Starting phenix.real_space_refine on Fri Jul 3 10:26:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lbd_62941/07_2026/9lbd_62941.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lbd_62941/07_2026/9lbd_62941.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9lbd_62941/07_2026/9lbd_62941.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lbd_62941/07_2026/9lbd_62941.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9lbd_62941/07_2026/9lbd_62941.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lbd_62941/07_2026/9lbd_62941.map" } resolution = 2.14 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 20 5.49 5 S 20 5.16 5 Cl 5 4.86 5 C 8865 2.51 5 N 2030 2.21 5 O 2430 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13370 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 2523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 2523 Classifications: {'peptide': 312} Link IDs: {'PTRANS': 18, 'TRANS': 293} Chain: "B" Number of atoms: 2523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 2523 Classifications: {'peptide': 312} Link IDs: {'PTRANS': 18, 'TRANS': 293} Chain: "C" Number of atoms: 2523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 2523 Classifications: {'peptide': 312} Link IDs: {'PTRANS': 18, 'TRANS': 293} Chain: "D" Number of atoms: 2523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 2523 Classifications: {'peptide': 312} Link IDs: {'PTRANS': 18, 'TRANS': 293} Chain: "E" Number of atoms: 2523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 2523 Classifications: {'peptide': 312} Link IDs: {'PTRANS': 18, 'TRANS': 293} Chain: "A" Number of atoms: 151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 150 Ad-hoc single atom residues: {' CL': 1} Unusual residues: {'PEE': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain breaks: 1 Unresolved non-hydrogen bonds: 105 Unresolved non-hydrogen angles: 111 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: 8 Chain: "B" Number of atoms: 151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 150 Ad-hoc single atom residues: {' CL': 1} Unusual residues: {'PEE': 5} Classifications: {'undetermined': 5} Link IDs: {None: 3} Chain breaks: 1 Unresolved non-hydrogen bonds: 105 Unresolved non-hydrogen angles: 111 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: 8 Chain: "C" Number of atoms: 151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 150 Ad-hoc single atom residues: {' CL': 1} Unusual residues: {'PEE': 5} Classifications: {'undetermined': 5} Link IDs: {None: 3} Chain breaks: 1 Unresolved non-hydrogen bonds: 105 Unresolved non-hydrogen angles: 111 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: 8 Chain: "D" Number of atoms: 151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 150 Ad-hoc single atom residues: {' CL': 1} Unusual residues: {'PEE': 5} Classifications: {'undetermined': 5} Link IDs: {None: 3} Chain breaks: 1 Unresolved non-hydrogen bonds: 105 Unresolved non-hydrogen angles: 111 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: 8 Chain: "E" Number of atoms: 151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 150 Ad-hoc single atom residues: {' CL': 1} Unusual residues: {'PEE': 5} Classifications: {'undetermined': 5} Link IDs: {None: 3} Chain breaks: 1 Unresolved non-hydrogen bonds: 105 Unresolved non-hydrogen angles: 111 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: 8 Time building chain proxies: 2.35, per 1000 atoms: 0.18 Number of scatterers: 13370 At special positions: 0 Unit cell: (92.72, 91.96, 128.44, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 5 17.00 S 20 16.00 P 20 15.00 O 2430 8.00 N 2030 7.00 C 8865 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: 1.01 Conformation dependent library (CDL) restraints added in 417.2 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: 45 helices and 20 sheets defined 41.0% alpha, 51.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'A' and resid 50 through 53 Processing helix chain 'A' and resid 55 through 60 Processing helix chain 'A' and resid 118 through 121 Processing helix chain 'A' and resid 146 through 149 removed outlier: 3.889A pdb=" N VAL A 149 " --> pdb=" O LEU A 146 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 146 through 149' Processing helix chain 'A' and resid 196 through 213 removed outlier: 3.513A pdb=" N ASN A 200 " --> pdb=" O SER A 196 " (cutoff:3.500A) removed outlier: 5.228A pdb=" N LEU A 203 " --> pdb=" O PRO A 199 " (cutoff:3.500A) Proline residue: A 204 - end of helix Processing helix chain 'A' and resid 214 through 218 Processing helix chain 'A' and resid 220 through 243 Processing helix chain 'A' and resid 253 through 282 Processing helix chain 'A' and resid 284 through 316 removed outlier: 3.626A pdb=" N ALA A 288 " --> pdb=" O GLN A 284 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ILE A 297 " --> pdb=" O ARG A 293 " (cutoff:3.500A) Proline residue: A 300 - end of helix Processing helix chain 'B' and resid 50 through 53 Processing helix chain 'B' and resid 55 through 60 Processing helix chain 'B' and resid 118 through 121 Processing helix chain 'B' and resid 146 through 149 removed outlier: 3.889A pdb=" N VAL B 149 " --> pdb=" O LEU B 146 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 146 through 149' Processing helix chain 'B' and resid 196 through 213 removed outlier: 3.513A pdb=" N ASN B 200 " --> pdb=" O SER B 196 " (cutoff:3.500A) removed outlier: 5.227A pdb=" N LEU B 203 " --> pdb=" O PRO B 199 " (cutoff:3.500A) Proline residue: B 204 - end of helix Processing helix chain 'B' and resid 214 through 218 Processing helix chain 'B' and resid 220 through 243 Processing helix chain 'B' and resid 253 through 282 Processing helix chain 'B' and resid 284 through 316 removed outlier: 3.626A pdb=" N ALA B 288 " --> pdb=" O GLN B 284 " (cutoff:3.500A) removed outlier: 3.822A 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: 3.889A pdb=" N VAL C 149 " --> pdb=" O LEU C 146 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 146 through 149' Processing helix chain 'C' and resid 196 through 213 removed outlier: 3.513A pdb=" N ASN C 200 " --> pdb=" O SER C 196 " (cutoff:3.500A) removed outlier: 5.228A pdb=" N LEU C 203 " --> pdb=" O PRO C 199 " (cutoff:3.500A) Proline residue: C 204 - end of helix Processing helix chain 'C' and resid 214 through 218 Processing helix chain 'C' and resid 220 through 243 Processing helix chain 'C' and resid 253 through 282 Processing helix chain 'C' and resid 284 through 316 removed outlier: 3.626A pdb=" N ALA C 288 " --> pdb=" O GLN C 284 " (cutoff:3.500A) removed outlier: 3.822A 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: 3.889A pdb=" N VAL D 149 " --> pdb=" O LEU D 146 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 146 through 149' Processing helix chain 'D' and resid 196 through 213 removed outlier: 3.513A pdb=" N ASN D 200 " --> pdb=" O SER D 196 " (cutoff:3.500A) removed outlier: 5.228A pdb=" N LEU D 203 " --> pdb=" O PRO D 199 " (cutoff:3.500A) Proline residue: D 204 - end of helix Processing helix chain 'D' and resid 214 through 218 Processing helix chain 'D' and resid 220 through 243 Processing helix chain 'D' and resid 253 through 282 Processing helix chain 'D' and resid 284 through 316 removed outlier: 3.626A pdb=" N ALA D 288 " --> pdb=" O GLN D 284 " (cutoff:3.500A) removed outlier: 3.821A 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: 3.888A pdb=" N VAL E 149 " --> pdb=" O LEU E 146 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 146 through 149' Processing helix chain 'E' and resid 196 through 213 removed outlier: 3.513A pdb=" N ASN E 200 " --> pdb=" O SER E 196 " (cutoff:3.500A) removed outlier: 5.228A pdb=" N LEU E 203 " --> pdb=" O PRO E 199 " (cutoff:3.500A) Proline residue: E 204 - end of helix Processing helix chain 'E' and resid 214 through 218 Processing helix chain 'E' and resid 220 through 243 Processing helix chain 'E' and resid 253 through 282 Processing helix chain 'E' and resid 284 through 316 removed outlier: 3.626A pdb=" N ALA E 288 " --> pdb=" O GLN E 284 " (cutoff:3.500A) removed outlier: 3.822A 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 64 through 65 removed outlier: 5.532A pdb=" N ALA A 87 " --> pdb=" O SER A 107 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N SER A 107 " --> pdb=" O ALA A 87 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N VAL A 89 " --> pdb=" O ARG A 105 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N ARG A 105 " --> pdb=" O VAL A 89 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASP A 91 " --> pdb=" O LEU A 103 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LYS A 38 " --> pdb=" O SER A 29 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N SER A 29 " --> pdb=" O LYS A 38 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N ASN A 40 " --> pdb=" O CYS A 27 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N CYS A 27 " --> pdb=" O ASN A 40 " (cutoff:3.500A) removed outlier: 8.489A pdb=" N PHE A 42 " --> pdb=" O ILE A 25 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N ILE A 25 " --> pdb=" O PHE A 42 " (cutoff:3.500A) removed outlier: 8.159A pdb=" N SER A 44 " --> pdb=" O TYR A 23 " (cutoff:3.500A) removed outlier: 8.083A pdb=" N TYR A 23 " --> pdb=" O SER A 44 " (cutoff:3.500A) removed outlier: 8.433A pdb=" N SER A 46 " --> pdb=" O GLY A 21 " (cutoff:3.500A) removed outlier: 8.593A pdb=" N GLY A 21 " --> pdb=" O SER A 46 " (cutoff:3.500A) removed outlier: 9.070A pdb=" N LYS A 48 " --> pdb=" O ASN A 19 " (cutoff:3.500A) removed outlier: 9.894A pdb=" N ASN A 19 " --> pdb=" O LYS A 48 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N LEU A 16 " --> pdb=" O VAL A 141 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N ALA A 143 " --> pdb=" O