Starting phenix.real_space_refine on Wed Feb 4 22:17:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lbe_62942/02_2026/9lbe_62942.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lbe_62942/02_2026/9lbe_62942.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.87 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9lbe_62942/02_2026/9lbe_62942.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lbe_62942/02_2026/9lbe_62942.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9lbe_62942/02_2026/9lbe_62942.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lbe_62942/02_2026/9lbe_62942.map" } resolution = 2.87 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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 16 5.49 5 S 20 5.16 5 Cl 5 4.86 5 C 8824 2.51 5 N 2026 2.21 5 O 2393 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13284 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 2522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 2522 Classifications: {'peptide': 312} Link IDs: {'PTRANS': 18, 'TRANS': 293} Chain: "B" Number of atoms: 2522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 2522 Classifications: {'peptide': 312} Link IDs: {'PTRANS': 18, 'TRANS': 293} Chain: "C" Number of atoms: 2522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 2522 Classifications: {'peptide': 312} Link IDs: {'PTRANS': 18, 'TRANS': 293} Chain: "D" Number of atoms: 2522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 2522 Classifications: {'peptide': 312} Link IDs: {'PTRANS': 18, 'TRANS': 293} Chain: "E" Number of atoms: 2522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 2522 Classifications: {'peptide': 312} Link IDs: {'PTRANS': 18, 'TRANS': 293} Chain: "A" Number of atoms: 125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 125 Unusual residues: {' CL': 1, 'PEE': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 80 Unresolved non-hydrogen angles: 86 Unresolved non-hydrogen dihedrals: 84 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PEE:plan-1': 1, 'PEE:plan-2': 1} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 100 Unusual residues: {' CL': 1, 'PEE': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 56 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PEE:plan-1': 1, 'PEE:plan-2': 1} Unresolved non-hydrogen planarities: 7 Chain: "C" Number of atoms: 189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 189 Unusual residues: {' CL': 1, 'PEE': 6} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 118 Unresolved non-hydrogen angles: 124 Unresolved non-hydrogen dihedrals: 124 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: 134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 134 Unusual residues: {' CL': 1, 'PEE': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 71 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 75 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: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 126 Unusual residues: {' CL': 1, 'PEE': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 79 Unresolved non-hydrogen angles: 85 Unresolved non-hydrogen dihedrals: 83 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PEE:plan-1': 1, 'PEE:plan-2': 1} Unresolved non-hydrogen planarities: 6 Time building chain proxies: 3.08, per 1000 atoms: 0.23 Number of scatterers: 13284 At special positions: 0 Unit cell: (91.96, 91.96, 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 16 15.00 O 2393 8.00 N 2026 7.00 C 8824 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 - 3.00 Amino acid : True - 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: 0.93 Conformation dependent library (CDL) restraints added in 510.5 milliseconds 3100 Ramachandran restraints generated. 1550 Oldfield, 0 Emsley, 1550 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3050 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 19 sheets defined 41.1% alpha, 37.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.55 Creating SS restraints... 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 145 through 149 Processing helix chain 'A' and resid 196 through 201 removed outlier: 3.634A pdb=" N ASN A 200 " --> pdb=" O SER A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 214 removed outlier: 3.536A pdb=" N MET A 205 " --> pdb=" O ILE A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 217 No H-bonds generated for 'chain 'A' and resid 215 through 217' Processing helix chain 'A' and resid 220 through 246 removed outlier: 3.683A pdb=" N LEU A 241 " --> pdb=" O ALA A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 282 Processing helix chain 'A' and resid 284 through 315 removed outlier: 3.616A pdb=" N ALA A 288 " --> pdb=" O GLN A 284 " (cutoff:3.500A) removed outlier: 3.915A 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: 3.532A 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 214 removed outlier: 3.601A pdb=" N ASN B 200 " --> pdb=" O SER B 196 " (cutoff:3.500A) removed outlier: 5.346A 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 215 through 218 removed outlier: 3.505A pdb=" N SER B 218 " --> pdb=" O ALA B 215 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 215 through 218' 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 315 removed outlier: 3.517A pdb=" N ALA B 288 " --> pdb=" O GLN B 284 " (cutoff:3.500A) removed outlier: 3.812A 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 removed outlier: 3.747A pdb=" N ALA C 53 " --> pdb=" O ARG C 50 " (cutoff:3.500A) No H-bonds generated for '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: 3.725A 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 214 removed outlier: 3.776A pdb=" N ASN C 200 " --> pdb=" O SER C 196 " (cutoff:3.500A) removed outlier: 5.229A 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 215 through 218 removed outlier: 3.544A pdb=" N SER C 218 " --> pdb=" O ALA C 215 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 215 through 218' Processing helix chain 'C' and resid 220 through 243 Processing helix chain 'C' and resid 253 through 282 removed outlier: 3.740A pdb=" N ALA C 257 " --> pdb=" O THR C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 284 through 316 removed outlier: 3.590A pdb=" N ALA C 288 " --> pdb=" O GLN C 284 " (cutoff:3.500A) removed outlier: 3.959A 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: 4.004A 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 214 removed outlier: 3.587A pdb=" N ASN D 200 " --> pdb=" O SER D 196 " (cutoff:3.500A) removed outlier: 5.073A 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 215 through 218 removed outlier: 3.615A pdb=" N SER D 218 " --> pdb=" O ALA D 215 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 215 through 218' Processing helix chain 'D' and resid 220 through 244 Processing helix chain 'D' and resid 253 through 282 Processing helix chain 'D' and resid 286 through 315 removed outlier: 3.880A pdb=" N ILE D 297 " --> pdb=" O ARG D 293 " (cutoff:3.500A) Proline residue: D 300 - end of helix 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: 3.677A 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 214 removed outlier: 3.678A pdb=" N ASN E 200 " --> pdb=" O SER E 196 " (cutoff:3.500A) removed outlier: 5.405A 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 215 through 218 removed outlier: 4.012A pdb=" N SER E 218 " --> pdb=" O ALA E 215 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 215 through 218' Processing helix chain 'E' and resid 220 through 244 removed outlier: 3.623A pdb=" N ALA E 237 " --> pdb=" O ILE E 233 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N PHE E 238 " --> pdb=" O ALA E 234 " (cutoff:3.500A) Processing helix chain 'E' and resid 253 through 282 Processing helix chain 'E' and resid 284 through 315 removed outlier: 3.725A pdb=" N ALA E 288 " --> pdb=" O GLN E 284 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ILE E 297 " --> pdb=" O ARG E 293 " (cutoff:3.500A) Proline residue: E 300 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 16 through 17 removed outlier: 6.132A pdb=" N LEU A 16 " --> pdb=" O VAL A 141 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 19 through 21 removed outlier: 3.778A pdb=" N TRP A 47 " --> pdb=" O VAL A 100 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASP A 91 " --> pdb=" O LEU A 103 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N ARG A 105 " --> pdb=" O VAL A 89 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N VAL A 89 " --> pdb=" O ARG A 105 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N VAL A 94 " --> pdb=" O LYS A 64 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LYS A 64 " --> pdb=" O VAL A 94 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 19 through 21 removed outlier: 6.579A pdb=" N THR A 36 " --> pdb=" O LEU A 30 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N LEU A 30 " --> pdb=" O THR A 36 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N PHE A 42 " --> pdb=" O LEU A 24 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N LEU A 24 " --> pdb=" O PHE A 42 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 76 through 78 removed outlier: 7.044A pdb=" N ASP A 185 " --> pdb=" O ALA A 167 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N ALA A 167 " --> pdb=" O ASP A 185 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N GLN A 187 " --> pdb=" O PHE A 165 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N PHE A 165 " --> pdb=" O GLN A 187 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ARG A 189 " --> pdb=" O GLU A 163 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 76 through 78 Processing sheet with id=AA6, first strand: chain 'B' and resid 86 through 94 removed outlier: 6.823A pdb=" N LEU B 103 " --> pdb=" O VAL B 90 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N ILE B 92 " --> pdb=" O GLN B 101 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N GLN B 101 " --> pdb=" O ILE B 92 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N VAL B 94 " --> pdb=" O