHE 0.011 0.001 PHE B 312 TYR 0.015 0.002 TYR C 102 ARG 0.001 0.000 ARG A 287 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 104 time to evaluate : 1.581 Fit side-chains REVERT: E 163 GLU cc_start: 0.8391 (OUTLIER) cc_final: 0.8132 (mt-10) REVERT: B 163 GLU cc_start: 0.8503 (OUTLIER) cc_final: 0.8069 (mt-10) outliers start: 27 outliers final: 16 residues processed: 121 average time/residue: 1.4704 time to fit residues: 193.7570 Evaluate side-chains 116 residues out of total 1395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 98 time to evaluate : 1.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 101 GLN Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 163 GLU Chi-restraints excluded: chain E residue 219 THR Chi-restraints excluded: chain E residue 292 THR Chi-restraints excluded: chain A residue 101 GLN Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 163 GLU Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 292 THR Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 219 THR Chi-restraints excluded: chain D residue 292 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 78 optimal weight: 5.9990 chunk 43 optimal weight: 4.9990 chunk 117 optimal weight: 0.4980 chunk 95 optimal weight: 2.9990 chunk 38 optimal weight: 0.0770 chunk 141 optimal weight: 1.9990 chunk 152 optimal weight: 0.9990 chunk 125 optimal weight: 0.6980 chunk 139 optimal weight: 5.9990 chunk 48 optimal weight: 5.9990 chunk 113 optimal weight: 5.9990 overall best weight: 0.8542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 284 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8782 moved from start: 0.0948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 14640 Z= 0.150 Angle : 0.541 7.468 19620 Z= 0.269 Chirality : 0.044 0.143 2120 Planarity : 0.004 0.040 2315 Dihedral : 23.725 165.504 3160 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.78 % Allowed : 16.51 % Favored : 81.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.49 (0.21), residues: 1555 helix: 3.50 (0.20), residues: 530 sheet: 0.46 (0.25), residues: 445 loop : -1.05 (0.24), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 47 HIS 0.002 0.001 HIS A 277 PHE 0.008 0.001 PHE B 42 TYR 0.014 0.001 TYR C 102 ARG 0.001 0.000 ARG A 133 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 114 time to evaluate : 1.404 Fit side-chains REVERT: E 14 GLU cc_start: 0.6799 (pm20) cc_final: 0.6499 (pm20) REVERT: A 14 GLU cc_start: 0.6691 (pm20) cc_final: 0.6286 (pm20) REVERT: B 163 GLU cc_start: 0.8463 (OUTLIER) cc_final: 0.8133 (mt-10) REVERT: D 14 GLU cc_start: 0.6750 (pm20) cc_final: 0.6507 (pm20) outliers start: 20 outliers final: 12 residues processed: 121 average time/residue: 1.5465 time to fit residues: 203.3498 Evaluate side-chains 111 residues out of total 1395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 98 time to evaluate : 1.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 219 THR Chi-restraints excluded: chain E residue 261 MET Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 163 GLU Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain D residue 101 GLN Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 219 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 139 optimal weight: 6.9990 chunk 106 optimal weight: 0.7980 chunk 73 optimal weight: 0.7980 chunk 15 optimal weight: 8.9990 chunk 67 optimal weight: 0.6980 chunk 94 optimal weight: 1.9990 chunk 141 optimal weight: 3.9990 chunk 149 optimal weight: 3.9990 chunk 134 optimal weight: 0.8980 chunk 40 optimal weight: 7.9990 chunk 124 optimal weight: 10.0000 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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: 0.8793 moved from start: 0.1097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 14640 Z= 0.161 Angle : 0.542 7.854 19620 Z= 0.269 Chirality : 0.044 0.164 2120 Planarity : 0.004 0.043 2315 Dihedral : 22.782 171.549 3159 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.71 % Allowed : 17.79 % Favored : 80.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.48 (0.21), residues: 1555 helix: 3.37 (0.20), residues: 535 sheet: 0.45 (0.25), residues: 445 loop : -0.96 (0.25), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 47 HIS 0.002 0.001 HIS B 277 PHE 0.010 0.001 PHE C 312 TYR 0.013 0.001 TYR C 102 ARG 0.001 0.000 ARG B 192 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 103 time to evaluate : 1.549 Fit side-chains REVERT: E 14 GLU cc_start: 0.6824 (pm20) cc_final: 0.6572 (pm20) REVERT: A 14 GLU cc_start: 0.6693 (pm20) cc_final: 0.6279 (pm20) REVERT: D 14 GLU cc_start: 0.6786 (pm20) cc_final: 0.6535 (pm20) outliers start: 19 outliers final: 11 residues processed: 110 average time/residue: 1.6548 time to fit residues: 196.8512 Evaluate side-chains 108 residues out of total 1395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 97 time to evaluate : 1.