LEU A 16 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N VAL A 18 " --> pdb=" O ALA A 143 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 64 through 65 removed outlier: 5.532A pdb=" N ALA A 87 " --> pdb=" O SER A 107 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N SER A 107 " --> pdb=" O ALA A 87 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N VAL A 89 " --> pdb=" O ARG A 105 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N ARG A 105 " --> pdb=" O VAL A 89 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASP A 91 " --> pdb=" O LEU A 103 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LYS A 38 " --> pdb=" O SER A 29 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N SER A 29 " --> pdb=" O LYS A 38 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N ASN A 40 " --> pdb=" O CYS A 27 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N CYS A 27 " --> pdb=" O ASN A 40 " (cutoff:3.500A) removed outlier: 8.489A pdb=" N PHE A 42 " --> pdb=" O ILE A 25 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N ILE A 25 " --> pdb=" O PHE A 42 " (cutoff:3.500A) removed outlier: 8.159A pdb=" N SER A 44 " --> pdb=" O TYR A 23 " (cutoff:3.500A) removed outlier: 8.083A pdb=" N TYR A 23 " --> pdb=" O SER A 44 " (cutoff:3.500A) removed outlier: 8.433A pdb=" N SER A 46 " --> pdb=" O GLY A 21 " (cutoff:3.500A) removed outlier: 8.593A pdb=" N GLY A 21 " --> pdb=" O SER A 46 " (cutoff:3.500A) removed outlier: 9.070A pdb=" N LYS A 48 " --> pdb=" O ASN A 19 " (cutoff:3.500A) removed outlier: 9.894A pdb=" N ASN A 19 " --> pdb=" O LYS A 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 76 through 78 removed outlier: 7.191A pdb=" N ASP A 185 " --> pdb=" O ALA A 167 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N ALA A 167 " --> pdb=" O ASP A 185 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N GLN A 187 " --> pdb=" O PHE A 165 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N PHE A 165 " --> pdb=" O GLN A 187 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N ARG A 189 " --> pdb=" O GLU A 163 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 76 through 78 Processing sheet with id=AA5, first strand: chain 'B' and resid 64 through 65 removed outlier: 5.532A pdb=" N ALA B 87 " --> pdb=" O SER B 107 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N SER B 107 " --> pdb=" O ALA B 87 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N VAL B 89 " --> pdb=" O ARG B 105 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N ARG B 105 " --> pdb=" O VAL B 89 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ASP B 91 " --> pdb=" O LEU B 103 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LYS B 38 " --> pdb=" O SER B 29 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N SER B 29 " --> pdb=" O LYS B 38 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N ASN B 40 " --> pdb=" O CYS B 27 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N CYS B 27 " --> pdb=" O ASN B 40 " (cutoff:3.500A) removed outlier: 8.490A pdb=" N PHE B 42 " --> pdb=" O ILE B 25 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N ILE B 25 " --> pdb=" O PHE B 42 " (cutoff:3.500A) removed outlier: 8.159A pdb=" N SER B 44 " --> pdb=" O TYR B 23 " (cutoff:3.500A) removed outlier: 8.083A pdb=" N TYR B 23 " --> pdb=" O SER B 44 " (cutoff:3.500A) removed outlier: 8.434A pdb=" N SER B 46 " --> pdb=" O GLY B 21 " (cutoff:3.500A) removed outlier: 8.593A pdb=" N GLY B 21 " --> pdb=" O SER B 46 " (cutoff:3.500A) removed outlier: 9.069A pdb=" N LYS B 48 " --> pdb=" O ASN B 19 " (cutoff:3.500A) removed outlier: 9.895A pdb=" N ASN B 19 " --> pdb=" O LYS B 48 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N LEU B 16 " --> pdb=" O VAL B 141 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N ALA B 143 " --> pdb=" O LEU B 16 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N VAL B 18 " --> pdb=" O ALA B 143 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 64 through 65 removed outlier: 5.532A pdb=" N ALA B 87 " --> pdb=" O SER B 107 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N SER B 107 " --> pdb=" O ALA B 87 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N VAL B 89 " --> pdb=" O ARG B 105 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N ARG B 105 " --> pdb=" O VAL B 89 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ASP B 91 " --> pdb=" O LEU B 103 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LYS B 38 " --> pdb=" O SER B 29 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N SER B 29 " --> pdb=" O LYS B 38 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N ASN B 40 " --> pdb=" O CYS B 27 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N CYS B 27 " --> pdb=" O ASN B 40 " (cutoff:3.500A) removed outlier: 8.490A pdb=" N PHE B 42 " --> pdb=" O ILE B 25 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N ILE B 25 " --> pdb=" O PHE B 42 " (cutoff:3.500A) removed outlier: 8.159A pdb=" N SER B 44 " --> pdb=" O TYR B 23 " (cutoff:3.500A) removed outlier: 8.083A pdb=" N TYR B 23 " --> pdb=" O SER B 44 " (cutoff:3.500A) removed outlier: 8.434A pdb=" N SER B 46 " --> pdb=" O GLY B 21 " (cutoff:3.500A) removed outlier: 8.593A pdb=" N GLY B 21 " --> pdb=" O SER B 46 " (cutoff:3.500A) removed outlier: 9.069A pdb=" N LYS B 48 " --> pdb=" O ASN B 19 " (cutoff:3.500A) removed outlier: 9.895A pdb=" N ASN B 19 " --> pdb=" O LYS B 48 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 76 through 78 removed outlier: 7.191A pdb=" N ASP B 185 " --> pdb=" O ALA B 167 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N ALA B 167 " --> pdb=" O ASP B 185 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N GLN B 187 " --> pdb=" O PHE B 165 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N PHE B 165 " --> pdb=" O GLN B 187 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N ARG B 189 " --> pdb=" O GLU B 163 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 76 through 78 Processing sheet with id=AA9, first strand: chain 'C' and resid 64 through 65 removed outlier: 5.532A pdb=" N ALA C 87 " --> pdb=" O SER C 107 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N SER C 107 " --> pdb=" O ALA C 87 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N VAL C 89 " --> pdb=" O ARG C 105 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N ARG C 105 " --> pdb=" O VAL C 89 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ASP C 91 " --> pdb=" O LEU C 103 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LYS C 38 " --> pdb=" O SER C 29 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N SER C 29 " --> pdb=" O LYS C 38 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N ASN C 40 " --> pdb=" O CYS C 27 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N CYS C 27 " --> pdb=" O ASN C 40 " (cutoff:3.500A) removed outlier: 8.490A pdb=" N PHE C 42 " --> pdb=" O ILE C 25 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N ILE C 25 " --> pdb=" O PHE C 42 " (cutoff:3.500A) removed outlier: 8.160A pdb=" N SER C 44 " --> pdb=" O TYR C 23 " (cutoff:3.500A) removed outlier: 8.083A pdb=" N TYR C 23 " --> pdb=" O SER C 44 " (cutoff:3.500A) removed outlier: 8.433A pdb=" N SER C 46 " --> pdb=" O GLY C 21 " (cutoff:3.500A) removed outlier: 8.592A pdb=" N GLY C 21 " --> pdb=" O SER C 46 " (cutoff:3.500A) removed outlier: 9.069A pdb=" N LYS C 48 " --> pdb=" O ASN C 19 " (cutoff:3.500A) removed outlier: 9.894A pdb=" N ASN C 19 " --> pdb=" O LYS C 48 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N LEU C 16 " --> pdb=" O VAL C 141 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N ALA C 143 " --> pdb=" O LEU C 16 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N VAL C 18 " --> pdb=" O ALA C 143 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 64 through 65 removed outlier: 5.532A pdb=" N ALA C 87 " --> pdb=" O SER C 107 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N SER C 107 " --> pdb=" O ALA C 87 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N VAL C 89 " --> pdb=" O ARG C 105 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N ARG C 105 " --> pdb=" O VAL C 89 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ASP C 91 " --> pdb=" O LEU C 103 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LYS C 38 " --> pdb=" O SER C 29 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N SER C 29 " --> pdb=" O LYS C 38 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N ASN C 40 " --> pdb=" O CYS C 27 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N CYS C 27 " --> pdb=" O ASN C 40 " (cutoff:3.500A) removed outlier: 8.490A pdb=" N PHE C 42 " --> pdb=" O ILE C 25 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N ILE C 25 " --> pdb=" O PHE C 42 " (cutoff:3.500A) removed outlier: 8.160A pdb=" N SER C 44 " --> pdb=" O TYR C 23 " (cutoff:3.500A) removed outlier: 8.083A pdb=" N TYR C 23 " --> pdb=" O SER C 44 " (cutoff:3.500A) removed outlier: 8.433A pdb=" N SER C 46 " --> pdb=" O GLY C 21 " (cutoff:3.500A) removed outlier: 8.592A pdb=" N GLY C 21 " --> pdb=" O SER C 46 " (cutoff:3.500A) removed outlier: 9.069A pdb=" N LYS C 48 " --> pdb=" O ASN C 19 " (cutoff:3.500A) removed outlier: 9.894A pdb=" N ASN C 19 " --> pdb=" O LYS C 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 76 through 78 removed outlier: 7.191A pdb=" N ASP C 185 " --> pdb=" O ALA C 167 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N ALA C 167 " --> pdb=" O ASP C 185 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N GLN C 187 " --> pdb=" O PHE C 165 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N PHE C 165 " --> pdb=" O GLN C 187 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N ARG C 189 " --> pdb=" O GLU C 163 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 76 through 78 Processing