Starting phenix.real_space_refine on Sat Oct 11 19:31:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5bki_9405/10_2025/5bki_9405.cif Found real_map, /net/cci-nas-00/data/ceres_data/5bki_9405/10_2025/5bki_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_9405/10_2025/5bki_9405.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5bki_9405/10_2025/5bki_9405.map" model { file = "/net/cci-nas-00/data/ceres_data/5bki_9405/10_2025/5bki_9405.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5bki_9405/10_2025/5bki_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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16933 Number of models: 1 Model: "" Number of chains: 8 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: "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: "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: 16 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: "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} Restraints were copied for chains: C, E, G, D, F, H Time building chain proxies: 3.15, per 1000 atoms: 0.19 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: 1.36 Conformation dependent library (CDL) restraints added in 888.0 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.66 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: 2.83 Time building geometry restraints manager: 1.82 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: 596 46.59 - 69.89: 100 69.89 - 93.18: 8 93.18 - 116.48: 16 Dihedral angle restraints: 10460 sinusoidal: 4308 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 10457 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: 0.850 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: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 15.680 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 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 : 15.839 116.480 6508 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 aren 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 covalent geometry : bond 0.00997 (17148) covalent geometry : angle 1.04335 (23156) hydrogen bonds : bond 0.30310 ( 696) hydrogen bonds : angle 9.73571 ( 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 : 0.673 Fit side-chains REVERT: A 25 LEU cc_start: 0.8263 (mt) cc_final: 0.8000 (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: 0.7816 (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: 0.7512 (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: 0.7737 (tt0) cc_final: 0.7480 (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: 0.7810 (tt0) cc_final: 0.7518 (tt0) REVERT: G 263 ARG cc_start: 0.8186 (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: 0.7821 (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: 0.1667 time to fit residues: 103.5766 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 : 0.660 ------------------------------------------------------------------------------- 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... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.156505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.114775 restraints weight = 11711.105| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 1.37 r_work: 0.2995 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2841 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.1646 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= 0.122 Angle : 0.513 5.107 23156 Z= 0.282 Chirality : 0.047 0.138 2692 Planarity : 0.004 0.030 3000 Dihedral : 11.010 98.752 2508 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 0.65 % Allowed : 9.26 % Favored : 90.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.16 (0.15), residues: 2140 helix: -2.23 (0.13), residues: 1020 sheet: -0.19 (0.27), residues: 328 loop : -2.55 (0.18), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 263 TYR 0.012 0.001 TYR B 310 PHE 0.006 0.001 PHE C 75 TRP 0.003 0.001 TRP G 46 HIS 0.002 0.001 HIS C 117 Details of bonding type rmsd covalent geometry : bond 0.00271 (17148) covalent geometry : angle 0.51346 (23156) hydrogen bonds : bond 0.04961 ( 696) hydrogen bonds : angle 5.12825 ( 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 : 0.691 Fit side-chains REVERT: A 25 LEU cc_start: 0.8167 (mt) cc_final: 0.7887 (tp) REVERT: A 96 GLU cc_start: 0.8629 (tt0) cc_final: 0.8423 (tt0) REVERT: A 