THR B 99 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N THR B 99 " --> pdb=" O VAL B 94 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N TRP B 47 " --> pdb=" O VAL B 100 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LYS B 38 " --> pdb=" O SER B 29 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N SER B 29 " --> pdb=" O LYS B 38 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N ASN B 40 " --> pdb=" O CYS B 27 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N CYS B 27 " --> pdb=" O ASN B 40 " (cutoff:3.500A) removed outlier: 8.614A pdb=" N PHE B 42 " --> pdb=" O ILE B 25 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N ILE B 25 " --> pdb=" O PHE B 42 " (cutoff:3.500A) removed outlier: 8.290A pdb=" N SER B 44 " --> pdb=" O TYR B 23 " (cutoff:3.500A) removed outlier: 8.304A pdb=" N TYR B 23 " --> pdb=" O SER B 44 " (cutoff:3.500A) removed outlier: 8.722A pdb=" N SER B 46 " --> pdb=" O GLY B 21 " (cutoff:3.500A) removed outlier: 8.903A pdb=" N GLY B 21 " --> pdb=" O SER B 46 " (cutoff:3.500A) removed outlier: 9.353A pdb=" N LYS B 48 " --> pdb=" O ASN B 19 " (cutoff:3.500A) removed outlier: 9.970A pdb=" N ASN B 19 " --> pdb=" O LYS B 48 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 86 through 94 removed outlier: 6.823A pdb=" N LEU B 103 " --> pdb=" O VAL B 90 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N ILE B 92 " --> pdb=" O GLN B 101 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N GLN B 101 " --> pdb=" O ILE B 92 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N VAL B 94 " --> pdb=" O THR B 99 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N THR B 99 " --> pdb=" O VAL B 94 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N TRP B 47 " --> pdb=" O VAL B 100 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LYS B 38 " --> pdb=" O SER B 29 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N SER B 29 " --> pdb=" O LYS B 38 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N ASN B 40 " --> pdb=" O CYS B 27 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N CYS B 27 " --> pdb=" O ASN B 40 " (cutoff:3.500A) removed outlier: 8.614A pdb=" N PHE B 42 " --> pdb=" O ILE B 25 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N ILE B 25 " --> pdb=" O PHE B 42 " (cutoff:3.500A) removed outlier: 8.290A pdb=" N SER B 44 " --> pdb=" O TYR B 23 " (cutoff:3.500A) removed outlier: 8.304A pdb=" N TYR B 23 " --> pdb=" O SER B 44 " (cutoff:3.500A) removed outlier: 8.722A pdb=" N SER B 46 " --> pdb=" O GLY B 21 " (cutoff:3.500A) removed outlier: 8.903A pdb=" N GLY B 21 " --> pdb=" O SER B 46 " (cutoff:3.500A) removed outlier: 9.353A pdb=" N LYS B 48 " --> pdb=" O ASN B 19 " (cutoff:3.500A) removed outlier: 9.970A pdb=" N ASN B 19 " --> pdb=" O LYS B 48 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 77 through 78 removed outlier: 3.518A pdb=" N SER B 182 " --> pdb=" O VAL B 132 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS B 183 " --> pdb=" O ALA B 172 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 123 through 128 removed outlier: 6.526A pdb=" N GLN B 187 " --> pdb=" O PHE B 165 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N PHE B 165 " --> pdb=" O GLN B 187 " (cutoff:3.500A) removed outlier: 6.819A 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: 3.550A pdb=" N ARG C 105 " --> pdb=" O ASP C 88 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N LEU C 103 " --> pdb=" O VAL C 90 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N ILE C 92 " --> pdb=" O GLN C 101 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N GLN C 101 " --> pdb=" O ILE C 92 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N VAL C 94 " --> pdb=" O THR C 99 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N THR C 99 " --> pdb=" O VAL C 94 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N TRP C 47 " --> pdb=" O VAL C 100 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N LYS C 38 " --> pdb=" O SER C 29 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N SER C 29 " --> pdb=" O LYS C 38 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N ASN C 40 " --> pdb=" O CYS C 27 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N CYS C 27 " --> pdb=" O ASN C 40 " (cutoff:3.500A) removed outlier: 8.450A pdb=" N PHE C 42 " --> pdb=" O ILE C 25 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N ILE C 25 " --> pdb=" O PHE C 42 " (cutoff:3.500A) removed outlier: 8.263A pdb=" N SER C 44 " --> pdb=" O TYR C 23 " (cutoff:3.500A) removed outlier: 8.229A pdb=" N TYR C 23 " --> pdb=" O SER C 44 " (cutoff:3.500A) removed outlier: 8.619A pdb=" N SER C 46 " --> pdb=" O GLY C 21 " (cutoff:3.500A) removed outlier: 8.813A pdb=" N GLY C 21 " --> pdb=" O SER C 46 " (cutoff:3.500A) removed outlier: 9.233A pdb=" N LYS C 48 " --> pdb=" O ASN C 19 " (cutoff:3.500A) removed outlier: 10.000A pdb=" N ASN C 19 " --> pdb=" O LYS C 48 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N LEU C 16 " --> pdb=" O VAL C 141 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N ALA C 143 " --> pdb=" O LEU C 16 " (cutoff:3.500A) removed outlier: 6.538A 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: 3.550A pdb=" N ARG C 105 " --> pdb=" O ASP C 88 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N LEU C 103 " --> pdb=" O VAL C 90 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N ILE C 92 " --> pdb=" O GLN C 101 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N GLN C 101 " --> pdb=" O ILE C 92 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N VAL C 94 " --> pdb=" O THR C 99 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N THR C 99 " --> pdb=" O VAL C 94 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N TRP C 47 " --> pdb=" O VAL C 100 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N LYS C 38 " --> pdb=" O SER C 29 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N SER C 29 " --> pdb=" O LYS C 38 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N ASN C 40 " --> pdb=" O CYS C 27 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N CYS C 27 " --> pdb=" O ASN C 40 " (cutoff:3.500A) removed outlier: 8.450A pdb=" N PHE C 42 " --> pdb=" O ILE C 25 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N ILE C 25 " --> pdb=" O PHE C 42 " (cutoff:3.500A) removed outlier: 8.263A pdb=" N SER C 44 " --> pdb=" O TYR C 23 " (cutoff:3.500A) removed outlier: 8.229A pdb=" N TYR C 23 " --> pdb=" O SER C 44 " (cutoff:3.500A) removed outlier: 8.619A pdb=" N SER C 46 " --> pdb=" O GLY C 21 " (cutoff:3.500A) removed outlier: 8.813A pdb=" N GLY C 21 " --> pdb=" O SER C 46 " (cutoff:3.500A) removed outlier: 9.233A pdb=" N LYS C 48 " --> pdb=" O ASN C 19 " (cutoff:3.500A) removed outlier: 10.000A pdb=" N ASN C 19 " --> pdb=" O LYS C 48 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLY C 150 " --> pdb=" O ILE C 22 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 77 through 78 removed outlier: 11.221A pdb=" N ARG C 179 " --> pdb=" O ASN C 173 " (cutoff:3.500A) removed outlier: 9.877A pdb=" N ASN C 173 " --> pdb=" O ARG C 179 " (cutoff:3.500A) removed outlier: 10.254A pdb=" N GLU C 181 " --> pdb=" O PRO C 171 " (cutoff:3.500A) removed outlier: 9.530A pdb=" N LYS C 183 " --> pdb=" O VAL C 169 " (cutoff:3.500A) removed outlier: 8.166A pdb=" N VAL C 169 " --> pdb=" O LYS C 183 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N ASP C 185 " --> pdb=" O ALA C 167 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N ALA C 167 " --> pdb=" O ASP C 185 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N GLN C 187 " --> pdb=" O PHE C 165 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N PHE C 165 " --> pdb=" O GLN C 187 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N ARG C 189 " --> pdb=" O GLU C 163 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 16 through 20 removed outlier: 6.218A pdb=" N LEU D 16 " --> pdb=" O VAL D 141 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N ALA D 143 " --> pdb=" O LEU D 16 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N VAL D 18 " --> pdb=" O ALA D 143 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'D' and resid 86 through 94 removed outlier: 6.064A pdb=" N ALA D 87 " --> pdb=" O SER D 107 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N SER D 107 " --> pdb=" O ALA D 87 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N VAL D 89 " --> pdb=" O ARG D 105 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N ARG D 105 " --> pdb=" O VAL D 89 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ASP D 91 " --> pdb=" O LEU D 103 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N TRP D 47 " --> pdb=" O VAL D 100 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N LYS D 38 " --> pdb=" O SER D 29 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N SER D 29 " --> pdb=" O LYS D 38 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N ASN D 40 " --> pdb=" O CYS D 27 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N CYS D 27 " --> pdb=" O ASN D 40 " (cutoff:3.500A) removed outlier: 8.623A pdb=" N PHE D 42 " --> pdb=" O ILE D 25 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N ILE D 25 " --> pdb=" O PHE D 42 " (cutoff:3.500A) removed outlier: 8.295A pdb=" N SER D 44 " --> pdb=" O TYR D 23 " (cutoff:3.500A) removed outlier: 8.247A pdb=" N TYR D 23 " --> pdb=" O SER D 44 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 76 through 78 removed outlier: 6.166A pdb=" N ASP D 185 " --> pdb=" O LYS D 170 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N LYS D 170 " --> pdb=" O ASP D 185 " (cutoff:3.500A) removed outlier: 8.196A pdb=" N GLN D 187 " --> pdb=" O VAL D 168 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N VAL D 168 " --> pdb=" O GLN D 187 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N ARG D 189 " --> pdb=" O THR D 166 " (cutoff:3.500A) removed outlier: 8.213A pdb=" N THR D 166 " --> pdb=" O ARG D 189 " (cutoff:3.500A) removed outlier: 8.658A pdb=" N SER D 191 " --> pdb=" O SER D 164 " (cutoff:3.500A) removed outlier: 9.823A