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 261 MET Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 191 SER Chi-restraints excluded: chain B residue 101 GLN Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 191 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 85 optimal weight: 5.9990 chunk 2 optimal weight: 4.9990 chunk 111 optimal weight: 4.9990 chunk 61 optimal weight: 6.9990 chunk 127 optimal weight: 6.9990 chunk 103 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 76 optimal weight: 0.3980 chunk 134 optimal weight: 0.6980 chunk 37 optimal weight: 8.9990 chunk 50 optimal weight: 0.4980 overall best weight: 2.1184 ------------------------------------------------------------------------------- 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: 0.8843 moved from start: 0.1178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 14640 Z= 0.254 Angle : 0.598 7.943 19620 Z= 0.300 Chirality : 0.046 0.179 2120 Planarity : 0.004 0.045 2315 Dihedral : 22.701 179.982 3155 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 2.35 % Allowed : 17.37 % Favored : 80.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.29 (0.21), residues: 1555 helix: 3.30 (0.21), residues: 525 sheet: 0.50 (0.25), residues: 410 loop : -1.14 (0.23), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 213 HIS 0.002 0.001 HIS D 277 PHE 0.009 0.001 PHE D 42 TYR 0.012 0.001 TYR C 102 ARG 0.001 0.000 ARG E 77 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 98 time to evaluate : 1.546 Fit side-chains REVERT: E 14 GLU cc_start: 0.6896 (pm20) cc_final: 0.6632 (pm20) REVERT: A 14 GLU cc_start: 0.6771 (pm20) cc_final: 0.6362 (pm20) REVERT: A 163 GLU cc_start: 0.8519 (OUTLIER) cc_final: 0.8227 (mt-10) REVERT: C 287 ARG cc_start: 0.7760 (OUTLIER) cc_final: 0.6941 (mtp180) REVERT: D 14 GLU cc_start: 0.6860 (pm20) cc_final: 0.6602 (pm20) outliers start: 28 outliers final: 21 residues processed: 111 average time/residue: 1.5989 time to fit residues: 192.6033 Evaluate side-chains 119 residues out of total 1395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 96 time to evaluate : 1.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 93 SER Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 146 LEU Chi-restraints excluded: chain E residue 191 SER Chi-restraints excluded: chain E residue 261 MET Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 101 GLN Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 163 GLU Chi-restraints excluded: chain A residue 191 SER Chi-restraints excluded: chain B residue 101 GLN Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 191 SER Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 287 ARG Chi-restraints excluded: chain D residue 101 GLN Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 191 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 134 optimal weight: 0.9980 chunk 29 optimal weight: 5.9990 chunk 87 optimal weight: 1.9990 chunk 36 optimal weight: 5.9990 chunk 149 optimal weight: 0.9990 chunk 124 optimal weight: 10.0000 chunk 69 optimal weight: 5.9990 chunk 12 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 78 optimal weight: 3.9990 chunk 144 optimal weight: 1.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 284 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8836 moved from start: 0.1210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 14640 Z= 0.238 Angle : 0.583 7.836 19620 Z= 0.291 Chirality : 0.046 0.187 2120 Planarity : 0.004 0.045 2315 Dihedral : 22.348 174.648 3155 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.28 % Allowed : 17.08 % Favored : 80.