sheet with id=AB4, first strand: chain 'D' and resid 64 through 65 removed outlier: 5.532A pdb=" N ALA D 87 " --> pdb=" O SER D 107 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N SER D 107 " --> pdb=" O ALA D 87 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N VAL D 89 " --> pdb=" O ARG D 105 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N ARG D 105 " --> pdb=" O VAL D 89 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASP D 91 " --> pdb=" O LEU D 103 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LYS D 38 " --> pdb=" O SER D 29 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N SER D 29 " --> pdb=" O LYS D 38 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N ASN D 40 " --> pdb=" O CYS D 27 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N CYS D 27 " --> pdb=" O ASN D 40 " (cutoff:3.500A) removed outlier: 8.490A pdb=" N PHE D 42 " --> pdb=" O ILE D 25 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N ILE D 25 " --> pdb=" O PHE D 42 " (cutoff:3.500A) removed outlier: 8.159A pdb=" N SER D 44 " --> pdb=" O TYR D 23 " (cutoff:3.500A) removed outlier: 8.084A pdb=" N TYR D 23 " --> pdb=" O SER D 44 " (cutoff:3.500A) removed outlier: 8.433A pdb=" N SER D 46 " --> pdb=" O GLY D 21 " (cutoff:3.500A) removed outlier: 8.593A pdb=" N GLY D 21 " --> pdb=" O SER D 46 " (cutoff:3.500A) removed outlier: 9.070A pdb=" N LYS D 48 " --> pdb=" O ASN D 19 " (cutoff:3.500A) removed outlier: 9.894A pdb=" N ASN D 19 " --> pdb=" O LYS D 48 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N LEU D 16 " --> pdb=" O VAL D 141 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N ALA D 143 " --> pdb=" O LEU D 16 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N VAL D 18 " --> pdb=" O ALA D 143 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 64 through 65 removed outlier: 5.532A pdb=" N ALA D 87 " --> pdb=" O SER D 107 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N SER D 107 " --> pdb=" O ALA D 87 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N VAL D 89 " --> pdb=" O ARG D 105 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N ARG D 105 " --> pdb=" O VAL D 89 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASP D 91 " --> pdb=" O LEU D 103 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LYS D 38 " --> pdb=" O SER D 29 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N SER D 29 " --> pdb=" O LYS D 38 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N ASN D 40 " --> pdb=" O CYS D 27 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N CYS D 27 " --> pdb=" O ASN D 40 " (cutoff:3.500A) removed outlier: 8.490A pdb=" N PHE D 42 " --> pdb=" O ILE D 25 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N ILE D 25 " --> pdb=" O PHE D 42 " (cutoff:3.500A) removed outlier: 8.159A pdb=" N SER D 44 " --> pdb=" O TYR D 23 " (cutoff:3.500A) removed outlier: 8.084A pdb=" N TYR D 23 " --> pdb=" O SER D 44 " (cutoff:3.500A) removed outlier: 8.433A pdb=" N SER D 46 " --> pdb=" O GLY D 21 " (cutoff:3.500A) removed outlier: 8.593A pdb=" N GLY D 21 " --> pdb=" O SER D 46 " (cutoff:3.500A) removed outlier: 9.070A pdb=" N LYS D 48 " --> pdb=" O ASN D 19 " (cutoff:3.500A) removed outlier: 9.894A pdb=" N ASN D 19 " --> pdb=" O LYS D 48 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 76 through 78 removed outlier: 7.191A pdb=" N ASP D 185 " --> pdb=" O ALA D 167 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N ALA D 167 " --> pdb=" O ASP D 185 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N GLN D 187 " --> pdb=" O PHE D 165 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N PHE D 165 " --> pdb=" O GLN D 187 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N ARG D 189 " --> pdb=" O GLU D 163 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 76 through 78 Processing sheet with id=AB8, first strand: chain 'E' and resid 64 through 65 removed outlier: 5.533A pdb=" N ALA E 87 " --> pdb=" O SER E 107 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N SER E 107 " --> pdb=" O ALA E 87 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N VAL E 89 " --> pdb=" O ARG E 105 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N ARG E 105 " --> pdb=" O VAL E 89 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASP E 91 " --> pdb=" O LEU E 103 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LYS E 38 " --> pdb=" O SER E 29 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N SER E 29 " --> pdb=" O LYS E 38 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N ASN E 40 " --> pdb=" O CYS E 27 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N CYS E 27 " --> pdb=" O ASN E 40 " (cutoff:3.500A) removed outlier: 8.489A pdb=" N PHE E 42 " --> pdb=" O ILE E 25 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N ILE E 25 " --> pdb=" O PHE E 42 " (cutoff:3.500A) removed outlier: 8.159A pdb=" N SER E 44 " --> pdb=" O TYR E 23 " (cutoff:3.500A) removed outlier: 8.083A pdb=" N TYR E 23 " --> pdb=" O SER E 44 " (cutoff:3.500A) removed outlier: 8.433A pdb=" N SER E 46 " --> pdb=" O GLY E 21 " (cutoff:3.500A) removed outlier: 8.592A pdb=" N GLY E 21 " --> pdb=" O SER E 46 " (cutoff:3.500A) removed outlier: 9.070A pdb=" N LYS E 48 " --> pdb=" O ASN E 19 " (cutoff:3.500A) removed outlier: 9.894A pdb=" N ASN E 19 " --> pdb=" O LYS E 48 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N LEU E 16 " --> pdb=" O VAL E 141 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N ALA E 143 " --> pdb=" O LEU E 16 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N VAL E 18 " --> pdb=" O ALA E 143 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 64 through 65 removed outlier: 5.533A pdb=" N ALA E 87 " --> pdb=" O SER E 107 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N SER E 107 " --> pdb=" O ALA E 87 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N VAL E 89 " --> pdb=" O ARG E 105 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N ARG E 105 " --> pdb=" O VAL E 89 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASP E 91 " --> pdb=" O LEU E 103 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LYS E 38 " --> pdb=" O SER E 29 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N SER E 29 " --> pdb=" O LYS E 38 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N ASN E 40 " --> pdb=" O CYS E 27 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N CYS E 27 " --> pdb=" O ASN E 40 " (cutoff:3.500A) removed outlier: 8.489A pdb=" N PHE E 42 " --> pdb=" O ILE E 25 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N ILE E 25 " --> pdb=" O PHE E 42 " (cutoff:3.500A) removed outlier: 8.159A pdb=" N SER E 44 " --> pdb=" O TYR E 23 " (cutoff:3.500A) removed outlier: 8.083A pdb=" N TYR E 23 " --> pdb=" O SER E 44 " (cutoff:3.500A) removed outlier: 8.433A pdb=" N SER E 46 " --> pdb=" O GLY E 21 " (cutoff:3.500A) removed outlier: 8.592A pdb=" N GLY E 21 " --> pdb=" O SER E 46 " (cutoff:3.500A) removed outlier: 9.070A pdb=" N LYS E 48 " --> pdb=" O ASN E 19 " (cutoff:3.500A) removed outlier: 9.894A pdb=" N ASN E 19 " --> pdb=" O LYS E 48 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 76 through 78 removed outlier: 7.191A pdb=" N ASP E 185 " --> pdb=" O ALA E 167 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N ALA E 167 " --> pdb=" O ASP E 185 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N GLN E 187 " --> pdb=" O PHE E 165 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N PHE E 165 " --> pdb=" O GLN E 187 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N ARG E 189 " --> pdb=" O GLU E 163 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 76 through 78 780 hydrogen bonds defined for protein. 2190 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.33 Time building geometry restraints manager: 1.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2162 1.33 - 1.45: 3612 1.45 - 1.57: 7826 1.57 - 1.69: 40 1.69 - 1.81: 35 Bond restraints: 13675 Sorted by residual: bond pdb=" N ASP D 88 " pdb=" CA ASP D 88 " ideal model delta sigma weight residual 1.455 1.489 -0.034 1.25e-02 6.40e+03 7.24e+00 bond pdb=" N ASP B 88 " pdb=" CA ASP B 88 " ideal model delta sigma weight residual 1.455 1.489 -0.034 1.25e-02 6.40e+03 7.24e+00 bond pdb=" N ASP A 88 " pdb=" CA ASP A 88 " ideal model delta sigma weight residual 1.455 1.489 -0.033 1.25e-02 6.40e+03 7.15e+00 bond pdb=" N ASP C 88 " pdb=" CA ASP C 88 " ideal model delta sigma weight residual 1.455 1.488 -0.033 1.25e-02 6.40e+03 7.13e+00 bond pdb=" N ASP E 88 " pdb=" CA ASP E 88 " ideal model delta sigma weight residual 1.455 1.488 -0.033 1.25e-02 6.40e+03 6.97e+00 ... (remaining 13670 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.10: 17945 1.10 - 2.20: 432 2.20 - 3.30: 103 3.30 - 4.40: 20 4.40 - 5.50: 25 Bond angle restraints: 18525 Sorted by residual: angle pdb=" CA ASP E 88 " pdb=" C ASP E 88 " pdb=" O ASP E 88 " ideal model delta sigma weight residual 120.60 117.56 3.04 1.20e+00 6.94e-01 6.42e+00 angle pdb=" CA ASP D 88 " pdb=" C ASP D 88 " pdb=" O ASP D 88 " ideal model delta sigma weight residual 120.60 117.56 3.04 1.20e+00 6.94e-01 6.41e+00 angle pdb=" CA ASP A 88 " pdb=" C ASP A 88 " pdb=" O ASP A 88 " ideal model delta sigma weight residual 120.60 117.57 3.03 1.20e+00 6.94e-01 6.36e+00 angle pdb=" CA ASP C 88 " pdb=" C ASP C 88 " pdb=" O ASP C 88 " ideal model delta sigma weight residual 120.60 117.61 2.99 1.20e+00 6.94e-01 6.21e+00 angle pdb=" CA ASP B 88 " pdb=" C ASP B 88 " pdb=" O ASP B 88 " ideal model delta sigma weight residual 120.60 117.61 2.99 1.20e+00 6.94e-01 6.21e+00 ... (remaining 18520 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.13: 7865 33.13 - 66.26: 335 66.26 - 99.40: 60 99.40 - 132.53: 20 132.53 - 165.66: 10 Dihedral angle restraints: 8290 sinusoidal: 3610 harmonic: 4680 Sorted by