Starting phenix.real_space_refine on Sun Oct 12 22:21:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9pfg_71601/10_2025/9pfg_71601.cif Found real_map, /net/cci-nas-00/data/ceres_data/9pfg_71601/10_2025/9pfg_71601.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.58 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9pfg_71601/10_2025/9pfg_71601.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9pfg_71601/10_2025/9pfg_71601.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9pfg_71601/10_2025/9pfg_71601.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9pfg_71601/10_2025/9pfg_71601.map" } resolution = 3.58 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= 0.002 sd= 0.058 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: 5 Type Number sf(0) Gaussians S 104 5.16 5 C 8707 2.51 5 N 2342 2.21 5 O 2755 1.98 5 H 13655 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 38 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: 27563 Number of models: 1 Model: "" Number of chains: 17 Chain: "A" Number of atoms: 1041 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 65, 1016 Classifications: {'peptide': 65} Link IDs: {'TRANS': 64} Conformer: "B" Number of residues, atoms: 65, 1016 Classifications: {'peptide': 65} Link IDs: {'TRANS': 64} bond proxies already assigned to first conformer: 989 Chain: "B" Number of atoms: 1100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 1100 Classifications: {'peptide': 68} Link IDs: {'TRANS': 67} Chain: "C" Number of atoms: 1027 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 64, 1002 Classifications: {'peptide': 64} Link IDs: {'TRANS': 63} Conformer: "B" Number of residues, atoms: 64, 1002 Classifications: {'peptide': 64} Link IDs: {'TRANS': 63} bond proxies already assigned to first conformer: 975 Chain: "D" Number of atoms: 1062 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 1062 Classifications: {'peptide': 68} Link IDs: {'TRANS': 67} Chain: "H" Number of atoms: 4450 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 284, 4425 Classifications: {'peptide': 284} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 280} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 284, 4425 Classifications: {'peptide': 284} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 280} Chain breaks: 1 bond proxies already assigned to first conformer: 4435 Chain: "E" Number of atoms: 4372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 4372 Classifications: {'peptide': 280} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 276} Chain breaks: 1 Chain: "F" Number of atoms: 4370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 4370 Classifications: {'peptide': 280} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 276} Chain breaks: 1 Chain: "G" Number of atoms: 4377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 4377 Classifications: {'peptide': 281} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 277} Chain breaks: 1 Chain: "J" Number of atoms: 2870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 2870 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 6, 'TRANS': 178} Chain breaks: 1 Chain: "K" Number of atoms: 2870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 2870 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 6, 'TRANS': 178} Chain breaks: 1 Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "F" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "G" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 3 residue: pdb=" N AARG A 59 " occ=0.63 ... (46 atoms not shown) pdb="HH22BARG A 59 " occ=0.37 residue: pdb=" N AARG C 45 " occ=0.32 ... (46 atoms not shown) pdb="HH22BARG C 45 " occ=0.68 residue: pdb=" N AARG H 271 " occ=0.80 ... (46 atoms not shown) pdb="HH22BARG H 271 " occ=0.20 Time building chain proxies: 6.30, per 1000 atoms: 0.23 Number of scatterers: 27563 At special positions: 0 Unit cell: (140.288, 145.768, 108.504, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 104 16.00 O 2755 8.00 N 2342 7.00 C 8707 6.00 H 13655 1.00 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: 2.78 Conformation dependent library (CDL) restraints added in 1.0 seconds Enol-peptide restraints added in 953.7 nanoseconds 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3388 Finding SS restraints... Secondary structure from input PDB file: 75 helices and 7 sheets defined 78.5% alpha, 8.