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.30 (0.21), residues: 1555 helix: 3.29 (0.20), residues: 530 sheet: 0.50 (0.25), residues: 410 loop : -1.15 (0.24), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 47 HIS 0.001 0.001 HIS E 277 PHE 0.008 0.001 PHE C 312 TYR 0.013 0.001 TYR C 102 ARG 0.001 0.000 ARG D 77 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 100 time to evaluate : 1.584 Fit side-chains REVERT: E 14 GLU cc_start: 0.6894 (pm20) cc_final: 0.6584 (pm20) REVERT: A 14 GLU cc_start: 0.6805 (pm20) cc_final: 0.6394 (pm20) REVERT: A 88 ASP cc_start: 0.8589 (p0) cc_final: 0.8350 (p0) REVERT: A 163 GLU cc_start: 0.8518 (OUTLIER) cc_final: 0.8239 (mt-10) REVERT: C 287 ARG cc_start: 0.7737 (OUTLIER) cc_final: 0.6922 (mtp180) REVERT: D 14 GLU cc_start: 0.6881 (pm20) cc_final: 0.6640 (pm20) outliers start: 27 outliers final: 22 residues processed: 114 average time/residue: 1.6512 time to fit residues: 204.0340 Evaluate side-chains 121 residues out of total 1395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 97 time to evaluate : 1.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 101 GLN Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 146 LEU Chi-restraints excluded: chain E residue 191 SER Chi-restraints excluded: chain E residue 261 MET Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 101 GLN Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 163 GLU Chi-restraints excluded: chain A residue 191 SER Chi-restraints excluded: chain B residue 101 GLN Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 191 SER Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 287 ARG Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 101 GLN Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 191 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 16 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 chunk 109 optimal weight: 1.9990 chunk 84 optimal weight: 0.7980 chunk 126 optimal weight: 7.9990 chunk 83 optimal weight: 4.9990 chunk 149 optimal weight: 2.9990 chunk 93 optimal weight: 10.0000 chunk 91 optimal weight: 1.9990 chunk 68 optimal weight: 0.6980 chunk 92 optimal weight: 6.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- 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: 0.8826 moved from start: 0.1235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14640 Z= 0.214 Angle : 0.570 7.841 19620 Z= 0.284 Chirality : 0.046 0.192 2120 Planarity : 0.004 0.044 2315 Dihedral : 21.990 172.446 3155 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.28 % Allowed : 17.01 % Favored : 80.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.32 (0.21), residues: 1555 helix: 3.33 (0.20), residues: 530 sheet: 0.49 (0.25), residues: 410 loop : -1.13 (0.24), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 47 HIS 0.002 0.001 HIS A 277 PHE 0.008 0.001 PHE A 42 TYR 0.013 0.001 TYR C 102 ARG 0.001 0.000 ARG D 77 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 99 time to evaluate : 1.486 Fit side-chains REVERT: E 14 GLU cc_start: 0.6900 (pm20) cc_final: 0.6594 (pm20) REVERT: A 14 GLU cc_start: 0.6812 (pm20) cc_final: 0.6400 (pm20) REVERT: A 88 ASP cc_start: 0.8569 (p0) cc_final: 0.8334 (p0) REVERT: A 93 SER cc_start: 0.8530 (OUTLIER) cc_final: 0.8300 (m) REVERT: A 163 GLU cc_start: 0.8520 (OUTLIER) cc_final: 0.8221 (mt-10) REVERT: C 287 ARG cc_start: 0.7698 (OUTLIER) cc_final: 0.6879 (mtp180) REVERT: D 14 GLU cc_start: 0.6862 (pm20) cc_final: 0.6630 (pm20) outliers start: 27 outliers final: 20 residues processed: 113 average time/residue: 1.6122 time to fit residues: 197.7403 Evaluate side-chains 121 residues out of total 1395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 98 time to evaluate : 1.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 146 LEU Chi-restraints excluded: chain E residue 191 SER Chi-restraints excluded: chain E residue 261 MET Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 101 GLN Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 163 GLU Chi-restraints excluded: chain A residue 191 SER Chi-restraints excluded: chain B residue 101 GLN Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 191 SER Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 287 ARG Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 101 GLN Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 191 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 59 optimal weight: 3.9990 chunk 89 optimal weight: 0.9980 chunk 45 optimal weight: 0.0470 chunk 29 optimal weight: 5.9990 chunk 28 optimal weight: 5.9990 chunk 94 optimal weight: 3.9990 chunk 101 optimal weight: 8.9990 chunk 73 optimal weight: 0.5980 chunk 13 optimal weight: 10.0000 chunk 117 optimal weight: 3.9990 chunk 135 optimal weight: 0.9980 overall best weight: 1.3280 ------------------------------------------------------------------------------- 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: 0.8807 moved from start: 0.1258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 14640 Z= 0.182 Angle : 0.551 7.824 19620 Z= 0.274 Chirality : 0.045 0.188 2120 Planarity : 0.004 0.044 2315 Dihedral : 21.583 171.313 3155 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.06 % Allowed : 17.22 % Favored : 80.