Starting phenix.real_space_refine on Wed Feb 4 22:39:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lb9_62937/02_2026/9lb9_62937.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lb9_62937/02_2026/9lb9_62937.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.16 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9lb9_62937/02_2026/9lb9_62937.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lb9_62937/02_2026/9lb9_62937.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9lb9_62937/02_2026/9lb9_62937.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lb9_62937/02_2026/9lb9_62937.map" } resolution = 3.16 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 8877 2.51 5 N 2028 2.21 5 O 2398 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 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: 13344 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 2529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 2529 Classifications: {'peptide': 312} Link IDs: {'PTRANS': 18, 'TRANS': 293} Chain: "B" Number of atoms: 2529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 2529 Classifications: {'peptide': 312} Link IDs: {'PTRANS': 18, 'TRANS': 293} Chain: "C" Number of atoms: 2529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 2529 Classifications: {'peptide': 312} Link IDs: {'PTRANS': 18, 'TRANS': 293} Chain: "D" Number of atoms: 2529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 2529 Classifications: {'peptide': 312} Link IDs: {'PTRANS': 18, 'TRANS': 293} Chain: "E" Number of atoms: 2529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 2529 Classifications: {'peptide': 312} Link IDs: {'PTRANS': 18, 'TRANS': 293} Chain: "A" Number of atoms: 109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 109 Unusual residues: {' CL': 1, 'PEE': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 51 Chain: "B" Number of atoms: 153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 153 Unusual residues: {' CL': 1, 'PEE': 5} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 103 Unresolved non-hydrogen angles: 109 Unresolved non-hydrogen dihedrals: 109 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PEE:plan-1': 1, 'PEE:plan-2': 1} Unresolved non-hydrogen planarities: 6 Chain: "C" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 129 Unusual residues: {' CL': 1, 'PEE': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 76 Unresolved non-hydrogen angles: 82 Unresolved non-hydrogen dihedrals: 78 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: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 154 Unusual residues: {' CL': 1, 'PEE': 5} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 102 Unresolved non-hydrogen angles: 114 Unresolved non-hydrogen dihedrals: 102 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PEE:plan-1': 2, 'PEE:plan-2': 2} Unresolved non-hydrogen planarities: 12 Chain: "E" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 154 Unusual residues: {' CL': 1, 'PEE': 5} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 102 Unresolved non-hydrogen angles: 114 Unresolved non-hydrogen dihedrals: 102 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PEE:plan-1': 2, 'PEE:plan-2': 2} Unresolved non-hydrogen planarities: 12 Time building chain proxies: 2.66, per 1000 atoms: 0.20 Number of scatterers: 13344 At special positions: 0 Unit cell: (91.2, 92.72, 129.2, 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 2398 8.00 N 2028 7.00 C 8877 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: 1.06 Conformation dependent library (CDL) restraints added in 491.4 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: 44 helices and 16 sheets defined 40.7% alpha, 42.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain 'A' and resid 55 through 60 Processing helix chain 'A' and resid 118 through 121 Processing helix chain 'A' and resid 146 through 149 removed outlier: 3.543A pdb=" N VAL A 149 " --> pdb=" O LEU A 146 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 146 through 149' Processing helix chain 'A' and resid 196 through 214 removed outlier: 3.550A pdb=" N ASN A 200 " --> pdb=" O SER A 196 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N LEU A 203 " --> pdb=" O PRO A 199 " (cutoff:3.500A) Proline residue: A 204 - end of helix Processing helix chain 'A' and resid 215 through 218 removed outlier: 3.909A pdb=" N SER A 218 " --> pdb=" O ALA A 215 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 215 through 218' Processing helix chain 'A' and resid 220 through 244 Processing helix chain 'A' and resid 253 through 282 removed outlier: 3.763A pdb=" N GLU A 282 " --> pdb=" O TYR A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 315 removed outlier: 3.655A pdb=" N ALA A 288 " --> pdb=" O GLN A 284 " (cutoff:3.500A) removed outlier: 4.032A 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 196 through 201 removed outlier: 3.523A pdb=" N ASN B 200 " --> pdb=" O SER B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 201 through 214 Processing helix chain 'B' and resid 215 through 218 removed outlier: 3.681A 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 316 removed outlier: 3.587A pdb=" N ALA B 288 " --> pdb=" O GLN B 284 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ILE B 297 " --> pdb=" O ARG B 293 " (cutoff:3.500A) Proline residue: B 300 - end of helix Processing helix chain 'C' and resid 50 through 53 Processing helix chain 'C' and resid 55 through 60 Processing helix chain 'C' and resid 118 through 121 Processing helix chain 'C' and resid 146 through 149 removed outlier: 3.787A 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: 3.506A pdb=" N ASN C 200 " --> pdb=" O SER C 196 " (cutoff:3.500A) removed outlier: 5.344A 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: 3.699A 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 244 Processing helix chain 'C' and resid 253 through 282 Processing helix chain 'C' and resid 284 through 316 removed outlier: 3.572A pdb=" N ALA C 288 " --> pdb=" O GLN C 284 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ILE C 297 " --> pdb=" O ARG C 293 " (cutoff:3.500A) Proline residue: C 300 - end of helix Processing helix chain 'D' and resid 50 through 53 Processing helix chain 'D' and resid 55 through 60 Processing helix chain 'D' and resid 118 through 121 Processing helix chain 'D' and resid 146 through 149 removed outlier: 3.790A 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: 3.622A pdb=" N ASN D 200 " --> pdb=" O SER D 196 " (cutoff:3.500A) removed outlier: 5.092A 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: 3.640A 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 316 removed outlier: 3.869A 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: 3.864A 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: 3.575A pdb=" N ASN E 200 " --> pdb=" O SER E 196 " (cutoff:3.500A) removed outlier: 5.177A 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: 3.994A 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 Processing helix chain 'E' and resid 253 through 282 Processing helix chain 'E' and resid 