Starting phenix.real_space_refine on Sat Jul 4 00:28:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/5bki_9405/07_2026/5bki_9405.cif Found real_map, /net/cci-nas-00/data/ceres_data/5bki_9405/07_2026/5bki_9405.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/5bki_9405/07_2026/5bki_9405.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5bki_9405/07_2026/5bki_9405.map" restraint_files = "/net/cci-nas-00/data/ceres_data/5bki_9405/07_2026/5bki_9405.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/5bki_9405/07_2026/5bki_9405.cif" model { file = "/net/cci-nas-00/data/ceres_data/5bki_9405/07_2026/5bki_9405.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5bki_9405/07_2026/5bki_9405.cif" } resolution = 3.1 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= 0.005 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 Cd 12 9.23 5 K 5 8.98 5 S 68 5.16 5 C 10688 2.51 5 N 2896 2.21 5 O 3264 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 132 residue(s): 0.01s 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: 16933 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 2467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2467 Classifications: {'peptide': 317} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 307} Chain: "C" Number of atoms: 2467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2467 Classifications: {'peptide': 317} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 307} Chain: "E" Number of atoms: 2467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2467 Classifications: {'peptide': 317} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 307} Chain: "G" Number of atoms: 2467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2467 Classifications: {'peptide': 317} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 307} Chain: "B" Number of atoms: 1725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1725 Classifications: {'peptide': 222} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 214} Chain: "D" Number of atoms: 1725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1725 Classifications: {'peptide': 222} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 214} Chain: "F" Number of atoms: 1725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1725 Classifications: {'peptide': 222} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 214} Chain: "H" Number of atoms: 1725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1725 Classifications: {'peptide': 222} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 214} Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 41 Ad-hoc single atom residues: {' CD': 1} Unusual residues: {' K': 5, 'PGW': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain breaks: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 36 Ad-hoc single atom residues: {' CD': 1} Unusual residues: {'PGW': 1} Classifications: {'undetermined': 1} Chain breaks: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 36 Ad-hoc single atom residues: {' CD': 1} Unusual residues: {'PGW': 1} Classifications: {'undetermined': 1} Chain breaks: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 36 Ad-hoc single atom residues: {' CD': 1} Unusual residues: {'PGW': 1} Classifications: {'undetermined': 1} Chain breaks: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' CD': 2} Chain breaks: 2 Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' CD': 2} Chain breaks: 2 Chain: "F" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' CD': 2} Chain breaks: 2 Chain: "H" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' CD': 2} Chain breaks: 2 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 2.91, per 1000 atoms: 0.17 Number of scatterers: 16933 At special positions: 0 Unit cell: (152.358, 152.358, 117.283, 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) Cd 12 47.96 K 5 19.00 S 68 16.00 O 3264 8.00 N 2896 7.00 C 10688 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.90 Conformation dependent library (CDL) restraints added in 856.4 milliseconds 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3952 Finding SS restraints... Secondary structure from input PDB file: 100 helices and 16 sheets defined 47.9% alpha, 12.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'A' and resid 21 through 43 removed outlier: 3.619A pdb=" N ALA A 36 " --> pdb=" O ILE A 32 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N PHE A 40 " --> pdb=" O ALA A 36 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ILE A 41 " --> pdb=" O GLY A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 58 removed outlier: 3.726A pdb=" N ALA A 58 " --> pdb=" O PHE A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 105 removed outlier: 3.636A pdb=" N VAL A 77 " --> pdb=" O MET A 73 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N THR A 78 " --> pdb=" O TYR A 74 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N VAL A 91 " --> pdb=" O PHE A 87 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLU A 92 " --> pdb=" O ALA A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 129 Processing helix chain 'A' and resid 146 through 156 removed outlier: 4.144A pdb=" N LYS A 150 " --> pdb=" O GLU A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 171 removed outlier: 3.568A pdb=" N GLU A 171 " --> pdb=" O VAL A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 178 removed outlier: 4.004A pdb=" N ALA A 178 " --> pdb=" O VAL A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 202 removed outlier: 3.516A pdb=" N THR A 191 " --> pdb=" O SER A 187 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LYS A 200 " --> pdb=" O LEU A 196 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ILE A 201 " --> pdb=" O GLY A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 215 No H-bonds generated for 'chain 'A' and resid 213 through 215' Processing helix chain 'A' and resid 216 through 223 Processing helix chain 'A' and resid 230 through 241 removed outlier: 3.570A pdb=" N SER A 240 " --> pdb=" O GLY A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 256 removed outlier: 3.502A pdb=" N PHE A 251 " --> pdb=" O TYR A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 284 Processing helix chain 'A' and resid 284 through 290 removed outlier: 3.569A pdb=" N VAL A 288 " --> pdb=" O ASP A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 332 removed outlier: 3.648A pdb=" N ASN A 332 " --> pdb=" O GLU A 328 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 43 removed outlier: 3.618A pdb=" N ALA C 36 " --> pdb=" O ILE C 32 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N PHE C 40 " --> pdb=" O ALA C 36 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILE C 41 " --> pdb=" O GLY C 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 58 removed outlier: 3.726A pdb=" N ALA C 58 " --> pdb=" O PHE C 54 " (cutoff:3.500A) Processing helix chain 'C' and resid 69 through 105 removed outlier: 3.636A pdb=" N VAL C 77 " --> pdb=" O MET C 73 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N THR C 78 " --> pdb=" O TYR C 74 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N VAL C 91 " --> pdb=" O PHE C 87 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLU C 92 " --> pdb=" O ALA C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 124 through 129 Processing helix chain 'C' and resid 146 through 156 removed outlier: 4.144A pdb=" N LYS C 150 " --> pdb=" O GLU C 146 " (cutoff:3.500A) Processing helix chain 'C' and resid 166 through 171 removed outlier: 3.568A pdb=" N GLU C 171 " --> pdb=" O VAL C 167 " (cutoff:3.500A) Processing helix chain 'C' and resid 174 through 178 removed outlier: 4.005A pdb=" N ALA C 178 " --> pdb=" O VAL C 175 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 202 removed outlier: 3.517A pdb=" N THR C 191 " --> pdb=" O SER C 187 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LYS C 200 " --> pdb=" O LEU C 196 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE C 201 " --> pdb=" O GLY C 197 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 215 No H-bonds generated for 'chain 'C' and resid 213 through 215' Processing helix chain 'C' and resid 216 through 223 Processing helix chain 'C' and resid 230 through 241 removed outlier: 3.571A pdb=" N SER C 240 " --> pdb=" O GLY C 236 " (cutoff:3.500A) Processing helix chain 'C' and resid 247 through 256 removed outlier: 3.502A pdb=" N PHE C 251 " --> pdb=" O TYR C 247 " (cutoff:3.500A) Processing helix chain 'C' and resid 279 through 284 Processing helix chain 'C' and resid 284 through 290 removed outlier: 3.569A pdb=" N VAL C 288 " --> pdb=" O ASP C 284 " (cutoff:3.500A) Processing helix chain 'C' and resid 327 through 332 removed