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.38 (0.21), residues: 1555 helix: 3.30 (0.20), residues: 535 sheet: 0.51 (0.25), residues: 410 loop : -1.06 (0.24), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 47 HIS 0.002 0.001 HIS D 235 PHE 0.009 0.001 PHE C 312 TYR 0.013 0.001 TYR D 102 ARG 0.002 0.000 ARG B 50 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 100 time to evaluate : 1.684 Fit side-chains REVERT: E 14 GLU cc_start: 0.6862 (pm20) cc_final: 0.6573 (pm20) REVERT: A 14 GLU cc_start: 0.6778 (pm20) cc_final: 0.6375 (pm20) REVERT: A 88 ASP cc_start: 0.8539 (p0) cc_final: 0.8321 (p0) REVERT: A 163 GLU cc_start: 0.8504 (OUTLIER) cc_final: 0.8203 (mt-10) REVERT: C 14 GLU cc_start: 0.6954 (pm20) cc_final: 0.6736 (pm20) REVERT: C 287 ARG cc_start: 0.7634 (OUTLIER) cc_final: 0.6800 (mtp180) REVERT: D 14 GLU cc_start: 0.6836 (pm20) cc_final: 0.6623 (pm20) outliers start: 24 outliers final: 19 residues processed: 111 average time/residue: 1.5689 time to fit residues: 189.2197 Evaluate side-chains 119 residues out of total 1395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 98 time to evaluate : 1.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 101 GLN Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 146 LEU Chi-restraints excluded: chain E residue 191 SER Chi-restraints excluded: chain E residue 261 MET Chi-restraints excluded: chain A residue 101 GLN Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 163 GLU Chi-restraints excluded: chain A residue 191 SER Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 191 SER Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 287 ARG Chi-restraints excluded: chain D residue 101 GLN Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 191 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 143 optimal weight: 4.9990 chunk 130 optimal weight: 8.9990 chunk 139 optimal weight: 4.9990 chunk 83 optimal weight: 0.6980 chunk 60 optimal weight: 5.9990 chunk 109 optimal weight: 3.9990 chunk 42 optimal weight: 0.3980 chunk 125 optimal weight: 2.9990 chunk 131 optimal weight: 3.9990 chunk 138 optimal weight: 4.9990 chunk 91 optimal weight: 4.9990 overall best weight: 2.4186 ------------------------------------------------------------------------------- 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: 0.8850 moved from start: 0.1324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 14640 Z= 0.280 Angle : 0.602 7.734 19620 Z= 0.302 Chirality : 0.046 0.191 2120 Planarity : 0.004 0.045 2315 Dihedral : 21.936 169.942 3155 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 2.06 % Allowed : 17.15 % Favored : 80.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.22 (0.21), residues: 1555 helix: 3.22 (0.21), residues: 525 sheet: 0.48 (0.25), residues: 410 loop : -1.17 (0.24), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 213 HIS 0.001 0.001 HIS E 277 PHE 0.008 0.001 PHE D 42 TYR 0.012 0.001 TYR C 102 ARG 0.002 0.000 ARG B 50 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 94 time to evaluate : 1.544 Fit side-chains REVERT: E 14 GLU cc_start: 0.6910 (pm20) cc_final: 0.6616 (pm20) REVERT: A 14 GLU cc_start: 0.6846 (pm20) cc_final: 0.6420 (pm20) REVERT: A 88 ASP cc_start: 0.8584 (p0) cc_final: 0.8363 (p0) REVERT: A 163 GLU cc_start: 0.8529 (OUTLIER) cc_final: 0.8231 (mt-10) REVERT: C 287 ARG cc_start: 0.7772 (OUTLIER) cc_final: 0.6955 (mtp180) outliers start: 24 outliers final: 21 residues processed: 106 average time/residue: 1.6818 time to fit residues: 192.8337 Evaluate side-chains 115 residues out of total 1395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 92 time to evaluate : 1.