263 ARG cc_start: 0.8423 (ttp80) cc_final: 0.8174 (ttp80) REVERT: C 25 LEU cc_start: 0.8172 (mt) cc_final: 0.7908 (tp) REVERT: C 74 TYR cc_start: 0.8445 (m-80) cc_final: 0.8214 (m-80) REVERT: E 25 LEU cc_start: 0.8167 (mt) cc_final: 0.7881 (tp) REVERT: E 74 TYR cc_start: 0.8444 (m-80) cc_final: 0.8179 (m-80) REVERT: E 210 GLU cc_start: 0.8467 (tt0) cc_final: 0.8193 (tt0) REVERT: G 74 TYR cc_start: 0.8430 (m-80) cc_final: 0.8178 (m-80) REVERT: G 96 GLU cc_start: 0.8637 (tt0) cc_final: 0.8422 (tt0) REVERT: G 263 ARG cc_start: 0.8378 (ttp80) cc_final: 0.8135 (ttp80) REVERT: G 266 GLU cc_start: 0.6830 (pt0) cc_final: 0.6531 (pt0) REVERT: B 250 MET cc_start: 0.8529 (mtt) cc_final: 0.8276 (mtt) REVERT: B 333 TYR cc_start: 0.8694 (t80) cc_final: 0.8386 (t80) REVERT: D 200 LYS cc_start: 0.8393 (mmtt) cc_final: 0.7736 (mtmt) REVERT: D 250 MET cc_start: 0.8514 (mtt) cc_final: 0.8263 (mtt) REVERT: D 333 TYR cc_start: 0.8695 (t80) cc_final: 0.8375 (t80) REVERT: F 250 MET cc_start: 0.8563 (mtt) cc_final: 0.8299 (mtt) REVERT: F 263 ARG cc_start: 0.7817 (ptt90) cc_final: 0.7319 (ptm-80) REVERT: H 200 LYS cc_start: 0.8399 (mmtt) cc_final: 0.7740 (mtmt) REVERT: H 250 MET cc_start: 0.8527 (mtt) cc_final: 0.8272 (mtt) REVERT: H 333 TYR cc_start: 0.8692 (t80) cc_final: 0.8384 (t80) outliers start: 12 outliers final: 6 residues processed: 413 average time/residue: 0.1540 time to fit residues: 91.1057 Evaluate side-chains 367 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 361 time to evaluate : 0.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 LEU 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: 0.7980 chunk 46 optimal weight: 5.9990 chunk 127 optimal weight: 4.9990 chunk 173 optimal weight: 0.7980 chunk 57 optimal weight: 0.7980 chunk 10 optimal weight: 0.8980 chunk 187 optimal weight: 0.3980 chunk 53 optimal weight: 0.7980 chunk 167 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 69 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.157602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.115659 restraints weight = 11774.203| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 1.38 r_work: 0.3022 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2867 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.2103 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= 0.102 Angle : 0.454 4.877 23156 Z= 0.247 Chirality : 0.046 0.132 2692 Planarity : 0.003 0.027 3000 Dihedral : 8.861 84.369 2504 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 0.76 % Allowed : 12.96 % Favored : 86.27 % 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 aren not related in a simple way. whole: -1.80 (0.17), residues: 2140 helix: -0.81 (0.15), residues: 1004 sheet: 0.13 (0.28), residues: 328 loop : -2.15 (0.19), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 237 TYR 0.018 0.001 TYR F 333 PHE 0.004 0.001 PHE A 40 TRP 0.002 0.000 TRP G 123 HIS 0.002 0.001 HIS H 117 Details of bonding type rmsd covalent geometry : bond 0.00227 (17148) covalent geometry : angle 0.45363 (23156) hydrogen bonds : bond 0.03719 ( 696) hydrogen bonds : angle 4.53502 ( 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 395 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 381 time to evaluate : 0.618 Fit side-chains REVERT: A 74 TYR cc_start: 0.8558 (m-80) cc_final: 0.7432 (m-80) REVERT: A 96 GLU cc_start: 0.8592 (tt0) cc_final: 0.8368 (tt0) REVERT: A 263 ARG cc_start: 0.8400 (ttp80) cc_final: 0.8103 (ttp80) REVERT: A 313 ARG cc_start: 0.7808 (mmm-85) cc_final: 0.7513 (mmm-85) REVERT: C 25 LEU cc_start: 0.8139 (mt) cc_final: 0.7897 (tp) REVERT: C 93 ARG cc_start: 0.7899 (tpt90) cc_final: 0.7678 (mmm160) REVERT: C 313 ARG cc_start: 0.7707 (mmm-85) cc_final: 0.7427 (mmm-85) REVERT: E 25 LEU cc_start: 0.8096 (mt) cc_final: 0.7834 (tp) REVERT: E 96 GLU cc_start: 0.8542 (tt0) cc_final: 0.8301 (tt0) REVERT: E 210 GLU cc_start: 0.8510 (tt0) cc_final: 0.8256 (tt0) REVERT: E 266 GLU cc_start: 0.6953 (pt0) cc_final: 0.6731 (pt0) REVERT: E 313 ARG cc_start: 0.7771 (mmm-85) cc_final: 0.7506 (mmm-85) REVERT: G 25 LEU cc_start: 0.8103 (mt) cc_final: 0.7830 (tp) REVERT: G 96 GLU cc_start: 0.8592 (tt0) cc_final: 0.8373 (tt0) REVERT: G 263 ARG cc_start: 0.8387 (ttp80) cc_final: 0.8088 (ttp80) REVERT: G 313 ARG cc_start: 0.7666 (mmm-85) cc_final: 0.7388 (mmm-85) REVERT: B 250 MET cc_start: 