284 through 316 removed outlier: 3.662A pdb=" N ALA E 288 " --> pdb=" O GLN E 284 " (cutoff:3.500A) removed outlier: 3.851A 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 20 removed outlier: 5.966A pdb=" N LEU A 16 " --> pdb=" O VAL A 141 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N ALA A 143 " --> pdb=" O LEU A 16 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N VAL A 18 " --> pdb=" O ALA A 143 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 86 through 94 removed outlier: 5.822A pdb=" N ALA A 87 " --> pdb=" O SER A 107 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N SER A 107 " --> pdb=" O ALA A 87 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N VAL A 89 " --> pdb=" O ARG A 105 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N ARG A 105 " --> pdb=" O VAL A 89 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASP A 91 " --> pdb=" O LEU A 103 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N TRP A 47 " --> pdb=" O VAL A 100 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N THR A 36 " --> pdb=" O LEU A 30 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N LEU A 30 " --> pdb=" O THR A 36 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N PHE A 42 " --> pdb=" O LEU A 24 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N LEU A 24 " --> pdb=" O PHE A 42 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 76 through 78 removed outlier: 3.521A pdb=" N VAL A 132 " --> pdb=" O SER A 182 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N SER A 182 " --> pdb=" O VAL A 132 " (cutoff:3.500A) removed outlier: 10.695A pdb=" N GLU A 181 " --> pdb=" O PRO A 171 " (cutoff:3.500A) removed outlier: 9.094A pdb=" N LYS A 183 " --> pdb=" O VAL A 169 " (cutoff:3.500A) removed outlier: 8.259A pdb=" N VAL A 169 " --> pdb=" O LYS A 183 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N ASP A 185 " --> pdb=" O ALA A 167 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N ALA A 167 " --> pdb=" O ASP A 185 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N GLN A 187 " --> pdb=" O PHE A 165 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N PHE A 165 " --> pdb=" O GLN A 187 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N ARG A 189 " --> pdb=" O GLU A 163 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 64 through 65 removed outlier: 5.753A pdb=" N ALA B 87 " --> pdb=" O SER B 107 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N SER B 107 " --> pdb=" O ALA B 87 " (cutoff:3.500A) removed outlier: 5.657A pdb=" N VAL B 89 " --> pdb=" O ARG B 105 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N ARG B 105 " --> pdb=" O VAL B 89 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N TRP B 47 " --> pdb=" O VAL B 100 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N THR B 36 " --> pdb=" O SER B 29 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N SER B 29 " --> pdb=" O THR B 36 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N LYS B 38 " --> pdb=" O CYS B 27 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N CYS B 27 " --> pdb=" O LYS B 38 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ASN B 40 " --> pdb=" O ILE B 25 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N LYS B 48 " --> pdb=" O THR B 17 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N THR B 17 " --> pdb=" O LYS B 48 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N LEU B 16 " --> pdb=" O VAL B 141 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N ALA B 143 " --> pdb=" O LEU B 16 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N VAL B 18 " --> pdb=" O ALA B 143 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 64 through 65 removed outlier: 5.753A pdb=" N ALA B 87 " --> pdb=" O SER B 107 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N SER B 107 " --> pdb=" O ALA B 87 " (cutoff:3.500A) removed outlier: 5.657A pdb=" N VAL B 89 " --> pdb=" O ARG B 105 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N ARG B 105 " --> pdb=" O VAL B 89 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N TRP B 47 " --> pdb=" O VAL B 100 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N THR B 36 " --> pdb=" O SER B 29 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N SER B 29 " --> pdb=" O THR B 36 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N LYS B 38 " --> pdb=" O CYS B 27 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N CYS B 27 " --> pdb=" O LYS B 38 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ASN B 40 " --> pdb=" O ILE B 25 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N LYS B 48 " --> pdb=" O THR B 17 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N THR B 17 " --> pdb=" O LYS B 48 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 76 through 78 removed outlier: 7.217A pdb=" N ASP B 185 " --> pdb=" O ALA B 167 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N ALA B 167 " --> pdb=" O ASP B 185 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N GLN B 187 " --> pdb=" O PHE B 165 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N PHE B 165 " --> pdb=" O GLN B 187 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ARG B 189 " --> pdb=" O GLU B 163 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 76 through 78 Processing sheet with id=AA8, first strand: chain 'C' and resid 88 through 94 removed outlier: 5.856A pdb=" N VAL C 89 " --> pdb=" O ARG C 105 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ARG C 105 " --> pdb=" O VAL C 89 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ASP C 91 " --> pdb=" O LEU C 103 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N TRP C 47 " --> pdb=" O VAL C 100 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA C 41 " --> pdb=" O PHE C 106 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N THR C 36 " --> pdb=" O LEU C 30 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N LEU C 30 " --> pdb=" O THR C 36 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N PHE C 42 " --> pdb=" O LEU C 24 " (cutoff:3.500A) removed outlier: 5.705A pdb=" N LEU C 24 " --> pdb=" O PHE C 42 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N SER C 44 " --> pdb=" O ILE C 22 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N ILE C 22 " --> pdb=" O SER C 44 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N SER C 46 " --> pdb=" O THR C 20 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N THR C 20 " --> pdb=" O SER C 46 " (cutoff:3.500A) removed outlier: 9.002A pdb=" N LYS C 48 " --> pdb=" O VAL C 18 " (cutoff:3.500A) removed outlier: 8.609A pdb=" N VAL C 18 " --> pdb=" O LYS C 48 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N LEU C 16 " --> pdb=" O VAL C 141 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N ALA C 143 " --> pdb=" O LEU C 16 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N VAL C 18 " --> pdb=" O ALA C 143 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 88 through 94 removed outlier: 5.856A pdb=" N VAL C 89 " --> pdb=" O ARG C 105 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ARG C 105 " --> pdb=" O VAL C 89 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ASP