outlier: 3.648A pdb=" N ASN C 332 " --> pdb=" O GLU C 328 " (cutoff:3.500A) Processing helix chain 'E' and resid 21 through 43 removed outlier: 3.619A pdb=" N ALA E 36 " --> pdb=" O ILE E 32 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N PHE E 40 " --> pdb=" O ALA E 36 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ILE E 41 " --> pdb=" O GLY E 37 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 58 removed outlier: 3.726A pdb=" N ALA E 58 " --> pdb=" O PHE E 54 " (cutoff:3.500A) Processing helix chain 'E' and resid 69 through 105 removed outlier: 3.635A pdb=" N VAL E 77 " --> pdb=" O MET E 73 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N THR E 78 " --> pdb=" O TYR E 74 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N VAL E 91 " --> pdb=" O PHE E 87 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLU E 92 " --> pdb=" O ALA E 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 124 through 129 Processing helix chain 'E' and resid 146 through 156 removed outlier: 4.144A pdb=" N LYS E 150 " --> pdb=" O GLU E 146 " (cutoff:3.500A) Processing helix chain 'E' and resid 166 through 171 removed outlier: 3.568A pdb=" N GLU E 171 " --> pdb=" O VAL E 167 " (cutoff:3.500A) Processing helix chain 'E' and resid 174 through 178 removed outlier: 4.005A pdb=" N ALA E 178 " --> pdb=" O VAL E 175 " (cutoff:3.500A) Processing helix chain 'E' and resid 187 through 202 removed outlier: 3.516A pdb=" N THR E 191 " --> pdb=" O SER E 187 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LYS E 200 " --> pdb=" O LEU E 196 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE E 201 " --> pdb=" O GLY E 197 " (cutoff:3.500A) Processing helix chain 'E' and resid 213 through 215 No H-bonds generated for 'chain 'E' and resid 213 through 215' Processing helix chain 'E' and resid 216 through 223 Processing helix chain 'E' and resid 230 through 241 removed outlier: 3.570A pdb=" N SER E 240 " --> pdb=" O GLY E 236 " (cutoff:3.500A) Processing helix chain 'E' and resid 247 through 256 removed outlier: 3.502A pdb=" N PHE E 251 " --> pdb=" O TYR E 247 " (cutoff:3.500A) Processing helix chain 'E' and resid 279 through 284 Processing helix chain 'E' and resid 284 through 290 removed outlier: 3.570A pdb=" N VAL E 288 " --> pdb=" O ASP E 284 " (cutoff:3.500A) Processing helix chain 'E' and resid 327 through 332 removed outlier: 3.648A pdb=" N ASN E 332 " --> pdb=" O GLU E 328 " (cutoff:3.500A) Processing helix chain 'G' and resid 21 through 43 removed outlier: 3.618A pdb=" N ALA G 36 " --> pdb=" O ILE G 32 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N PHE G 40 " --> pdb=" O ALA G 36 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILE G 41 " --> pdb=" O GLY G 37 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 58 removed outlier: 3.726A pdb=" N ALA G 58 " --> pdb=" O PHE G 54 " (cutoff:3.500A) Processing helix chain 'G' and resid 69 through 105 removed outlier: 3.635A pdb=" N VAL G 77 " --> pdb=" O MET G 73 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N THR G 78 " --> pdb=" O TYR G 74 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N VAL G 91 " --> pdb=" O PHE G 87 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLU G 92 " --> pdb=" O ALA G 88 " (cutoff:3.500A) Processing helix chain 'G' and resid 124 through 129 Processing helix chain 'G' and resid 146 through 156 removed outlier: 4.143A pdb=" N LYS G 150 " --> pdb=" O GLU G 146 " (cutoff:3.500A) Processing helix chain 'G' and resid 166 through 171 removed outlier: 3.567A pdb=" N GLU G 171 " --> pdb=" O VAL G 167 " (cutoff:3.500A) Processing helix chain 'G' and resid 174 through 178 removed outlier: 4.004A pdb=" N ALA G 178 " --> pdb=" O VAL G 175 " (cutoff:3.500A) Processing helix chain 'G' and resid 187 through 202 removed outlier: 3.516A pdb=" N THR G 191 " --> pdb=" O SER G 187 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LYS G 200 " --> pdb=" O LEU G 196 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE G 201 " --> pdb=" O GLY G 197 " (cutoff:3.500A) Processing helix chain 'G' and resid 213 through 215 No H-bonds generated for 'chain 'G' and resid 213 through 215' Processing helix chain 'G' and resid 216 through 223 Processing helix chain 'G' and resid 230 through 241 removed outlier: 3.570A pdb=" N SER G 240 " --> pdb=" O GLY G 236 " (cutoff:3.500A) Processing helix chain 'G' and resid 247 through 256 removed outlier: 3.503A pdb=" N PHE G 251 " --> pdb=" O TYR G 247 " (cutoff:3.500A) Processing helix chain 'G' and resid 279 through 284 Processing helix chain 'G' and resid 284 through 290 removed outlier: 3.569A pdb=" N VAL G 288 " --> pdb=" O ASP G 284 " (cutoff:3.500A) Processing helix chain 'G' and resid 327 through 332 removed outlier: 3.648A pdb=" N ASN G 332 " --> pdb=" O GLU G 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 124 through 129 Processing helix chain 'B' and resid 130 through 134 removed outlier: 3.828A pdb=" N GLU B 133 " --> pdb=" O CYS B 130 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU B 134 " --> pdb=" O LEU B 131 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 130 through 134' Processing helix chain 'B' and resid 147 through 155 removed outlier: 4.282A pdb=" N LYS B 151 " --> pdb=" O ASN B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 171 Processing helix chain 'B' and resid 187 through 202 removed outlier: 3.525A pdb=" N GLY B 197 " --> pdb=" O HIS B 193 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LYS B 200 " --> pdb=" O LEU B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 224 removed outlier: 3.534A pdb=" N ARG B 221 " --> pdb=" O ILE B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 238 removed outlier: 3.544A pdb=" N ILE B 234 " --> pdb=" O SER B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 256 removed outlier: 3.576A pdb=" N PHE B 251 " --> pdb=" O TYR B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 289 Processing helix chain 'B' and resid 323 through 334 removed outlier: 3.952A pdb=" N GLU B 328 " --> pdb=" O PRO B 324 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ARG B 329 " --> pdb=" O GLU B 325 " (cutoff:3.500A) Processing helix chain 'D' and resid 124 through 129 Processing helix chain 'D' and resid 130 through 134 removed outlier: 3.828A pdb=" N GLU D 133 " --> pdb=" O CYS D 130 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU D 134 " --> pdb=" O LEU D 131 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 130 through 134' Processing helix chain 'D' and resid 147 through 155 removed outlier: 4.282A pdb=" N LYS D 151 " --> pdb=" O ASN D 147 " (cutoff:3.500A) Processing helix chain 'D' and resid 166 through 171 Processing helix chain 'D' and resid 187 through 202 removed outlier: 3.525A pdb=" N GLY D 197 " --> pdb=" O HIS D 193 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LYS D 200 " --> pdb=" O LEU D 196 " (cutoff:3.500A) Processing helix chain 'D' and resid 216 through 224 removed outlier: 3.534A pdb=" N ARG D 221 " --> pdb=" O ILE D 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 230 through 238 removed outlier: 3.543A pdb=" N ILE D 234 " --> pdb=" O SER D 230 " (cutoff:3.500A) Processing helix chain 'D' and resid 247 through 256 removed outlier: 3.576A pdb=" N PHE D 251 " --> pdb=" O TYR D 247 " (cutoff:3.500A) Processing helix chain 'D' and resid 284 through 289 Processing helix chain 'D' and resid 323 through 334 removed outlier: 3.953A pdb=" N GLU D 328 " --> pdb=" O PRO D 324 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ARG D 329 " --> pdb=" O GLU D 325 " (cutoff:3.500A) Processing helix chain 'F' and resid 124 through 129 Processing helix chain 'F' and resid 130 through 134 removed outlier: 3.829A pdb=" N GLU F 133 " --> pdb=" O CYS F 130 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU F 134 " --> pdb=" O LEU F 131 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 130 through 134' Processing helix chain 'F' and resid 147 through 155 removed outlier: 4.282A pdb=" N LYS F 151 " --> pdb=" O ASN F 147 " (cutoff:3.500A) Processing helix chain 'F' and resid 166 through 171 Processing helix chain 'F' and resid 187 through 202 removed outlier: 3.525A pdb=" N GLY F 197 " --> pdb=" O HIS F 193 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LYS F 200 " --> pdb=" O LEU F 196 " (cutoff:3.500A) Processing helix chain 'F' and resid 216 through 224 removed outlier: 3.534A pdb=" N ARG F 221 " --> pdb=" O ILE F 217 " (cutoff:3.500A) Processing helix chain 'F' and resid 230 through 238 removed outlier: 3.544A pdb=" N ILE F 234 " --> pdb=" O SER F 230 " (cutoff:3.500A) Processing helix chain 'F' and resid 247 through 256 removed outlier: 3.576A pdb=" N PHE F 251 " --> pdb=" O TYR F 247 " (cutoff:3.500A) Processing helix chain 'F' and resid 284 through 289 Processing helix chain 'F' and resid 323 through 334 removed outlier: 3.951A pdb=" N GLU F 328 " --> pdb=" O PRO F 324 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ARG F 329 " --> pdb=" O GLU F 325 " (cutoff:3.500A) Processing helix chain 'H' and resid 124 through 129 Processing helix chain 'H' and resid 130 through 134 removed outlier: 3.829A pdb=" N GLU H 133 " --> pdb=" O CYS H 130 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU H 134 " --> pdb=" O LEU H 131 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 130 through 134' Processing helix chain 'H' and resid 147 through 155 removed outlier: 4.282A pdb=" N LYS H 151 " --> pdb=" O ASN H 147 " (cutoff:3.500A) Processing helix chain 'H' and resid 166 through 171 Processing helix chain 'H' and resid 187 through 202 removed outlier: 3.525A pdb=" N GLY H 197 " --> pdb=" O HIS H 193 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LYS H 200 " --> pdb=" O LEU H 196 " (cutoff:3.500A) Processing helix chain 'H' and resid 216 through 224 removed outlier: 3.534A pdb=" N ARG H 221 " --> pdb=" O ILE H 217 " (cutoff:3.500A) Processing helix chain 'H' and resid 230 through 238 removed outlier: 3.544A pdb=" N ILE H 234 " --> pdb=" O SER H 230 " (cutoff:3.500A) Processing helix chain 'H' and resid 247 through 256 removed outlier: 3.576A pdb=" N PHE H 251 " --> pdb=" O TYR H 247 " (cutoff:3.500A) Processing helix chain 'H' and resid 284 through 289 Processing helix chain 'H' and resid 323 through 334 removed outlier: 3.952A pdb=" N GLU H 328 " --> pdb=" O PRO H 324 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ARG H 329 " --> pdb=" O GLU H 325 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 158 through 161 removed outlier: 6.693A pdb=" N VAL A 119 " --> pdb=" O ILE A 182 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 263 through 268 removed outlier: 6.884A pdb=" N ILE A 321 " --> pdb=" O ILE A 293 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N ILE A 293 " --> pdb=" O ILE A 321 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL A 296 " --> pdb=" O ILE A 303 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 158 through 161 removed outlier: 6.693A pdb=" N VAL C 119 " --> pdb=" O ILE C 182 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 263 through 268 removed outlier: 6.884A pdb=" N ILE C 321 " --> pdb=" O ILE C 293 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N ILE C 293 " --> pdb=" O ILE C 321 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL C 296 " --> pdb=" O ILE C 303 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 158 through 161 removed outlier: 6.694A pdb=" N VAL E 119 " --> pdb=" O ILE E 182 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 263 through 268 removed outlier: 6.884A pdb=" N ILE E 321 " --> pdb=" O ILE E 293 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N ILE E 293 " --> pdb=" O ILE E 321 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL E 296 " --> pdb=" O ILE E 303 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 158 through 161 removed outlier: 6.693A pdb=" N VAL G 119 " --> pdb=" O ILE G 182 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'G' and resid 263 through 268 removed outlier: 6.885A pdb=" N ILE G 321 " --> pdb=" O ILE G 293 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N ILE G 293 " --> pdb=" O ILE G 321 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL G 296 " --> pdb=" O ILE G 303 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 158 through 161 removed outlier: 6.652A pdb=" N VAL B 139 " --> pdb=" O ASN B 158 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N VAL B 160 " --> pdb=" O VAL B 139 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N VAL B 141 " --> pdb=" O VAL B 160 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N VAL B 118 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N LEU B 142 " --> pdb=" O VAL B 118 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ILE B 120 " --> pdb=" O LEU B 142 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N VAL B 181 " --> pdb=" O ILE B 208 " (cutoff:3.500A) removed outlier: 8.071A pdb=" N GLU B 210 " --> pdb=" O VAL B 181 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N VAL B 183 " --> pdb=" O GLU B 210 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 263 through 268 removed outlier: 6.991A pdb=" N ILE B 321 " --> pdb=" O ILE B 293 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N ILE B 293 " --> pdb=" O ILE B 321 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 158 through 161 removed outlier: 6.653A pdb=" N VAL D 139 " --> pdb=" O ASN D 158 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N VAL D 160 " --> pdb=" O VAL D 139 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N VAL D 141 " --> pdb=" O VAL D 160 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N VAL D 118 " --> pdb=" O PHE D 140 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N LEU D 142 " --> pdb=" O VAL D 118 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ILE D 120 " --> pdb=" O LEU D 142 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N VAL D 181 " --> pdb=" O ILE D 208 " (cutoff:3.500A) removed outlier: 8.071A pdb=" N GLU D 210 " --> pdb=" O VAL D 181 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N VAL D 183 " --> pdb=" O GLU D 210 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 263 through 268 removed outlier: 6.991A pdb=" N ILE D 321 " --> pdb=" O ILE D 293 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N ILE D 293 " --> pdb=" O ILE D 321 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 158 through 161 removed outlier: 6.652A pdb=" N VAL F 139 " --> pdb=" O ASN F 158 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N VAL F 160 " --> pdb=" O VAL F 139 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N VAL F 141 " --> pdb=" O VAL F 160 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N VAL F 118 " --> pdb=" O PHE F 140 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N LEU F 142 " --> pdb=" O VAL F 118 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ILE F 120 " --> pdb=" O LEU F 142 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N VAL F 181 " --> pdb=" O ILE F 208 " (cutoff:3.500A) removed outlier: 8.071A pdb=" N GLU F 210 " --> pdb=" O VAL F 181 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N VAL F 183 " --> pdb=" O GLU F 210 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 263 through 268 removed outlier: 6.991A pdb=" N ILE F 321 " --> pdb=" O ILE F 293 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N ILE F 293 " --> pdb=" O ILE F 321 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 158 through 161 removed outlier: 6.652A pdb=" N VAL H 139 " --> pdb=" O ASN H 158 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N VAL H 160 " --> pdb=" O VAL H 139 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N VAL H 141 " --> pdb=" O VAL H 160 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N VAL H 118 " --> pdb=" O PHE H 140 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N LEU H 142 " --> pdb=" O VAL H 118 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ILE H 120 " --> pdb=" O LEU H 142 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N VAL H 181 " --> pdb=" O ILE H 208 " (cutoff:3.500A) removed outlier: 8.071A pdb=" N GLU H 210 " --> pdb=" O VAL H 181 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N VAL H 183 " --> pdb=" O GLU H 210 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 263 through 268 removed outlier: 6.991A pdb=" N ILE H 321 " --> pdb=" O ILE H 293 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N ILE H 293 " --> pdb=" O ILE H 321 " (cutoff:3.500A) 696 hydrogen bonds defined for protein. 1992 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: 2.53 Time building geometry restraints manager: 1.