0.8659 (mtt) cc_final: 0.8440 (mtt) REVERT: B 333 TYR cc_start: 0.8624 (t80) cc_final: 0.8385 (t80) REVERT: D 250 MET cc_start: 0.8644 (mtt) cc_final: 0.8424 (mtt) REVERT: D 333 TYR cc_start: 0.8626 (t80) cc_final: 0.8378 (t80) REVERT: F 263 ARG cc_start: 0.7844 (ptt90) cc_final: 0.7331 (ptm-80) REVERT: H 250 MET cc_start: 0.8664 (mtt) cc_final: 0.8436 (mtt) REVERT: H 333 TYR cc_start: 0.8626 (t80) cc_final: 0.8383 (t80) outliers start: 14 outliers final: 13 residues processed: 385 average time/residue: 0.1503 time to fit residues: 84.0853 Evaluate side-chains 365 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 352 time to evaluate : 0.788 ------------------------------------------------------------------------------- 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 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 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 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: 4.9990 chunk 50 optimal weight: 0.8980 chunk 3 optimal weight: 3.9990 chunk 126 optimal weight: 5.9990 chunk 66 optimal weight: 7.9990 chunk 114 optimal weight: 2.9990 chunk 60 optimal weight: 7.9990 chunk 43 optimal weight: 2.9990 chunk 198 optimal weight: 0.9990 chunk 189 optimal weight: 6.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.158222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.117694 restraints weight = 11304.743| |-----------------------------------------------------------------------------| r_work (start): 0.3160 rms_B_bonded: 1.29 r_work: 0.2999 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2846 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.2149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 17148 Z= 0.228 Angle : 0.542 4.684 23156 Z= 0.288 Chirality : 0.050 0.137 2692 Planarity : 0.004 0.029 3000 Dihedral : 8.600 71.461 2504 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 1.47 % Allowed : 14.05 % Favored : 84.48 % 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 aren not related in a simple way. whole: -1.46 (0.17), residues: 2140 helix: -0.47 (0.16), residues: 1020 sheet: 0.19 (0.28), residues: 328 loop : -2.04 (0.20), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 241 TYR 0.015 0.002 TYR D 310 PHE 0.024 0.001 PHE C 97 TRP 0.003 0.001 TRP E 123 HIS 0.006 0.001 HIS G 117 Details of bonding type rmsd covalent geometry : bond 0.00566 (17148) covalent geometry : angle 0.54181 (23156) hydrogen bonds : bond 0.04597 ( 696) hydrogen bonds : angle 4.65172 ( 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 405 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 378 time to evaluate : 0.657 Fit side-chains REVERT: A 25 LEU cc_start: 0.8127 (mt) cc_final: 0.7850 (tp) REVERT: A 74 TYR cc_start: 0.8572 (m-80) cc_final: 0.7480 (m-80) REVERT: A 96 GLU cc_start: 0.8599 (tt0) cc_final: 0.8336 (tt0) REVERT: A 263 ARG cc_start: 0.8465 (ttp80) cc_final: 0.8108 (ttp80) REVERT: A 313 ARG cc_start: 0.7824 (mmm-85) cc_final: 0.7558 (mmm-85) REVERT: C 25 LEU cc_start: 0.8175 (mt) cc_final: 0.7909 (tp) REVERT: C 74 TYR cc_start: 0.8583 (m-80) cc_final: 0.7531 (m-80) REVERT: C 93 ARG cc_start: 0.7879 (tpt90) cc_final: 0.7632 (tpt170) REVERT: C 313 ARG cc_start: 0.7809 (mmm-85) cc_final: 0.7538 (mmm-85) REVERT: E 25 LEU cc_start: 0.8139 (mt) cc_final: 0.7867 (tp) REVERT: E 313 ARG cc_start: 0.7816 (mmm-85) cc_final: 0.7548 (mmm-85) REVERT: G 25 LEU cc_start: 0.8130 (mt) cc_final: 0.7853 (tp) REVERT: G 74 TYR cc_start: 0.8557 (m-80) cc_final: 0.7475 (m-80) REVERT: G 96 GLU cc_start: 0.8612 (tt0) cc_final: 0.8362 (tt0) REVERT: G 263 ARG cc_start: 0.8462 (ttp80) cc_final: 0.8102 (ttp80) REVERT: G 313 ARG cc_start: 0.7804 (mmm-85) cc_final: 0.7537 (mmm-85) outliers start: 27 outliers final: 23 residues processed: 396 average time/residue: 0.1595 time to fit residues: 90.7289 Evaluate side-chains 384 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 361 time to evaluate : 0.629 ------------------------------------------------------------------------------- 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 68 SER Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 98 LEU 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 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 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 H residue 133 GLU Chi-restraints excluded: chain H residue 325 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: 4.9990 chunk 6 optimal weight: 0.9980 chunk 73 optimal weight: 5.9990 chunk 197 optimal weight: 0.7980 chunk 122 optimal weight: 6.9990 chunk 143 optimal weight: 1.9990 chunk 87 optimal weight: 0.9980 chunk 37 optimal weight: 5.9990 chunk 9 optimal weight: 3.9990 chunk 150 optimal weight: 7.