C 91 " --> pdb=" O LEU C 103 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N TRP C 47 " --> pdb=" O VAL C 100 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA C 41 " --> pdb=" O PHE C 106 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N THR C 36 " --> pdb=" O LEU C 30 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N LEU C 30 " --> pdb=" O THR C 36 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N PHE C 42 " --> pdb=" O LEU C 24 " (cutoff:3.500A) removed outlier: 5.705A pdb=" N LEU C 24 " --> pdb=" O PHE C 42 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N SER C 44 " --> pdb=" O ILE C 22 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N ILE C 22 " --> pdb=" O SER C 44 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N SER C 46 " --> pdb=" O THR C 20 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N THR C 20 " --> pdb=" O SER C 46 " (cutoff:3.500A) removed outlier: 9.002A pdb=" N LYS C 48 " --> pdb=" O VAL C 18 " (cutoff:3.500A) removed outlier: 8.609A pdb=" N VAL C 18 " --> pdb=" O LYS C 48 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 76 through 78 removed outlier: 10.432A pdb=" N GLU C 181 " --> pdb=" O PRO C 171 " (cutoff:3.500A) removed outlier: 9.563A pdb=" N LYS C 183 " --> pdb=" O VAL C 169 " (cutoff:3.500A) removed outlier: 8.307A pdb=" N VAL C 169 " --> pdb=" O LYS C 183 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N ASP C 185 " --> pdb=" O ALA C 167 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N ALA C 167 " --> pdb=" O ASP C 185 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N GLN C 187 " --> pdb=" O PHE C 165 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N PHE C 165 " --> pdb=" O GLN C 187 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N ARG C 189 " --> pdb=" O GLU C 163 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 64 through 65 removed outlier: 5.719A pdb=" N VAL D 89 " --> pdb=" O ARG D 105 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N ARG D 105 " --> pdb=" O VAL D 89 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ASP D 91 " --> pdb=" O LEU D 103 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N THR D 36 " --> pdb=" O LEU D 30 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N LEU D 30 " --> pdb=" O THR D 36 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N PHE D 42 " --> pdb=" O LEU D 24 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N LEU D 24 " --> pdb=" O PHE D 42 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N SER D 44 " --> pdb=" O ILE D 22 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N ILE D 22 " --> pdb=" O SER D 44 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N SER D 46 " --> pdb=" O THR D 20 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N THR D 20 " --> pdb=" O SER D 46 " (cutoff:3.500A) removed outlier: 8.951A pdb=" N LYS D 48 " --> pdb=" O VAL D 18 " (cutoff:3.500A) removed outlier: 8.521A pdb=" N VAL D 18 " --> pdb=" O LYS D 48 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N LEU D 16 " --> pdb=" O VAL D 141 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N ALA D 143 " --> pdb=" O LEU D 16 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N VAL D 18 " --> pdb=" O ALA D 143 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 64 through 65 removed outlier: 5.719A pdb=" N VAL D 89 " --> pdb=" O ARG D 105 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N ARG D 105 " --> pdb=" O VAL D 89 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ASP D 91 " --> pdb=" O LEU D 103 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N THR D 36 " --> pdb=" O LEU D 30 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N LEU D 30 " --> pdb=" O THR D 36 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N PHE D 42 " --> pdb=" O LEU D 24 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N LEU D 24 " --> pdb=" O PHE D 42 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N SER D 44 " --> pdb=" O ILE D 22 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N ILE D 22 " --> pdb=" O SER D 44 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N SER D 46 " --> pdb=" O THR D 20 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N THR D 20 " --> pdb=" O SER D 46 " (cutoff:3.500A) removed outlier: 8.951A pdb=" N LYS D 48 " --> pdb=" O VAL D 18 " (cutoff:3.500A) removed outlier: 8.521A pdb=" N VAL D 18 " --> pdb=" O LYS D 48 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 76 through 78 removed outlier: 10.045A pdb=" N GLU D 181 " --> pdb=" O PRO D 171 " (cutoff:3.500A) removed outlier: 8.886A pdb=" N LYS D 183 " --> pdb=" O VAL D 169 " (cutoff:3.500A) removed outlier: 8.213A pdb=" N VAL D 169 " --> pdb=" O LYS D 183 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N ASP D 185 " --> pdb=" O ALA D 167 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N ALA D 167 " --> pdb=" O ASP D 185 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N GLN D 187 " --> pdb=" O PHE D 165 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N PHE D 165 " --> pdb=" O GLN D 187 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N ARG D 189 " --> pdb=" O GLU D 163 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 64 through 65 removed outlier: 3.550A pdb=" N LYS E 64 " --> pdb=" O VAL E 94 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N ALA E 87 " --> pdb=" O SER E 107 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N SER E 107 " --> pdb=" O ALA E 87 " (cutoff:3.500A) removed outlier: 5.753A pdb=" N VAL E 89 " --> pdb=" O ARG E 105 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N ARG E 105 " --> pdb=" O VAL E 89 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ASP E 91 " --> pdb=" O LEU E 103 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N TRP E 47 " --> pdb=" O VAL E 100 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N THR E 36 " --> pdb=" O SER E 29 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N SER E 29 " --> pdb=" O THR E 36 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N LYS E 38 " --> pdb=" O CYS E 27 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N CYS E 27 " --> pdb=" O LYS E 38 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ASN E 40 " --> pdb=" O ILE E 25 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N LYS E 48 " --> pdb=" O THR E 17 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N THR E 17 " --> pdb=" O LYS E 48 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N LEU E 16 " --> pdb=" O VAL E 141 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N ALA E 143 " --> pdb=" O LEU E 16 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N VAL E 18 " --> pdb=" O ALA E 143 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 64 through 65 removed outlier: 3.550A pdb=" N LYS E 64 " --> pdb=" O VAL E 94 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N ALA E 87 " --> pdb=" O SER E 107 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N SER E 107 " --> pdb=" O ALA E 87 " (cutoff:3.500A) removed outlier: 5.753A pdb=" N VAL E 89 " --> pdb=" O ARG E 105 