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 2961 1.31 - 1.43: 4079 1.43 - 1.56: 9978 1.56 - 1.68: 18 1.68 - 1.81: 112 Bond restraints: 17148 Sorted by residual: bond pdb=" C10 PGW C 402 " pdb=" C9 PGW C 402 " ideal model delta sigma weight residual 1.333 1.536 -0.203 2.00e-02 2.50e+03 1.03e+02 bond pdb=" C10 PGW E 402 " pdb=" C9 PGW E 402 " ideal model delta sigma weight residual 1.333 1.536 -0.203 2.00e-02 2.50e+03 1.03e+02 bond pdb=" C10 PGW G 402 " pdb=" C9 PGW G 402 " ideal model delta sigma weight residual 1.333 1.536 -0.203 2.00e-02 2.50e+03 1.03e+02 bond pdb=" C10 PGW A 402 " pdb=" C9 PGW A 402 " ideal model delta sigma weight residual 1.333 1.535 -0.202 2.00e-02 2.50e+03 1.02e+02 bond pdb=" C1 PGW E 402 " pdb=" O01 PGW E 402 " ideal model delta sigma weight residual 1.332 1.433 -0.101 2.00e-02 2.50e+03 2.54e+01 ... (remaining 17143 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.39: 23116 6.39 - 12.79: 28 12.79 - 19.18: 8 19.18 - 25.58: 0 25.58 - 31.97: 4 Bond angle restraints: 23156 Sorted by residual: angle pdb=" C06 PGW C 402 " pdb=" C07 PGW C 402 " pdb=" C08 PGW C 402 " ideal model delta sigma weight residual 112.92 80.95 31.97 3.00e+00 1.11e-01 1.14e+02 angle pdb=" C06 PGW A 402 " pdb=" C07 PGW A 402 " pdb=" C08 PGW A 402 " ideal model delta sigma weight residual 112.92 80.96 31.96 3.00e+00 1.11e-01 1.14e+02 angle pdb=" C06 PGW G 402 " pdb=" C07 PGW G 402 " pdb=" C08 PGW G 402 " ideal model delta sigma weight residual 112.92 80.96 31.96 3.00e+00 1.11e-01 1.13e+02 angle pdb=" C06 PGW E 402 " pdb=" C07 PGW E 402 " pdb=" C08 PGW E 402 " ideal model delta sigma weight residual 112.92 80.96 31.96 3.00e+00 1.11e-01 1.13e+02 angle pdb=" N PHE E 38 " pdb=" CA PHE E 38 " pdb=" C PHE E 38 " ideal model delta sigma weight residual 111.36 119.29 -7.93 1.09e+00 8.42e-01 5.30e+01 ... (remaining 23151 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.30: 9740 23.30 - 46.59: 584 46.59 - 69.89: 96 69.89 - 93.18: 8 93.18 - 116.48: 8 Dihedral angle restraints: 10436 sinusoidal: 4284 harmonic: 6152 Sorted by residual: dihedral pdb=" CA GLY G 108 " pdb=" C GLY G 108 " pdb=" N LEU G 109 " pdb=" CA LEU G 109 " ideal model delta harmonic sigma weight residual 180.00 154.74 25.26 0 5.00e+00 4.00e-02 2.55e+01 dihedral pdb=" CA GLY E 108 " pdb=" C GLY E 108 " pdb=" N LEU E 109 " pdb=" CA LEU E 109 " ideal model delta harmonic sigma weight residual 180.00 154.75 25.25 0 5.00e+00 4.00e-02 2.55e+01 dihedral pdb=" CA GLY A 108 " pdb=" C GLY A 108 " pdb=" N LEU A 109 " pdb=" CA LEU A 109 " ideal model delta harmonic sigma weight residual 180.00 154.79 25.21 0 5.00e+00 4.00e-02 2.54e+01 ... (remaining 10433 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1680 0.052 - 0.104: 789 0.104 - 0.156: 195 0.156 - 0.208: 8 0.208 - 0.259: 20 Chirality restraints: 2692 Sorted by residual: chirality pdb=" CA PHE C 38 " pdb=" N PHE C 38 " pdb=" C PHE C 38 " pdb=" CB PHE C 38 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.68e+00 chirality pdb=" CA PHE E 38 " pdb=" N PHE E 38 " pdb=" C PHE E 38 " pdb=" CB PHE E 38 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.67e+00 chirality pdb=" CA PHE A 38 " pdb=" N PHE A 38 " pdb=" C PHE A 38 " pdb=" CB PHE A 38 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.67e+00 ... (remaining 2689 not shown) Planarity restraints: 3000 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C06 PGW C 402 " -0.306 2.00e-02 2.50e+03 3.09e-01 9.52e+02 pdb=" C10 PGW C 402 " 0.307 2.00e-02 2.50e+03 pdb=" C8 PGW C 402 " -0.311 2.00e-02 2.50e+03 pdb=" C9 PGW C 402 " 0.310 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C06 PGW E 402 " -0.306 2.00e-02 2.50e+03 3.09e-01 9.52e+02 pdb=" C10 PGW E 402 " 0.307 2.00e-02 2.50e+03 pdb=" C8 PGW E 402 " -0.311 2.00e-02 2.50e+03 pdb=" C9 PGW E 402 " 0.310 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C06 PGW A 402 " 0.306 2.00e-02 2.50e+03 3.08e-01 9.52e+02 pdb=" C10 PGW A 402 " -0.307 2.00e-02 2.50e+03 pdb=" C8 PGW A 402 " 0.311 2.00e-02 2.50e+03 pdb=" C9 PGW A 402 " -0.310 2.00e-02 2.50e+03 ... (remaining 2997 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.83: 5257 2.83 - 3.41: 16532 3.41 - 3.98: 30183 3.98 - 4.56: 43486 4.56 - 5.14: 66930 Nonbonded interactions: 162388 Sorted by model distance: nonbonded pdb=" O PHE E 75 " pdb=" CG2 THR E 78 " model vdw 2.252 3.460 nonbonded pdb=" O PHE C 75 " pdb=" CG2 THR C 78 " model vdw 2.252 3.460 nonbonded pdb=" O PHE A 75 " pdb=" CG2 THR A 78 " model vdw 2.253 3.460 nonbonded pdb=" O PHE G 75 " pdb=" CG2 THR G 78 " model vdw 2.253 3.460 nonbonded pdb=" OG SER A 124 " pdb=" OD2 ASP A 184 " model vdw 2.254 3.040 ... (remaining 162383 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 20 through 402) selection = chain 'C' selection = chain 'E' selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' } 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: 0.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 13.200 Find NCS groups from input model: 0.380 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: 0.010 Load rotamer database and sin/cos tables:1.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 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 : 0.010 0.203 17148 Z= 0.439 Angle : 1.043 31.969 23156 Z= 0.541 Chirality : 0.060 0.259 2692 Planarity : 0.012 0.309 3000 Dihedral : 15.270 116.480 6484 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 0.44 % Allowed : 6.54 % Favored : 93.03 % 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: -5.10 (0.13), residues: 2140 helix: -4.22 (0.08), residues: 1060 sheet: -0.47 (0.26), residues: 356 loop : -3.22 (0.17), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 116 TYR 0.015 0.002 TYR F 214 PHE 0.009 0.002 PHE G 97 TRP 0.009 0.001 TRP C 123 HIS 0.005 0.002 HIS E 117 Details of bonding type rmsd/Z covalent geometry : bond 0.00997 / 0.44 (17148) covalent geometry : angle 1.04335 / 0.54 (23156) hydrogen bonds : bond 0.30310 / 19.50 ( 696) hydrogen bonds : angle 9.73571 / 6.80 ( 1992) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 433 time to evaluate : 0.623 Fit side-chains REVERT: A 25 LEU cc_start: 0.8263 (mt) cc_final: 0.7999 (tp) REVERT: A 74 TYR cc_start: 0.8203 (m-80) cc_final: 0.7477 (m-80) REVERT: A 96 GLU cc_start: 0.8217 (tt0) cc_final: 0.7948 (tt0) REVERT: A 210 GLU cc_start: 0.7817 (tt0) cc_final: 0.7556 (tt0) REVERT: A 263 ARG cc_start: 0.8246 (ttp80) cc_final: 0.8046 (ttp80) REVERT: C 25 LEU cc_start: 0.8271 (mt) cc_final: 0.8010 (tp) REVERT: C 74 TYR cc_start: 0.8235 (m-80) cc_final: 0.7513 (m-80) REVERT: C 210 GLU cc_start: 0.7811 (tt0) cc_final: 0.7544 (tt0) REVERT: C 310 TYR cc_start: 0.8492 (t80) cc_final: 0.8259 (t80) REVERT: E 25 LEU cc_start: 0.8253 (mt) cc_final: 0.7975 (tp) REVERT: E 74 TYR cc_start: 0.8189 (m-80) cc_final: 0.7488 (m-80) REVERT: E 210 GLU cc_start: 0.7736 (tt0) cc_final: 0.7481 (tt0) REVERT: E 294 ILE cc_start: 0.8423 (mm) cc_final: 0.8220 (mm) REVERT: G 25 LEU cc_start: 0.8257 (mt) cc_final: 0.7987 (tp) REVERT: G 74 TYR cc_start: 0.8207 (m-80) cc_final: 0.7483 (m-80) REVERT: G 96 GLU cc_start: 0.8200 (tt0) cc_final: 0.7936 (tt0) REVERT: G 210 GLU cc_start: 0.7811 (tt0) cc_final: 0.7518 (tt0) REVERT: G 263 ARG cc_start: 0.8187 (ttp80) cc_final: 0.7946 (ttp80) REVERT: G 294 ILE cc_start: 0.8422 (mm) cc_final: 0.8219 (mm) REVERT: B 190 GLU cc_start: 0.8059 (mt-10) cc_final: 0.7849 (mt-10) REVERT: B 250 MET cc_start: 0.8790 (mtt) cc_final: 0.8570 (mtt) REVERT: D 190 GLU cc_start: 0.8038 (mt-10) cc_final: 0.7822 (mt-10) REVERT: D 250 MET cc_start: 0.8788 (mtt) cc_final: 0.8584 (mtt) REVERT: F 190 GLU cc_start: 0.8015 (mt-10) cc_final: 0.7802 (mt-10) REVERT: F 200 LYS cc_start: 0.8713 (mmtt) cc_final: 0.8287 (mtmt) REVERT: F 250 MET cc_start: 0.8835 (mtt) cc_final: 0.8618 (mtt) REVERT: F 263 ARG cc_start: 0.7626 (ptt90) cc_final: 0.7229 (ptm-80) REVERT: H 190 GLU cc_start: 0.8078 (mt-10) cc_final: 0.7873 (mt-10) REVERT: H 250 MET cc_start: 0.8810 (mtt) cc_final: 0.8594 (mtt) outliers start: 8 outliers final: 4 residues processed: 437 average time/residue: 0.1363 time to fit residues: 85.6547 Evaluate side-chains 373 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 369 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain G residue 77 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 2.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 0.9990 chunk 200 optimal weight: 0.6980 chunk 77 optimal weight: 0.3980 chunk 122 optimal weight: 0.