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.158729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.117996 restraints weight = 11439.411| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 1.31 r_work: 0.2996 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2843 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.2359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 17148 Z= 0.174 Angle : 0.497 4.813 23156 Z= 0.265 Chirality : 0.048 0.132 2692 Planarity : 0.003 0.029 3000 Dihedral : 8.112 62.003 2504 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 1.31 % Allowed : 15.58 % Favored : 83.12 % 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 aren not related in a simple way. whole: -1.12 (0.17), residues: 2140 helix: -0.09 (0.16), residues: 1020 sheet: 0.21 (0.27), residues: 320 loop : -1.94 (0.20), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 241 TYR 0.014 0.001 TYR C 51 PHE 0.024 0.001 PHE A 97 TRP 0.003 0.001 TRP G 123 HIS 0.004 0.001 HIS A 117 Details of bonding type rmsd covalent geometry : bond 0.00430 (17148) covalent geometry : angle 0.49680 (23156) hydrogen bonds : bond 0.03951 ( 696) hydrogen bonds : angle 4.45254 ( 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 409 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 385 time to evaluate : 0.549 Fit side-chains REVERT: A 25 LEU cc_start: 0.8115 (mt) cc_final: 0.7836 (tp) REVERT: A 74 TYR cc_start: 0.8583 (m-80) cc_final: 0.7500 (m-80) REVERT: A 96 GLU cc_start: 0.8495 (tt0) cc_final: 0.8292 (tt0) REVERT: A 263 ARG cc_start: 0.8451 (ttp80) cc_final: 0.8136 (ttp80) REVERT: A 313 ARG cc_start: 0.7884 (mmm-85) cc_final: 0.7622 (mmm-85) REVERT: C 25 LEU cc_start: 0.8160 (mt) cc_final: 0.7891 (tp) REVERT: C 74 TYR cc_start: 0.8583 (m-80) cc_final: 0.7539 (m-80) REVERT: C 313 ARG cc_start: 0.7873 (mmm-85) cc_final: 0.7614 (mmm-85) REVERT: E 25 LEU cc_start: 0.8123 (mt) cc_final: 0.7844 (tp) REVERT: E 74 TYR cc_start: 0.8569 (m-80) cc_final: 0.7553 (m-80) REVERT: E 313 ARG cc_start: 0.7907 (mmm-85) cc_final: 0.7500 (mtt180) REVERT: G 25 LEU cc_start: 0.8119 (mt) cc_final: 0.7839 (tp) REVERT: G 74 TYR cc_start: 0.8556 (m-80) cc_final: 0.7480 (m-80) REVERT: G 96 GLU cc_start: 0.8502 (tt0) cc_final: 0.8284 (tt0) REVERT: G 263 ARG cc_start: 0.8441 (ttp80) cc_final: 0.8124 (ttp80) REVERT: G 313 ARG cc_start: 0.7883 (mmm-85) cc_final: 0.7635 (mmm-85) REVERT: B 263 ARG cc_start: 0.7805 (ptt90) cc_final: 0.7321 (ptm-80) REVERT: D 263 ARG cc_start: 0.7817 (ptt90) cc_final: 0.7336 (ptm-80) REVERT: F 263 ARG cc_start: 0.7867 (ptt90) cc_final: 0.7381 (ptm-80) REVERT: H 263 ARG cc_start: 0.7823 (ptt90) cc_final: 0.7341 (ptm-80) outliers start: 24 outliers final: 18 residues processed: 395 average time/residue: 0.1650 time to fit residues: 92.6603 Evaluate side-chains 385 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 367 time to evaluate : 0.657 ------------------------------------------------------------------------------- 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 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 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 244 ASP Chi-restraints excluded: chain B residue 133 GLU Chi-restraints excluded: chain D residue 133 GLU Chi-restraints excluded: chain H residue 133 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 80 optimal weight: 0.0770 chunk 126 optimal weight: 5.9990 chunk 57 optimal weight: 1.9990 chunk 145 optimal weight: 0.0170 chunk 74 optimal weight: 0.9980 chunk 113 optimal weight: 1.9990 chunk 201 optimal weight: 0.9990 chunk 18 optimal weight: 0.0870 chunk 27 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 overall best weight: 0.4356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.162213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.121490 restraints weight = 11585.144| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 1.33 r_work: 0.3030 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2878 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.2617 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= 0.082 Angle : 0.427 4.467 23156 Z= 0.232 Chirality : 0.045 0.132 2692 Planarity : 0.003 0.029 3000 Dihedral : 7.310 59.795 2504 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 0.87 % Allowed : 16.83 % Favored : 82.