residual: dihedral pdb=" C4 PEE C 406 " pdb=" O4P PEE C 406 " pdb=" P PEE C 406 " pdb=" O2P PEE C 406 " ideal model delta sinusoidal sigma weight residual 284.22 118.56 165.66 1 3.00e+01 1.11e-03 2.10e+01 dihedral pdb=" C4 PEE B 406 " pdb=" O4P PEE B 406 " pdb=" P PEE B 406 " pdb=" O2P PEE B 406 " ideal model delta sinusoidal sigma weight residual 284.22 118.58 165.64 1 3.00e+01 1.11e-03 2.10e+01 dihedral pdb=" C4 PEE A 405 " pdb=" O4P PEE A 405 " pdb=" P PEE A 405 " pdb=" O2P PEE A 405 " ideal model delta sinusoidal sigma weight residual 284.22 118.59 165.63 1 3.00e+01 1.11e-03 2.10e+01 ... (remaining 8287 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1378 0.032 - 0.065: 459 0.065 - 0.097: 156 0.097 - 0.129: 93 0.129 - 0.162: 9 Chirality restraints: 2095 Sorted by residual: chirality pdb=" CA ILE B 71 " pdb=" N ILE B 71 " pdb=" C ILE B 71 " pdb=" CB ILE B 71 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.53e-01 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 2.59 -0.16 2.00e-01 2.50e+01 6.46e-01 chirality pdb=" CA ILE C 71 " pdb=" N ILE C 71 " pdb=" C ILE C 71 " pdb=" CB ILE C 71 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.40e-01 ... (remaining 2092 not shown) Planarity restraints: 2260 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG D 50 " 0.138 9.50e-02 1.11e+02 6.25e-02 3.07e+00 pdb=" NE ARG D 50 " -0.013 2.00e-02 2.50e+03 pdb=" CZ ARG D 50 " 0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG D 50 " -0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG D 50 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 50 " 0.139 9.50e-02 1.11e+02 6.27e-02 3.07e+00 pdb=" NE ARG C 50 " -0.013 2.00e-02 2.50e+03 pdb=" CZ ARG C 50 " 0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG C 50 " -0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG C 50 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 50 " -0.138 9.50e-02 1.11e+02 6.25e-02 3.06e+00 pdb=" NE ARG A 50 " 0.013 2.00e-02 2.50e+03 pdb=" CZ ARG A 50 " -0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG A 50 " 0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG A 50 " -0.000 2.00e-02 2.50e+03 ... (remaining 2257 not shown) Histogram of nonbonded interaction distances: 2.41 - 2.91: 5065 2.91 - 3.41: 11573 3.41 - 3.91: 21778 3.91 - 4.40: 24052 4.40 - 4.90: 41551 Nonbonded interactions: 104019 Sorted by model distance: nonbonded pdb=" O SER C 6 " pdb=" NH2 ARG C 51 " model vdw 2.414 3.120 nonbonded pdb=" O SER D 6 " pdb=" NH2 ARG D 51 " model vdw 2.415 3.120 nonbonded pdb=" O SER A 6 " pdb=" NH2 ARG A 51 " model vdw 2.415 3.120 nonbonded pdb=" O SER E 6 " pdb=" NH2 ARG E 51 " model vdw 2.415 3.120 nonbonded pdb=" O SER B 6 " pdb=" NH2 ARG B 51 " model vdw 2.415 3.120 ... (remaining 104014 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: 0.01 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 5 through 316 or (resid 403 and (name C1 or name C10 or na \ me C11 or name C12 or name C13 or name C14 or name C15 or name C16 or name C17 o \ r name C2 or name C3 or name C30 or name C31 or name C32 or name C33 or name C34 \ or name C35 or name C36 or name O1P or name O2 or name O2P or name O3 or name O \ 3P or name O4 or name O4P or name O5 or name P )) or (resid 404 and (name C12 or \ name C13 or name C14 or name C15 or name C16 or name C17 or name C18 or name C1 \ 9 or name C20 or name C21 or name C22 or name C23)) or (resid 406 and (name C1 o \ r name C10 or name C11 or name C12 or name C13 or name C14 or name C15 or name C \ 16 or name C2 or name C3 or name C30 or name C31 or name C32 or name C33 or name \ C34 or name C35 or name C36 or name C37 or name O1P or name O2 or name O2P or n \ ame O3 or name O3P or name O4 or name O4P or name O5 or name P )))) selection = (chain 'B' and (resid 5 through 316 or resid 403 or (resid 404 and (name C12 or \ name C13 or name C14 or name C15 or name C16 or name C17 or name C18 or name C19 \ or name C20 or name C21 or name C22 or name C23)) or (resid 406 and (name C1 or \ name C10 or name C11 or name C12 or name C13 or name C14 or name C15 or name C1 \ 6 or name C2 or name C3 or name C30 or name C31 or name C32 or name C33 or name \ C34 or name C35 or name C36 or name C37 or name O1P or name O2 or name O2P or na \ me O3 or name O3P or name O4 or name O4P or name O5 or name P )))) selection = (chain 'C' and (resid 5 through 316 or resid 403 or (resid 404 and (name C12 or \ name C13 or name C14 or name C15 or name C16 or name C17 or name C18 or name C19 \ or name C20 or name C21 or name C22 or name C23)) or (resid 406 and (name C1 or \ name C10 or name C11 or name C12 or name C13 or name C14 or name C15 or name C1 \ 6 or name C2 or name C3 or name C30 or name C31 or name C32 or name C33 or name \ C34 or name C35 or name C36 or name C37 or name O1P or name O2 or name O2P or na \ me O3 or name O3P or name O4 or name O4P or name O5 or name P )))) selection = (chain 'D' and (resid 5 through 316 or resid 403 or (resid 404 and (name C12 or \ name C13 or name C14 or name C15 or name C16 or name C17 or name C18 or name C19 \ or name C20 or name C21 or name C22 or name C23)) or (resid 406 and (name C1 or \ name C10 or name C11 or name C12 or name C13 or name C14 or name C15 or name C1 \ 6 or name C2 or name C3 or name C30 or name C31 or name C32 or name C33 or name \ C34 or name C35 or name C36 or name C37 or name O1P or name O2 or name O2P or na \ me O3 or name O3P or name O4 or name O4P or name O5 or name P )))) selection = (chain 'E' and (resid 5 through 316 or resid 403 or (resid 404 and (name C12 or \ name C13 or name C14 or name C15 or name C16 or name C17 or name C18 or name C19 \ or name C20 or name C21 or name C22 or name C23)) or (resid 406 and (name C1 or \ name C10 or name C11 or name C12 or name C13 or name C14 or name C15 or name C1 \ 6 or name C2 or name C3 or name C30 or name C31 or name C32 or name C33 or name \ C34 or name C35 or name C36 or name C37 or name O1P or name O2 or name O2P or na \ me O3 or name O3P or name O4 or name O4P or name O5 or name P )))) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 1.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 11.260 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.030 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:8.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8898 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 : 0.002 0.034 13675 Z= 0.131 Angle : 0.498 5.503 18525 Z= 0.277 Chirality : 0.042 0.162 2095 Planarity : 0.005 0.063 2260 Dihedral : 20.378 165.662 5240 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 0.00 % Allowed : 19.00 % Favored : 81.00 % 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: 1.59 (0.22), residues: 1550 helix: 3.04 (0.20), residues: 515 sheet: 0.12 (0.25), residues: 480 loop : 0.10 (0.27), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG D 50 TYR 0.012 0.001 TYR C 197 PHE 0.007 0.001 PHE E 195 TRP 0.004 0.001 TRP B 47 HIS 0.002 0.001 HIS B 277 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.13 (13675) covalent geometry : angle 0.49796 / 0.28 (18525) hydrogen bonds : bond 0.16949 / 11.61 ( 625) hydrogen bonds : angle 5.92349 / 4.02 ( 2190) *********************** 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 143 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 143 time to evaluate : 0.402 Fit side-chains REVERT: A 50 ARG cc_start: 0.7999 (ptp-110) cc_final: 0.7663 (ptp90) REVERT: A 147 GLU cc_start: 0.8277 (mp0) cc_final: 0.8074 (mm-30) REVERT: A 180 LEU cc_start: 0.7771 (mm) cc_final: 0.7328 (tp) REVERT: A 312 PHE cc_start: 0.7872 (t80) cc_final: 0.6983 (m-10) REVERT: B 50 ARG cc_start: 0.7885 (ptp-110) cc_final: 0.7444 (ptp90) REVERT: B 67 GLU cc_start: 0.7962 (tp30) cc_final: 0.7672 (tp30) REVERT: B 69 GLU cc_start: 0.7324 (mp0) cc_final: 0.7045 (pm20) REVERT: B 147 GLU cc_start: 0.8426 (mp0) cc_final: 0.8165 (mm-30) REVERT: B 252 MET cc_start: 0.8774 (tpp) cc_final: 0.8550 (tpp) REVERT: B 312 PHE cc_start: 0.7829 (t80) cc_final: 0.6870 (m-10) REVERT: C 50 ARG cc_start: 0.7890 (ptp-110) cc_final: 0.7381 (ptp90) REVERT: C 147 GLU cc_start: 0.8422 (mp0) cc_final: 0.8151 (mm-30) REVERT: C 312 PHE cc_start: 0.7659 (t80) cc_final: 0.6772 (m-10) REVERT: D 50 ARG cc_start: 0.7871 (ptp-110) cc_final: 0.7554 (ptp90) REVERT: D 147 GLU cc_start: 0.8452 (mp0) cc_final: 0.8166 (mm-30) REVERT: D 179 ARG cc_start: 0.6282 (mmt-90) cc_final: 0.5907 (mmt-90) REVERT: D 312 PHE cc_start: 0.7636 (t80) cc_final: 0.6802 (m-10) REVERT: E 50 ARG cc_start: 0.7762 (ptp-110) cc_final: 0.7289 (ptp90) REVERT: E 147 GLU cc_start: 0.8332 (mp0) cc_final: 0.8061 (mm-30) REVERT: E 312 PHE cc_start: 0.7469 (t80) cc_final: 0.6752 (m-10) outliers start: 0 outliers final: 0 residues processed: 143 average time/residue: 0.6963 time to fit residues: 106.5960 Evaluate side-chains 131 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 131 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 98 optimal weight: 7.9990 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 9.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 9.9990 chunk 77 optimal weight: 0.2980 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 5.9990 chunk 149 optimal weight: 5.9990 overall best weight: 4.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.125929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.080832 restraints weight = 14667.440| |-----------------------------------------------------------------------------| r_work (start): 0.2905 rms_B_bonded: 1.89 r_work: 0.2775 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2657 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9102 moved from start: 0.1662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 13675 Z= 0.258 Angle : 0.691 6.770 18525 Z= 0.368 Chirality : 0.048 0.140 2095 Planarity : 0.005 0.041 2260 Dihedral : 20.543 167.597 2325 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 1.