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N ARG E 105 " --> pdb=" O VAL E 89 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ASP E 91 " --> pdb=" O LEU E 103 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N TRP E 47 " --> pdb=" O VAL E 100 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N THR E 36 " --> pdb=" O SER E 29 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N SER E 29 " --> pdb=" O THR E 36 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N LYS E 38 " --> pdb=" O CYS E 27 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N CYS E 27 " --> pdb=" O LYS E 38 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ASN E 40 " --> pdb=" O ILE E 25 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N LYS E 48 " --> pdb=" O THR E 17 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N THR E 17 " --> pdb=" O LYS E 48 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 77 through 78 removed outlier: 6.037A pdb=" N ASP E 185 " --> pdb=" O LYS E 170 " (cutoff:3.500A) removed outlier: 7.711A pdb=" N LYS E 170 " --> pdb=" O ASP E 185 " (cutoff:3.500A) removed outlier: 8.238A pdb=" N GLN E 187 " --> pdb=" O VAL E 168 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N VAL E 168 " --> pdb=" O GLN E 187 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N ARG E 189 " --> pdb=" O THR E 166 " (cutoff:3.500A) removed outlier: 8.407A pdb=" N THR E 166 " --> pdb=" O ARG E 189 " (cutoff:3.500A) removed outlier: 8.696A pdb=" N SER E 191 " --> pdb=" O SER E 164 " (cutoff:3.500A) removed outlier: 9.950A pdb=" N SER E 164 " --> pdb=" O SER E 191 " (cutoff:3.500A) 709 hydrogen bonds defined for protein. 2067 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: 1.90 Time building geometry restraints manager: 1.43 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: 2074 1.32 - 1.44: 3691 1.44 - 1.56: 7825 1.56 - 1.69: 32 1.69 - 1.81: 35 Bond restraints: 13657 Sorted by residual: bond pdb=" N PHE E 238 " pdb=" CA PHE E 238 " ideal model delta sigma weight residual 1.459 1.486 -0.026 1.19e-02 7.06e+03 4.90e+00 bond pdb=" CA ASP E 178 " pdb=" C ASP E 178 " ideal model delta sigma weight residual 1.523 1.537 -0.014 1.45e-02 4.76e+03 9.84e-01 bond pdb=" CA LEU B 203 " pdb=" C LEU B 203 " ideal model delta sigma weight residual 1.521 1.531 -0.010 1.14e-02 7.69e+03 8.13e-01 bond pdb=" CB GLU B 243 " pdb=" CG GLU B 243 " ideal model delta sigma weight residual 1.520 1.544 -0.024 3.00e-02 1.11e+03 6.21e-01 bond pdb=" CA ASP E 178 " pdb=" CB ASP E 178 " ideal model delta sigma weight residual 1.532 1.544 -0.012 1.53e-02 4.27e+03 6.12e-01 ... (remaining 13652 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.56: 18187 1.56 - 3.11: 256 3.11 - 4.67: 37 4.67 - 6.23: 15 6.23 - 7.79: 1 Bond angle restraints: 18496 Sorted by residual: angle pdb=" CA PHE E 238 " pdb=" C PHE E 238 " pdb=" O PHE E 238 " ideal model delta sigma weight residual 120.82 118.03 2.79 1.05e+00 9.07e-01 7.06e+00 angle pdb=" N TYR A 119 " pdb=" CA TYR A 119 " pdb=" C TYR A 119 " ideal model delta sigma weight residual 109.81 114.85 -5.04 2.21e+00 2.05e-01 5.21e+00 angle pdb=" CA LEU A 246 " pdb=" CB LEU A 246 " pdb=" CG LEU A 246 " ideal model delta sigma weight residual 116.30 124.09 -7.79 3.50e+00 8.16e-02 4.95e+00 angle pdb=" N ASP E 178 " pdb=" CA ASP E 178 " pdb=" CB ASP E 178 " ideal model delta sigma weight residual 112.63 109.48 3.15 1.61e+00 3.86e-01 3.83e+00 angle pdb=" C ASP C 88 " pdb=" N VAL C 89 " pdb=" CA VAL C 89 " ideal model delta sigma weight residual 122.93 120.48 2.45 1.26e+00 6.30e-01 3.77e+00 ... (remaining 18491 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.95: 8024 34.95 - 69.91: 195 69.91 - 104.86: 31 104.86 - 139.82: 3 139.82 - 174.77: 12 Dihedral angle restraints: 8265 sinusoidal: 3585 harmonic: 4680 Sorted by residual: dihedral pdb=" C3 PEE E 405 " pdb=" C1 PEE E 405 " pdb=" C2 PEE E 405 " pdb=" O3P PEE E 405 " ideal model delta sinusoidal sigma weight residual 62.73 -112.04 174.77 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" O2 PEE E 405 " pdb=" C1 PEE E 405 " pdb=" C2 PEE E 405 " pdb=" O3P PEE E 405 " ideal model delta sinusoidal sigma weight residual 300.04 125.67 174.37 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C4 PEE D 405 " pdb=" O4P PEE D 405 " pdb=" P PEE D 405 " pdb=" O2P PEE D 405 " ideal model delta sinusoidal sigma weight residual -75.78 87.97 -163.75 1 3.00e+01 1.11e-03 2.09e+01 ... (remaining 8262 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1266 0.028 - 0.056: 510 0.056 - 0.085: 157 0.085 - 0.113: 126 0.113 - 0.141: 32 Chirality restraints: 2091 Sorted by residual: chirality pdb=" CA ILE A 71 " pdb=" N ILE A 71 " pdb=" C ILE A 71 " pdb=" CB ILE A 71 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.96e-01 chirality pdb=" CA ILE C 128 " pdb=" N ILE C 128 " pdb=" C ILE C 128 " pdb=" CB ILE C 128 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.57e-01 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 2.38 0.13 2.00e-01 2.50e+01 4.41e-01 ... (remaining 2088 not shown) Planarity restraints: 2257 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A 170 " -0.036 5.00e-02 4.00e+02 5.40e-02 4.67e+00 pdb=" N PRO A 171 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO A 171 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 171 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 95 " -0.032 5.00e-02 4.00e+02 4.84e-02 3.76e+00 pdb=" N PRO A 96 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO A 96 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 96 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU E 67 " 0.031 5.00e-02 4.00e+02 4.76e-02 3.63e+00 pdb=" N PRO E 68 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO E 68 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO E 68 " 0.027 5.00e-02 4.00e+02 ... (remaining 2254 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 500 2.72 - 3.27: 12108 3.27 - 3.81: 20131 3.81 - 4.36: 24862 4.36 - 4.90: 45051 Nonbonded interactions: 102652 Sorted by model distance: nonbonded pdb=" N GLU E 69 " pdb=" OE1 GLU E 69 " model vdw 2.176 3.120 nonbonded pdb=" N GLU B 14 " pdb=" OE1 GLU B 14 " model vdw 2.212 3.120 nonbonded pdb=" O LEU C 241 " pdb=" OG1 THR C 244 " model vdw 2.265 3.040 nonbonded pdb=" OG1 THR A 65 " pdb=" OD2 ASP B 136 " model vdw 2.285 3.040 nonbonded pdb=" O PRO B 8 " pdb=" NH1 ARG B 138 " model vdw 2.312 3.120 ... (remaining 102647 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 C10 or name C11 or n \ ame C12 or name C13 or name C14 or name C15 or name C16)))) selection = (chain 'B' and (resid 5 through 316 or (resid 404 and (name C10 or name C11 or n \ ame C12 or name C13 or name C14 or name C15 or name C16)))) selection = (chain 'C' and (resid 5 through 316 or (resid 404 and (name C10 or name C11 or n \ ame C12 or name C13 or name C14 or name C15 or name C16)))) selection = (chain 'D' and (resid 5 through 316 or (resid 404 and (name C10 or name C11 or n \ ame C12 or name C13 or name C14 or name C15 or name C16)))) selection = (chain 'E' and (resid 5 through 316 or (resid 404 and (name C10 or name C11 or n \ ame C12 or name C13 or name C14 or name C15 or name C16)))) } 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: 1.640 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: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 11.090 Find NCS groups from input model: 0.280 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:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8746 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 0.028 13657 Z= 0.132 Angle : 0.488 7.786 18496 Z= 0.253 Chirality : 0.041 0.141 2091 Planarity : 0.004 0.054 2257 Dihedral : 17.393 174.774 5215 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 0.07 % Allowed : 10.21 % Favored : 89.