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.56 (0.18), residues: 2140 helix: 0.51 (0.16), residues: 1016 sheet: 0.36 (0.27), residues: 320 loop : -1.80 (0.20), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 241 TYR 0.011 0.001 TYR A 51 PHE 0.021 0.001 PHE E 97 TRP 0.003 0.000 TRP C 123 HIS 0.001 0.000 HIS D 117 Details of bonding type rmsd covalent geometry : bond 0.00176 (17148) covalent geometry : angle 0.42737 (23156) hydrogen bonds : bond 0.02910 ( 696) hydrogen bonds : angle 4.11810 ( 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 402 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 386 time to evaluate : 0.696 Fit side-chains REVERT: A 25 LEU cc_start: 0.8081 (mt) cc_final: 0.7807 (tp) REVERT: A 74 TYR cc_start: 0.8553 (m-80) cc_final: 0.7433 (m-80) REVERT: A 96 GLU cc_start: 0.8417 (tt0) cc_final: 0.8206 (tt0) REVERT: A 263 ARG cc_start: 0.8422 (ttp80) cc_final: 0.8108 (ttp80) REVERT: A 313 ARG cc_start: 0.7939 (mmm-85) cc_final: 0.7678 (mmm-85) REVERT: C 25 LEU cc_start: 0.8118 (mt) cc_final: 0.7857 (tp) REVERT: C 74 TYR cc_start: 0.8518 (m-80) cc_final: 0.7490 (m-80) REVERT: C 313 ARG cc_start: 0.7841 (mmm-85) cc_final: 0.7447 (mtt180) REVERT: E 25 LEU cc_start: 0.8151 (mt) cc_final: 0.7878 (tp) REVERT: E 74 TYR cc_start: 0.8489 (m-80) cc_final: 0.7409 (m-80) REVERT: E 313 ARG cc_start: 0.7875 (mmm-85) cc_final: 0.7457 (mtt180) REVERT: G 74 TYR cc_start: 0.8538 (m-80) cc_final: 0.7500 (m-80) REVERT: G 96 GLU cc_start: 0.8482 (tt0) cc_final: 0.8194 (tt0) REVERT: G 263 ARG cc_start: 0.8387 (ttp80) cc_final: 0.8093 (ttp80) REVERT: G 313 ARG cc_start: 0.7826 (mmm-85) cc_final: 0.7558 (mmm-85) outliers start: 16 outliers final: 13 residues processed: 393 average time/residue: 0.1563 time to fit residues: 88.1254 Evaluate side-chains 378 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 365 time to evaluate : 0.689 ------------------------------------------------------------------------------- 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 98 LEU Chi-restraints excluded: chain C residue 244 ASP Chi-restraints excluded: chain E residue 244 ASP Chi-restraints excluded: chain G residue 91 VAL 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 47 optimal weight: 3.9990 chunk 31 optimal weight: 10.0000 chunk 61 optimal weight: 3.9990 chunk 72 optimal weight: 0.7980 chunk 33 optimal weight: 7.9990 chunk 43 optimal weight: 2.9990 chunk 177 optimal weight: 4.9990 chunk 167 optimal weight: 4.9990 chunk 144 optimal weight: 0.0020 chunk 169 optimal weight: 0.0170 chunk 73 optimal weight: 0.8980 overall best weight: 0.9428 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.154498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.109921 restraints weight = 11836.188| |-----------------------------------------------------------------------------| r_work (start): 0.3117 rms_B_bonded: 1.52 r_work: 0.2957 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2800 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.2636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 17148 Z= 0.110 Angle : 0.446 4.742 23156 Z= 0.238 Chirality : 0.046 0.137 2692 Planarity : 0.003 0.032 3000 Dihedral : 7.134 59.986 2504 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 1.03 % Allowed : 16.72 % Favored : 82.24 % 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 aren not related in a simple way. whole: -0.26 (0.18), residues: 2140 helix: 0.79 (0.17), residues: 1020 sheet: 0.45 (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 B 241 TYR 0.012 0.001 TYR C 51 PHE 0.016 0.001 PHE A 97 TRP 0.002 0.000 TRP G 123 HIS 0.002 0.001 HIS G 117 Details of bonding type rmsd covalent geometry : bond 0.00262 (17148) covalent geometry : angle 0.44576 (23156) hydrogen bonds : bond 0.03198 ( 696) hydrogen bonds : angle 4.09672 ( 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 393 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 374 time to evaluate : 0.598 Fit side-chains REVERT: A 74 TYR