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.44 % Allowed : 14.19 % Favored : 83.37 % 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 (0.21), residues: 1550 helix: 2.88 (0.20), residues: 510 sheet: 0.18 (0.25), residues: 405 loop : -0.37 (0.24), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 296 TYR 0.020 0.002 TYR C 197 PHE 0.019 0.002 PHE B 195 TRP 0.010 0.002 TRP B 213 HIS 0.002 0.001 HIS A 127 Details of bonding type rmsd/Z covalent geometry : bond 0.00606 / 0.26 (13675) covalent geometry : angle 0.69122 / 0.37 (18525) hydrogen bonds : bond 0.11052 / 7.40 ( 625) hydrogen bonds : angle 4.84452 / 3.28 ( 2190) *********************** 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 161 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 127 time to evaluate : 0.475 Fit side-chains revert: symmetry clash REVERT: A 50 ARG cc_start: 0.7969 (ptp-110) cc_final: 0.7597 (ptp90) REVERT: A 147 GLU cc_start: 0.8350 (mp0) cc_final: 0.8135 (mm-30) REVERT: A 222 GLU cc_start: 0.8329 (OUTLIER) cc_final: 0.7993 (mm-30) REVERT: A 280 LYS cc_start: 0.8632 (OUTLIER) cc_final: 0.8416 (tttp) REVERT: B 50 ARG cc_start: 0.7901 (ptp-110) cc_final: 0.7463 (ptp90) REVERT: B 147 GLU cc_start: 0.8401 (mp0) cc_final: 0.8145 (mm-30) REVERT: B 222 GLU cc_start: 0.8353 (OUTLIER) cc_final: 0.8077 (mm-30) REVERT: B 312 PHE cc_start: 0.8080 (t80) cc_final: 0.7351 (m-10) REVERT: B 313 LEU cc_start: 0.8667 (OUTLIER) cc_final: 0.8221 (mp) REVERT: C 24 LEU cc_start: 0.9297 (OUTLIER) cc_final: 0.8845 (mp) REVERT: C 26 GLU cc_start: 0.8729 (OUTLIER) cc_final: 0.8480 (mm-30) REVERT: C 50 ARG cc_start: 0.7869 (ptp-110) cc_final: 0.7467 (ptm160) REVERT: C 147 GLU cc_start: 0.8451 (mp0) cc_final: 0.8223 (mm-30) REVERT: C 222 GLU cc_start: 0.8327 (OUTLIER) cc_final: 0.8077 (mm-30) REVERT: C 248 LYS cc_start: 0.8516 (mttp) cc_final: 0.8180 (mmtm) REVERT: C 312 PHE cc_start: 0.8096 (t80) cc_final: 0.7326 (m-10) REVERT: D 24 LEU cc_start: 0.9265 (OUTLIER) cc_final: 0.8834 (mp) REVERT: D 50 ARG cc_start: 0.7905 (ptp-110) cc_final: 0.7498 (ptm160) REVERT: D 147 GLU cc_start: 0.8592 (mp0) cc_final: 0.8322 (mm-30) REVERT: D 163 GLU cc_start: 0.8614 (mt-10) cc_final: 0.8357 (mp0) REVERT: D 179 ARG cc_start: 0.6689 (mmt-90) cc_final: 0.5982 (mmt-90) REVERT: D 222 GLU cc_start: 0.8297 (OUTLIER) cc_final: 0.8000 (mm-30) REVERT: D 313 LEU cc_start: 0.8739 (OUTLIER) cc_final: 0.8521 (mt) REVERT: E 24 LEU cc_start: 0.9289 (OUTLIER) cc_final: 0.8891 (mp) REVERT: E 147 GLU cc_start: 0.8431 (mp0) cc_final: 0.8184 (mm-30) REVERT: E 163 GLU cc_start: 0.8628 (OUTLIER) cc_final: 0.8070 (mt-10) REVERT: E 179 ARG cc_start: 0.6634 (mmt-90) cc_final: 0.6374 (mmt-90) REVERT: E 222 GLU cc_start: 0.8320 (OUTLIER) cc_final: 0.8017 (mm-30) outliers start: 34 outliers final: 7 residues processed: 149 average time/residue: 0.6604 time to fit residues: 105.6245 Evaluate side-chains 140 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 120 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 222 GLU Chi-restraints excluded: chain A residue 280 LYS Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 222 GLU Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 26 GLU Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 222 GLU Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 222 GLU Chi-restraints excluded: chain D residue 313 LEU Chi-restraints excluded: chain E residue 24 LEU Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 163 GLU Chi-restraints excluded: chain E residue 222 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 122 optimal weight: 4.9990 chunk 48 optimal weight: 9.9990 chunk 19 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 149 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 chunk 107 optimal weight: 0.6980 chunk 38 optimal weight: 3.9990 chunk 126 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.129266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.084640 restraints weight = 14719.009| |-----------------------------------------------------------------------------| r_work (start): 0.2964 rms_B_bonded: 1.90 r_work: 0.2838 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2721 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9049 moved from start: 0.1667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 13675 Z= 0.143 Angle : 0.547 6.410 18525 Z= 0.292 Chirality : 0.044 0.139 2095 Planarity : 0.004 0.041 2260 Dihedral : 19.649 170.500 2325 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 1.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.29 % Allowed : 13.19 % Favored : 84.52 % 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: 1.45 (0.21), residues: 1550 helix: 3.06 (0.20), residues: 515 sheet: 0.40 (0.25), residues: 410 loop : -0.44 (0.25), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 50 TYR 0.018 0.001 TYR B 197 PHE 0.013 0.001 PHE B 195 TRP 0.009 0.001 TRP C 47 HIS 0.002 0.001 HIS B 277 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.14 (13675) covalent geometry : angle 0.54734 / 0.29 (18525) hydrogen bonds : bond 0.07918 / 5.26 ( 625) hydrogen bonds : angle 4.34960 / 2.95 ( 2190) *********************** 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 164 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 132 time to evaluate : 0.512 Fit side-chains REVERT: A 147 GLU cc_start: 0.8361 (mp0) cc_final: 0.8147 (mm-30) REVERT: A 222 GLU cc_start: 0.8055 (OUTLIER) cc_final: 0.7641 (mm-30) REVERT: A 280 LYS cc_start: 0.8413 (tttm) cc_final: 0.8187 (tttp) REVERT: B 67 GLU cc_start: 0.8300 (tp30) cc_final: 0.8072 (tp30) REVERT: B 69 GLU cc_start: 0.7789 (mp0) cc_final: 0.7439 (pm20) REVERT: B 147 GLU cc_start: 0.8398 (mp0) cc_final: 0.8161 (mm-30) REVERT: B 163 GLU cc_start: 0.8616 (mt-10) cc_final: 0.8381 (mm-30) REVERT: B 312 PHE cc_start: 0.8034 (t80) cc_final: 0.7251 (m-10) REVERT: C 147 GLU cc_start: 0.8461 (mp0) cc_final: 0.8246 (mm-30) REVERT: C 312 PHE cc_start: 0.8036 (t80) cc_final: 0.7181 (m-10) REVERT: D 50 ARG cc_start: 0.7861 (ptp-110) cc_final: 0.7543 (ptm160) REVERT: D 147 GLU cc_start: 0.8598 (mp0) cc_final: 0.8374 (mm-30) REVERT: D 179 ARG cc_start: 0.6766 (mmt-90) cc_final: 0.6076 (mmt-90) REVERT: D 222 GLU cc_start: 0.8019 (OUTLIER) cc_final: 0.7716 (mm-30) REVERT: D 313 LEU cc_start: 0.8669 (OUTLIER) cc_final: 0.8427 (mt) REVERT: E 50 ARG cc_start: 0.7824 (ptp-110) cc_final: 0.7386 (ptp90) REVERT: E 147 GLU cc_start: 0.8389 (mp0) cc_final: 0.8163 (mm-30) REVERT: E 163 GLU cc_start: 0.8625 (OUTLIER) cc_final: 0.8066 (mt-10) REVERT: E 179 ARG cc_start: 0.6717 (mmt-90) cc_final: 0.6453 (mmt-90) REVERT: E 222 GLU cc_start: 0.8051 (OUTLIER) cc_final: 0.7714 (mm-30) outliers start: 32 outliers final: 2 residues processed: 159 average time/residue: 0.7361 time to fit residues: 125.2979 Evaluate side-chains 133 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 126 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 222 GLU Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 222 GLU Chi-restraints excluded: chain D residue 313 LEU Chi-restraints excluded: chain E residue 163 GLU Chi-restraints excluded: chain E residue 222 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 33 optimal weight: 4.9990 chunk 93 optimal weight: 10.0000 chunk 76 optimal weight: 0.9980 chunk 71 optimal weight: 4.9990 chunk 92 optimal weight: 6.9990 chunk 48 optimal weight: 9.9990 chunk 44 optimal weight: 6.9990 chunk 47 optimal weight: 4.9990 chunk 146 optimal weight: 4.9990 chunk 125 optimal weight: 4.9990 chunk 13 optimal weight: 7.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 284 GLN E 284 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.125953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.080809 restraints weight = 14593.876| |-----------------------------------------------------------------------------| r_work (start): 0.2900 rms_B_bonded: 1.90 r_work: 0.2772 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2653 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9105 moved from start: 0.2093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 13675 Z= 0.242 Angle : 0.669 7.283 18525 Z= 0.355 Chirality : 0.048 0.139 2095 Planarity : 0.005 0.039 2260 Dihedral : 20.505 173.154 2325 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 1.