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- 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 = 0.3680 r_free = 0.3680 target = 0.156807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.115101 restraints weight = 11735.995| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 1.37 r_work: 0.3000 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2846 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.1690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 17148 Z= 0.120 Angle : 0.514 5.023 23156 Z= 0.283 Chirality : 0.046 0.137 2692 Planarity : 0.004 0.029 3000 Dihedral : 9.047 81.756 2484 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 0.65 % Allowed : 9.53 % Favored : 89.81 % 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: -3.09 (0.15), residues: 2140 helix: -2.16 (0.13), residues: 1020 sheet: -0.17 (0.27), residues: 328 loop : -2.54 (0.18), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 241 TYR 0.013 0.001 TYR B 310 PHE 0.006 0.001 PHE C 75 TRP 0.004 0.001 TRP G 46 HIS 0.002 0.001 HIS C 117 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 (17148) covalent geometry : angle 0.51407 / 0.28 (23156) hydrogen bonds : bond 0.04476 / 2.91 ( 696) hydrogen bonds : angle 5.05313 / 3.51 ( 1992) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 410 time to evaluate : 0.551 Fit side-chains REVERT: A 263 ARG cc_start: 0.8416 (ttp80) cc_final: 0.8171 (ttp80) REVERT: C 25 LEU cc_start: 0.8174 (mt) cc_final: 0.7915 (tp) REVERT: E 25 LEU cc_start: 0.8155 (mt) cc_final: 0.7875 (tp) REVERT: E 74 TYR cc_start: 0.8443 (m-80) cc_final: 0.8176 (m-80) REVERT: E 210 GLU cc_start: 0.8462 (tt0) cc_final: 0.8187 (tt0) REVERT: G 74 TYR cc_start: 0.8432 (m-80) cc_final: 0.8219 (m-80) REVERT: G 210 GLU cc_start: 0.8466 (tt0) cc_final: 0.8186 (tt0) REVERT: G 263 ARG cc_start: 0.8370 (ttp80) cc_final: 0.8131 (ttp80) REVERT: G 266 GLU cc_start: 0.6822 (pt0) cc_final: 0.6541 (pt0) REVERT: B 250 MET cc_start: 0.8520 (mtt) cc_final: 0.8264 (mtt) REVERT: B 333 TYR cc_start: 0.8712 (t80) cc_final: 0.8397 (t80) REVERT: D 200 LYS cc_start: 0.8379 (mmtt) cc_final: 0.7731 (mtmt) REVERT: D 250 MET cc_start: 0.8506 (mtt) cc_final: 0.8252 (mtt) REVERT: D 333 TYR cc_start: 0.8712 (t80) cc_final: 0.8382 (t80) REVERT: F 250 MET cc_start: 0.8552 (mtt) cc_final: 0.8290 (mtt) REVERT: F 263 ARG cc_start: 0.7800 (ptt90) cc_final: 0.7299 (ptm-80) REVERT: H 200 LYS cc_start: 0.8373 (mmtt) cc_final: 0.7718 (mtmt) REVERT: H 250 MET cc_start: 0.8528 (mtt) cc_final: 0.8284 (mtt) REVERT: H 333 TYR cc_start: 0.8711 (t80) cc_final: 0.8399 (t80) outliers start: 12 outliers final: 5 residues processed: 413 average time/residue: 0.1366 time to fit residues: 80.8393 Evaluate side-chains 362 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 357 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 244 ASP Chi-restraints excluded: chain E residue 244 ASP Chi-restraints excluded: chain G residue 95 LEU Chi-restraints excluded: chain G residue 244 ASP Chi-restraints excluded: chain H residue 133 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 116 optimal weight: 0.6980 chunk 46 optimal weight: 5.9990 chunk 127 optimal weight: 5.9990 chunk 173 optimal weight: 0.6980 chunk 57 optimal weight: 0.0970 chunk 10 optimal weight: 0.7980 chunk 187 optimal weight: 0.6980 chunk 53 optimal weight: 2.9990 chunk 167 optimal weight: 8.9990 chunk 8 optimal weight: 2.9990 chunk 69 optimal weight: 0.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- 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 = 0.3689 r_free = 0.3689 target = 0.157766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.115525 restraints weight = 11807.286| |-----------------------------------------------------------------------------| r_work (start): 0.3173 rms_B_bonded: 1.40 r_work: 0.3017 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2862 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.2194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 17148 Z= 0.094 Angle : 0.446 4.809 23156 Z= 0.243 Chirality : 0.046 0.135 2692 Planarity : 0.003 0.029 3000 Dihedral : 7.020 59.538 2480 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 0.87 % Allowed : 12.69 % Favored : 86.44 % 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: -1.67 (0.17), residues: 2140 helix: -0.67 (0.16), residues: 1012 sheet: 0.21 (0.28), residues: 328 loop : -2.16 (0.19), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 241 TYR 0.017 0.001 TYR F 333 PHE 0.003 0.001 PHE G 40 TRP 0.002 0.000 TRP G 123 HIS 0.001 0.000 HIS H 117 Details of bonding type rmsd/Z covalent geometry : bond 0.00206 / 0.09 (17148) covalent geometry : angle 0.44606 / 0.24 (23156) hydrogen bonds : bond 0.03556 / 2.31 ( 696) hydrogen bonds : angle 4.45439 / 3.10 ( 1992) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 383 time to evaluate : 0.531 Fit side-chains REVERT: A 74 TYR cc_start: 0.8522 (m-80) cc_final: 0.7357 (m-80) REVERT: A 96 GLU cc_start: 0.8483 (tt0) cc_final: 0.8243 (tt0) REVERT: A 263 ARG cc_start: 0.8367 (ttp80) cc_final: 0.8053 (ttp80) REVERT: A 313 ARG cc_start: 0.7807 (mmm-85) cc_final: 0.7500 (mmm-85) REVERT: C 313 ARG cc_start: 0.7695 (mmm-85) cc_final: 0.7234 (mtt180) REVERT: E 25 LEU cc_start: 0.8113 (mt) cc_final: 0.7856 (tp) REVERT: E 96 GLU cc_start: 0.8470 (tt0) cc_final: 0.8260 (tt0) REVERT: E 210 GLU cc_start: 0.8498 (tt0) cc_final: 0.8232 (tt0) REVERT: E 313 ARG cc_start: 0.7809 (mmm-85) cc_final: 0.7531 (mmm-85) REVERT: G 210 GLU cc_start: 0.8452 (tt0) cc_final: 0.8189 (tt0) REVERT: G 263 ARG cc_start: 0.8349 (ttp80) cc_final: 0.8034 (ttp80) REVERT: G 313 ARG cc_start: 0.7675 (mmm-85) cc_final: 0.7396 (mmm-85) REVERT: B 276 GLU cc_start: 0.7848 (mt-10) cc_final: 0.7620 (mt-10) REVERT: B 333 TYR cc_start: 0.8613 (t80) cc_final: 0.8354 (t80) REVERT: D 250 MET cc_start: 0.8557 (mtt) cc_final: 0.8329 (mtt) REVERT: D 276 GLU cc_start: 0.7853 (mt-10) cc_final: 0.7621 (mt-10) REVERT: D 333 TYR cc_start: 0.8608 (t80) cc_final: 0.8339 (t80) REVERT: F 263 ARG cc_start: 0.7745 (ptt90) cc_final: 0.7221 (ptm-80) REVERT: H 276 GLU cc_start: 0.7864 (mt-10) cc_final: 0.7641 (mt-10) REVERT: H 333 TYR cc_start: 0.8611 (t80) cc_final: 0.8355 (t80) outliers start: 16 outliers final: 15 residues processed: 389 average time/residue: 0.1405 time to fit residues: 79.3630 Evaluate side-chains 377 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 362 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 SER Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 244 ASP Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 244 ASP Chi-restraints excluded: chain G residue 68 SER Chi-restraints excluded: chain G residue 95 LEU Chi-restraints excluded: chain G residue 244 ASP Chi-restraints excluded: chain B residue 133 GLU Chi-restraints excluded: chain D residue 133 GLU Chi-restraints excluded: chain F residue 133 GLU Chi-restraints excluded: chain H residue 133 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 207 optimal weight: 5.9990 chunk 163 optimal weight: 3.9990 chunk 50 optimal weight: 0.7980 chunk 3 optimal weight: 3.9990 chunk 126 optimal weight: 6.9990 chunk 66 optimal weight: 5.9990 chunk 114 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 198 optimal weight: 0.9980 chunk 189 optimal weight: 0.8980 overall best weight: 1.7384 ------------------------------------------------------------------------------- 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 = 0.3713 r_free = 0.3713 target = 0.159475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.118851 restraints weight = 11368.733| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 1.31 r_work: 0.3027 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2873 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8640 moved from start: 0.2218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 17148 Z= 0.175 Angle : 0.494 5.077 23156 Z= 0.264 Chirality : 0.048 0.134 2692 Planarity : 0.004 0.030 3000 Dihedral : 6.958 59.125 2480 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 1.53 % Allowed : 13.62 % Favored : 84.86 % 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: -1.20 (0.17), residues: 2140 helix: -0.21 (0.16), residues: 1020 sheet: 0.38 (0.28), residues: 320 loop : -2.01 (0.19), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 101 TYR 0.015 0.001 TYR D 310 PHE 0.024 0.001 PHE C 97 TRP 0.003 0.001 TRP A 52 HIS 0.005 0.001 HIS G 117 Details of bonding type rmsd/Z covalent geometry : bond 0.00430 / 0.17 (17148) covalent geometry : angle 0.49378 / 0.26 (23156) hydrogen bonds : bond 0.04084 / 2.65 ( 696) hydrogen bonds : angle 4.48803 / 3.12 ( 1992) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 382 time to evaluate : 0.602 Fit side-chains REVERT: A 25 LEU cc_start: 0.8092 (mt) cc_final: 0.7834 (tp) REVERT: A 74 TYR cc_start: 0.8577 (m-80) cc_final: 0.7449 (m-80) REVERT: A 263 ARG cc_start: 0.8439 (ttp80) cc_final: 0.8128 (ttp80) REVERT: A 313 ARG cc_start: 0.7836 (mmm-85) cc_final: 0.7555 (mmm-85) REVERT: C 313 ARG cc_start: 0.7791 (mmm-85) cc_final: 0.7357 (mtt180) REVERT: E 25 LEU cc_start: 0.8109 (mt) cc_final: 0.7848 (tp) REVERT: E 96 GLU cc_start: 0.8487 (tt0) cc_final: 0.8279 (tt0) REVERT: E 313 ARG cc_start: 0.7808 (mmm-85) cc_final: 0.7537 (mmm-85) REVERT: G 25 LEU cc_start: 0.8106 (mt) cc_final: 0.7843 (tp) REVERT: G 210 GLU cc_start: 0.8402 (tt0) cc_final: 0.8184 (tt0) REVERT: G 263 ARG cc_start: 0.8427 (ttp80) cc_final: 0.8154 (ttp80) REVERT: G 313 ARG cc_start: 0.7784 (mmm-85) cc_final: 0.7512 (mmm-85) REVERT: D 250 MET cc_start: 0.8684 (mtt) cc_final: 0.8477 (mtt) REVERT: F 263 ARG cc_start: 