cc_start: 0.8516 (m-80) cc_final: 0.7358 (m-80) REVERT: A 96 GLU cc_start: 0.8468 (tt0) cc_final: 0.8217 (tt0) REVERT: A 263 ARG cc_start: 0.8423 (ttp80) cc_final: 0.8074 (ttp80) REVERT: A 313 ARG cc_start: 0.8038 (mmm-85) cc_final: 0.7560 (mtt180) REVERT: C 25 LEU cc_start: 0.8152 (mt) cc_final: 0.7889 (tp) REVERT: C 74 TYR cc_start: 0.8515 (m-80) cc_final: 0.7447 (m-80) REVERT: C 313 ARG cc_start: 0.7878 (mmm-85) cc_final: 0.7390 (mtt180) REVERT: E 25 LEU cc_start: 0.8146 (mt) cc_final: 0.7878 (tp) REVERT: E 74 TYR cc_start: 0.8476 (m-80) cc_final: 0.7380 (m-80) REVERT: E 313 ARG cc_start: 0.7876 (mmm-85) cc_final: 0.7361 (mtt180) REVERT: G 25 LEU cc_start: 0.8146 (mt) cc_final: 0.7875 (tp) REVERT: G 74 TYR cc_start: 0.8511 (m-80) cc_final: 0.7433 (m-80) REVERT: G 96 GLU cc_start: 0.8470 (tt0) cc_final: 0.8230 (tt0) REVERT: G 263 ARG cc_start: 0.8385 (ttp80) cc_final: 0.8061 (ttp80) REVERT: G 313 ARG cc_start: 0.7883 (mmm-85) cc_final: 0.7368 (mtt180) REVERT: F 284 ASP cc_start: 0.5722 (OUTLIER) cc_final: 0.5472 (t0) outliers start: 19 outliers final: 15 residues processed: 385 average time/residue: 0.1567 time to fit residues: 86.4081 Evaluate side-chains 379 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 363 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 244 ASP 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 244 ASP Chi-restraints excluded: chain G residue 68 SER Chi-restraints excluded: chain G residue 91 VAL 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 F residue 284 ASP 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: 0.9990 chunk 175 optimal weight: 0.7980 chunk 104 optimal weight: 3.9990 chunk 4 optimal weight: 4.9990 chunk 34 optimal weight: 0.9980 chunk 68 optimal weight: 1.9990 chunk 79 optimal weight: 0.6980 chunk 191 optimal weight: 0.0980 chunk 26 optimal weight: 0.9990 chunk 126 optimal weight: 4.9990 chunk 145 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.156037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.112377 restraints weight = 11909.451| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 1.46 r_work: 0.2985 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2829 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.2765 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= 0.094 Angle : 0.434 4.552 23156 Z= 0.232 Chirality : 0.045 0.139 2692 Planarity : 0.003 0.031 3000 Dihedral : 6.834 58.853 2504 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 0.93 % Allowed : 17.05 % Favored : 82.03 % 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 aren not related in a simple way. whole: 0.01 (0.18), residues: 2140 helix: 1.06 (0.17), residues: 1016 sheet: 0.54 (0.27), residues: 320 loop : -1.61 (0.20), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 241 TYR 0.011 0.001 TYR E 51 PHE 0.015 0.001 PHE A 97 TRP 0.003 0.000 TRP C 123 HIS 0.001 0.000 HIS B 117 Details of bonding type rmsd covalent geometry : bond 0.00218 (17148) covalent geometry : angle 0.43375 (23156) hydrogen bonds : bond 0.02965 ( 696) hydrogen bonds : angle 4.01283 ( 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 386 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 369 time to evaluate : 0.698 Fit side-chains REVERT: A 25 LEU cc_start: 0.8136 (mt) cc_final: 0.7875 (tp) REVERT: A 74 TYR cc_start: 0.8516 (m-80) cc_final: 0.7359 (m-80) REVERT: A 96 GLU cc_start: 0.8452 (tt0) cc_final: 0.8178 (tt0) REVERT: A 263 ARG cc_start: 0.8398 (ttp80) cc_final: 0.8065 (ttp80) REVERT: A 313 ARG cc_start: 0.7999 (mmm-85) cc_final: 0.7556 (mtt180) REVERT: C 25 LEU cc_start: 0.8132 (mt) cc_final: 0.7880 (tp) REVERT: C 74 TYR cc_start: 0.8488 (m-80) cc_final: 0.7412 (m-80) REVERT: C 313 ARG cc_start: 0.7913 (mmm-85) cc_final: 0.7437 (mtt180) REVERT: E 74 TYR cc_start: 0.8477 (m-80) cc_final: 0.7386 (m-80) REVERT: E 93 ARG cc_start: 0.7638 (mmm160) cc_final: 0.7271 (mmm160) REVERT: E 313 ARG cc_start: 0.7954 (mmm-85) cc_final: 0.7464 (mtt180) REVERT: G 74 TYR cc_start: 0.8483 (m-80) cc_final: 0.7337 (m-80) REVERT: G 263 ARG cc_start: 0.8360 (ttp80) cc_final: 0.8041 (ttp80) REVERT: G 313 ARG cc_start: 0.7954 (mmm-85) cc_final: 0.7466 (mtt180) REVERT: F 284 ASP cc_start: 0.5724 (OUTLIER) cc_final: 0.5440 (t0) outliers start: 17 outliers final: 15 residues processed: 377 average time/residue: 0.1624 time to fit residues: 87.4026 Evaluate side-chains 375 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 359 time to evaluate : 0.