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 3.37 % Allowed : 11.47 % Favored : 85.16 % 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: 1.17 (0.21), residues: 1550 helix: 2.83 (0.20), residues: 515 sheet: 0.34 (0.24), residues: 405 loop : -0.68 (0.24), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 50 TYR 0.021 0.002 TYR B 197 PHE 0.020 0.002 PHE A 195 TRP 0.008 0.002 TRP D 160 HIS 0.002 0.001 HIS A 127 Details of bonding type rmsd/Z covalent geometry : bond 0.00571 / 0.24 (13675) covalent geometry : angle 0.66892 / 0.36 (18525) hydrogen bonds : bond 0.10658 / 7.13 ( 625) hydrogen bonds : angle 4.67199 / 3.17 ( 2190) *********************** 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 171 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 124 time to evaluate : 0.455 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 101 GLN cc_start: 0.8532 (OUTLIER) cc_final: 0.8019 (mt0) REVERT: A 147 GLU cc_start: 0.8397 (mp0) cc_final: 0.8172 (mm-30) REVERT: A 177 GLU cc_start: 0.7624 (OUTLIER) cc_final: 0.6590 (mt-10) REVERT: A 222 GLU cc_start: 0.8361 (OUTLIER) cc_final: 0.8038 (mm-30) REVERT: A 280 LYS cc_start: 0.8611 (OUTLIER) cc_final: 0.8401 (tttp) REVERT: A 312 PHE cc_start: 0.8119 (t80) cc_final: 0.7370 (m-10) REVERT: A 313 LEU cc_start: 0.8698 (OUTLIER) cc_final: 0.8218 (mp) REVERT: B 50 ARG cc_start: 0.7825 (ptp-110) cc_final: 0.7424 (ptp90) REVERT: B 62 ARG cc_start: 0.7958 (mmm-85) cc_final: 0.7509 (mmt90) REVERT: B 69 GLU cc_start: 0.7790 (mp0) cc_final: 0.7399 (pm20) REVERT: B 97 ASP cc_start: 0.8284 (OUTLIER) cc_final: 0.7984 (p0) REVERT: B 101 GLN cc_start: 0.8533 (OUTLIER) cc_final: 0.7994 (mt0) REVERT: B 147 GLU cc_start: 0.8455 (mp0) cc_final: 0.8230 (mm-30) REVERT: B 177 GLU cc_start: 0.7772 (OUTLIER) cc_final: 0.6430 (mt-10) REVERT: B 222 GLU cc_start: 0.8241 (OUTLIER) cc_final: 0.7972 (mm-30) REVERT: B 312 PHE cc_start: 0.8078 (t80) cc_final: 0.7331 (m-10) REVERT: C 26 GLU cc_start: 0.8760 (OUTLIER) cc_final: 0.8472 (mm-30) REVERT: C 101 GLN cc_start: 0.8563 (OUTLIER) cc_final: 0.7912 (mt0) REVERT: C 147 GLU cc_start: 0.8443 (mp0) cc_final: 0.8231 (mm-30) REVERT: C 177 GLU cc_start: 0.7669 (OUTLIER) cc_final: 0.6132 (mt-10) REVERT: C 222 GLU cc_start: 0.8261 (OUTLIER) cc_final: 0.7940 (mm-30) REVERT: C 312 PHE cc_start: 0.8065 (t80) cc_final: 0.7347 (m-10) REVERT: D 50 ARG cc_start: 0.7953 (ptp-110) cc_final: 0.7681 (ptm160) REVERT: D 62 ARG cc_start: 0.7859 (mmm-85) cc_final: 0.7637 (tpp-160) REVERT: D 101 GLN cc_start: 0.8572 (OUTLIER) cc_final: 0.8004 (mt0) REVERT: D 147 GLU cc_start: 0.8595 (mp0) cc_final: 0.8369 (mm-30) REVERT: D 177 GLU cc_start: 0.7702 (OUTLIER) cc_final: 0.6593 (mt-10) REVERT: D 179 ARG cc_start: 0.6876 (mmt-90) cc_final: 0.6223 (mmt-90) REVERT: D 222 GLU cc_start: 0.8304 (OUTLIER) cc_final: 0.7990 (mm-30) REVERT: E 147 GLU cc_start: 0.8447 (mp0) cc_final: 0.8227 (mm-30) REVERT: E 163 GLU cc_start: 0.8628 (OUTLIER) cc_final: 0.8055 (mt-10) REVERT: E 222 GLU cc_start: 0.8353 (OUTLIER) cc_final: 0.8044 (mm-30) outliers start: 47 outliers final: 7 residues processed: 154 average time/residue: 0.7590 time to fit residues: 124.6848 Evaluate side-chains 146 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 121 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 101 GLN Chi-restraints excluded: chain A residue 177 GLU Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 222 GLU Chi-restraints excluded: chain A residue 280 LYS Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 97 ASP Chi-restraints excluded: chain B residue 101 GLN Chi-restraints excluded: chain B residue 177 GLU Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 222 GLU Chi-restraints excluded: chain C residue 26 GLU Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 101 GLN Chi-restraints excluded: chain C residue 177 GLU Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 222 GLU Chi-restraints excluded: chain D residue 101 GLN Chi-restraints excluded: chain D residue 177 GLU Chi-restraints excluded: chain D residue 222 GLU Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 163 GLU Chi-restraints excluded: chain E residue 222 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 67 optimal weight: 0.3980 chunk 125 optimal weight: 4.9990 chunk 136 optimal weight: 8.9990 chunk 40 optimal weight: 9.9990 chunk 101 optimal weight: 9.9990 chunk 56 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 58 optimal weight: 0.2980 chunk 82 optimal weight: 0.9980 chunk 130 optimal weight: 4.9990 chunk 83 optimal weight: 0.6980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.131127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.087193 restraints weight = 14687.470| |-----------------------------------------------------------------------------| r_work (start): 0.2998 rms_B_bonded: 1.89 r_work: 0.2875 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2758 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9017 moved from start: 0.1919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 13675 Z= 0.121 Angle : 0.522 6.395 18525 Z= 0.276 Chirality : 0.043 0.137 2095 Planarity : 0.004 0.039 2260 Dihedral : 19.491 176.561 2325 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 2.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.22 % Allowed : 13.62 % Favored : 85.16 % 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: 1.60 (0.21), residues: 1550 helix: 3.22 (0.20), residues: 520 sheet: 0.32 (0.24), residues: 445 loop : -0.32 (0.26), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 50 TYR 0.017 0.001 TYR B 197 PHE 0.010 0.001 PHE E 195 TRP 0.010 0.001 TRP C 47 HIS 0.002 0.001 HIS B 277 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.12 (13675) covalent geometry : angle 0.52153 / 0.28 (18525) hydrogen bonds : bond 0.06664 / 4.39 ( 625) hydrogen bonds : angle 4.16776 / 2.84 ( 2190) *********************** 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 146 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 129 time to evaluate : 0.504 Fit side-chains REVERT: A 50 ARG cc_start: 0.7847 (ptp-110) cc_final: 0.7385 (ptp90) REVERT: A 222 GLU cc_start: 0.7943 (OUTLIER) cc_final: 0.7538 (mm-30) REVERT: B 50 ARG cc_start: 0.7745 (ptp-110) cc_final: 0.7507 (ptm160) REVERT: B 62 ARG cc_start: 0.7917 (mmm-85) cc_final: 0.7519 (mmt90) REVERT: B 69 GLU cc_start: 0.7787 (mp0) cc_final: 0.7372 (pm20) REVERT: B 147 GLU cc_start: 0.8445 (mp0) cc_final: 0.8230 (mm-30) REVERT: B 163 GLU cc_start: 0.8624 (mt-10) cc_final: 0.8398 (mp0) REVERT: B 177 GLU cc_start: 0.7736 (OUTLIER) cc_final: 0.6281 (mt-10) REVERT: B 312 PHE cc_start: 0.8004 (t80) cc_final: 0.7252 (m-10) REVERT: C 50 ARG cc_start: 0.7811 (ptp-110) cc_final: 0.7497 (ptm160) REVERT: C 67 GLU cc_start: 0.8383 (tp30) cc_final: 0.8089 (tp30) REVERT: C 69 GLU cc_start: 0.7863 (mp0) cc_final: 0.7411 (pm20) REVERT: C 177 GLU cc_start: 0.7613 (OUTLIER) cc_final: 0.6120 (mt-10) REVERT: C 222 GLU cc_start: 0.7887 (OUTLIER) cc_final: 0.7620 (mm-30) REVERT: C 312 PHE cc_start: 0.8013 (t80) cc_final: 0.7195 (m-10) REVERT: D 147 GLU cc_start: 0.8575 (mp0) cc_final: 0.8367 (mm-30) REVERT: D 177 GLU cc_start: 0.7703 (OUTLIER) cc_final: 0.6592 (mt-10) REVERT: D 179 ARG cc_start: 0.6849 (mmt-90) cc_final: 0.6228 (mmt-90) REVERT: D 222 GLU cc_start: 0.7892 (OUTLIER) cc_final: 0.7591 (mm-30) REVERT: E 50 ARG cc_start: 0.7834 (ptp-110) cc_final: 0.7425 (ptp90) REVERT: E 147 GLU cc_start: 0.8419 (mp0) cc_final: 0.8214 (mm-30) REVERT: E 163 GLU cc_start: 0.8647 (OUTLIER) cc_final: 0.8144 (mp0) REVERT: E 222 GLU cc_start: 0.7943 (OUTLIER) cc_final: 0.7622 (mm-30) outliers start: 17 outliers final: 5 residues processed: 144 average time/residue: 0.8118 time to fit residues: 124.0451 Evaluate side-chains 139 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 126 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 222 GLU Chi-restraints excluded: chain B residue 177 GLU Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 177 GLU Chi-restraints excluded: chain C residue 222 GLU Chi-restraints excluded: chain C residue 297 ILE Chi-restraints excluded: chain D residue 177 GLU Chi-restraints excluded: chain D residue 222 GLU Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 163 GLU Chi-restraints excluded: chain E residue 222 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 59 optimal weight: 0.8980 chunk 129 optimal weight: 0.0980 chunk 78 optimal weight: 10.0000 chunk 109 optimal weight: 10.0000 chunk 116 optimal weight: 10.0000 chunk 115 optimal weight: 0.7980 chunk 52 optimal weight: 1.9990 chunk 55 optimal weight: 0.0020 chunk 120 optimal weight: 4.9990 chunk 85 optimal weight: 6.9990 chunk 123 optimal weight: 6.9990 overall best weight: 0.7590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 284 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.133132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.089382 restraints weight = 14737.889| |-----------------------------------------------------------------------------| r_work (start): 0.3032 rms_B_bonded: 1.89 r_work: 0.2912 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2797 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8988 moved from start: 0.1955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 13675 Z= 0.111 Angle : 0.500 6.058 18525 Z= 0.262 Chirality : 0.043 0.137 2095 Planarity : 0.004 0.039 2260 Dihedral : 18.901 179.286 2325 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 2.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.22 % Allowed : 13.41 % Favored : 85.38 % 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: 1.84 (0.22), residues: 1550 helix: 3.36 (0.20), residues: 520 sheet: 0.40 (0.24), residues: 445 loop : -0.07 (0.27), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 50 TYR 0.014 0.001 TYR B 197 PHE 0.009 0.001 PHE A 195 TRP 0.009 0.001 TRP C 47 HIS 0.002 0.001 HIS B 277 Details of bonding type rmsd/Z covalent geometry : bond 0.00214 / 0.11 (13675) covalent geometry : angle 0.49999 / 0.26 (18525) hydrogen bonds : bond 0.06028 / 3.98 ( 625) hydrogen bonds : angle 3.94534 / 2.69 ( 2190) *********************** 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 157 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 140 time to evaluate : 0.415 Fit side-chains REVERT: A 222 GLU cc_start: 0.7820 (OUTLIER) cc_final: 0.7442 (mm-30) REVERT: B 62 ARG cc_start: 0.7939 (mmm-85) cc_final: 0.7501 (mmt90) REVERT: B 147 GLU cc_start: 0.8447 (mp0) cc_final: 0.8233 (mm-30) REVERT: B 177 GLU cc_start: 0.7680 (OUTLIER) cc_final: 0.6169 (mt-10) REVERT: B 312 PHE cc_start: 0.7996 (t80) cc_final: 0.7182 (m-10) REVERT: C 50 ARG cc_start: 0.7767 (ptp-110) cc_final: 0.7481 (ptm160) REVERT: C 62 ARG cc_start: 0.8099 (tpp-160) cc_final: 0.7870 (tpp80) REVERT: C 177 GLU cc_start: 0.7626 (OUTLIER) cc_final: 0.6108 (mt-10) REVERT: C 312 PHE cc_start: 0.7978 (t80) cc_final: 0.7096 (m-10) REVERT: D 50 ARG cc_start: 0.7803 (ptp-110) cc_final: 0.7454 (ptm160) REVERT: D 147 GLU cc_start: 0.8580 (mp0) cc_final: 0.8377 (mm-30) REVERT: D 177 GLU cc_start: 0.7642 (OUTLIER) cc_final: 0.6482 (mt-10) REVERT: D 179 ARG cc_start: 0.6827 (mmt-90) cc_final: 0.6487 (mmt-90) REVERT: D 222 GLU cc_start: 0.7777 (OUTLIER) cc_final: 0.7478 (mm-30) REVERT: E 50 ARG cc_start: 0.7806 (ptp-110) cc_final: 0.7404 (ptm160) REVERT: E 163 GLU cc_start: 0.8667 (OUTLIER) cc_final: 0.8268 (mp0) REVERT: E 222 GLU cc_start: 0.7863 (OUTLIER) cc_final: 0.7558 (mm-30) outliers start: 17 outliers final: 4 residues processed: 154 average time/residue: 0.7088 time to fit residues: 116.3824 Evaluate side-chains 147 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 136 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 222 GLU Chi-restraints excluded: chain B residue 177 GLU Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 177 GLU Chi-restraints excluded: chain D residue 177 GLU Chi-restraints excluded: chain D residue 222 GLU Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 163 GLU Chi-restraints excluded: chain E residue 222 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 107 optimal weight: 4.9990 chunk 70 optimal weight: 8.9990 chunk 81 optimal weight: 7.9990 chunk 62 optimal weight: 10.0000 chunk 34 optimal weight: 9.9990 chunk 38 optimal weight: 0.5980 chunk 9 optimal weight: 0.4980 chunk 44 optimal weight: 9.9990 chunk 32 optimal weight: 4.9990 chunk 98 optimal weight: 0.0020 chunk 61 optimal weight: 6.9990 overall best weight: 2.2192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 284 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.128809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.083943 restraints weight = 14499.766| |-----------------------------------------------------------------------------| r_work (start): 0.2947 rms_B_bonded: 1.90 r_work: 0.2820 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2701 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9060 moved from start: 0.2145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 13675 Z= 0.162 Angle : 0.564 6.518 18525 Z= 0.299 Chirality : 0.044 0.134 2095 Planarity : 0.004 0.039 2260 Dihedral : 19.281 178.518 2325 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 2.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.72 % Allowed : 13.41 % Favored : 84.87 % 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: 1.63 (0.21), residues: 1550 helix: 3.11 (0.20), residues: 515 sheet: 0.57 (0.25), residues: 410 loop : -0.29 (0.25), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 50 TYR 0.017 0.002 TYR B 197 PHE 0.013 0.001 PHE E 195 TRP 0.007 0.001 TRP D 160 HIS 0.002 0.001 HIS B 277 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.16 (13675) covalent geometry : angle 0.56404 / 0.30 (18525) hydrogen bonds : bond 0.08537 / 5.68 ( 625) hydrogen bonds : angle 4.24751 / 2.89 ( 2190) *********************** 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 153 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 129 time to evaluate : 0.389 Fit side-chains revert: symmetry clash REVERT: A 50 ARG cc_start: 0.7864 (ptp-110) cc_final: 0.7413 (ptp90) REVERT: A 222 GLU cc_start: 0.8134 (OUTLIER) cc_final: 0.7778 (mm-30) REVERT: B 62 ARG cc_start: 0.7934 (mmm-85) cc_final: 0.7511 (mmt90) REVERT: B 147 GLU cc_start: 0.8454 (mp0) cc_final: 0.8238 (mm-30) REVERT: B 177 GLU cc_start: 0.7752 (OUTLIER) cc_final: 0.6374 (mt-10) REVERT: B 222 GLU cc_start: 0.7999 (OUTLIER) cc_final: 0.7640 (mm-30) REVERT: B 312 PHE cc_start: 0.8027 (t80) cc_final: 0.7253 (m-10) REVERT: C 50 ARG cc_start: 0.7782 (ptp-110) cc_final: 0.7540 (ptm160) REVERT: C 67 GLU cc_start: 0.8333 (tp30) cc_final: 0.8071 (tp30) REVERT: C 69 GLU cc_start: 0.7816 (mp0) cc_final: 0.7406 (pm20) REVERT: C 177 GLU cc_start: 0.7634 (OUTLIER) cc_final: 0.6767 (mt-10) REVERT: C 312 PHE cc_start: 0.8031 (t80) cc_final: 0.7216 (m-10) REVERT: D 50 ARG cc_start: 0.7813 (ptp-110) cc_final: 0.7508 (ptm160) REVERT: D 147 GLU cc_start: 0.8605 (mp0) cc_final: 0.8402 (mm-30) REVERT: D 177 GLU cc_start: 0.7709 (OUTLIER) cc_final: 0.6604 (mt-10) REVERT: D 179 ARG cc_start: 0.6859 (mmt-90) cc_final: 0.6246 (mmt-90) REVERT: D 222 GLU cc_start: 0.8074 (OUTLIER) cc_final: 0.7751 (mm-30) REVERT: D 252 MET cc_start: 0.8963 (tpp) cc_final: 0.8617 (tpp) REVERT: E 163 GLU cc_start: 0.8652 (OUTLIER) cc_final: 0.8194 (mp0) REVERT: E 222 GLU cc_start: 0.8103 (OUTLIER) cc_final: 0.7773 (mm-30) outliers start: 24 outliers final: 7 residues processed: 146 average time/residue: 0.7943 time to fit residues: 123.2623 Evaluate side-chains 142 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 127 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 222 GLU Chi-restraints excluded: chain B residue 177 GLU Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 222 GLU Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 177 GLU Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 297 ILE Chi-restraints excluded: chain D residue 177 GLU Chi-restraints excluded: chain D residue 222 GLU Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 163 GLU Chi-restraints excluded: chain E residue 222 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 59 optimal weight: 0.9990 chunk 47 optimal weight: 10.0000 chunk 50 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 148 optimal weight: 0.2980 chunk 43 optimal weight: 8.9990 chunk 77 optimal weight: 5.9990 chunk 28 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 152 optimal weight: 4.9990 chunk 108 optimal weight: 5.9990 overall best weight: 1.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.129455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.084784 restraints weight = 14556.754| |-----------------------------------------------------------------------------| r_work (start): 0.2962 rms_B_bonded: 1.90 r_work: 0.2837 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2718 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9049 moved from start: 0.2168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 13675 Z= 0.146 Angle : 0.552 6.474 18525 Z= 0.291 Chirality : 0.044 0.135 2095 Planarity : 0.004 0.039 2260 Dihedral : 19.326 178.514 2325 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 2.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 1.43 % Allowed : 13.55 % Favored : 85.02 % 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: 1.65 (0.21), residues: 1550 helix: 3.15 (0.20), residues: 515 sheet: 0.41 (0.24), residues: 445 loop : -0.20 (0.26), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 50 TYR 0.017 0.001 TYR B 197 PHE 0.012 0.001 PHE A 195 TRP 0.007 0.001 TRP C 47 HIS 0.002 0.001 HIS B 277 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.15 (13675) covalent geometry : angle 0.55173 / 0.29 (18525) hydrogen bonds : bond 0.07911 / 5.25 ( 625) hydrogen bonds : angle 4.19642 / 2.85 ( 2190) *********************** 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 148 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 128 time to evaluate : 0.494 Fit side-chains revert: symmetry clash REVERT: A 50 ARG cc_start: 0.7863 (ptp-110) cc_final: 0.7524 (ptm160) REVERT: A 222 GLU cc_start: 0.8056 (OUTLIER) cc_final: 0.7653 (mm-30) REVERT: B 50 ARG cc_start: 0.7701 (ptp-110) cc_final: 0.7304 (ptp90) REVERT: B 62 ARG cc_start: 0.7905 (mmm-85) cc_final: 0.7472 (mmt90) REVERT: B 147 GLU cc_start: 0.8474 (mp0) cc_final: 0.8265 (mm-30) REVERT: B 177 GLU cc_start: 0.7752 (OUTLIER) cc_final: 0.6369 (mt-10) REVERT: B 312 PHE cc_start: 0.8010 (t80) cc_final: 0.7256 (m-10) REVERT: C 50 ARG cc_start: 0.7781 (ptp-110) cc_final: 0.7558 (ptm160) REVERT: C 69 GLU cc_start: 0.7829 (mp0) cc_final: 0.7396 (pm20) REVERT: C 163 GLU cc_start: 0.8545 (OUTLIER) cc_final: 0.7207 (mp0) REVERT: C 177 GLU cc_start: 0.7660 (OUTLIER) cc_final: 0.6781 (mt-10) REVERT: C 222 GLU cc_start: 0.8002 (OUTLIER) cc_final: 0.7770 (mm-30) REVERT: C 312 PHE cc_start: 0.8020 (t80) cc_final: 0.7239 (m-10) REVERT: D 50 ARG cc_start: 0.7811 (ptp-110) cc_final: 0.7528 (ptm160) REVERT: D 163 GLU cc_start: 0.8507 (OUTLIER) cc_final: 0.7380 (mp0) REVERT: D 177 GLU cc_start: 0.7720 (OUTLIER) cc_final: 0.6601 (mt-10) REVERT: D 179 ARG cc_start: 0.6893 (mmt-90) cc_final: 0.6282 (mmt-90) REVERT: D 222 GLU cc_start: 0.8020 (OUTLIER) cc_final: 0.7688 (mm-30) REVERT: D 252 MET cc_start: 0.8962 (tpp) cc_final: 0.8611 (tpp) REVERT: E 50 ARG cc_start: 0.7875 (ptp-110) cc_final: 0.7443 (ptp90) REVERT: E 62 ARG cc_start: 0.7926 (mmm-85) cc_final: 0.7529 (mmt90) REVERT: E 163 GLU cc_start: 0.8648 (OUTLIER) cc_final: 0.8196 (mp0) REVERT: E 222 GLU cc_start: 0.8025 (OUTLIER) cc_final: 0.7709 (mm-30) outliers start: 20 outliers final: 7 residues processed: 144 average time/residue: 0.8078 time to fit residues: 123.6369 Evaluate side-chains 145 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 128 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 222 GLU Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 177 GLU Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 163 GLU Chi-restraints excluded: chain C residue 177 GLU Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 222 GLU Chi-restraints excluded: chain D residue 163 GLU Chi-restraints excluded: chain D residue 177 GLU Chi-restraints excluded: chain D residue 222 GLU Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 163 GLU Chi-restraints excluded: chain E residue 222 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 77 optimal weight: 5.9990 chunk 149 optimal weight: 5.9990 chunk 46 optimal weight: 3.9990 chunk 87 optimal weight: 5.9990 chunk 142 optimal weight: 5.9990 chunk 112 optimal weight: 0.7980 chunk 58 optimal weight: 0.9990 chunk 145 optimal weight: 4.9990 chunk 17 optimal weight: 4.9990 chunk 98 optimal weight: 0.0050 chunk 97 optimal weight: 10.0000 overall best weight: 2.1600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.128330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.083595 restraints weight = 14674.262| |-----------------------------------------------------------------------------| r_work (start): 0.2944 rms_B_bonded: 1.91 r_work: 0.2816 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2695 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9067 moved from start: 0.2242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 13675 Z= 0.161 Angle : 0.575 6.623 18525 Z= 0.304 Chirality : 0.044 0.133 2095 Planarity : 0.004 0.046 2260 Dihedral : 19.540 179.847 2325 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 1.