pdb=" N SER D 164 " --> pdb=" O SER D 191 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 16 through 20 removed outlier: 6.240A pdb=" N LEU E 16 " --> pdb=" O VAL E 141 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N ALA E 143 " --> pdb=" O LEU E 16 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N VAL E 18 " --> pdb=" O ALA E 143 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'E' and resid 64 through 65 removed outlier: 3.541A pdb=" N LYS E 64 " --> pdb=" O VAL E 94 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N VAL E 89 " --> pdb=" O ARG E 105 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N ARG E 105 " --> pdb=" O VAL E 89 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASP E 91 " --> pdb=" O LEU E 103 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N TRP E 47 " --> pdb=" O VAL E 100 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA E 41 " --> pdb=" O PHE E 106 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N THR E 36 " --> pdb=" O LEU E 30 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N LEU E 30 " --> pdb=" O THR E 36 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N PHE E 42 " --> pdb=" O LEU E 24 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N LEU E 24 " --> pdb=" O PHE E 42 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 76 through 78 removed outlier: 7.103A pdb=" N ASP E 185 " --> pdb=" O ALA E 167 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N ALA E 167 " --> pdb=" O ASP E 185 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N GLN E 187 " --> pdb=" O PHE E 165 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N PHE E 165 " --> pdb=" O GLN E 187 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ARG E 189 " --> pdb=" O GLU E 163 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 76 through 78 671 hydrogen bonds defined for protein. 1908 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: 2.00 Time building geometry restraints manager: 1.14 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: 2127 1.32 - 1.44: 3601 1.44 - 1.56: 7798 1.56 - 1.69: 32 1.69 - 1.81: 35 Bond restraints: 13593 Sorted by residual: bond pdb=" CB TRP A 213 " pdb=" CG TRP A 213 " ideal model delta sigma weight residual 1.498 1.471 0.027 3.10e-02 1.04e+03 7.38e-01 bond pdb=" CB TRP D 213 " pdb=" CG TRP D 213 " ideal model delta sigma weight residual 1.498 1.473 0.025 3.10e-02 1.04e+03 6.59e-01 bond pdb=" CB TRP E 213 " pdb=" CG TRP E 213 " ideal model delta sigma weight residual 1.498 1.474 0.024 3.10e-02 1.04e+03 6.18e-01 bond pdb=" CB TRP C 213 " pdb=" CG TRP C 213 " ideal model delta sigma weight residual 1.498 1.475 0.023 3.10e-02 1.04e+03 5.67e-01 bond pdb=" CA PHE D 299 " pdb=" C PHE D 299 " ideal model delta sigma weight residual 1.520 1.529 -0.009 1.23e-02 6.61e+03 5.25e-01 ... (remaining 13588 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.17: 18014 1.17 - 2.35: 299 2.35 - 3.52: 78 3.52 - 4.70: 12 4.70 - 5.87: 15 Bond angle restraints: 18418 Sorted by residual: angle pdb=" N TYR A 119 " pdb=" CA TYR A 119 " pdb=" C TYR A 119 " ideal model delta sigma weight residual 109.81 114.83 -5.02 2.21e+00 2.05e-01 5.16e+00 angle pdb=" N ILE B 11 " pdb=" CA ILE B 11 " pdb=" C ILE B 11 " ideal model delta sigma weight residual 110.42 108.56 1.86 9.40e-01 1.13e+00 3.93e+00 angle pdb=" C ASN D 245 " pdb=" N LEU D 246 " pdb=" CA LEU D 246 " ideal model delta sigma weight residual 120.67 123.29 -2.62 1.34e+00 5.57e-01 3.83e+00 angle pdb=" N VAL D 90 " pdb=" CA VAL D 90 " pdb=" C VAL D 90 " ideal model delta sigma weight residual 111.67 109.95 1.72 9.50e-01 1.11e+00 3.27e+00 angle pdb=" N LEU A 203 " pdb=" CA LEU A 203 " pdb=" C LEU A 203 " ideal model delta sigma weight residual 109.81 113.60 -3.79 2.21e+00 2.05e-01 2.93e+00 ... (remaining 18413 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.49: 8087 35.49 - 70.99: 106 70.99 - 106.48: 17 106.48 - 141.97: 8 141.97 - 177.46: 6 Dihedral angle restraints: 8224 sinusoidal: 3549 harmonic: 4675 Sorted by residual: dihedral pdb=" CA GLU C 243 " pdb=" C GLU C 243 " pdb=" N THR C 244 " pdb=" CA THR C 244 " ideal model delta harmonic sigma weight residual 180.00 156.39 23.61 0 5.00e+00 4.00e-02 2.23e+01 dihedral pdb=" C3 PEE C 406 " pdb=" C1 PEE C 406 " pdb=" C2 PEE C 406 " pdb=" O3P PEE C 406 " ideal model delta sinusoidal sigma weight residual 62.73 -114.73 177.46 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" O2 PEE C 406 " pdb=" C1 PEE C 406 " pdb=" C2 PEE C 406 " pdb=" O3P PEE C 406 " ideal model delta sinusoidal sigma weight residual 300.04 123.43 176.61 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 8221 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1258 0.028 - 0.057: 523 0.057 - 0.085: 151 0.085 - 0.113: 132 0.113 - 0.142: 27 Chirality restraints: 2091 Sorted by residual: chirality pdb=" CA PHE C 299 " pdb=" N PHE C 299 " pdb=" C PHE C 299 " pdb=" CB PHE C 299 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.02e-01 chirality pdb=" CA ILE E 128 " pdb=" N ILE E 128 " pdb=" C ILE E 128 " pdb=" CB ILE E 128 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.52e-01 chirality pdb=" CA PHE B 299 " pdb=" N PHE B 299 " pdb=" C PHE B 299 " pdb=" CB PHE B 299 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.40e-01 ... (remaining 2088 not shown) Planarity restraints: 2252 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU A 67 " 0.032 5.00e-02 4.00e+02 4.81e-02 3.70e+00 pdb=" N PRO A 68 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO A 68 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 68 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 203 " 0.023 5.00e-02 4.00e+02 3.52e-02 1.99e+00 pdb=" N PRO A 204 " -0.061 5.00e-02 4.00e+02 pdb=" CA PRO A 204 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 204 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER B 95 " -0.023 5.00e-02 4.00e+02 3.47e-02 1.93e+00 pdb=" N PRO B 96 " 0.060 5.00e-02 4.00e+02 pdb=" CA PRO B 96 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 96 " -0.019 5.00e-02 4.00e+02 ... (remaining 2249 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 119 2.65 - 3.21: 11382 3.21 - 3.78: 18664 3.78 - 4.34: 25899 4.34 - 4.90: 45250 Nonbonded interactions: 101314 Sorted by model distance: nonbonded pdb=" O ILE C 240 " pdb=" OG1 THR C 244 " model vdw 2.090 3.040 nonbonded pdb=" OD2 ASP A 91 " pdb=" NH1 ARG B 133 " model vdw 2.233 3.120 nonbonded pdb=" OE2 GLU B 163 " pdb=" OG SER B 191 " model vdw 2.242 3.040 nonbonded pdb=" O LEU D 241 " pdb=" OG1 THR D 244 " model vdw 2.254 3.040 nonbonded pdb=" OD1 ASN B 173 " pdb=" OG SER B 182 " model vdw 2.257 3.040 ... (remaining 101309 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 316 or (resid 404 and (name C12 or name C13 or n \ ame C14 or name C15 or name C16 or name C17)))) selection = (chain 'B' and (resid 5 through 316 or (resid 404 and (name C12 or name C13 or n \ ame C14 or name C15 or name C16 or name C17)))) selection = (chain 'C' and (resid 5 through 316 or (resid 404 and (name C12 or name C13 or n \ ame C14 or name C15 or name C16 or name C17)))) selection = (chain 'D' and (resid 5 through 316 or (resid 404 and (name C12 or name C13 or n \ ame C14 or name C15 or name C16 or name C17)))) selection = (chain 'E' and (resid 5 through 316 or (resid 404 and (name C12 or name C13 or n \ ame C14 or name C15 or name C16 or name C17)))) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.340 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: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.310 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.020 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: 0.000 Load rotamer database and sin/cos tables:6.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 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 : 0.003 0.029 13593 Z= 0.131 Angle : 0.463 5.872 18418 Z= 0.239 Chirality : 0.041 0.142 2091 Planarity : 0.004 0.048 2252 Dihedral : 14.764 177.463 5174 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 2.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 0.36 % Allowed : 4.95 % Favored : 94.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.12 (0.22), residues: 1550 helix: 2.41 (0.21), residues: 555 sheet: 0.14 (0.25), residues: 465 loop : -0.45 (0.27), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 51 TYR 0.011 0.001 TYR A 254 PHE 0.009 0.001 PHE E 37 TRP 0.005 0.001 TRP A 160 HIS 0.003 0.001 HIS E 277 Details of bonding type rmsd covalent geometry : bond 0.00296 (13593) covalent geometry : angle 0.46311 (18418) hydrogen bonds : bond 0.18388 ( 608) hydrogen bonds : angle 6.38522 ( 1908) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3100 Ramachandran restraints generated. 1550 Oldfield, 0 Emsley, 1550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3100 Ramachandran restraints generated. 