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.22 (0.22), residues: 1550 helix: 3.13 (0.21), residues: 515 sheet: 0.41 (0.26), residues: 440 loop : -1.02 (0.24), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 189 TYR 0.011 0.001 TYR E 254 PHE 0.011 0.001 PHE E 42 TRP 0.010 0.001 TRP E 47 HIS 0.002 0.001 HIS E 277 Details of bonding type rmsd covalent geometry : bond 0.00298 (13657) covalent geometry : angle 0.48798 (18496) hydrogen bonds : bond 0.17817 ( 613) hydrogen bonds : angle 6.78847 ( 2067) *********************** 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 176 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 175 time to evaluate : 0.456 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 175 average time/residue: 0.1439 time to fit residues: 33.9601 Evaluate side-chains 176 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 175 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 297 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 0.2980 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 0.7980 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.123425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.091857 restraints weight = 15941.562| |-----------------------------------------------------------------------------| r_work (start): 0.2871 rms_B_bonded: 1.74 r_work: 0.2745 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2608 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8763 moved from start: 0.0536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 13657 Z= 0.161 Angle : 0.554 7.264 18496 Z= 0.289 Chirality : 0.043 0.148 2091 Planarity : 0.004 0.048 2257 Dihedral : 17.744 173.740 2292 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 2.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.07 % Allowed : 9.00 % Favored : 88.93 % 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: 1.28 (0.22), residues: 1550 helix: 3.30 (0.21), residues: 515 sheet: 0.49 (0.25), residues: 440 loop : -1.15 (0.24), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 50 TYR 0.013 0.001 TYR A 102 PHE 0.015 0.001 PHE E 42 TRP 0.009 0.001 TRP A 47 HIS 0.002 0.001 HIS D 127 Details of bonding type rmsd covalent geometry : bond 0.00389 (13657) covalent geometry : angle 0.55430 (18496) hydrogen bonds : bond 0.06769 ( 613) hydrogen bonds : angle 4.52040 ( 2067) *********************** 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 197 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 168 time to evaluate : 0.494 Fit side-chains REVERT: A 76 ILE cc_start: 0.8301 (mt) cc_final: 0.8059 (mm) REVERT: B 48 LYS cc_start: 0.8549 (OUTLIER) cc_final: 0.8188 (tptp) REVERT: B 146 LEU cc_start: 0.8747 (OUTLIER) cc_final: 0.8482 (mm) REVERT: D 40 ASN cc_start: 0.9320 (t0) cc_final: 0.9094 (t0) REVERT: E 178 ASP cc_start: 0.7064 (t70) cc_final: 0.6758 (m-30) outliers start: 29 outliers final: 12 residues processed: 189 average time/residue: 0.1359 time to fit residues: 35.2759 Evaluate side-chains 181 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 167 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain B residue 48 LYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain C residue 104 GLU Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 219 THR Chi-restraints excluded: chain D residue 283 SER Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 111 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 34 optimal weight: 5.9990 chunk 98 optimal weight: 5.9990 chunk 131 optimal weight: 4.9990 chunk 17 optimal weight: 0.9990 chunk 150 optimal weight: 4.9990 chunk 15 optimal weight: 0.0010 chunk 95 optimal weight: 2.9990 chunk 120 optimal weight: 4.9990 chunk 74 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 overall best weight: 1.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.123574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.091880 restraints weight = 16098.754| |-----------------------------------------------------------------------------| r_work (start): 0.2871 rms_B_bonded: 1.75 r_work: 0.2746 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2608 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8768 moved from start: 0.0736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 13657 Z= 0.156 Angle : 0.538 6.612 18496 Z= 0.279 Chirality : 0.043 0.143 2091 Planarity : 0.004 0.050 2257 Dihedral : 16.689 173.043 2290 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 1.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.00 % Allowed : 10.00 % Favored : 88.00 % 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: 1.27 (0.22), residues: 1550 helix: 3.31 (0.21), residues: 515 sheet: 0.52 (0.25), residues: 440 loop : -1.23 (0.24), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 50 TYR 0.013 0.001 TYR D 102 PHE 0.012 0.001 PHE E 42 TRP 0.008 0.001 TRP A 47 HIS 0.002 0.001 HIS C 277 Details of bonding type rmsd covalent geometry : bond 0.00378 (13657) covalent geometry : angle 0.53811 (18496) hydrogen bonds : bond 0.06747 ( 613) hydrogen bonds : angle 4.21748 ( 2067) *********************** 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 198 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 170 time to evaluate : 0.322 Fit side-chains REVERT: A 26 GLU cc_start: 0.7992 (mm-30) cc_final: 0.7451 (mt-10) REVERT: B 146 LEU cc_start: 0.8724 (OUTLIER) cc_final: 0.8457 (mm) REVERT: D 63 VAL cc_start: 0.8843 (m) cc_final: 0.8520 (p) REVERT: E 178 ASP cc_start: 0.7168 (t70) cc_final: 0.6793 (m-30) outliers start: 28 outliers final: 18 residues processed: 189 average time/residue: 0.1350 time to fit residues: 35.0087 Evaluate side-chains 185 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 166 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain C residue 104 GLU Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain D residue 71 ILE Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 219 THR Chi-restraints excluded: chain D residue 241 LEU Chi-restraints excluded: chain D residue 283 SER Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 146 LEU Chi-restraints excluded: chain E residue 238 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 35 optimal weight: 0.9990 chunk 71 optimal weight: 0.5980 chunk 133 optimal weight: 0.6980 chunk 5 optimal weight: 5.9990 chunk 43 optimal weight: 3.9990 chunk 67 optimal weight: 0.8980 chunk 39 optimal weight: 6.9990 chunk 13 optimal weight: 10.0000 chunk 100 optimal weight: 2.9990 chunk 2 optimal weight: 6.9990 chunk 7 optimal weight: 6.