0.7840 (ptt90) cc_final: 0.7359 (ptm-80) outliers start: 28 outliers final: 22 residues processed: 398 average time/residue: 0.1422 time to fit residues: 82.1689 Evaluate side-chains 387 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 365 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 68 SER Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 187 SER Chi-restraints excluded: chain C residue 244 ASP Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 98 LEU Chi-restraints excluded: chain E residue 187 SER Chi-restraints excluded: chain E residue 244 ASP Chi-restraints excluded: chain G residue 55 VAL Chi-restraints excluded: chain G residue 95 LEU Chi-restraints excluded: chain G residue 98 LEU Chi-restraints excluded: chain G residue 244 ASP Chi-restraints excluded: chain B residue 133 GLU Chi-restraints excluded: chain D residue 133 GLU Chi-restraints excluded: chain F residue 133 GLU Chi-restraints excluded: chain H residue 133 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 164 optimal weight: 7.9990 chunk 208 optimal weight: 0.9990 chunk 6 optimal weight: 0.9980 chunk 73 optimal weight: 1.9990 chunk 197 optimal weight: 1.9990 chunk 122 optimal weight: 3.9990 chunk 143 optimal weight: 9.9990 chunk 87 optimal weight: 0.9990 chunk 37 optimal weight: 3.9990 chunk 9 optimal weight: 0.1980 chunk 150 optimal weight: 3.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 147 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.160675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.120045 restraints weight = 11430.384| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 1.32 r_work: 0.3012 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2860 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.2431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 17148 Z= 0.116 Angle : 0.449 4.706 23156 Z= 0.242 Chirality : 0.046 0.132 2692 Planarity : 0.003 0.028 3000 Dihedral : 6.582 59.699 2480 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 1.42 % Allowed : 15.14 % Favored : 83.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.84 (0.17), residues: 2140 helix: 0.18 (0.16), residues: 1016 sheet: 0.41 (0.27), residues: 320 loop : -1.89 (0.20), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 241 TYR 0.012 0.001 TYR A 51 PHE 0.023 0.001 PHE E 97 TRP 0.002 0.001 TRP E 123 HIS 0.002 0.001 HIS G 117 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 (17148) covalent geometry : angle 0.44914 / 0.24 (23156) hydrogen bonds : bond 0.03414 / 2.22 ( 696) hydrogen bonds : angle 4.25789 / 2.96 ( 1992) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 374 time to evaluate : 0.578 Fit side-chains REVERT: A 25 LEU cc_start: 0.8084 (mt) cc_final: 0.7815 (tp) REVERT: A 74 TYR cc_start: 0.8515 (m-80) cc_final: 0.7397 (m-80) REVERT: A 263 ARG cc_start: 0.8435 (ttp80) cc_final: 0.8101 (ttp80) REVERT: A 313 ARG cc_start: 0.7824 (mmm-85) cc_final: 0.7529 (mmm-85) REVERT: C 74 TYR cc_start: 0.8526 (m-80) cc_final: 0.7515 (m-80) REVERT: C 313 ARG cc_start: 0.7836 (mmm-85) cc_final: 0.7410 (mtt180) REVERT: E 25 LEU cc_start: 0.8123 (mt) cc_final: 0.7867 (tp) REVERT: E 96 GLU cc_start: 0.8441 (tt0) cc_final: 0.8209 (tt0) REVERT: E 313 ARG cc_start: 0.7838 (mmm-85) cc_final: 0.7332 (mtt180) REVERT: G 25 LEU cc_start: 0.8100 (mt) cc_final: 0.7828 (tp) REVERT: G 74 TYR cc_start: 0.8530 (m-80) cc_final: 0.7444 (m-80) REVERT: G 263 ARG cc_start: 0.8413 (ttp80) cc_final: 0.8083 (ttp80) REVERT: G 313 ARG cc_start: 0.7780 (mmm-85) cc_final: 0.7511 (mmm-85) REVERT: B 210 GLU cc_start: 0.8495 (tt0) cc_final: 0.8271 (tt0) REVERT: D 210 GLU cc_start: 0.8510 (tt0) cc_final: 0.8284 (tt0) REVERT: F 263 ARG cc_start: 0.7768 (ptt90) cc_final: 0.7277 (ptm-80) outliers start: 26 outliers final: 22 residues processed: 386 average time/residue: 0.1488 time to fit residues: 82.6185 Evaluate side-chains 385 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 363 time to evaluate : 0.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 SER Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 187 SER Chi-restraints excluded: chain C residue 244 ASP Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 244 ASP Chi-restraints excluded: chain G residue 55 VAL Chi-restraints excluded: chain G residue 68 SER Chi-restraints excluded: chain G residue 95 LEU Chi-restraints excluded: chain G residue 187 SER Chi-restraints excluded: chain G residue 244 ASP Chi-restraints excluded: chain B residue 133 GLU Chi-restraints excluded: chain D residue 133 GLU Chi-restraints excluded: chain F residue 133 GLU Chi-restraints excluded: chain H residue 133 GLU Chi-restraints excluded: chain H residue 325 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 80 optimal weight: 0.5980 chunk 126 optimal weight: 5.9990 chunk 57 optimal weight: 0.7980 chunk 145 optimal weight: 0.9980 chunk 74 optimal weight: 0.8980 chunk 113 optimal weight: 0.5980 chunk 201 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 chunk 27 optimal weight: 6.9990 chunk 97 optimal weight: 4.9990 chunk 58 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 147 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.161774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.120913 restraints weight = 11595.550| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 1.35 r_work: 0.3011 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2858 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.2577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 17148 Z= 0.097 Angle : 0.429 4.500 23156 Z= 0.232 Chirality : 0.045 0.130 2692 Planarity : 0.003 0.029 3000 Dihedral : 6.145 58.416 2480 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 1.25 % Allowed : 16.01 % Favored : 82.73 % 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: -0.47 (0.18), residues: 2140 helix: 0.56 (0.16), residues: 1020 sheet: 0.46 (0.27), residues: 320 loop : -1.76 (0.20), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 241 TYR 0.011 0.001 TYR G 51 PHE 0.017 0.001 PHE A 97 TRP 0.002 0.000 TRP E 123 HIS 0.001 0.000 HIS H 117 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.10 (17148) covalent geometry : angle 0.42938 / 0.23 (23156) hydrogen bonds : bond 0.03097 / 2.02 ( 696) hydrogen bonds : angle 4.12282 / 2.87 ( 1992) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 381 time to evaluate : 0.654 Fit side-chains REVERT: A 25 LEU cc_start: 0.8117 (mt) cc_final: 0.7854 (tp) REVERT: A 74 TYR cc_start: 0.8531 (m-80) cc_final: 0.7433 (m-80) REVERT: A 93 ARG cc_start: 0.7765 (tpt90) cc_final: 0.7487 (tpt170) REVERT: A 263 ARG cc_start: 0.8427 (ttp80) cc_final: 0.8099 (ttp80) REVERT: A 313 ARG cc_start: 0.7939 (mmm-85) cc_final: 0.7665 (mmm-85) REVERT: C 74 TYR cc_start: 0.8499 (m-80) cc_final: 0.7502 (m-80) REVERT: C 313 ARG cc_start: 0.7867 (mmm-85) cc_final: 0.7462 (mtt180) REVERT: E 25 LEU cc_start: 0.8130 (mt) cc_final: 0.7869 (tp) REVERT: E 74 TYR cc_start: 0.8469 (m-80) cc_final: 0.7436 (m-80) REVERT: E 93 ARG cc_start: 0.7672 (mmm160) cc_final: 0.7315 (mmm160) REVERT: E 96 GLU cc_start: 0.8429 (tt0) cc_final: 0.8126 (tt0) REVERT: E 313 ARG cc_start: 0.7850 (mmm-85) cc_final: 0.7373 (mtt180) REVERT: G 25 LEU cc_start: 0.8126 (mt) cc_final: 0.7855 (tp) REVERT: G 74 TYR cc_start: 0.8469 (m-80) cc_final: 0.7393 (m-80) REVERT: G 93 ARG cc_start: 0.7594 (mmm160) cc_final: 0.7384 (mmm160) REVERT: G 263 ARG cc_start: 0.8392 (ttp80) cc_final: 0.8077 (ttp80) REVERT: G 313 ARG cc_start: 0.7817 (mmm-85) cc_final: 0.7539 (mmm-85) REVERT: D 287 ASP cc_start: 0.8091 (m-30) cc_final: 0.7882 (m-30) outliers start: 23 outliers final: 21 residues processed: 390 average time/residue: 0.1544 time to fit residues: 86.5020 Evaluate side-chains 397 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 376 time to evaluate : 0.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 SER Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain C residue 187 SER Chi-restraints excluded: chain C residue 244 ASP Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 98 LEU Chi-restraints excluded: chain E residue 187 SER Chi-restraints excluded: chain E residue 244 ASP Chi-restraints excluded: chain G residue 68 SER Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 95 LEU Chi-restraints excluded: chain G residue 98 LEU Chi-restraints excluded: chain G residue 187 SER Chi-restraints excluded: chain G residue 244 ASP Chi-restraints excluded: chain B residue 133 GLU Chi-restraints excluded: chain D residue 133 GLU Chi-restraints excluded: chain F residue 133 GLU Chi-restraints excluded: chain H residue 133 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 47 optimal weight: 0.8980 chunk 31 optimal weight: 10.0000 chunk 61 optimal weight: 5.9990 chunk 72 optimal weight: 0.9990 chunk 33 optimal weight: 6.9990 chunk 43 optimal weight: 2.9990 chunk 177 optimal weight: 0.7980 chunk 167 optimal weight: 1.9990 chunk 144 optimal weight: 8.9990 chunk 169 optimal weight: 0.3980 chunk 73 optimal weight: 0.