1550 Oldfield, 0 Emsley, 1550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 230 time to evaluate : 0.351 Fit side-chains REVERT: A 20 THR cc_start: 0.8450 (m) cc_final: 0.8145 (p) REVERT: A 38 LYS cc_start: 0.9182 (mtmm) cc_final: 0.8954 (mttm) REVERT: A 75 GLU cc_start: 0.8045 (mt-10) cc_final: 0.7709 (pm20) REVERT: A 77 ARG cc_start: 0.8328 (mtm-85) cc_final: 0.7908 (mtt-85) REVERT: A 195 PHE cc_start: 0.7768 (t80) cc_final: 0.7352 (m-80) REVERT: B 64 LYS cc_start: 0.7964 (mttp) cc_final: 0.7658 (mttt) REVERT: B 97 ASP cc_start: 0.8111 (m-30) cc_final: 0.7836 (p0) REVERT: B 101 GLN cc_start: 0.7684 (mm-40) cc_final: 0.7226 (mt0) REVERT: B 109 ARG cc_start: 0.8034 (ttt90) cc_final: 0.7755 (ttp80) REVERT: B 243 GLU cc_start: 0.7995 (mm-30) cc_final: 0.7436 (tp30) REVERT: B 252 MET cc_start: 0.6395 (mtp) cc_final: 0.5285 (tpt) REVERT: C 151 LYS cc_start: 0.8891 (pttp) cc_final: 0.8550 (ptmm) REVERT: C 195 PHE cc_start: 0.7983 (t80) cc_final: 0.7624 (t80) REVERT: C 280 LYS cc_start: 0.8040 (tttm) cc_final: 0.7745 (tttm) REVERT: C 293 ARG cc_start: 0.8405 (ttm-80) cc_final: 0.8068 (mtp180) REVERT: D 50 ARG cc_start: 0.7445 (mtp85) cc_final: 0.7138 (mtt-85) REVERT: D 66 TYR cc_start: 0.8167 (m-80) cc_final: 0.7840 (m-80) REVERT: D 71 ILE cc_start: 0.8012 (mm) cc_final: 0.7722 (tt) REVERT: D 151 LYS cc_start: 0.8457 (pttm) cc_final: 0.8129 (pttp) REVERT: D 195 PHE cc_start: 0.7429 (t80) cc_final: 0.7113 (m-80) REVERT: E 48 LYS cc_start: 0.7985 (tptt) cc_final: 0.7777 (tppt) REVERT: E 64 LYS cc_start: 0.8144 (mttt) cc_final: 0.7381 (mtpp) REVERT: E 67 GLU cc_start: 0.7076 (pt0) cc_final: 0.6800 (tt0) REVERT: E 86 ASP cc_start: 0.8100 (t0) cc_final: 0.7863 (t70) REVERT: E 95 SER cc_start: 0.7907 (m) cc_final: 0.7327 (p) REVERT: E 97 ASP cc_start: 0.7611 (p0) cc_final: 0.7287 (p0) REVERT: E 99 THR cc_start: 0.8118 (m) cc_final: 0.7866 (m) REVERT: E 101 GLN cc_start: 0.8060 (mm-40) cc_final: 0.7628 (mp10) REVERT: E 139 ASN cc_start: 0.8236 (m-40) cc_final: 0.7980 (m-40) REVERT: E 195 PHE cc_start: 0.7613 (t80) cc_final: 0.7007 (m-80) outliers start: 5 outliers final: 6 residues processed: 235 average time/residue: 0.7570 time to fit residues: 189.7782 Evaluate side-chains 145 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 139 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 ASP Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain E residue 214 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 98 optimal weight: 0.0040 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 0.2980 chunk 77 optimal weight: 8.9990 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 0.7980 overall best weight: 0.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 GLN B 200 ASN C 307 ASN E 152 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.132304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.099107 restraints weight = 18121.091| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 2.36 r_work: 0.3074 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2936 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.1414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 13593 Z= 0.112 Angle : 0.541 10.957 18418 Z= 0.278 Chirality : 0.043 0.153 2091 Planarity : 0.004 0.050 2252 Dihedral : 15.960 175.440 2266 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.22 % Allowed : 10.61 % Favored : 87.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.43 (0.22), residues: 1550 helix: 3.06 (0.21), residues: 535 sheet: 0.17 (0.26), residues: 455 loop : -0.45 (0.26), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 179 TYR 0.014 0.001 TYR A 102 PHE 0.010 0.001 PHE B 106 TRP 0.005 0.000 TRP C 213 HIS 0.003 0.001 HIS A 277 Details of bonding type rmsd covalent geometry : bond 0.00225 (13593) covalent geometry : angle 0.54097 (18418) hydrogen bonds : bond 0.05192 ( 608) hydrogen bonds : angle 4.40895 ( 1908) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3100 Ramachandran restraints generated. 1550 Oldfield, 0 Emsley, 1550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3100 Ramachandran restraints generated. 1550 Oldfield, 0 Emsley, 1550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 150 time to evaluate : 0.527 Fit side-chains REVERT: A 38 LYS cc_start: 0.9104 (mtmm) cc_final: 0.8863 (mttm) REVERT: A 48 LYS cc_start: 0.7592 (mttt) cc_final: 0.7297 (mmtt) REVERT: A 75 GLU cc_start: 0.8026 (mt-10) cc_final: 0.7686 (pm20) REVERT: A 77 ARG cc_start: 0.8408 (mtm-85) cc_final: 0.7955 (mpt-90) REVERT: A 195 PHE cc_start: 0.7704 (t80) cc_final: 0.7304 (m-80) REVERT: A 276 GLN cc_start: 0.9228 (OUTLIER) cc_final: 0.8690 (tt0) REVERT: A 280 LYS cc_start: 0.7453 (OUTLIER) cc_final: 0.7120 (ttpt) REVERT: B 64 LYS cc_start: 0.7957 (mttp) cc_final: 0.7635 (mttt) REVERT: B 97 ASP cc_start: 0.8077 (m-30) cc_final: 0.7798 (p0) REVERT: B 101 GLN cc_start: 0.7779 (mm-40) cc_final: 0.7353 (mt0) REVERT: B 109 ARG cc_start: 0.8159 (ttt90) cc_final: 0.7808 (ttp-170) REVERT: B 243 GLU cc_start: 0.7932 (mm-30) cc_final: 0.7570 (tp30) REVERT: B 252 MET cc_start: 0.6239 (mtp) cc_final: 0.5174 (tpt) REVERT: C 151 LYS cc_start: 0.8905 (pttp) cc_final: 0.8588 (ptmm) REVERT: C 238 PHE cc_start: 0.9082 (OUTLIER) cc_final: 0.8594 (m-80) REVERT: C 280 LYS cc_start: 0.7990 (tttm) cc_final: 0.7694 (tttm) REVERT: C 293 ARG cc_start: 0.8390 (ttm-80) cc_final: 0.8046 (mtp180) REVERT: D 14 GLU cc_start: 0.6904 (tp30) cc_final: 0.6591 (tp30) REVERT: D 50 ARG cc_start: 0.7411 (mtp85) cc_final: 0.7129 (mtt-85) REVERT: D 55 ASP cc_start: 0.7479 (t0) cc_final: 0.6927 (t0) REVERT: D 66 TYR cc_start: 0.8227 (m-80) cc_final: 0.7855 (m-80) REVERT: D 151 LYS cc_start: 0.8305 (pttm) cc_final: 0.7976 (pttp) REVERT: D 195 PHE cc_start: 0.7499 (t80) cc_final: 0.7102 (m-80) REVERT: E 55 ASP cc_start: 0.5850 (p0) cc_final: 0.5643 (p0) REVERT: E 67 GLU cc_start: 0.7014 (pt0) cc_final: 0.6710 (tt0) REVERT: E 95 SER cc_start: 0.8104 (m) cc_final: 0.7517 (p) REVERT: E 97 ASP cc_start: 0.7415 (p0) cc_final: 0.7050 (p0) REVERT: E 101 GLN cc_start: 0.7993 (mm-40) cc_final: 0.7590 (mp10) REVERT: E 139 ASN cc_start: 0.8351 (m-40) cc_final: 0.8034 (m-40) REVERT: E 195 PHE cc_start: 0.7675 (t80) cc_final: 0.7023 (m-80) outliers start: 31 outliers final: 14 residues processed: 171 average time/residue: 0.5933 time to fit residues: 109.4511 Evaluate side-chains 151 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 134 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 ASP Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 117 ARG Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 276 GLN Chi-restraints excluded: chain A residue 280 LYS Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain C residue 91 ASP Chi-restraints excluded: chain C residue 117 ARG Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 252 MET Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 214 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 70 optimal weight: 9.9990 chunk 137 optimal weight: 10.0000 chunk 4 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 15 optimal weight: 8.9990 chunk 35 optimal weight: 8.9990 chunk 79 optimal weight: 0.9980 chunk 101 optimal weight: 8.9990 chunk 25 optimal weight: 4.9990 chunk 110 optimal weight: 5.9990 chunk 59 optimal weight: 9.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 GLN B 277 HIS D 40 ASN D 307 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.124011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.089530 restraints weight = 18507.008| |-----------------------------------------------------------------------------| r_work (start): 0.3043 rms_B_bonded: 2.37 r_work: 0.2906 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2766 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8734 moved from start: 0.2264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 13593 Z= 0.246 Angle : 0.646 8.043 18418 Z= 0.335 Chirality : 0.045 0.153 2091 Planarity : 0.005 0.050 2252 Dihedral : 16.053 168.594 2265 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 2.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 3.15 % Allowed : 10.90 % Favored : 85.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.06 (0.22), residues: 1550 helix: 2.57 (0.21), residues: 535 sheet: 0.24 (0.25), residues: 445 loop : -0.72 (0.26), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 62 TYR 0.015 0.002 TYR D 66 PHE 0.020 0.002 PHE B 42 TRP 0.008 0.002 TRP E 213 HIS 0.005 0.002 HIS E 127 Details of bonding type rmsd covalent geometry : bond 0.00600 (13593) covalent geometry : angle 0.64597 (18418) hydrogen bonds : bond 0.08773 ( 608) hydrogen bonds : angle 4.55507 ( 1908) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3100 Ramachandran restraints generated. 1550 Oldfield, 0 Emsley, 1550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3100 Ramachandran restraints generated. 1550 Oldfield, 0 Emsley, 1550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 140 time to evaluate : 0.456 Fit side-chains REVERT: A 38 LYS cc_start: 0.9110 (mtmm) cc_final: 0.8842 (mttm) REVERT: A 75 GLU cc_start: 0.8105 (mt-10) cc_final: 0.7746 (pm20) REVERT: A 77 ARG cc_start: 0.8498 (mtm-85) cc_final: 0.8074 (mtt-85) REVERT: A 153 ASP cc_start: 0.7728 (p0) cc_final: 0.7468 (p0) REVERT: A 154 ASP cc_start: 0.7659 (m-30) cc_final: 0.7296 (m-30) REVERT: B 64 LYS cc_start: 0.7924 (mttp) cc_final: 0.7597 (mttt) REVERT: B 97 ASP cc_start: 0.8203 (m-30) cc_final: 0.7837 (p0) REVERT: B 101 GLN cc_start: 0.7791 (mm-40) cc_final: 0.7340 (mt0) REVERT: B 109 ARG cc_start: 0.8246 (ttt90) cc_final: 0.7868 (ttp80) REVERT: B 154 ASP cc_start: 0.7513 (m-30) cc_final: 0.7122 (m-30) REVERT: B 170 LYS cc_start: 0.8846 (OUTLIER) cc_final: 0.8633 (ttpt) REVERT: B 243 GLU cc_start: 0.8057 (mm-30) cc_final: 0.7522 (tp30) REVERT: B 252 MET cc_start: 0.6462 (mtp) cc_final: 0.5110 (mmt) REVERT: C 30 LEU cc_start: 0.9348 (OUTLIER) cc_final: 0.9087 (tp) REVERT: C 109 ARG cc_start: 0.8102 (OUTLIER) cc_final: 0.7828 (ttt-90) REVERT: C 151 LYS cc_start: 0.8940 (pttp) cc_final: 0.8624 (ptmm) REVERT: C 238 PHE cc_start: 0.9254 (OUTLIER) cc_final: 0.8629 (m-80) REVERT: D 14 GLU cc_start: 0.7031 (tp30) cc_final: 0.6737 (tp30) REVERT: D 50 ARG cc_start: 0.7456 (mtp85) cc_final: 0.7158 (mtt-85) REVERT: D 55 ASP cc_start: 0.7480 (t0) cc_final: 0.6939 (t0) REVERT: D 66 TYR cc_start: 0.8293 (m-80) cc_final: 0.7985 (m-80) REVERT: D 71 ILE cc_start: 0.8026 (mm) cc_final: 0.7784 (tt) REVERT: D 151 LYS cc_start: 0.8348 (pttm) cc_final: 0.8016 (pttp) REVERT: D 246 LEU cc_start: 0.7481 (tt) cc_final: 0.7039 (pp) REVERT: E 55 ASP cc_start: 0.5861 (p0) cc_final: 0.5646 (p0) REVERT: E 67 GLU cc_start: 0.7161 (pt0) cc_final: 0.6583 (mm-30) REVERT: E 95 SER cc_start: 0.8321 (m) cc_final: 0.7759 (p) REVERT: E 97 ASP cc_start: 0.7505 (p0) cc_final: 0.7245 (p0) REVERT: E 101 GLN cc_start: 0.7997 (mm-40) cc_final: 0.7514 (mp10) REVERT: E 109 ARG cc_start: 0.8474 (mtp180) cc_final: 0.7869 (mtp180) REVERT: E 139 ASN cc_start: 0.8559 (m-40) cc_final: 0.8332 (m-40) REVERT: E 195 PHE cc_start: 0.7602 (t80) cc_final: 0.6875 (m-80) outliers start: 44 outliers final: 21 residues processed: 170 average time/residue: 0.6206 time to fit residues: 113.8602 Evaluate