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.125333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.093733 restraints weight = 15898.060| |-----------------------------------------------------------------------------| r_work (start): 0.2902 rms_B_bonded: 1.75 r_work: 0.2776 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2639 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8741 moved from start: 0.0814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 13657 Z= 0.124 Angle : 0.507 6.090 18496 Z= 0.263 Chirality : 0.042 0.142 2091 Planarity : 0.004 0.049 2257 Dihedral : 15.846 175.149 2290 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 1.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.14 % Allowed : 10.29 % Favored : 87.57 % 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: 1.40 (0.22), residues: 1550 helix: 3.44 (0.21), residues: 515 sheet: 0.57 (0.25), residues: 440 loop : -1.15 (0.24), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 189 TYR 0.013 0.001 TYR D 102 PHE 0.011 0.001 PHE E 42 TRP 0.008 0.001 TRP A 47 HIS 0.002 0.001 HIS C 277 Details of bonding type rmsd covalent geometry : bond 0.00286 (13657) covalent geometry : angle 0.50715 (18496) hydrogen bonds : bond 0.05836 ( 613) hydrogen bonds : angle 3.99483 ( 2067) *********************** 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 199 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 169 time to evaluate : 0.343 Fit side-chains REVERT: A 26 GLU cc_start: 0.7970 (mm-30) cc_final: 0.7415 (mt-10) REVERT: B 146 LEU cc_start: 0.8695 (OUTLIER) cc_final: 0.8434 (mm) REVERT: C 101 GLN cc_start: 0.8593 (mm-40) cc_final: 0.8211 (mt0) REVERT: E 101 GLN cc_start: 0.7929 (OUTLIER) cc_final: 0.7009 (mt0) outliers start: 30 outliers final: 21 residues processed: 193 average time/residue: 0.1354 time to fit residues: 35.5465 Evaluate side-chains 187 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 164 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 91 ASP Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain C residue 104 GLU Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 219 THR Chi-restraints excluded: chain D residue 283 SER Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 101 GLN Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 146 LEU Chi-restraints excluded: chain E residue 219 THR Chi-restraints excluded: chain E residue 238 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 117 optimal weight: 4.9990 chunk 76 optimal weight: 6.9990 chunk 145 optimal weight: 5.9990 chunk 154 optimal weight: 2.9990 chunk 147 optimal weight: 5.9990 chunk 19 optimal weight: 3.9990 chunk 141 optimal weight: 0.9980 chunk 36 optimal weight: 6.9990 chunk 79 optimal weight: 2.9990 chunk 86 optimal weight: 4.9990 chunk 68 optimal weight: 4.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.120733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.088931 restraints weight = 16226.580| |-----------------------------------------------------------------------------| r_work (start): 0.2841 rms_B_bonded: 1.75 r_work: 0.2710 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2572 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8804 moved from start: 0.0995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 13657 Z= 0.248 Angle : 0.616 10.300 18496 Z= 0.317 Chirality : 0.045 0.145 2091 Planarity : 0.005 0.045 2257 Dihedral : 16.281 175.253 2290 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 2.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 2.57 % Allowed : 10.36 % Favored : 87.07 % 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: 1.04 (0.21), residues: 1550 helix: 2.99 (0.21), residues: 520 sheet: 0.43 (0.25), residues: 440 loop : -1.29 (0.24), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 189 TYR 0.013 0.002 TYR A 102 PHE 0.012 0.002 PHE E 42 TRP 0.010 0.001 TRP A 47 HIS 0.003 0.001 HIS D 127 Details of bonding type rmsd covalent geometry : bond 0.00632 (13657) covalent geometry : angle 0.61599 (18496) hydrogen bonds : bond 0.08119 ( 613) hydrogen bonds : angle 4.28867 ( 2067) *********************** 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 203 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 167 time to evaluate : 0.327 Fit side-chains REVERT: A 26 GLU cc_start: 0.8020 (mm-30) cc_final: 0.7476 (mt-10) REVERT: B 146 LEU cc_start: 0.8765 (OUTLIER) cc_final: 0.8502 (mm) REVERT: B 200 ASN cc_start: 0.9000 (m110) cc_final: 0.8751 (m110) REVERT: C 101 GLN cc_start: 0.8633 (mm-40) cc_final: 0.8282 (mt0) REVERT: D 63 VAL cc_start: 0.8796 (m) cc_final: 0.8459 (p) REVERT: E 101 GLN cc_start: 0.7992 (OUTLIER) cc_final: 0.7023 (mt0) outliers start: 36 outliers final: 26 residues processed: 197 average time/residue: 0.1337 time to fit residues: 35.7871 Evaluate side-chains 189 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 161 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 91 ASP Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain C residue 104 GLU Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 71 ILE Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 219 THR Chi-restraints excluded: chain D residue 283 SER Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 101 GLN Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 146 LEU Chi-restraints excluded: chain E residue 214 THR Chi-restraints excluded: chain E residue 219 THR Chi-restraints excluded: chain E residue 238 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 62 optimal weight: 8.9990 chunk 65 optimal weight: 4.9990 chunk 77 optimal weight: 0.0970 chunk 34 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 72 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 9 optimal weight: 4.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 284 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.124540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.092937 restraints weight = 15935.363| |-----------------------------------------------------------------------------| r_work (start): 0.2888 rms_B_bonded: 1.75 r_work: 0.2761 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2624 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8753 moved from start: 0.0933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 13657 Z= 0.126 Angle : 0.515 5.807 18496 Z= 0.268 Chirality : 0.042 0.144 2091 Planarity : 0.004 0.048 2257 Dihedral : 15.689 178.425 2290 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 2.