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 101 GLN Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 146 LEU Chi-restraints excluded: chain E residue 191 SER Chi-restraints excluded: chain E residue 261 MET Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 101 GLN Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 163 GLU Chi-restraints excluded: chain A residue 191 SER Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 191 SER Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 287 ARG Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 101 GLN Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 191 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 147 optimal weight: 0.9980 chunk 89 optimal weight: 0.5980 chunk 69 optimal weight: 2.9990 chunk 102 optimal weight: 0.9990 chunk 154 optimal weight: 6.9990 chunk 142 optimal weight: 1.9990 chunk 122 optimal weight: 3.9990 chunk 12 optimal weight: 5.9990 chunk 94 optimal weight: 0.9990 chunk 75 optimal weight: 5.9990 chunk 97 optimal weight: 1.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 284 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8803 moved from start: 0.1287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 14640 Z= 0.172 Angle : 0.552 7.756 19620 Z= 0.275 Chirality : 0.045 0.192 2120 Planarity : 0.004 0.044 2315 Dihedral : 21.468 172.572 3155 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.78 % Allowed : 17.37 % Favored : 80.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.38 (0.21), residues: 1555 helix: 3.37 (0.20), residues: 530 sheet: 0.42 (0.24), residues: 445 loop : -1.09 (0.25), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 47 HIS 0.002 0.001 HIS E 277 PHE 0.008 0.001 PHE B 42 TYR 0.013 0.001 TYR B 102 ARG 0.001 0.000 ARG D 77 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 94 time to evaluate : 1.491 Fit side-chains REVERT: E 14 GLU cc_start: 0.6869 (pm20) cc_final: 0.6582 (pm20) REVERT: A 14 GLU cc_start: 0.6791 (pm20) cc_final: 0.6384 (pm20) REVERT: A 88 ASP cc_start: 0.8560 (p0) cc_final: 0.8332 (p0) REVERT: A 163 GLU cc_start: 0.8513 (OUTLIER) cc_final: 0.8211 (mt-10) REVERT: C 14 GLU cc_start: 0.6923 (pm20) cc_final: 0.6703 (pm20) REVERT: C 287 ARG cc_start: 0.7622 (OUTLIER) cc_final: 0.6783 (mtp180) outliers start: 20 outliers final: 17 residues processed: 103 average time/residue: 1.6709 time to fit residues: 185.9102 Evaluate side-chains 113 residues out of total 1395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 94 time to evaluate : 1.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 146 LEU Chi-restraints excluded: chain E residue 191 SER Chi-restraints excluded: chain E residue 261 MET Chi-restraints excluded: chain A residue 101 GLN Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 163 GLU Chi-restraints excluded: chain A residue 191 SER Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 191 SER Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 287 ARG Chi-restraints excluded: chain D residue 101 GLN Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 191 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 130 optimal weight: 10.0000 chunk 37 optimal weight: 0.9990 chunk 113 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 34 optimal weight: 5.9990 chunk 123 optimal weight: 6.9990 chunk 51 optimal weight: 2.9990 chunk 126 optimal weight: 8.9990 chunk 15 optimal weight: 0.9990 chunk 22 optimal weight: 4.9990 chunk 108 optimal weight: 2.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- 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 = 0.3465 r_free = 0.3465 target = 0.124740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.087065 restraints weight = 28610.254| |-----------------------------------------------------------------------------| r_work (start): 0.2925 rms_B_bonded: 2.47 r_work: 0.2777 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2771 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2771 r_free = 0.2771 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2770 r_free = 0.2770 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2770 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8677 moved from start: 0.1337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 14640 Z= 0.260 Angle : 0.594 7.735 19620 Z= 0.298 Chirality : 0.046 0.193 2120 Planarity : 0.004 0.045 2315 Dihedral : 21.702 172.117 3155 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 1.92 % Allowed : 17.30 % Favored : 80.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.23 (0.21), residues: 1555 helix: 3.26 (0.21), residues: 525 sheet: 0.45 (0.25), residues: 410 loop : -1.15 (0.24), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 213 HIS 0.001 0.001 HIS E 277 PHE 0.008 0.001 PHE D 42 TYR 0.012 0.001 TYR C 102 ARG 0.001 0.000 ARG D 85 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4109.36 seconds wall clock time: 73 minutes 10.96 seconds (4390.96 seconds total)