side-chains 156 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 131 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 32 ASP Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 117 ARG Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain B residue 38 LYS Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 117 ARG Chi-restraints excluded: chain B residue 170 LYS Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 109 ARG Chi-restraints excluded: chain C residue 117 ARG Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 214 THR Chi-restraints excluded: chain D residue 219 THR Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 214 THR Chi-restraints excluded: chain E residue 305 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 129 optimal weight: 40.0000 chunk 138 optimal weight: 0.0870 chunk 152 optimal weight: 7.9990 chunk 69 optimal weight: 3.9990 chunk 144 optimal weight: 1.9990 chunk 99 optimal weight: 6.9990 chunk 55 optimal weight: 0.0470 chunk 52 optimal weight: 5.9990 chunk 137 optimal weight: 10.0000 chunk 65 optimal weight: 6.9990 chunk 104 optimal weight: 1.9990 overall best weight: 1.6262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 GLN D 40 ASN D 307 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.126614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.092352 restraints weight = 18181.505| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 2.37 r_work: 0.2965 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2827 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 moved from start: 0.2311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13593 Z= 0.135 Angle : 0.535 7.392 18418 Z= 0.277 Chirality : 0.042 0.139 2091 Planarity : 0.004 0.051 2252 Dihedral : 15.235 161.557 2265 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 2.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 2.87 % Allowed : 11.90 % Favored : 85.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.26 (0.22), residues: 1550 helix: 2.91 (0.21), residues: 535 sheet: 0.28 (0.25), residues: 445 loop : -0.73 (0.26), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 62 TYR 0.014 0.001 TYR D 102 PHE 0.020 0.001 PHE D 54 TRP 0.005 0.001 TRP A 160 HIS 0.003 0.001 HIS E 277 Details of bonding type rmsd covalent geometry : bond 0.00308 (13593) covalent geometry : angle 0.53512 (18418) hydrogen bonds : bond 0.06510 ( 608) hydrogen bonds : angle 4.20226 ( 1908) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3100 Ramachandran restraints generated. 1550 Oldfield, 0 Emsley, 1550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3100 Ramachandran restraints generated. 1550 Oldfield, 0 Emsley, 1550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 139 time to evaluate : 0.477 Fit side-chains REVERT: A 38 LYS cc_start: 0.9147 (mtmm) cc_final: 0.8873 (mttm) REVERT: A 75 GLU cc_start: 0.8078 (mt-10) cc_final: 0.7818 (pm20) REVERT: A 77 ARG cc_start: 0.8496 (mtm-85) cc_final: 0.8132 (mtt-85) REVERT: A 153 ASP cc_start: 0.7664 (p0) cc_final: 0.7419 (p0) REVERT: A 154 ASP cc_start: 0.7538 (m-30) cc_final: 0.7194 (m-30) REVERT: A 187 GLN cc_start: 0.9063 (OUTLIER) cc_final: 0.8835 (mt0) REVERT: A 276 GLN cc_start: 0.9294 (OUTLIER) cc_final: 0.8904 (tt0) REVERT: B 31 ASP cc_start: 0.8828 (t0) cc_final: 0.8567 (t70) REVERT: B 64 LYS cc_start: 0.7968 (mttp) cc_final: 0.7620 (mttt) REVERT: B 97 ASP cc_start: 0.8160 (m-30) cc_final: 0.7858 (p0) REVERT: B 101 GLN cc_start: 0.7752 (mm-40) cc_final: 0.7357 (mt0) REVERT: B 109 ARG cc_start: 0.8159 (ttt90) cc_final: 0.7797 (ttp80) REVERT: B 154 ASP cc_start: 0.7459 (m-30) cc_final: 0.7057 (m-30) REVERT: B 170 LYS cc_start: 0.8853 (OUTLIER) cc_final: 0.8647 (ttpt) REVERT: B 243 GLU cc_start: 0.8016 (mm-30) cc_final: 0.7614 (tp30) REVERT: B 252 MET cc_start: 0.6429 (mtp) cc_final: 0.5097 (mmt) REVERT: C 64 LYS cc_start: 0.7765 (mtpt) cc_final: 0.7327 (mttt) REVERT: C 151 LYS cc_start: 0.8908 (pttp) cc_final: 0.8585 (ptmm) REVERT: C 162 ILE cc_start: 0.9205 (OUTLIER) cc_final: 0.8923 (mp) REVERT: C 238 PHE cc_start: 0.9209 (OUTLIER) cc_final: 0.8670 (m-80) REVERT: C 243 GLU cc_start: 0.8473 (mm-30) cc_final: 0.8194 (tp30) REVERT: C 252 MET cc_start: 0.6833 (OUTLIER) cc_final: 0.5625 (mtp) REVERT: D 14 GLU cc_start: 0.6872 (tp30) cc_final: 0.6593 (tp30) REVERT: D 50 ARG cc_start: 0.7395 (mtp85) cc_final: 0.7081 (mtt-85) REVERT: D 55 ASP cc_start: 0.7454 (t0) cc_final: 0.6908 (t0) REVERT: D 66 TYR cc_start: 0.8284 (m-80) cc_final: 0.7938 (m-80) REVERT: D 71 ILE cc_start: 0.7946 (mm) cc_final: 0.7722 (tt) REVERT: D 151 LYS cc_start: 0.8318 (pttm) cc_final: 0.7984 (pttp) REVERT: D 195 PHE cc_start: 0.7463 (t80) cc_final: 0.7034 (m-80) REVERT: E 67 GLU cc_start: 0.7030 (pt0) cc_final: 0.6434 (mm-30) REVERT: E 95 SER cc_start: 0.8231 (m) cc_final: 0.7644 (p) REVERT: E 97 ASP cc_start: 0.7380 (p0) cc_final: 0.7084 (p0) REVERT: E 101 GLN cc_start: 0.8023 (mm-40) cc_final: 0.7534 (mp10) REVERT: E 109 ARG cc_start: 0.8400 (mtp180) cc_final: 0.7892 (mtp180) REVERT: E 139 ASN cc_start: 0.8560 (m-40) cc_final: 0.8336 (m-40) REVERT: E 195 PHE cc_start: 0.7564 (t80) cc_final: 0.6884 (m-80) outliers start: 40 outliers final: 23 residues processed: 165 average time/residue: 0.6064 time to fit residues: 108.0380 Evaluate side-chains 159 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 130 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 32 ASP Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 117 ARG Chi-restraints excluded: chain A residue 187 GLN Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 276 GLN Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 117 ARG Chi-restraints excluded: chain B residue 170 LYS Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain C residue 14 GLU Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 104 GLU Chi-restraints excluded: chain C residue 117 ARG Chi-restraints excluded: chain C residue 162 ILE Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 252 MET Chi-restraints excluded: chain D residue 40 ASN Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 214 THR Chi-restraints excluded: chain E residue 38 LYS Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 214 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 146 optimal weight: 2.9990 chunk 4 optimal weight: 0.0670 chunk 46 optimal weight: 0.8980 chunk 91 optimal weight: 0.0870 chunk 129 optimal weight: 30.0000 chunk 131 optimal weight: 6.9990 chunk 92 optimal weight: 0.8980 chunk 1 optimal weight: 4.9990 chunk 49 optimal weight: 4.9990 chunk 52 optimal weight: 6.9990 chunk 99 optimal weight: 6.9990 overall best weight: 0.9898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 GLN D 307 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.128259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.094187 restraints weight = 18386.659| |-----------------------------------------------------------------------------| r_work (start): 0.3114 rms_B_bonded: 2.37 r_work: 0.2985 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2847 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8649 moved from start: 0.2394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 13593 Z= 0.111 Angle : 0.511 7.986 18418 Z= 0.263 Chirality : 0.042 0.139 2091 Planarity : 0.004 0.051 2252 Dihedral : 14.388 154.336 2265 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 3.01 % Allowed : 11.90 % Favored : 85.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.43 (0.22), residues: 1550 helix: 3.02 (0.21), residues: 540 sheet: 0.22 (0.24), residues: 480 loop : -0.53 (0.27), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 62 TYR 0.015 0.001 TYR D 102 PHE 0.011 0.001 PHE E 54 TRP 0.004 0.001 TRP C 47 HIS 0.003 0.001 HIS E 277 Details of bonding type rmsd covalent geometry : bond 0.00238 (13593) covalent geometry : angle 0.51053 (18418) hydrogen bonds : bond 0.05608 ( 608) hydrogen bonds : angle 4.00454 ( 1908) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3100 Ramachandran restraints generated. 1550 Oldfield, 0 Emsley, 1550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3100 Ramachandran restraints generated. 1550 Oldfield, 0 Emsley, 1550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 139 time to evaluate : 0.497 Fit side-chains REVERT: A 38 LYS cc_start: 0.9052 (mtmm) cc_final: 0.8777 (mttm) REVERT: A 75 GLU cc_start: 0.8060 (mt-10) cc_final: 0.7772 (pm20) REVERT: A 77 ARG cc_start: 0.8454 (mtm-85) cc_final: 0.8062 (mpt-90) REVERT: A 151 LYS cc_start: 0.9023 (OUTLIER) cc_final: 0.8735 (ttpp) REVERT: A 153 ASP cc_start: 0.7609 (p0) cc_final: 0.7351 (p0) REVERT: A 154 ASP cc_start: 0.7515 (m-30) cc_final: 0.7061 (m-30) REVERT: A 187 GLN cc_start: 0.9029 (OUTLIER) cc_final: 0.8603 (mt0) REVERT: B 31 ASP cc_start: 0.8802 (t0) cc_final: 0.8571 (t70) REVERT: B 64 LYS cc_start: 0.7937 (mttp) cc_final: 0.7570 (mttt) REVERT: B 97 ASP cc_start: 0.8157 (m-30) cc_final: 0.7867 (p0) REVERT: B 101 GLN cc_start: 0.7705 (mm-40) cc_final: 0.7304 (mt0) REVERT: B 109 ARG cc_start: 0.8120 (ttt90) cc_final: 0.7696 (ttp-170) REVERT: B 154 ASP cc_start: 0.7477 (m-30) cc_final: 0.7077 (m-30) REVERT: B 170 LYS cc_start: 0.8870 (OUTLIER) cc_final: 0.8644 (ttpt) REVERT: B 243 GLU cc_start: 0.8022 (mm-30) cc_final: 0.7613 (tp30) REVERT: B 252 MET cc_start: 0.6415 (mtp) cc_final: 0.5198 (tpt) REVERT: C 64 LYS cc_start: 0.7777 (mtpt) cc_final: 0.7386 (mtpt) REVERT: C 151 LYS cc_start: 0.8906 (pttp) cc_final: 0.8578 (ptmm) REVERT: C 238 PHE cc_start: 0.9147 (OUTLIER) cc_final: 0.8695 (m-80) REVERT: C 243 GLU cc_start: 0.8418 (mm-30) cc_final: 0.8194 (tp30) REVERT: C 252 MET cc_start: 0.6788 (OUTLIER) cc_final: 0.5723 (mtp) REVERT: D 14 GLU cc_start: 0.6801 (tp30) cc_final: 0.6503 (tp30) REVERT: D 50 ARG cc_start: 0.7360 (mtp85) cc_final: 0.7038 (mtt-85) REVERT: D 55 ASP cc_start: 0.7389 (t0) cc_final: 0.6892 (t0) REVERT: D 66 TYR cc_start: 0.8213 (m-80) cc_final: 0.7827 (m-80) REVERT: D 151 LYS cc_start: 0.8251 (pttm) cc_final: 0.7940 (pttp) REVERT: D 180 LEU cc_start: 0.7464 (OUTLIER) cc_final: 