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.79 Creating SS restraints... Processing helix chain 'A' and resid 19 through 83 removed outlier: 3.839A pdb=" N ASP A 23 " --> pdb=" O ASP A 19 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLU A 24 " --> pdb=" O GLN A 20 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N SER A 25 " --> pdb=" O LEU A 21 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLU A 62 " --> pdb=" O GLU A 58 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLY A 63 " --> pdb=" O AARG A 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 192 through 258 removed outlier: 3.812A pdb=" N TYR B 235 " --> pdb=" O ASP B 231 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ASN B 236 " --> pdb=" O ARG B 232 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA B 240 " --> pdb=" O ASN B 236 " (cutoff:3.500A) Processing helix chain 'C' and resid 20 through 82 removed outlier: 3.564A pdb=" N ASP C 65 " --> pdb=" O GLU C 61 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLN C 66 " --> pdb=" O GLU C 62 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA C 74 " --> pdb=" O ASP C 70 " (cutoff:3.500A) Processing helix chain 'D' and resid 192 through 258 removed outlier: 3.621A pdb=" N ARG D 198 " --> pdb=" O GLU D 194 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ILE D 203 " --> pdb=" O HIS D 199 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N LYS D 204 " --> pdb=" O SER D 200 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N LEU D 205 " --> pdb=" O GLU D 201 " (cutoff:3.500A) Processing helix chain 'H' and resid 2 through 26 removed outlier: 3.636A pdb=" N LYS H 6 " --> pdb=" O ASP H 2 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N SER H 26 " --> pdb=" O LYS H 22 " (cutoff:3.500A) Processing helix chain 'H' and resid 36 through 55 removed outlier: 3.996A pdb=" N GLU H 40 " --> pdb=" O SER H 36 " (cutoff:3.500A) Processing helix chain 'H' and resid 57 through 75 removed outlier: 3.645A pdb=" N LEU H 75 " --> pdb=" O LEU H 71 " (cutoff:3.500A) Processing helix chain 'H' and resid 78 through 93 Processing helix chain 'H' and resid 96 through 115 Processing helix chain 'H' and resid 117 through 134 Processing helix chain 'H' and resid 137 through 155 Processing helix chain 'H' and resid 157 through 175 removed outlier: 3.938A pdb=" N ALA H 161 " --> pdb=" O SER H 157 " (cutoff:3.500A) Processing helix chain 'H' and resid 177 through 194 removed outlier: 3.682A pdb=" N ALA H 181 " --> pdb=" O GLN H 177 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE H 184 " --> pdb=" O LYS H 180 " (cutoff:3.500A) Processing helix chain 'H' and resid 197 through 200 removed outlier: 3.661A pdb=" N TYR H 200 " --> pdb=" O LEU H 197 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 197 through 200' Processing helix chain 'H' and resid 201 through 217 removed outlier: 4.065A pdb=" N TYR H 205 " --> pdb=" O SER H 201 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N PHE H 206 " --> pdb=" O ALA H 202 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE H 216 " --> pdb=" O CYS H 212 " (cutoff:3.500A) Processing helix chain 'H' and resid 217 through 232 Processing helix chain 'H' and resid 233 through 237 Processing helix chain 'H' and resid 238 through 254 removed outlier: 3.738A pdb=" N LYS H 242 " --> pdb=" O SER H 238 " (cutoff:3.500A) Processing helix chain 'H' and resid 255 through 270 removed outlier: 3.548A pdb=" N TYR H 259 " --> pdb=" O ASN H 255 " (cutoff:3.500A) Processing helix chain 'H' and resid 273 through 291 removed outlier: 3.619A pdb=" N GLY H 289 " --> pdb=" O LYS H 285 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ASP H 290 " --> pdb=" O THR H 286 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 24 removed outlier: 4.122A pdb=" N LYS E 6 " --> pdb=" O ASP E 2 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N SER E 24 " --> pdb=" O LYS E 20 " (cutoff:3.500A) Processing helix chain 'E' and resid 35 through 55 Processing helix chain 'E' and resid 57 through 75 removed outlier: 3.670A pdb=" N ALA E 61 " --> pdb=" O ASN E 57 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LEU E 75 " --> pdb=" O LEU E 71 " (cutoff:3.500A) Processing helix chain 'E' and resid 78 through 93 removed outlier: 3.986A pdb=" N THR E 83 " --> pdb=" O HIS E 79 " (cutoff:3.500A) Processing helix chain 'E' and resid 96 through 115 removed outlier: 4.011A pdb=" N ALA E 100 " --> pdb=" O ASP E 96 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE E 110 " --> pdb=" O ARG E 106 " (cutoff:3.500A) Processing helix chain 'E' and resid 117 through 135 removed outlier: 4.047A pdb=" N LYS E 122 " --> pdb=" O THR E 118 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N HIS E 123 " --> pdb=" O ILE E 119 " (cutoff:3.500A) Processing