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.79 % Allowed : 13.76 % Favored : 84.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.59 (0.21), residues: 1550 helix: 3.08 (0.20), residues: 515 sheet: 0.59 (0.25), residues: 410 loop : -0.36 (0.25), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 50 TYR 0.018 0.002 TYR B 197 PHE 0.013 0.001 PHE B 195 TRP 0.007 0.001 TRP D 160 HIS 0.002 0.001 HIS B 277 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.16 (13675) covalent geometry : angle 0.57526 / 0.30 (18525) hydrogen bonds : bond 0.08583 / 5.71 ( 625) hydrogen bonds : angle 4.28372 / 2.91 ( 2190) *********************** 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 154 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 129 time to evaluate : 0.388 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 ARG cc_start: 0.7875 (ptp-110) cc_final: 0.7551 (ptm160) REVERT: A 222 GLU cc_start: 0.8158 (OUTLIER) cc_final: 0.7762 (mm-30) REVERT: B 50 ARG cc_start: 0.7721 (ptp-110) cc_final: 0.7338 (ptp90) REVERT: B 62 ARG cc_start: 0.7908 (mmm-85) cc_final: 0.7472 (mmt90) REVERT: B 147 GLU cc_start: 0.8533 (mp0) cc_final: 0.8311 (mm-30) REVERT: B 177 GLU cc_start: 0.7773 (OUTLIER) cc_final: 0.6396 (mt-10) REVERT: B 312 PHE cc_start: 0.8021 (t80) cc_final: 0.7253 (m-10) REVERT: C 50 ARG cc_start: 0.7782 (ptp-110) cc_final: 0.7563 (ptm160) REVERT: C 163 GLU cc_start: 0.8597 (OUTLIER) cc_final: 0.7188 (mp0) REVERT: C 177 GLU cc_start: 0.7665 (OUTLIER) cc_final: 0.6836 (mt-10) REVERT: C 222 GLU cc_start: 0.8078 (OUTLIER) cc_final: 0.7862 (mm-30) REVERT: C 312 PHE cc_start: 0.8032 (t80) cc_final: 0.7254 (m-10) REVERT: D 50 ARG cc_start: 0.7803 (ptp-110) cc_final: 0.7533 (ptm160) REVERT: D 163 GLU cc_start: 0.8540 (OUTLIER) cc_final: 0.7406 (mp0) REVERT: D 177 GLU cc_start: 0.7675 (OUTLIER) cc_final: 0.6655 (mt-10) REVERT: D 179 ARG cc_start: 0.6909 (mmt-90) cc_final: 0.6304 (mmt-90) REVERT: D 222 GLU cc_start: 0.8105 (OUTLIER) cc_final: 0.7773 (mm-30) REVERT: D 252 MET cc_start: 0.8970 (tpp) cc_final: 0.8604 (tpp) REVERT: E 50 ARG cc_start: 0.7875 (ptp-110) cc_final: 0.7432 (ptp90) REVERT: E 62 ARG cc_start: 0.7940 (mmm-85) cc_final: 0.7541 (mmt90) REVERT: E 163 GLU cc_start: 0.8665 (OUTLIER) cc_final: 0.8109 (mt-10) REVERT: E 222 GLU cc_start: 0.8105 (OUTLIER) cc_final: 0.7777 (mm-30) outliers start: 25 outliers final: 11 residues processed: 148 average time/residue: 0.7740 time to fit residues: 121.7508 Evaluate side-chains 150 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 129 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 222 GLU Chi-restraints excluded: chain A residue 280 LYS Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 177 GLU Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 163 GLU Chi-restraints excluded: chain C residue 177 GLU Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 222 GLU Chi-restraints excluded: chain D residue 163 GLU Chi-restraints excluded: chain D residue 177 GLU Chi-restraints excluded: chain D residue 212 SER Chi-restraints excluded: chain D residue 222 GLU Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 163 GLU Chi-restraints excluded: chain E residue 212 SER Chi-restraints excluded: chain E residue 222 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 136 optimal weight: 7.9990 chunk 154 optimal weight: 5.9990 chunk 122 optimal weight: 3.9990 chunk 112 optimal weight: 1.9990 chunk 148 optimal weight: 0.3980 chunk 117 optimal weight: 7.9990 chunk 67 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 7 optimal weight: 6.9990 chunk 99 optimal weight: 6.9990 chunk 146 optimal weight: 3.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.129202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.084731 restraints weight = 14580.089| |-----------------------------------------------------------------------------| r_work (start): 0.2960 rms_B_bonded: 1.90 r_work: 0.2833 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2713 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9052 moved from start: 0.2239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13675 Z= 0.149 Angle : 0.561 6.595 18525 Z= 0.296 Chirality : 0.044 0.134 2095 Planarity : 0.004 0.042 2260 Dihedral : 19.403 179.998 2325 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 1.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 1.65 % Allowed : 13.84 % Favored : 84.52 % 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: 1.63 (0.21), residues: 1550 helix: 3.15 (0.20), residues: 515 sheet: 0.41 (0.24), residues: 445 loop : -0.24 (0.26), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 50 TYR 0.017 0.001 TYR B 197 PHE 0.012 0.001 PHE B 195 TRP 0.007 0.001 TRP C 47 HIS 0.002 0.001 HIS B 277 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.15 (13675) covalent geometry : angle 0.56111 / 0.30 (18525) hydrogen bonds : bond 0.07981 / 5.30 ( 625) hydrogen bonds : angle 4.20307 / 2.86 ( 2190) ********************** 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 153 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 130 time to evaluate : 0.475 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 ARG cc_start: 0.7865 (ptp-110) cc_final: 0.7555 (ptm160) REVERT: A 222 GLU cc_start: 0.8076 (OUTLIER) cc_final: 0.7663 (mm-30) REVERT: B 50 ARG cc_start: 0.7740 (ptp-110) cc_final: 0.7415 (ptm160) REVERT: B 62 ARG cc_start: 0.7905 (mmm-85) cc_final: 0.7469 (mmt90) REVERT: B 147 GLU cc_start: 0.8516 (mp0) cc_final: 0.8297 (mm-30) REVERT: B 177 GLU cc_start: 0.7772 (OUTLIER) cc_final: 0.6435 (mt-10) REVERT: B 312 PHE cc_start: 0.8021 (t80) cc_final: 0.7242 (m-10) REVERT: C 50 ARG cc_start: 0.7778 (ptp-110) cc_final: 0.7565 (ptm160) REVERT: C 177 GLU cc_start: 0.7651 (OUTLIER) cc_final: 0.6815 (mt-10) REVERT: C 222 GLU cc_start: 0.8011 (OUTLIER) cc_final: 0.7802 (mm-30) REVERT: C 312 PHE cc_start: 0.8025 (t80) cc_final: 0.7238 (m-10) REVERT: D 50 ARG cc_start: 0.7808 (ptp-110) cc_final: 0.7545 (ptm160) REVERT: D 163 GLU cc_start: 0.8537 (OUTLIER) cc_final: 0.7404 (mp0) REVERT: D 177 GLU cc_start: 0.7646 (OUTLIER) cc_final: 0.6597 (mt-10) REVERT: D 179 ARG cc_start: 0.6936 (mmt-90) cc_final: 0.6330 (mmt-90) REVERT: D 222 GLU cc_start: 0.8037 (OUTLIER) cc_final: 0.7714 (mm-30) REVERT: D 252 MET cc_start: 0.8955 (tpp) cc_final: 0.8595 (tpp) REVERT: E 50 ARG cc_start: 0.7858 (ptp-110) cc_final: 0.7415 (ptp90) REVERT: E 62 ARG cc_start: 0.7922 (mmm-85) cc_final: 0.7521 (mmt90) REVERT: E 163 GLU cc_start: 0.8648 (OUTLIER) cc_final: 0.8101 (mt-10) REVERT: E 222 GLU cc_start: 0.8032 (OUTLIER) cc_final: 0.7718 (mm-30) outliers start: 23 outliers final: 10 residues processed: 148 average time/residue: 0.7785 time to fit residues: 122.4592 Evaluate side-chains 149 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 130 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 222 GLU Chi-restraints excluded: chain A residue 280 LYS Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 177 GLU Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 177 GLU Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 222 GLU Chi-restraints excluded: chain D residue 163 GLU Chi-restraints excluded: chain D residue 177 GLU Chi-restraints excluded: chain D residue 222 GLU Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 163 GLU Chi-restraints excluded: chain E residue 212 SER Chi-restraints excluded: chain E residue 222 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 3 optimal weight: 10.0000 chunk 88 optimal weight: 6.9990 chunk 84 optimal weight: 0.9980 chunk 16 optimal weight: 10.0000 chunk 153 optimal weight: 3.9990 chunk 117 optimal weight: 7.9990 chunk 66 optimal weight: 9.9990 chunk 92 optimal weight: 6.9990 chunk 123 optimal weight: 5.9990 chunk 76 optimal weight: 5.9990 chunk 28 optimal weight: 1.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.126443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.081423 restraints weight = 14652.297| |-----------------------------------------------------------------------------| r_work (start): 0.2910 rms_B_bonded: 1.91 r_work: 0.2780 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2658 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9099 moved from start: 0.2408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 13675 Z= 0.224 Angle : 0.650 7.161 18525 Z= 0.345 Chirality : 0.047 0.140 2095 Planarity : 0.005 0.039 2260 Dihedral : 19.945 179.793 2325 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 1.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 1.79 % Allowed : 13.62 % Favored : 84.59 % 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: 1.39 (0.21), residues: 1550 helix: 2.92 (0.20), residues: 515 sheet: 0.56 (0.24), residues: 410 loop : -0.55 (0.24), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 50 TYR 0.019 0.002 TYR C 197 PHE 0.016 0.002 PHE B 195 TRP 0.011 0.002 TRP E 213 HIS 0.002 0.001 HIS A 127 Details of bonding type rmsd/Z covalent geometry : bond 0.00523 / 0.22 (13675) covalent geometry : angle 0.64971 / 0.34 (18525) hydrogen bonds : bond 0.10132 / 6.77 ( 625) hydrogen bonds : angle 4.48421 / 3.05 ( 2190) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5623.88 seconds wall clock time: 95 minutes 56.45 seconds (5756.45 seconds total)