0.7201 (mt) REVERT: D 195 PHE cc_start: 0.7509 (t80) cc_final: 0.7032 (m-80) REVERT: D 246 LEU cc_start: 0.7300 (OUTLIER) cc_final: 0.6892 (pp) REVERT: E 67 GLU cc_start: 0.6991 (pt0) cc_final: 0.6410 (mm-30) REVERT: E 95 SER cc_start: 0.8096 (m) cc_final: 0.7476 (p) REVERT: E 97 ASP cc_start: 0.7358 (p0) cc_final: 0.7027 (p0) REVERT: E 101 GLN cc_start: 0.7945 (mm-40) cc_final: 0.7439 (mp10) REVERT: E 109 ARG cc_start: 0.8320 (mtp180) cc_final: 0.7851 (mtp180) REVERT: E 139 ASN cc_start: 0.8521 (m-40) cc_final: 0.8301 (m-40) REVERT: E 195 PHE cc_start: 0.7535 (t80) cc_final: 0.6866 (m-80) outliers start: 42 outliers final: 20 residues processed: 170 average time/residue: 0.5976 time to fit residues: 109.7851 Evaluate side-chains 161 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 134 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 117 ARG Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 151 LYS Chi-restraints excluded: chain A residue 187 GLN Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 117 ARG Chi-restraints excluded: chain B residue 170 LYS Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain C residue 14 GLU Chi-restraints excluded: chain C residue 104 GLU Chi-restraints excluded: chain C residue 117 ARG Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 252 MET Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 214 THR Chi-restraints excluded: chain D residue 246 LEU Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 214 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 15 optimal weight: 0.6980 chunk 107 optimal weight: 6.9990 chunk 6 optimal weight: 0.3980 chunk 111 optimal weight: 5.9990 chunk 135 optimal weight: 2.9990 chunk 72 optimal weight: 7.9990 chunk 109 optimal weight: 6.9990 chunk 4 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 chunk 50 optimal weight: 5.9990 chunk 56 optimal weight: 1.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 GLN D 40 ASN D 307 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.127113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.092789 restraints weight = 18395.061| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 2.38 r_work: 0.2965 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2826 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8670 moved from start: 0.2500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 13593 Z= 0.136 Angle : 0.528 8.155 18418 Z= 0.271 Chirality : 0.042 0.138 2091 Planarity : 0.004 0.051 2252 Dihedral : 13.953 146.204 2263 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 2.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 3.37 % Allowed : 12.62 % Favored : 84.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.35 (0.22), residues: 1550 helix: 2.91 (0.21), residues: 540 sheet: 0.22 (0.24), residues: 480 loop : -0.55 (0.27), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 62 TYR 0.016 0.001 TYR D 102 PHE 0.026 0.001 PHE D 54 TRP 0.004 0.001 TRP D 47 HIS 0.003 0.001 HIS E 277 Details of bonding type rmsd covalent geometry : bond 0.00319 (13593) covalent geometry : angle 0.52764 (18418) hydrogen bonds : bond 0.06144 ( 608) hydrogen bonds : angle 4.00817 ( 1908) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3100 Ramachandran restraints generated. 1550 Oldfield, 0 Emsley, 1550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3100 Ramachandran restraints generated. 1550 Oldfield, 0 Emsley, 1550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 135 time to evaluate : 0.494 Fit side-chains REVERT: A 38 LYS cc_start: 0.9056 (mtmm) cc_final: 0.8715 (mttm) REVERT: A 75 GLU cc_start: 0.8053 (mt-10) cc_final: 0.7782 (pm20) REVERT: A 77 ARG cc_start: 0.8464 (mtm-85) cc_final: 0.8099 (mpt-90) REVERT: A 151 LYS cc_start: 0.9020 (OUTLIER) cc_final: 0.8642 (ttpp) REVERT: A 153 ASP cc_start: 0.7597 (p0) cc_final: 0.7382 (p0) REVERT: A 154 ASP cc_start: 0.7496 (m-30) cc_final: 0.7046 (m-30) REVERT: A 179 ARG cc_start: 0.6452 (mmt-90) cc_final: 0.6102 (mmp80) REVERT: A 187 GLN cc_start: 0.9034 (OUTLIER) cc_final: 0.8713 (mt0) REVERT: B 64 LYS cc_start: 0.7933 (mttp) cc_final: 0.7553 (mttt) REVERT: B 97 ASP cc_start: 0.8147 (m-30) cc_final: 0.7870 (p0) REVERT: B 101 GLN cc_start: 0.7716 (mm-40) cc_final: 0.7221 (mt0) REVERT: B 109 ARG cc_start: 0.8136 (ttt90) cc_final: 0.7730 (ttp-170) REVERT: B 154 ASP cc_start: 0.7487 (m-30) cc_final: 0.7044 (m-30) REVERT: B 170 LYS cc_start: 0.8872 (OUTLIER) cc_final: 0.8645 (ttpt) REVERT: B 243 GLU cc_start: 0.8043 (mm-30) cc_final: 0.7604 (tp30) REVERT: B 252 MET cc_start: 0.6416 (mtp) cc_final: 0.5062 (mmt) REVERT: C 91 ASP cc_start: 0.8348 (t0) cc_final: 0.8103 (t0) REVERT: C 151 LYS cc_start: 0.8927 (pttp) cc_final: 0.8604 (ptmm) REVERT: C 162 ILE cc_start: 0.9217 (OUTLIER) cc_final: 0.8935 (mp) REVERT: C 238 PHE cc_start: 0.9191 (OUTLIER) cc_final: 0.8740 (m-80) REVERT: C 252 MET cc_start: 0.6803 (OUTLIER) cc_final: 0.5678 (mtp) REVERT: D 14 GLU cc_start: 0.6848 (tp30) cc_final: 0.6527 (tp30) REVERT: D 50 ARG cc_start: 0.7346 (mtp85) cc_final: 0.7025 (mtt-85) REVERT: D 55 ASP cc_start: 0.7418 (t0) cc_final: 0.6884 (t0) REVERT: D 66 TYR cc_start: 0.8221 (m-80) cc_final: 0.7859 (m-80) REVERT: D 151 LYS cc_start: 0.8285 (pttm) cc_final: 0.7971 (pttp) REVERT: D 180 LEU cc_start: 0.7430 (OUTLIER) cc_final: 0.7163 (mt) REVERT: D 195 PHE cc_start: 0.7528 (t80) cc_final: 0.7001 (m-80) REVERT: D 246 LEU cc_start: 0.7351 (OUTLIER) cc_final: 0.6945 (pp) REVERT: E 67 GLU cc_start: 0.6998 (pt0) cc_final: 0.6399 (mm-30) REVERT: E 101 GLN cc_start: 0.7970 (mm-40) cc_final: 0.7458 (mp10) REVERT: E 109 ARG cc_start: 0.8372 (mtp180) cc_final: 0.7933 (mtp180) REVERT: E 139 ASN cc_start: 0.8530 (m-40) cc_final: 0.8306 (m-40) REVERT: E 195 PHE cc_start: 0.7551 (t80) cc_final: 0.6869 (m-80) REVERT: E 252 MET cc_start: 0.6407 (tpt) cc_final: 0.5977 (ttt) outliers start: 47 outliers final: 26 residues processed: 170 average time/residue: 0.6359 time to fit residues: 116.8954 Evaluate side-chains 161 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 127 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 117 ARG Chi-restraints excluded: chain A residue 151 LYS Chi-restraints excluded: chain A residue 187 GLN Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 117 ARG Chi-restraints excluded: chain B residue 170 LYS Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain C residue 14 GLU Chi-restraints excluded: chain C residue 104 GLU Chi-restraints excluded: chain C residue 109 ARG Chi-restraints excluded: chain C residue 117 ARG Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 162 ILE Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 252 MET Chi-restraints excluded: chain D residue 40 ASN Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 214 THR Chi-restraints excluded: chain D residue 219 THR Chi-restraints excluded: chain D residue 246 LEU Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 214 THR Chi-restraints excluded: chain E residue 282 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 136 optimal weight: 8.9990 chunk 121 optimal weight: 8.9990 chunk 142 optimal weight: 0.9990 chunk 118 optimal weight: 4.9990 chunk 111 optimal weight: 8.9990 chunk 58 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 77 optimal weight: 4.9990 chunk 100 optimal weight: 4.9990 chunk 25 optimal weight: 2.9990 chunk 12 optimal weight: 7.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 GLN D 40 ASN D 307 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.124342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.089648 restraints weight = 18213.039| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 2.38 r_work: 0.2919 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2780 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8725 moved from start: 0.2687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 13593 Z= 0.212 Angle : 0.601 8.983 18418 Z= 0.310 Chirality : 0.044 0.144 2091 Planarity : 0.005 0.050 2252 Dihedral : 14.435 137.062 2263 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 2.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 3.66 % Allowed : 12.54 % Favored : 83.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.12 (0.22), residues: 1550 helix: 2.67 (0.21), residues: 540 sheet: 0.23 (0.24), residues: 445 loop : -0.73 (0.26), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 62 TYR 0.017 0.002 TYR D 102 PHE 0.014 0.001 PHE E 37 TRP 0.008 0.001 TRP E 213 HIS 0.004 0.001 HIS E 127 Details of bonding type rmsd covalent geometry : bond 0.00526 (13593) covalent geometry : angle 0.60132 (18418) hydrogen bonds : bond 0.07856 ( 608) hydrogen bonds : angle 4.26944 ( 1908) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3100 Ramachandran restraints generated. 1550 Oldfield, 0 Emsley, 1550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3100 Ramachandran restraints generated. 