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 LEU 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 E residue 95 LEU Chi-restraints excluded: chain E residue 98 LEU 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 81 optimal weight: 0.9990 chunk 40 optimal weight: 0.0870 chunk 178 optimal weight: 0.9980 chunk 75 optimal weight: 2.9990 chunk 145 optimal weight: 0.9990 chunk 208 optimal weight: 7.9990 chunk 146 optimal weight: 3.9990 chunk 175 optimal weight: 1.9990 chunk 59 optimal weight: 10.0000 chunk 91 optimal weight: 6.9990 chunk 36 optimal weight: 0.1980 overall best weight: 0.6562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.156158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.111590 restraints weight = 11863.393| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 1.52 r_work: 0.2981 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2825 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.2834 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 5.056 23156 Z= 0.231 Chirality : 0.046 0.144 2692 Planarity : 0.003 0.033 3000 Dihedral : 6.667 58.320 2504 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 0.98 % Allowed : 17.27 % 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 aren not related in a simple way. whole: 0.17 (0.18), residues: 2140 helix: 1.25 (0.17), residues: 1012 sheet: 0.61 (0.27), residues: 320 loop : -1.59 (0.20), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 241 TYR 0.011 0.001 TYR G 51 PHE 0.017 0.001 PHE E 97 TRP 0.002 0.000 TRP C 123 HIS 0.001 0.000 HIS D 117 Details of bonding type rmsd covalent geometry : bond 0.00210 (17148) covalent geometry : angle 0.43276 (23156) hydrogen bonds : bond 0.02889 ( 696) hydrogen bonds : angle 3.97573 ( 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 385 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 367 time to evaluate : 0.688 Fit side-chains REVERT: A 74 TYR cc_start: 0.8514 (m-80) cc_final: 0.7355 (m-80) REVERT: A 263 ARG cc_start: 0.8393 (ttp80) cc_final: 0.8056 (ttp80) REVERT: A 313 ARG cc_start: 0.8002 (mmm-85) cc_final: 0.7717 (mmm-85) REVERT: C 25 LEU cc_start: 0.8145 (mt) cc_final: 0.7893 (tp) REVERT: C 74 TYR cc_start: 0.8484 (m-80) cc_final: 0.7405 (m-80) REVERT: C 313 ARG cc_start: 0.7934 (mmm-85) cc_final: 0.7645 (mmm-85) REVERT: E 25 LEU cc_start: 0.8146 (mt) cc_final: 0.7887 (tp) REVERT: E 74 TYR cc_start: 0.8478 (m-80) cc_final: 0.7386 (m-80) REVERT: E 313 ARG cc_start: 0.7967 (mmm-85) cc_final: 0.7687 (mmm-85) REVERT: G 25 LEU cc_start: 0.8139 (mt) cc_final: 0.7882 (tp) REVERT: G 74 TYR cc_start: 0.8483 (m-80) cc_final: 0.7337 (m-80) REVERT: G 263 ARG cc_start: 0.8360 (ttp80) cc_final: 0.8031 (ttp80) REVERT: G 313 ARG cc_start: 0.7955 (mmm-85) cc_final: 0.7672 (mmm-85) REVERT: F 276 GLU cc_start: 0.7727 (mt-10) cc_final: 0.7475 (mt-10) REVERT: F 284 ASP cc_start: 0.5710 (OUTLIER) cc_final: 0.5426 (t0) REVERT: H 310 TYR cc_start: 0.7934 (t80) cc_final: 0.7732 (t80) outliers start: 18 outliers final: 16 residues processed: 377 average time/residue: 0.1675 time to fit residues: 89.3083 Evaluate side-chains 378 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 361 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 296 VAL 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 E residue 95 LEU 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 68 SER Chi-restraints excluded: chain G residue 95 LEU 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: 0.9980 chunk 68 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 54 optimal weight: 0.8980 chunk 140 optimal weight: 8.9990 chunk 96 optimal weight: 4.9990 chunk 4 optimal weight: 4.9990 chunk 110 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 chunk 142 optimal weight: 5.9990 chunk 169 optimal weight: 0.5980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.155347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.110699 restraints weight = 11881.891| |-----------------------------------------------------------------------------| r_work (start): 0.3184 rms_B_bonded: 1.52 r_work: 0.3040 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2888 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.2879 