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- 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 = 0.3660 r_free = 0.3660 target = 0.155274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.110632 restraints weight = 11851.920| |-----------------------------------------------------------------------------| r_work (start): 0.3129 rms_B_bonded: 1.53 r_work: 0.2969 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2811 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.2657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 17148 Z= 0.101 Angle : 0.431 4.363 23156 Z= 0.232 Chirality : 0.046 0.133 2692 Planarity : 0.003 0.028 3000 Dihedral : 5.887 56.558 2480 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 1.31 % Allowed : 16.88 % Favored : 81.81 % 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: -0.20 (0.18), residues: 2140 helix: 0.86 (0.17), residues: 1020 sheet: 0.50 (0.27), residues: 320 loop : -1.70 (0.20), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 241 TYR 0.011 0.001 TYR A 51 PHE 0.017 0.001 PHE A 97 TRP 0.002 0.000 TRP C 123 HIS 0.001 0.000 HIS F 117 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.10 (17148) covalent geometry : angle 0.43094 / 0.23 (23156) hydrogen bonds : bond 0.03083 / 2.01 ( 696) hydrogen bonds : angle 4.07043 / 2.84 ( 1992) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 377 time to evaluate : 0.683 Fit side-chains REVERT: A 74 TYR cc_start: 0.8518 (m-80) cc_final: 0.7392 (m-80) REVERT: A 93 ARG cc_start: 0.7673 (tpt90) cc_final: 0.7387 (tpt170) REVERT: A 263 ARG cc_start: 0.8411 (ttp80) cc_final: 0.8066 (ttp80) REVERT: A 313 ARG cc_start: 0.8012 (mmm-85) cc_final: 0.7729 (mmm-85) REVERT: C 74 TYR cc_start: 0.8474 (m-80) cc_final: 0.7388 (m-80) REVERT: C 237 ARG cc_start: 0.8098 (ttm-80) cc_final: 0.7755 (ttm-80) REVERT: C 313 ARG cc_start: 0.7910 (mmm-85) cc_final: 0.7480 (mtt180) REVERT: E 74 TYR cc_start: 0.8468 (m-80) cc_final: 0.7439 (m-80) REVERT: E 96 GLU cc_start: 0.8471 (tt0) cc_final: 0.8262 (tt0) REVERT: E 313 ARG cc_start: 0.7878 (mmm-85) cc_final: 0.7323 (mtt180) REVERT: G 25 LEU cc_start: 0.8138 (mt) cc_final: 0.7874 (tp) REVERT: G 74 TYR cc_start: 0.8469 (m-80) cc_final: 0.7389 (m-80) REVERT: G 93 ARG cc_start: 0.7506 (mmm160) cc_final: 0.7298 (mmm160) REVERT: G 263 ARG cc_start: 0.8387 (ttp80) cc_final: 0.8033 (ttp80) REVERT: G 313 ARG cc_start: 0.7866 (mmm-85) cc_final: 0.7330 (mtt180) outliers start: 24 outliers final: 21 residues processed: 388 average time/residue: 0.1552 time to fit residues: 86.5684 Evaluate side-chains 389 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 368 time to evaluate : 0.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 SER Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 187 SER Chi-restraints excluded: chain C residue 244 ASP Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 98 LEU Chi-restraints excluded: chain E residue 187 SER Chi-restraints excluded: chain E residue 244 ASP Chi-restraints excluded: chain G residue 68 SER Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 95 LEU Chi-restraints excluded: chain G residue 98 LEU Chi-restraints excluded: chain G residue 244 ASP Chi-restraints excluded: chain B residue 133 GLU Chi-restraints excluded: chain D residue 133 GLU Chi-restraints excluded: chain F residue 133 GLU Chi-restraints excluded: chain H residue 133 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 84 optimal weight: 2.9990 chunk 175 optimal weight: 2.9990 chunk 104 optimal weight: 3.9990 chunk 4 optimal weight: 4.9990 chunk 34 optimal weight: 3.9990 chunk 68 optimal weight: 0.9990 chunk 79 optimal weight: 0.9980 chunk 191 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 126 optimal weight: 4.9990 chunk 145 optimal weight: 0.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- 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 = 0.3709 r_free = 0.3709 target = 0.159148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.118062 restraints weight = 11493.116| |-----------------------------------------------------------------------------| r_work (start): 0.3145 rms_B_bonded: 1.32 r_work: 0.2987 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2833 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.2605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 17148 Z= 0.160 Angle : 0.477 6.628 23156 Z= 0.254 Chirality : 0.048 0.139 2692 Planarity : 0.004 0.029 3000 Dihedral : 5.963 55.633 2480 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 1.42 % Allowed : 16.67 % Favored : 81.92 % 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: -0.21 (0.18), residues: 2140 helix: 0.79 (0.16), residues: 1024 sheet: 0.54 (0.27), residues: 320 loop : -1.65 (0.21), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 241 TYR 0.012 0.001 TYR G 51 PHE 0.017 0.001 PHE E 97 TRP 0.003 0.001 TRP G 123 HIS 0.003 0.001 HIS E 117 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.16 (17148) covalent geometry : angle 0.47706 / 0.25 (23156) hydrogen bonds : bond 0.03643 / 2.37 ( 696) hydrogen bonds : angle 4.18143 / 2.92 ( 1992) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 373 time to evaluate : 0.671 Fit side-chains REVERT: A 25 LEU cc_start: 0.8148 (mt) cc_final: 0.7887 (tp) REVERT: A 74 TYR cc_start: 0.8550 (m-80) cc_final: 0.7523 (m-80) REVERT: A 93 ARG cc_start: 0.7764 (tpt90) cc_final: 0.7469 (tpt170) REVERT: A 263 ARG cc_start: 0.8452 (ttp80) cc_final: 0.8121 (ttp80) REVERT: A 313 ARG cc_start: 0.7967 (mmm-85) cc_final: 0.7696 (mmm-85) REVERT: C 74 TYR cc_start: 0.8547 (m-80) cc_final: 0.7561 (m-80) REVERT: C 313 ARG cc_start: 0.7887 (mmm-85) cc_final: 0.7483 (mtt180) REVERT: E 25 LEU cc_start: 0.8155 (mt) cc_final: 0.7894 (tp) REVERT: E 74 TYR cc_start: 0.8542 (m-80) cc_final: 0.7551 (m-80) REVERT: E 313 ARG cc_start: 0.7907 (mmm-85) cc_final: 0.7634 (mmm-85) REVERT: G 25 LEU cc_start: 0.8139 (mt) cc_final: 0.7876 (tp) REVERT: G 74 TYR cc_start: 0.8577 (m-80) cc_final: 0.7531 (m-80) REVERT: G 93 ARG cc_start: 0.7634 (mmm160) cc_final: 0.7429 (mmm160) REVERT: G 263 ARG cc_start: 0.8425 (ttp80) cc_final: 0.8083 (ttp80) REVERT: G 313 ARG cc_start: 0.7888 (mmm-85) cc_final: 0.7484 (mtt180) REVERT: F 276 GLU cc_start: 0.7684 (mt-10) cc_final: 0.7472 (mt-10) outliers start: 26 outliers final: 26 residues processed: 387 average time/residue: 0.1532 time to fit residues: 85.6740 Evaluate side-chains 393 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 367 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 SER Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 187 SER Chi-restraints excluded: chain C residue 244 ASP Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 98 LEU Chi-restraints excluded: chain E residue 187 SER Chi-restraints excluded: chain E residue 244 ASP Chi-restraints excluded: chain G residue 55 VAL Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 95 LEU Chi-restraints excluded: chain G residue 98 LEU Chi-restraints excluded: chain G residue 187 SER Chi-restraints excluded: chain G residue 244 ASP Chi-restraints excluded: chain B residue 133 GLU Chi-restraints excluded: chain D residue 133 GLU Chi-restraints excluded: chain F residue 133 GLU Chi-restraints excluded: chain H residue 133 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 81 optimal weight: 0.7980 chunk 40 optimal weight: 0.7980 chunk 178 optimal weight: 0.6980 chunk 75 optimal weight: 1.9990 chunk 145 optimal weight: 1.9990 chunk 208 optimal weight: 4.9990 chunk 146 optimal weight: 6.9990 chunk 175 optimal weight: 0.9980 chunk 59 optimal weight: 0.0050 chunk 91 optimal weight: 8.9990 chunk 36 optimal weight: 2.9990 overall best weight: 0.6594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 174 ASN H 174 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.155507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.110769 restraints weight = 11909.163| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 1.54 r_work: 0.3054 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2901 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.2739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 17148 Z= 0.092 Angle : 0.433 5.359 23156 Z= 0.233 Chirality : 0.046 0.142 2692 Planarity : 0.003 0.029 3000 Dihedral : 5.682 54.727 2480 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 1.25 % Allowed : 16.83 % Favored : 81.92 % 