1550 Oldfield, 0 Emsley, 1550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 129 time to evaluate : 0.502 Fit side-chains REVERT: A 38 LYS cc_start: 0.9157 (mtmm) cc_final: 0.8808 (mttm) REVERT: A 75 GLU cc_start: 0.8132 (mt-10) cc_final: 0.7866 (pm20) REVERT: A 77 ARG cc_start: 0.8471 (mtm-85) cc_final: 0.8116 (mpt-90) REVERT: A 151 LYS cc_start: 0.9006 (OUTLIER) cc_final: 0.8603 (ttpp) REVERT: A 153 ASP cc_start: 0.7661 (p0) cc_final: 0.7449 (p0) REVERT: A 154 ASP cc_start: 0.7486 (m-30) cc_final: 0.7077 (m-30) REVERT: A 179 ARG cc_start: 0.6555 (mmt-90) cc_final: 0.6137 (mmp80) REVERT: A 187 GLN cc_start: 0.9060 (OUTLIER) cc_final: 0.8833 (mt0) REVERT: B 64 LYS cc_start: 0.7917 (mttp) cc_final: 0.7575 (mttt) REVERT: B 101 GLN cc_start: 0.7768 (mm-40) cc_final: 0.7280 (mt0) REVERT: B 109 ARG cc_start: 0.8119 (ttt90) cc_final: 0.7793 (ttp80) REVERT: B 154 ASP cc_start: 0.7448 (m-30) cc_final: 0.7041 (m-30) REVERT: B 170 LYS cc_start: 0.8895 (OUTLIER) cc_final: 0.8689 (ttpt) REVERT: B 243 GLU cc_start: 0.8098 (mm-30) cc_final: 0.7629 (tp30) REVERT: B 252 MET cc_start: 0.6405 (mtp) cc_final: 0.4984 (mmt) REVERT: C 91 ASP cc_start: 0.8436 (t0) cc_final: 0.8150 (t0) REVERT: C 109 ARG cc_start: 0.8050 (OUTLIER) cc_final: 0.7834 (ttt180) REVERT: C 151 LYS cc_start: 0.8928 (pttp) cc_final: 0.8590 (ptmm) REVERT: C 162 ILE cc_start: 0.9229 (OUTLIER) cc_final: 0.8940 (mp) REVERT: C 238 PHE cc_start: 0.9280 (OUTLIER) cc_final: 0.8692 (m-80) REVERT: D 14 GLU cc_start: 0.6828 (tp30) cc_final: 0.6564 (tp30) REVERT: D 50 ARG cc_start: 0.7357 (mtp85) cc_final: 0.7043 (mtt-85) REVERT: D 55 ASP cc_start: 0.7387 (t0) cc_final: 0.6818 (t0) REVERT: D 63 VAL cc_start: 0.8541 (m) cc_final: 0.8245 (p) REVERT: D 66 TYR cc_start: 0.8295 (m-80) cc_final: 0.7930 (m-80) REVERT: D 71 ILE cc_start: 0.7987 (mm) cc_final: 0.7768 (tt) REVERT: D 151 LYS cc_start: 0.8313 (pttm) cc_final: 0.7984 (pttp) REVERT: E 67 GLU cc_start: 0.7190 (pt0) cc_final: 0.6532 (mm-30) REVERT: E 101 GLN cc_start: 0.7975 (mm-40) cc_final: 0.7522 (mp10) REVERT: E 109 ARG cc_start: 0.8398 (mtp180) cc_final: 0.7967 (mtp180) REVERT: E 252 MET cc_start: 0.6441 (tpt) cc_final: 0.6040 (ttt) outliers start: 51 outliers final: 31 residues processed: 165 average time/residue: 0.6882 time to fit residues: 122.5830 Evaluate side-chains 164 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 127 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 83 ASN Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 117 ARG Chi-restraints excluded: chain A residue 151 LYS Chi-restraints excluded: chain A residue 187 GLN Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 117 ARG Chi-restraints excluded: chain B residue 170 LYS Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain C residue 104 GLU Chi-restraints excluded: chain C residue 109 ARG Chi-restraints excluded: chain C residue 117 ARG Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 162 ILE Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain D residue 40 ASN Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 214 THR Chi-restraints excluded: chain D residue 219 THR Chi-restraints excluded: chain D residue 241 LEU Chi-restraints excluded: chain E residue 38 LYS Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 146 LEU Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 214 THR Chi-restraints excluded: chain E residue 282 GLU Chi-restraints excluded: chain E residue 305 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 138 optimal weight: 3.9990 chunk 10 optimal weight: 8.9990 chunk 55 optimal weight: 0.6980 chunk 26 optimal weight: 3.9990 chunk 15 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 132 optimal weight: 10.0000 chunk 128 optimal weight: 0.3980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 GLN D 40 ASN D 307 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.127742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.093502 restraints weight = 18342.452| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 2.38 r_work: 0.2979 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2842 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8654 moved from start: 0.2675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 13593 Z= 0.110 Angle : 0.522 8.506 18418 Z= 0.268 Chirality : 0.042 0.139 2091 Planarity : 0.004 0.051 2252 Dihedral : 13.663 127.542 2263 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 2.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 3.01 % Allowed : 13.48 % Favored : 83.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.42 (0.22), residues: 1550 helix: 3.02 (0.21), residues: 540 sheet: 0.25 (0.24), residues: 480 loop : -0.58 (0.27), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 50 TYR 0.019 0.001 TYR D 102 PHE 0.029 0.001 PHE D 54 TRP 0.006 0.001 TRP A 213 HIS 0.003 0.001 HIS E 277 Details of bonding type rmsd covalent geometry : bond 0.00232 (13593) covalent geometry : angle 0.52237 (18418) hydrogen bonds : bond 0.05657 ( 608) hydrogen bonds : angle 3.96825 ( 1908) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3100 Ramachandran restraints generated. 1550 Oldfield, 0 Emsley, 1550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3100 Ramachandran restraints generated. 1550 Oldfield, 0 Emsley, 1550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 135 time to evaluate : 0.542 Fit side-chains REVERT: A 38 LYS cc_start: 0.9106 (mtmm) cc_final: 0.8740 (mttm) REVERT: A 75 GLU cc_start: 0.8132 (mt-10) cc_final: 0.7861 (pm20) REVERT: A 77 ARG cc_start: 0.8444 (mtm-85) cc_final: 0.8034 (mpt-90) REVERT: A 151 LYS cc_start: 0.9022 (OUTLIER) cc_final: 0.8653 (ttpp) REVERT: A 153 ASP cc_start: 0.7562 (p0) cc_final: 0.7315 (p0) REVERT: A 154 ASP cc_start: 0.7512 (m-30) cc_final: 0.7023 (m-30) REVERT: A 179 ARG cc_start: 0.6606 (mmt-90) cc_final: 0.6237 (mmp80) REVERT: A 187 GLN cc_start: 0.9026 (OUTLIER) cc_final: 0.8797 (mt0) REVERT: B 64 LYS cc_start: 0.7906 (mttp) cc_final: 0.7551 (mttt) REVERT: B 101 GLN cc_start: 0.7707 (mm-40) cc_final: 0.7213 (mt0) REVERT: B 109 ARG cc_start: 0.8083 (ttt90) cc_final: 0.7710 (ttp-170) REVERT: B 154 ASP cc_start: 0.7448 (m-30) cc_final: 0.7029 (m-30) REVERT: B 170 LYS cc_start: 0.8864 (OUTLIER) cc_final: 0.8637 (ttpt) REVERT: B 243 GLU cc_start: 0.8045 (mm-30) cc_final: 0.7603 (tp30) REVERT: B 252 MET cc_start: 0.6429 (mtp) cc_final: 0.5029 (mmt) REVERT: C 91 ASP cc_start: 0.8342 (t0) cc_final: 0.8071 (t0) REVERT: C 151 LYS cc_start: 0.8916 (pttp) cc_final: 0.8582 (ptmm) REVERT: C 162 ILE cc_start: 0.9199 (OUTLIER) cc_final: 0.8911 (mp) REVERT: C 243 GLU cc_start: 0.8424 (mm-30) cc_final: 0.8174 (tp30) REVERT: C 252 MET cc_start: 0.6847 (OUTLIER) cc_final: 0.5732 (mtp) REVERT: C 280 LYS cc_start: 0.8355 (ttpp) cc_final: 0.7765 (tttm) REVERT: D 14 GLU cc_start: 0.6800 (tp30) cc_final: 0.6496 (tp30) REVERT: D 50 ARG cc_start: 0.7285 (mtp85) cc_final: 0.6948 (mtt-85) REVERT: D 55 ASP cc_start: 0.7375 (t0) cc_final: 0.6840 (t0) REVERT: D 63 VAL cc_start: 0.8500 (m) cc_final: 0.8205 (p) REVERT: D 66 TYR cc_start: 0.8233 (m-80) cc_final: 0.7844 (m-80) REVERT: D 151 LYS cc_start: 0.8268 (pttm) cc_final: 0.7953 (pttp) REVERT: D 180 LEU cc_start: 0.7417 (OUTLIER) cc_final: 0.7152 (mt) REVERT: D 195 PHE cc_start: 0.7534 (t80) cc_final: 0.6990 (m-80) REVERT: D 246 LEU cc_start: 0.7334 (OUTLIER) cc_final: 0.7060 (pp) REVERT: E 67 GLU cc_start: 0.7125 (pt0) cc_final: 0.6441 (mm-30) REVERT: E 101 GLN cc_start: 0.7988 (mm-40) cc_final: 0.7479 (mp10) REVERT: E 109 ARG cc_start: 0.8278 (mtp180) cc_final: 0.7884 (mtp180) REVERT: E 139 ASN cc_start: 0.8533 (m-40) cc_final: 0.8095 (t0) REVERT: E 195 PHE cc_start: 0.7521 (t80) cc_final: 0.6836 (m-80) REVERT: E 252 MET cc_start: 0.6292 (tpt) cc_final: 0.5885 (ttt) outliers start: 42 outliers final: 22 residues processed: 162 average time/residue: 0.6864 time to fit residues: 119.9574 Evaluate side-chains 156 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 127 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 117 ARG Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 151 LYS Chi-restraints excluded: chain A residue 187 GLN Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 117 ARG Chi-restraints excluded: chain B residue 170 LYS Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain C residue 14 GLU Chi-restraints excluded: chain C residue 104 GLU Chi-restraints excluded: chain C residue 117 ARG Chi-restraints excluded: chain C residue 162 ILE Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 252 MET Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain D residue 40 ASN Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 214 THR Chi-restraints excluded: chain D residue 241 LEU Chi-restraints excluded: chain D residue 246 LEU Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 214 THR Chi-restraints excluded: chain E residue 305 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 18 optimal weight: 2.9990 chunk 89 optimal weight: 6.9990 chunk 66 optimal weight: 0.9990 chunk 24 optimal weight: 0.7980 chunk 80 optimal weight: 5.9990 chunk 98 optimal weight: 0.0070 chunk 3 optimal weight: 8.9990 chunk 79 optimal weight: 5.9990 chunk 35 optimal weight: 0.3980 chunk 92 optimal weight: 0.9990 chunk 143 optimal weight: 3.9990 overall best weight: 0.6402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 GLN D 40 ASN D 307 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.129177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.095192 restraints weight = 18399.786| |-----------------------------------------------------------------------------| r_work (start): 0.3131 rms_B_bonded: 2.38 r_work: 0.3003 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2867 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 moved from start: 0.2715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 13593 Z= 0.102 Angle : 0.507 8.307 18418 Z= 0.261 Chirality : 0.042 0.138 2091 Planarity : 0.004 0.051 2252 Dihedral : 13.123 123.383 2262 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.37 % Allowed : 14.19 % Favored : 83.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.52 (0.22), residues: 1550 helix: 3.12 (0.21), residues: 540 sheet: 0.31 (0.24), residues: 480 loop : -0.55 (0.28), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 50 TYR 0.019 0.001 TYR D 102 PHE 0.027 0.001 PHE D 54 TRP 0.005 0.001 TRP C 47 HIS 0.003 0.001 HIS E 277 Details of bonding type rmsd covalent geometry : bond 0.00214 (13593) covalent geometry : angle 0.50735 (18418) hydrogen bonds : bond 0.05002 ( 608) hydrogen bonds : angle 3.83379 ( 1908) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3100 Ramachandran restraints generated. 1550 Oldfield, 0 Emsley, 1550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3100 Ramachandran restraints generated. 