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.07 % Allowed : 11.14 % Favored : 86.79 % 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: 1.29 (0.21), residues: 1550 helix: 3.38 (0.21), residues: 515 sheet: 0.64 (0.25), residues: 415 loop : -1.28 (0.23), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 50 TYR 0.015 0.001 TYR D 102 PHE 0.011 0.001 PHE E 42 TRP 0.007 0.001 TRP D 47 HIS 0.002 0.001 HIS D 127 Details of bonding type rmsd covalent geometry : bond 0.00289 (13657) covalent geometry : angle 0.51474 (18496) hydrogen bonds : bond 0.06066 ( 613) hydrogen bonds : angle 3.99874 ( 2067) *********************** 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 192 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 163 time to evaluate : 0.477 Fit side-chains REVERT: A 26 GLU cc_start: 0.7974 (mm-30) cc_final: 0.7440 (mt-10) REVERT: B 146 LEU cc_start: 0.8723 (OUTLIER) cc_final: 0.8456 (mm) REVERT: C 101 GLN cc_start: 0.8614 (mm-40) cc_final: 0.8279 (mt0) REVERT: D 63 VAL cc_start: 0.8781 (m) cc_final: 0.8442 (p) REVERT: E 101 GLN cc_start: 0.7923 (OUTLIER) cc_final: 0.7007 (mt0) outliers start: 29 outliers final: 21 residues processed: 187 average time/residue: 0.1497 time to fit residues: 37.9955 Evaluate side-chains 182 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 159 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 91 ASP Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain C residue 104 GLU Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 219 THR Chi-restraints excluded: chain D residue 283 SER Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 101 GLN Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 214 THR Chi-restraints excluded: chain E residue 238 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 133 optimal weight: 5.9990 chunk 153 optimal weight: 4.9990 chunk 126 optimal weight: 7.9990 chunk 139 optimal weight: 0.8980 chunk 45 optimal weight: 6.9990 chunk 137 optimal weight: 7.9990 chunk 121 optimal weight: 0.7980 chunk 149 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 27 optimal weight: 6.9990 chunk 118 optimal weight: 0.8980 overall best weight: 1.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.123270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.091579 restraints weight = 15899.195| |-----------------------------------------------------------------------------| r_work (start): 0.2869 rms_B_bonded: 1.75 r_work: 0.2741 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2602 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8766 moved from start: 0.0972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 13657 Z= 0.153 Angle : 0.531 5.893 18496 Z= 0.275 Chirality : 0.043 0.141 2091 Planarity : 0.004 0.047 2257 Dihedral : 15.551 179.210 2290 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 2.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.14 % Allowed : 11.43 % Favored : 86.43 % 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: 1.25 (0.21), residues: 1550 helix: 3.23 (0.21), residues: 520 sheet: 0.64 (0.25), residues: 415 loop : -1.23 (0.24), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 189 TYR 0.014 0.001 TYR D 102 PHE 0.012 0.001 PHE E 42 TRP 0.008 0.001 TRP A 47 HIS 0.002 0.001 HIS D 127 Details of bonding type rmsd covalent geometry : bond 0.00372 (13657) covalent geometry : angle 0.53095 (18496) hydrogen bonds : bond 0.06529 ( 613) hydrogen bonds : angle 4.02017 ( 2067) *********************** 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 194 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 164 time to evaluate : 0.542 Fit side-chains REVERT: A 26 GLU cc_start: 0.7985 (mm-30) cc_final: 0.7447 (mt-10) REVERT: B 146 LEU cc_start: 0.8714 (OUTLIER) cc_final: 0.8447 (mm) REVERT: C 101 GLN cc_start: 0.8611 (mm-40) cc_final: 0.8288 (mt0) REVERT: D 63 VAL cc_start: 0.8804 (m) cc_final: 0.8463 (p) REVERT: E 101 GLN cc_start: 0.7917 (OUTLIER) cc_final: 0.7017 (mt0) outliers start: 30 outliers final: 24 residues processed: 188 average time/residue: 0.1524 time to fit residues: 39.2447 Evaluate side-chains 187 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 161 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 91 ASP Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain C residue 104 GLU Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 219 THR Chi-restraints excluded: chain D residue 283 SER Chi-restraints excluded: chain E residue 13 ASP Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 101 GLN Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 219 THR Chi-restraints excluded: chain E residue 238 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 76 optimal weight: 5.9990 chunk 98 optimal weight: 2.9990 chunk 4 optimal weight: 7.9990 chunk 108 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 39 optimal weight: 4.9990 chunk 28 optimal weight: 0.9990 chunk 147 optimal weight: 2.9990 chunk 125 optimal weight: 2.9990 chunk 138 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.121397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.089707 restraints weight = 15896.452| |-----------------------------------------------------------------------------| r_work (start): 0.2851 rms_B_bonded: 1.74 r_work: 0.2722 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2584 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8795 moved from start: 0.1083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 13657 Z= 0.206 Angle : 0.587 7.913 18496 Z= 0.302 Chirality : 0.044 0.143 2091 Planarity : 0.005 0.046 2257 Dihedral : 15.741 179.618 2290 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 2.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 2.29 % Allowed : 12.14 % Favored : 85.57 % 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: 1.07 (0.21), residues: 1550 helix: 3.07 (0.21), residues: 520 sheet: 0.55 (0.25), residues: 415 loop : -1.36 (0.23), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 189 TYR 0.014 0.001 TYR D 102 PHE 0.012 0.001 PHE E 42 TRP 0.009 0.001 TRP A 47 HIS 0.003 0.001 HIS D 127 Details of bonding type rmsd covalent geometry : bond 0.00516 (13657) covalent geometry : angle 0.58667 (18496) hydrogen bonds : bond 0.07696 ( 613) hydrogen bonds : angle 4.21090 ( 2067) *********************** 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 192 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 160 time to evaluate : 0.457 Fit side-chains REVERT: A 26 GLU cc_start: 0.8015 (mm-30) cc_final: 0.7461 (mt-10) REVERT: B 146 LEU cc_start: 0.8761 (OUTLIER) cc_final: 0.8506 (mm) REVERT: C 101 GLN cc_start: 0.8616 (mm-40) cc_final: 0.8294 (mt0) REVERT: D 63 VAL cc_start: 0.8781 (m) cc_final: 0.8436 (p) REVERT: E 101 GLN cc_start: 0.7927 (OUTLIER) cc_final: 0.6990 (mt0) outliers start: 32 outliers final: 26 residues processed: 186 average time/residue: 0.1507 time to fit residues: 38.6736 Evaluate side-chains 185 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 157 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 91 ASP Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain C residue 104 GLU Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 71 ILE Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 219 THR Chi-restraints excluded: chain D residue 283 SER Chi-restraints excluded: chain E residue 13 ASP Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 101 GLN Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 214 THR Chi-restraints excluded: chain E residue 219 THR Chi-restraints excluded: chain E residue 238 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 33 optimal weight: 2.9990 chunk 8 optimal weight: 6.9990 chunk 130 optimal weight: 0.9980 chunk 144 optimal weight: 0.9980 chunk 69 optimal weight: 2.9990 chunk 142 optimal weight: 4.9990 chunk 110 optimal weight: 5.9990 chunk 21 optimal weight: 5.9990 chunk 42 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 111 optimal weight: 4.