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: 0.08 (0.18), residues: 2140 helix: 1.12 (0.17), residues: 1020 sheet: 0.59 (0.27), residues: 320 loop : -1.59 (0.21), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 241 TYR 0.010 0.001 TYR G 51 PHE 0.015 0.001 PHE A 97 TRP 0.002 0.000 TRP E 123 HIS 0.001 0.000 HIS H 117 Details of bonding type rmsd/Z covalent geometry : bond 0.00211 / 0.09 (17148) covalent geometry : angle 0.43304 / 0.23 (23156) hydrogen bonds : bond 0.02969 / 1.94 ( 696) hydrogen bonds : angle 4.03875 / 2.81 ( 1992) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 373 time to evaluate : 0.675 Fit side-chains REVERT: A 74 TYR cc_start: 0.8543 (m-80) cc_final: 0.7429 (m-80) REVERT: A 93 ARG cc_start: 0.7696 (tpt90) cc_final: 0.7401 (tpt170) REVERT: A 110 ILE cc_start: 0.8344 (tp) cc_final: 0.7696 (pt) REVERT: A 263 ARG cc_start: 0.8392 (ttp80) cc_final: 0.8067 (ttp80) REVERT: A 313 ARG cc_start: 0.7960 (mmm-85) cc_final: 0.7690 (mmm-85) REVERT: C 74 TYR cc_start: 0.8502 (m-80) cc_final: 0.7441 (m-80) REVERT: C 110 ILE cc_start: 0.8346 (tp) cc_final: 0.7711 (pt) REVERT: C 313 ARG cc_start: 0.7925 (mmm-85) cc_final: 0.7575 (mtt180) REVERT: E 25 LEU cc_start: 0.8128 (mt) cc_final: 0.7870 (tp) REVERT: E 74 TYR cc_start: 0.8501 (m-80) cc_final: 0.7427 (m-80) REVERT: E 110 ILE cc_start: 0.8351 (tp) cc_final: 0.7712 (pt) REVERT: E 313 ARG cc_start: 0.7923 (mmm-85) cc_final: 0.7495 (mtt180) REVERT: G 25 LEU cc_start: 0.8143 (mt) cc_final: 0.7876 (tp) REVERT: G 74 TYR cc_start: 0.8510 (m-80) cc_final: 0.7442 (m-80) REVERT: G 93 ARG cc_start: 0.7518 (mmm160) cc_final: 0.7305 (mmm160) REVERT: G 110 ILE cc_start: 0.8353 (tp) cc_final: 0.7711 (pt) REVERT: G 263 ARG cc_start: 0.8387 (ttp80) cc_final: 0.8057 (ttp80) REVERT: G 313 ARG cc_start: 0.7898 (mmm-85) cc_final: 0.7494 (mtt180) REVERT: B 276 GLU cc_start: 0.7649 (mt-10) cc_final: 0.7394 (mt-10) REVERT: F 276 GLU cc_start: 0.7580 (mt-10) cc_final: 0.7367 (mt-10) REVERT: F 284 ASP cc_start: 0.5792 (OUTLIER) cc_final: 0.5530 (t0) outliers start: 23 outliers final: 19 residues processed: 385 average time/residue: 0.1563 time to fit residues: 85.5857 Evaluate side-chains 384 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 364 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 SER Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 244 ASP Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 98 LEU Chi-restraints excluded: chain E residue 244 ASP Chi-restraints excluded: chain E residue 296 VAL Chi-restraints excluded: chain G residue 244 ASP Chi-restraints excluded: chain G residue 296 VAL Chi-restraints excluded: chain B residue 133 GLU Chi-restraints excluded: chain D residue 133 GLU Chi-restraints excluded: chain F residue 133 GLU Chi-restraints excluded: chain F residue 284 ASP Chi-restraints excluded: chain H residue 133 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 28 optimal weight: 8.9990 chunk 68 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 54 optimal weight: 0.6980 chunk 140 optimal weight: 0.1980 chunk 96 optimal weight: 4.9990 chunk 4 optimal weight: 4.9990 chunk 110 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 142 optimal weight: 5.9990 chunk 169 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3664 r_free = 0.3664 target = 0.155686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.110925 restraints weight = 11940.851| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 1.53 r_work: 0.3042 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2889 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.2861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 17148 Z= 0.094 Angle : 0.433 5.265 23156 Z= 0.232 Chirality : 0.046 0.144 2692 Planarity : 0.003 0.030 3000 Dihedral : 5.554 54.220 2480 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 1.03 % Allowed : 17.27 % Favored : 81.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.18), residues: 2140 helix: 1.32 (0.17), residues: 1020 sheet: 0.65 (0.27), residues: 320 loop : -1.56 (0.21), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 241 TYR 0.010 0.001 TYR E 51 PHE 0.015 0.001 PHE G 97 TRP 0.001 0.000 TRP C 123 HIS 0.001 0.000 HIS D 117 Details of bonding type rmsd/Z covalent geometry : bond 0.00218 / 0.09 (17148) covalent geometry : angle 0.43280 / 0.23 (23156) hydrogen bonds : bond 0.02951 / 1.92 ( 696) hydrogen bonds : angle 3.99346 / 2.78 ( 1992) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 374 time to evaluate : 0.603 Fit side-chains REVERT: A 25 LEU cc_start: 0.8132 (mt) cc_final: 0.7880 (tp) REVERT: A 74 TYR cc_start: 0.8541 (m-80) cc_final: 0.7427 (m-80) REVERT: A 93 ARG cc_start: 0.7696 (tpt90) cc_final: 0.7399 (tpt170) REVERT: A 110 ILE cc_start: 0.8325 (tp) cc_final: 0.7691 (pt) REVERT: A 263 ARG cc_start: 0.8378 (ttp80) cc_final: 0.8077 (ttp80) REVERT: A 313 ARG cc_start: 0.7967 (mmm-85) cc_final: 0.7599 (mtt180) REVERT: C 74 TYR cc_start: 0.8503 (m-80) cc_final: 0.7437 (m-80) REVERT: C 110 ILE cc_start: 0.8393 (tp) cc_final: 0.7764 (pt) REVERT: C 313 ARG cc_start: 0.7932 (mmm-85) cc_final: 0.7592 (mtt180) REVERT: E 25 LEU cc_start: 0.8145 (mt) cc_final: 0.7888 (tp) REVERT: E 74 TYR cc_start: 0.8503 (m-80) cc_final: 0.7436 (m-80) REVERT: E 110 ILE cc_start: 0.8339 (tp) cc_final: 0.7714 (pt) REVERT: E 313 ARG cc_start: 0.7971 (mmm-85) cc_final: 0.7596 (mtt180) REVERT: G 25 LEU cc_start: 0.8132 (mt) cc_final: 0.7870 (tp) REVERT: G 74 TYR cc_start: 0.8512 (m-80) cc_final: 0.7443 (m-80) REVERT: G 93 ARG cc_start: 0.7518 (mmm160) cc_final: 0.7295 (mmm160) REVERT: G 110 ILE cc_start: 0.8337 (tp) cc_final: 0.7713 (pt) REVERT: G 263 ARG cc_start: 0.8365 (ttp80) cc_final: 0.8033 (ttp80) REVERT: G 313 ARG cc_start: 0.7942 (mmm-85) cc_final: 0.7598 (mtt180) REVERT: B 276 GLU cc_start: 0.7648 (mt-10) cc_final: 0.7385 (mt-10) REVERT: F 276 GLU cc_start: 0.7558 (mt-10) cc_final: 0.7329 (mt-10) REVERT: F 284 ASP cc_start: 0.5798 (OUTLIER) cc_final: 0.5492 (t0) REVERT: H 276 GLU cc_start: 0.7727 (mt-10) cc_final: 0.7435 (mt-10) outliers start: 19 outliers final: 17 residues processed: 385 average time/residue: 0.1433 time to fit residues: 79.1808 Evaluate side-chains 386 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 368 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 SER Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 244 ASP Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 244 ASP Chi-restraints excluded: chain E residue 296 VAL Chi-restraints excluded: chain G residue 244 ASP Chi-restraints excluded: chain B residue 133 GLU Chi-restraints excluded: chain D residue 133 GLU Chi-restraints excluded: chain F residue 133 GLU Chi-restraints excluded: chain F residue 284 ASP Chi-restraints excluded: chain H residue 133 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 179 optimal weight: 0.3980 chunk 91 optimal weight: 6.9990 chunk 178 optimal weight: 0.7980 chunk 122 optimal weight: 7.9990 chunk 204 optimal weight: 0.8980 chunk 130 optimal weight: 3.9990 chunk 14 optimal weight: 0.7980 chunk 203 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 chunk 162 optimal weight: 0.0050 chunk 28 optimal weight: 9.9990 overall best weight: 0.5794 ------------------------------------------------------------------------------- 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 = 0.3669 r_free = 0.3669 target = 0.156310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.111741 restraints weight = 11893.775| |-----------------------------------------------------------------------------| r_work (start): 0.3145 rms_B_bonded: 1.52 r_work: 0.2984 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2827 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.2917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 17148 Z= 0.086 Angle : 0.425 5.084 23156 Z= 0.229 Chirality : 0.045 0.142 2692 Planarity : 0.003 0.030 3000 Dihedral : 5.416 53.139 2480 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 1.14 % Allowed : 17.10 % Favored : 81.75 % 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: 0.44 (0.18), residues: 2140 helix: 1.53 (0.17), residues: 1012 sheet: 0.71 (0.27), residues: 320 loop : -1.54 (0.21), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 241 TYR 0.010 0.001 TYR E 51 PHE 0.015 0.001 PHE E 97 TRP 0.002 0.000 TRP B 123 HIS 0.001 0.000 HIS B 117 Details of bonding type rmsd/Z covalent geometry : bond 0.00195 / 0.09 (17148) covalent geometry : angle 0.42544 / 0.23 (23156) hydrogen bonds : bond 0.02787 / 1.82 ( 696) hydrogen bonds : angle 3.93575 / 2.74 ( 1992) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5044.43 seconds wall clock time: 86 minutes 38.38 seconds (5198.38 seconds total)