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= 0.103 Angle : 0.441 5.161 23156 Z= 0.236 Chirality : 0.046 0.148 2692 Planarity : 0.003 0.031 3000 Dihedral : 6.572 57.249 2504 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 0.93 % Allowed : 17.54 % Favored : 81.54 % 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 aren not related in a simple way. whole: 0.26 (0.18), residues: 2140 helix: 1.29 (0.17), residues: 1016 sheet: 0.66 (0.27), residues: 320 loop : -1.53 (0.21), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 241 TYR 0.011 0.001 TYR G 51 PHE 0.016 0.001 PHE E 97 TRP 0.002 0.000 TRP G 123 HIS 0.001 0.000 HIS H 117 Details of bonding type rmsd covalent geometry : bond 0.00241 (17148) covalent geometry : angle 0.44117 (23156) hydrogen bonds : bond 0.03000 ( 696) hydrogen bonds : angle 3.97975 ( 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 385 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 368 time to evaluate : 0.641 Fit side-chains REVERT: A 25 LEU cc_start: 0.8145 (mt) cc_final: 0.7887 (tp) REVERT: A 74 TYR cc_start: 0.8550 (m-80) cc_final: 0.7407 (m-80) REVERT: A 263 ARG cc_start: 0.8404 (ttp80) cc_final: 0.8083 (ttp80) REVERT: A 313 ARG cc_start: 0.7959 (mmm-85) cc_final: 0.7692 (mmm-85) REVERT: C 25 LEU cc_start: 0.8132 (mt) cc_final: 0.7883 (tp) REVERT: C 74 TYR cc_start: 0.8523 (m-80) cc_final: 0.7460 (m-80) REVERT: C 203 GLU cc_start: 0.7671 (tm-30) cc_final: 0.7336 (tm-30) REVERT: C 313 ARG cc_start: 0.7888 (mmm-85) cc_final: 0.7616 (mmm-85) REVERT: E 25 LEU cc_start: 0.8131 (mt) cc_final: 0.7876 (tp) REVERT: E 74 TYR cc_start: 0.8506 (m-80) cc_final: 0.7440 (m-80) REVERT: E 93 ARG cc_start: 0.7672 (mmm160) cc_final: 0.7431 (mmm160) REVERT: E 313 ARG cc_start: 0.7932 (mmm-85) cc_final: 0.7669 (mmm-85) REVERT: G 25 LEU cc_start: 0.8135 (mt) cc_final: 0.7873 (tp) REVERT: G 74 TYR cc_start: 0.8513 (m-80) cc_final: 0.7382 (m-80) REVERT: G 263 ARG cc_start: 0.8365 (ttp80) cc_final: 0.8048 (ttp80) REVERT: G 313 ARG cc_start: 0.7913 (mmm-85) cc_final: 0.7649 (mmm-85) REVERT: F 276 GLU cc_start: 0.7640 (mt-10) cc_final: 0.7351 (mt-10) REVERT: F 284 ASP cc_start: 0.5808 (OUTLIER) cc_final: 0.5527 (t0) outliers start: 17 outliers final: 16 residues processed: 378 average time/residue: 0.1569 time to fit residues: 84.6012 Evaluate side-chains 387 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 370 time to evaluate : 0.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 296 VAL 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 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 244 ASP Chi-restraints excluded: chain E residue 296 VAL Chi-restraints excluded: chain G residue 68 SER 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 179 optimal weight: 0.5980 chunk 91 optimal weight: 7.9990 chunk 178 optimal weight: 0.0770 chunk 122 optimal weight: 1.9990 chunk 204 optimal weight: 0.0470 chunk 130 optimal weight: 3.9990 chunk 14 optimal weight: 0.6980 chunk 203 optimal weight: 0.6980 chunk 63 optimal weight: 2.9990 chunk 162 optimal weight: 5.9990 chunk 28 optimal weight: 8.9990 overall best weight: 0.4236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.158245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.114620 restraints weight = 11884.097| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 1.47 r_work: 0.3001 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2846 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.2989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 17148 Z= 0.079 Angle : 0.425 5.328 23156 Z= 0.228 Chirality : 0.045 0.140 2692 Planarity : 0.003 0.031 3000 Dihedral : 6.330 59.244 2504 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 0.98 % Allowed : 17.59 % Favored : 81.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.48 (0.18), residues: 2140 helix: 1.54 (0.17), residues: 1012 sheet: 0.77 (0.28), residues: 320 loop : -1.50 (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 0.016 0.001 PHE E 97 TRP 0.002 0.000 TRP F 123 HIS 0.001 0.000 HIS F 117 Details of bonding type rmsd covalent geometry : bond 0.00172 (17148) covalent geometry : angle 0.42472 (23156) hydrogen bonds : bond 0.02634 ( 696) hydrogen bonds : angle 3.88807 ( 1992) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5496.36 seconds wall clock time: 94 minutes 15.52 seconds (5655.52 seconds total)