1550 Oldfield, 0 Emsley, 1550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 135 time to evaluate : 0.317 Fit side-chains REVERT: A 38 LYS cc_start: 0.9082 (mtmm) cc_final: 0.8717 (mttm) REVERT: A 75 GLU cc_start: 0.8108 (mt-10) cc_final: 0.7857 (pm20) REVERT: A 77 ARG cc_start: 0.8441 (mtm-85) cc_final: 0.8039 (mpt-90) REVERT: A 151 LYS cc_start: 0.8988 (OUTLIER) cc_final: 0.8666 (ttpp) REVERT: A 154 ASP cc_start: 0.7472 (m-30) cc_final: 0.7019 (m-30) REVERT: A 179 ARG cc_start: 0.6617 (mmt-90) cc_final: 0.6248 (mmp80) REVERT: A 187 GLN cc_start: 0.9028 (OUTLIER) cc_final: 0.8793 (mt0) REVERT: B 64 LYS cc_start: 0.7935 (mttp) cc_final: 0.7574 (mttt) REVERT: B 88 ASP cc_start: 0.7427 (OUTLIER) cc_final: 0.7181 (m-30) REVERT: B 101 GLN cc_start: 0.7677 (mm-40) cc_final: 0.7231 (mt0) REVERT: B 109 ARG cc_start: 0.8045 (ttt90) cc_final: 0.7664 (ttp-170) REVERT: B 154 ASP cc_start: 0.7441 (m-30) cc_final: 0.7027 (m-30) REVERT: B 243 GLU cc_start: 0.7988 (mm-30) cc_final: 0.7585 (tp30) REVERT: B 252 MET cc_start: 0.6364 (mtp) cc_final: 0.4996 (mmt) REVERT: C 91 ASP cc_start: 0.8296 (t0) cc_final: 0.8021 (t0) REVERT: C 151 LYS cc_start: 0.8921 (pttp) cc_final: 0.8597 (ptmm) REVERT: C 162 ILE cc_start: 0.9196 (OUTLIER) cc_final: 0.8915 (mp) REVERT: C 243 GLU cc_start: 0.8387 (mm-30) cc_final: 0.8177 (tp30) REVERT: C 252 MET cc_start: 0.6807 (OUTLIER) cc_final: 0.5680 (mtp) REVERT: C 280 LYS cc_start: 0.8230 (ttpp) cc_final: 0.7617 (tttm) REVERT: D 50 ARG cc_start: 0.7306 (mtp85) cc_final: 0.6975 (mtt-85) REVERT: D 55 ASP cc_start: 0.7446 (t0) cc_final: 0.6958 (t0) REVERT: D 63 VAL cc_start: 0.8484 (m) cc_final: 0.8187 (p) REVERT: D 66 TYR cc_start: 0.8185 (m-80) cc_final: 0.7800 (m-80) REVERT: D 151 LYS cc_start: 0.8293 (pttm) cc_final: 0.7981 (pttp) REVERT: D 180 LEU cc_start: 0.7407 (OUTLIER) cc_final: 0.7135 (mt) REVERT: D 195 PHE cc_start: 0.7541 (t80) cc_final: 0.6992 (m-80) REVERT: D 246 LEU cc_start: 0.7320 (OUTLIER) cc_final: 0.7009 (pp) REVERT: E 67 GLU cc_start: 0.7128 (pt0) cc_final: 0.6459 (mm-30) REVERT: E 101 GLN cc_start: 0.7963 (mm-40) cc_final: 0.7451 (mp10) REVERT: E 109 ARG cc_start: 0.8212 (mtp180) cc_final: 0.7827 (mtp180) REVERT: E 139 ASN cc_start: 0.8492 (m-40) cc_final: 0.8157 (m-40) REVERT: E 195 PHE cc_start: 0.7546 (t80) cc_final: 0.6868 (m-80) REVERT: E 252 MET cc_start: 0.6297 (tpt) cc_final: 0.5839 (ttm) outliers start: 33 outliers final: 18 residues processed: 160 average time/residue: 0.6810 time to fit residues: 117.6344 Evaluate side-chains 155 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 130 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 117 ARG Chi-restraints excluded: chain A residue 151 LYS Chi-restraints excluded: chain A residue 187 GLN Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 117 ARG Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain C residue 117 ARG Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 162 ILE Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 252 MET Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain D residue 40 ASN Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 214 THR Chi-restraints excluded: chain D residue 241 LEU Chi-restraints excluded: chain D residue 246 LEU Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 214 THR Chi-restraints excluded: chain E residue 305 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 1 optimal weight: 4.9990 chunk 17 optimal weight: 9.9990 chunk 30 optimal weight: 0.9990 chunk 121 optimal weight: 0.9980 chunk 7 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 154 optimal weight: 0.9990 chunk 85 optimal weight: 3.9990 chunk 90 optimal weight: 6.9990 chunk 47 optimal weight: 1.9990 chunk 101 optimal weight: 2.9990 overall best weight: 1.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 GLN D 40 ASN D 307 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.128316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.094415 restraints weight = 18326.440| |-----------------------------------------------------------------------------| r_work (start): 0.3123 rms_B_bonded: 2.37 r_work: 0.2995 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2858 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.2733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13593 Z= 0.115 Angle : 0.517 8.396 18418 Z= 0.265 Chirality : 0.042 0.146 2091 Planarity : 0.004 0.050 2252 Dihedral : 12.994 120.733 2262 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 2.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.08 % Allowed : 14.62 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.51 (0.22), residues: 1550 helix: 3.09 (0.21), residues: 540 sheet: 0.32 (0.24), residues: 480 loop : -0.55 (0.27), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 62 TYR 0.020 0.001 TYR D 102 PHE 0.027 0.001 PHE D 54 TRP 0.004 0.001 TRP C 47 HIS 0.003 0.001 HIS E 277 Details of bonding type rmsd covalent geometry : bond 0.00261 (13593) covalent geometry : angle 0.51686 (18418) hydrogen bonds : bond 0.05329 ( 608) hydrogen bonds : angle 3.83647 ( 1908) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3100 Ramachandran restraints generated. 1550 Oldfield, 0 Emsley, 1550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3100 Ramachandran restraints generated. 1550 Oldfield, 0 Emsley, 1550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 129 time to evaluate : 0.532 Fit side-chains revert: symmetry clash REVERT: A 38 LYS cc_start: 0.9095 (mtmm) cc_final: 0.8727 (mttm) REVERT: A 75 GLU cc_start: 0.8108 (mt-10) cc_final: 0.7855 (pm20) REVERT: A 77 ARG cc_start: 0.8436 (mtm-85) cc_final: 0.8045 (mpt-90) REVERT: A 151 LYS cc_start: 0.8999 (OUTLIER) cc_final: 0.8712 (ttpp) REVERT: A 154 ASP cc_start: 0.7644 (m-30) cc_final: 0.7434 (m-30) REVERT: A 179 ARG cc_start: 0.6603 (mmt-90) cc_final: 0.6235 (mmp80) REVERT: A 187 GLN cc_start: 0.9031 (OUTLIER) cc_final: 0.8610 (mt0) REVERT: B 64 LYS cc_start: 0.7938 (mttp) cc_final: 0.7531 (mttt) REVERT: B 88 ASP cc_start: 0.7439 (OUTLIER) cc_final: 0.7206 (m-30) REVERT: B 101 GLN cc_start: 0.7658 (mm-40) cc_final: 0.7226 (mt0) REVERT: B 109 ARG cc_start: 0.8066 (ttt90) cc_final: 0.7684 (ttp-170) REVERT: B 154 ASP cc_start: 0.7444 (m-30) cc_final: 0.7030 (m-30) REVERT: B 243 GLU cc_start: 0.7996 (mm-30) cc_final: 0.7588 (tp30) REVERT: B 252 MET cc_start: 0.6388 (mtp) cc_final: 0.5034 (mmt) REVERT: C 91 ASP cc_start: 0.8339 (t0) cc_final: 0.8044 (t0) REVERT: C 151 LYS cc_start: 0.8929 (pttp) cc_final: 0.8612 (ptmm) REVERT: C 162 ILE cc_start: 0.9205 (OUTLIER) cc_final: 0.8924 (mp) REVERT: C 243 GLU cc_start: 0.8397 (mm-30) cc_final: 0.8197 (tp30) REVERT: C 280 LYS cc_start: 0.8238 (ttpp) cc_final: 0.7623 (tttm) REVERT: D 50 ARG cc_start: 0.7302 (mtp85) cc_final: 0.6966 (mtt-85) REVERT: D 55 ASP cc_start: 0.7485 (t0) cc_final: 0.6939 (t0) REVERT: D 63 VAL cc_start: 0.8461 (m) cc_final: 0.8167 (p) REVERT: D 66 TYR cc_start: 0.8187 (m-80) cc_final: 0.7782 (m-80) REVERT: D 151 LYS cc_start: 0.8307 (pttm) cc_final: 0.8000 (pttp) REVERT: D 180 LEU cc_start: 0.7419 (OUTLIER) cc_final: 0.7147 (mt) REVERT: D 195 PHE cc_start: 0.7552 (t80) cc_final: 0.6993 (m-80) REVERT: D 246 LEU cc_start: 0.7314 (OUTLIER) cc_final: 0.7006 (pp) REVERT: E 67 GLU cc_start: 0.7126 (pt0) cc_final: 0.6456 (mm-30) REVERT: E 101 GLN cc_start: 0.7963 (mm-40) cc_final: 0.7434 (mp10) REVERT: E 109 ARG cc_start: 0.8225 (mtp180) cc_final: 0.7807 (ttt180) REVERT: E 139 ASN cc_start: 0.8465 (m-40) cc_final: 0.8159 (m-40) REVERT: E 195 PHE cc_start: 0.7558 (t80) cc_final: 0.6873 (m-80) REVERT: E 252 MET cc_start: 0.6343 (tpt) cc_final: 0.5894 (ttm) outliers start: 29 outliers final: 20 residues processed: 155 average time/residue: 0.6908 time to fit residues: 115.7313 Evaluate side-chains 152 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 126 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 117 ARG Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 151 LYS Chi-restraints excluded: chain A residue 187 GLN Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 117 ARG Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain C residue 117 ARG Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 162 ILE Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain D residue 40 ASN Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 214 THR Chi-restraints excluded: chain D residue 241 LEU Chi-restraints excluded: chain D residue 246 LEU Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 104 GLU Chi-restraints excluded: chain E residue 214 THR Chi-restraints excluded: chain E residue 305 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 69 optimal weight: 5.9990 chunk 102 optimal weight: 7.9990 chunk 109 optimal weight: 8.9990 chunk 65 optimal weight: 10.0000 chunk 144 optimal weight: 3.9990 chunk 150 optimal weight: 4.9990 chunk 44 optimal weight: 0.9990 chunk 105 optimal weight: 8.9990 chunk 20 optimal weight: 3.9990 chunk 9 optimal weight: 9.9990 chunk 106 optimal weight: 6.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 GLN D 40 ASN D 307 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.122796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.088133 restraints weight = 18558.270| |-----------------------------------------------------------------------------| r_work (start): 0.3031 rms_B_bonded: 2.37 r_work: 0.2895 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2758 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8749 moved from start: 0.2913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 13593 Z= 0.258 Angle : 0.656 9.333 18418 Z= 0.339 Chirality : 0.046 0.151 2091 Planarity : 0.005 0.048 2252 Dihedral : 14.233 134.197 2262 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.44 % Allowed : 14.12 % Favored : 83.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.21), residues: 1550 helix: 2.58 (0.21), residues: 540 sheet: 0.21 (0.24), residues: 445 loop : -0.86 (0.26), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 62 TYR 0.020 0.002 TYR D 102 PHE 0.016 0.002 PHE E 37 TRP 0.013 0.002 TRP E 213 HIS 0.005 0.001 HIS D 277 Details of bonding type rmsd covalent geometry : bond 0.00641 (13593) covalent geometry : angle 0.65635 (18418) hydrogen bonds : bond 0.08844 ( 608) hydrogen bonds : angle 4.40002 ( 1908) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4511.82 seconds wall clock time: 77 minutes 24.60 seconds (4644.60 seconds total)