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.122912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.091287 restraints weight = 16052.486| |-----------------------------------------------------------------------------| r_work (start): 0.2868 rms_B_bonded: 1.74 r_work: 0.2739 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2601 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8781 moved from start: 0.1059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 13657 Z= 0.157 Angle : 0.545 8.157 18496 Z= 0.281 Chirality : 0.043 0.143 2091 Planarity : 0.004 0.047 2257 Dihedral : 15.418 178.390 2290 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 2.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.07 % Allowed : 12.71 % Favored : 85.21 % 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: 1.16 (0.21), residues: 1550 helix: 3.19 (0.21), residues: 520 sheet: 0.57 (0.25), residues: 415 loop : -1.32 (0.23), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 189 TYR 0.016 0.001 TYR D 102 PHE 0.012 0.001 PHE E 42 TRP 0.008 0.001 TRP A 47 HIS 0.002 0.001 HIS C 277 Details of bonding type rmsd covalent geometry : bond 0.00380 (13657) covalent geometry : angle 0.54490 (18496) hydrogen bonds : bond 0.06723 ( 613) hydrogen bonds : angle 4.06804 ( 2067) *********************** 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 185 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 156 time to evaluate : 0.470 Fit side-chains REVERT: A 26 GLU cc_start: 0.8003 (mm-30) cc_final: 0.7449 (mt-10) REVERT: B 146 LEU cc_start: 0.8735 (OUTLIER) cc_final: 0.8476 (mm) REVERT: C 101 GLN cc_start: 0.8620 (mm-40) cc_final: 0.8298 (mt0) REVERT: D 63 VAL cc_start: 0.8768 (m) cc_final: 0.8426 (p) REVERT: E 101 GLN cc_start: 0.7935 (OUTLIER) cc_final: 0.7026 (mt0) outliers start: 29 outliers final: 23 residues processed: 180 average time/residue: 0.1435 time to fit residues: 35.5121 Evaluate side-chains 177 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 152 time to evaluate : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 ASP Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain C residue 104 GLU Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 71 ILE Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 219 THR Chi-restraints excluded: chain D residue 283 SER Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 101 GLN Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 214 THR Chi-restraints excluded: chain E residue 219 THR Chi-restraints excluded: chain E residue 238 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 142 optimal weight: 4.9990 chunk 46 optimal weight: 0.3980 chunk 73 optimal weight: 0.3980 chunk 85 optimal weight: 4.9990 chunk 40 optimal weight: 5.9990 chunk 63 optimal weight: 6.9990 chunk 80 optimal weight: 0.9980 chunk 123 optimal weight: 1.9990 chunk 34 optimal weight: 5.9990 chunk 77 optimal weight: 0.9980 chunk 135 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.126886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.095631 restraints weight = 15871.113| |-----------------------------------------------------------------------------| r_work (start): 0.2936 rms_B_bonded: 1.74 r_work: 0.2811 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2674 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8708 moved from start: 0.1121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 13657 Z= 0.104 Angle : 0.500 8.784 18496 Z= 0.258 Chirality : 0.042 0.143 2091 Planarity : 0.004 0.050 2257 Dihedral : 14.693 174.059 2290 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 2.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.29 % Allowed : 13.29 % Favored : 85.43 % 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: 1.40 (0.22), residues: 1550 helix: 3.39 (0.21), residues: 520 sheet: 0.67 (0.25), residues: 415 loop : -1.16 (0.24), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 189 TYR 0.016 0.001 TYR D 102 PHE 0.011 0.001 PHE E 42 TRP 0.008 0.001 TRP D 47 HIS 0.002 0.001 HIS C 277 Details of bonding type rmsd covalent geometry : bond 0.00223 (13657) covalent geometry : angle 0.49969 (18496) hydrogen bonds : bond 0.05011 ( 613) hydrogen bonds : angle 3.79693 ( 2067) ********************** 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 191 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 173 time to evaluate : 0.445 Fit side-chains REVERT: A 26 GLU cc_start: 0.7942 (mm-30) cc_final: 0.7403 (mt-10) REVERT: B 146 LEU cc_start: 0.8651 (OUTLIER) cc_final: 0.8397 (mm) REVERT: C 101 GLN cc_start: 0.8504 (mm-40) cc_final: 0.8176 (mt0) REVERT: E 101 GLN cc_start: 0.7852 (OUTLIER) cc_final: 0.7021 (mt0) outliers start: 18 outliers final: 14 residues processed: 188 average time/residue: 0.1344 time to fit residues: 34.6437 Evaluate side-chains 177 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 161 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain E residue 101 GLN Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 219 THR Chi-restraints excluded: chain E residue 238 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 154 optimal weight: 1.9990 chunk 35 optimal weight: 5.9990 chunk 46 optimal weight: 0.8980 chunk 122 optimal weight: 4.9990 chunk 62 optimal weight: 8.9990 chunk 30 optimal weight: 0.9990 chunk 83 optimal weight: 5.9990 chunk 17 optimal weight: 5.9990 chunk 89 optimal weight: 1.9990 chunk 124 optimal weight: 10.0000 chunk 91 optimal weight: 1.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.124359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.092833 restraints weight = 15859.034| |-----------------------------------------------------------------------------| r_work (start): 0.2888 rms_B_bonded: 1.73 r_work: 0.2761 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2623 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8757 moved from start: 0.1104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 13657 Z= 0.145 Angle : 0.531 9.022 18496 Z= 0.274 Chirality : 0.043 0.143 2091 Planarity : 0.004 0.048 2257 Dihedral : 14.771 173.690 2290 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 2.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 1.57 % Allowed : 13.43 % Favored : 85.00 % 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: 1.34 (0.22), residues: 1550 helix: 3.32 (0.21), residues: 520 sheet: 0.65 (0.25), residues: 415 loop : -1.18 (0.24), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 50 TYR 0.017 0.001 TYR B 102 PHE 0.030 0.001 PHE D 54 TRP 0.009 0.001 TRP A 47 HIS 0.002 0.001 HIS E 277 Details of bonding type rmsd covalent geometry : bond 0.00348 (13657) covalent geometry : angle 0.53077 (18496) hydrogen bonds : bond 0.06146 ( 613) hydrogen bonds : angle 3.91158 ( 2067) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3053.53 seconds wall clock time: 52 minutes 54.08 seconds (3174.08 seconds total)