helix chain 'E' and resid 138 through 155 removed outlier: 3.608A pdb=" N GLU E 155 " --> pdb=" O TYR E 151 " (cutoff:3.500A) Processing helix chain 'E' and resid 157 through 175 Processing helix chain 'E' and resid 177 through 194 removed outlier: 3.722A pdb=" N ALA E 181 " --> pdb=" O GLN E 177 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ASP E 194 " --> pdb=" O THR E 190 " (cutoff:3.500A) Processing helix chain 'E' and resid 197 through 200 removed outlier: 3.657A pdb=" N TYR E 200 " --> pdb=" O LEU E 197 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 197 through 200' Processing helix chain 'E' and resid 201 through 217 removed outlier: 4.140A pdb=" N TYR E 205 " --> pdb=" O SER E 201 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N PHE E 206 " --> pdb=" O ALA E 202 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILE E 216 " --> pdb=" O CYS E 212 " (cutoff:3.500A) Processing helix chain 'E' and resid 217 through 232 Processing helix chain 'E' and resid 233 through 237 removed outlier: 3.717A pdb=" N ASP E 237 " --> pdb=" O ALA E 234 " (cutoff:3.500A) Processing helix chain 'E' and resid 238 through 252 removed outlier: 3.624A pdb=" N LYS E 242 " --> pdb=" O SER E 238 " (cutoff:3.500A) Processing helix chain 'E' and resid 255 through 270 removed outlier: 3.730A pdb=" N TYR E 259 " --> pdb=" O ASN E 255 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ILE E 269 " --> pdb=" O GLU E 265 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N SER E 270 " --> pdb=" O TYR E 266 " (cutoff:3.500A) Processing helix chain 'E' and resid 273 through 287 removed outlier: 3.616A pdb=" N ILE E 287 " --> pdb=" O ILE E 283 " (cutoff:3.500A) Processing helix chain 'F' and resid 1 through 25 Processing helix chain 'F' and resid 35 through 55 removed outlier: 3.503A pdb=" N MET F 54 " --> pdb=" O ASN F 50 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ALA F 55 " --> pdb=" O MET F 51 " (cutoff:3.500A) Processing helix chain 'F' and resid 57 through 75 removed outlier: 3.554A pdb=" N ALA F 61 " --> pdb=" O ASN F 57 " (cutoff:3.500A) Processing helix chain 'F' and resid 78 through 93 Processing helix chain 'F' and resid 96 through 115 removed outlier: 3.701A pdb=" N ALA F 100 " --> pdb=" O ASP F 96 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N MET F 114 " --> pdb=" O ILE F 110 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLY F 115 " --> pdb=" O TYR F 111 " (cutoff:3.500A) Processing helix chain 'F' and resid 117 through 135 removed outlier: 3.911A pdb=" N ALA F 121 " --> pdb=" O PHE F 117 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LYS F 122 " --> pdb=" O THR F 118 " (cutoff:3.500A) Processing helix chain 'F' and resid 138 through 155 removed outlier: 3.781A pdb=" N GLU F 155 " --> pdb=" O TYR F 151 " (cutoff:3.500A) Processing helix chain 'F' and resid 157 through 175 removed outlier: 3.563A pdb=" N ALA F 161 " --> pdb=" O SER F 157 " (cutoff:3.500A) Processing helix chain 'F' and resid 177 through 195 removed outlier: 4.096A pdb=" N ALA F 181 " --> pdb=" O GLN F 177 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ASP F 194 " --> pdb=" O THR F 190 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N SER F 195 " --> pdb=" O SER F 191 " (cutoff:3.500A) Processing helix chain 'F' and resid 197 through 200 removed outlier: 4.422A pdb=" N TYR F 200 " --> pdb=" O LEU F 197 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 197 through 200' Processing helix chain 'F' and resid 201 through 217 removed outlier: 3.950A pdb=" N TYR F 205 " --> pdb=" O SER F 201 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE F 216 " --> pdb=" O CYS F 212 " (cutoff:3.500A) Processing helix chain 'F' and resid 217 through 232 Processing helix chain 'F' and resid 233 through 236 Processing helix chain 'F' and resid 237 through 253 removed outlier: 3.640A pdb=" N CYS F 241 " --> pdb=" O ASP F 237 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N LEU F 243 " --> pdb=" O ARG F 239 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLU F 253 " --> pdb=" O GLU F 249 " (cutoff:3.500A) Processing helix chain 'F' and resid 255 through 270 removed outlier: 3.759A pdb=" N TYR F 259 " --> pdb=" O ASN F 255 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ILE F 269 " --> pdb=" O GLU F 265 " (cutoff:3.500A) Processing helix chain 'F' and resid 273 through 287 Processing helix chain 'G' and resid 1 through 23 removed outlier: 4.171A pdb=" N GLY G 5 " --> pdb=" O MET G 1 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LYS G 6 " --> pdb=" O ASP G 2 " (cutoff:3.500A) Processing helix chain 'G' and resid 35 through 56 Processing helix chain 'G' and resid 59 through 75 Processing helix chain 'G' and resid 78 through 96 removed outlier: 4.775A pdb=" N LYS G 94 " --> pdb=" O ASN G 90 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N ALA G 95 " --> pdb=" O ALA G 91 " (cutoff:3.500A) Processing helix chain 'G' and resid 96 through 114 removed outlier: 3.825A pdb=" N ASP G 113 " --> pdb=" O GLU G 109 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N MET G 114 " --> pdb=" O ILE G 110 " (cutoff:3.500A) Processing helix chain 'G' and resid 116 through 134 removed outlier: 3.666A pdb=" N ALA G 120 " --> pdb=" O ARG G 116 " (cutoff:3.500A) Processing helix chain 'G' and resid 137 through 154 Processing helix chain 'G' and resid 162 through 175 Processing helix chain 'G' and resid 177 through 195 removed outlier: 3.801A pdb=" N ALA G 181 " --> pdb=" O GLN G 177 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ASP G 194 " --> pdb=" O THR G 190 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N SER G 195 " --> pdb=" O SER G 191 " (cutoff:3.500A) Processing helix chain 'G' and resid 198 through 217 removed outlier: 3.502A pdb=" N ALA G 202 " --> pdb=" O LEU G 198 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N LYS G 203 " --> pdb=" O LYS G 199 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N ASP G 204 " --> pdb=" O TYR G 200 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N TYR G 205 " --> pdb=" O SER G 201 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N PHE G 206 " --> pdb=" O ALA G 202 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N PHE G 207 " --> pdb=" O LYS G 203 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N CYS G 212 " --> pdb=" O LYS G 208 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ILE G 216 " --> pdb=" O CYS G 212 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASP G 217 " --> pdb=" O HIS G 213 " (cutoff:3.500A) Processing helix chain 'G' and resid 217 through 232 Processing helix chain 'G' and resid 233 through 237 Processing helix chain 'G' and resid 238 through 251 removed outlier: 4.028A pdb=" N LYS G 242 " --> pdb=" O SER G 238 " (cutoff:3.500A) Processing helix chain 'G' and resid 255 through 270 removed outlier: 3.535A pdb=" N TYR G 259 " --> pdb=" O ASN G 255 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ILE G 269 " --> pdb=" O GLU G 265 " (cutoff:3.500A) Processing helix chain 'G' and resid 273 through 289 removed outlier: 4.299A pdb=" N GLY G 289 " --> pdb=" O LYS G 285 " (cutoff:3.500A) Processing helix chain 'J' and resid 13 through 19 removed outlier: 3.500A pdb=" N SER J 17 " --> pdb=" O THR J 13 " (cutoff:3.500A) Processing helix chain 'J' and resid 63 through 71 Processing helix chain 'J' and resid 103 through 107 removed outlier: 3.913A pdb=" N ASN J 106 " --> pdb=" O GLN J 103 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ILE J 107 " --> pdb=" O LYS J 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 103 through 107' Processing helix chain 'J' and resid 114 through 126 Processing helix chain 'K' and resid 13 through 19 Processing helix chain 'K' and resid 63 through 71 Processing helix chain 'K' and resid 103 through 107 removed outlier: 3.593A pdb=" N ILE K 107 " --> pdb=" O LYS K 104 " (cutoff:3.500A) Processing helix chain 'K' and resid 114 through 126 removed outlier: 3.669A pdb=" N ALA K 118 " --> pdb=" O THR K 114 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ALA K 119 " --> pdb=" O ASP K 115 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N GLU K 120 " --> pdb=" O LYS K 116 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'J' and resid 4 through 10 removed outlier: 8.034A pdb=" N VAL J 60 " --> pdb=" O SER J 5 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N GLN J 7 " --> pdb=" O VAL J 60 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N PHE J 62 " --> pdb=" O GLN J 7 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N ALA J 9 " --> pdb=" O PHE J 62 " (cutoff:3.500A) removed outlier: 8.728A pdb=" N SER J 59 " --> pdb=" O SER J 25 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N SER J 25 " --> pdb=" O SER J 59 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N HIS J 43 " --> pdb=" O THR J 39 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N THR J 39 " --> pdb=" O HIS J 43 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N SER J 40 " --> pdb=" O GLU J 77 " (cutoff:3.500A) removed outlier: 12.056A pdb=" N GLU J 77 " --> pdb=" O SER J 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'J' and resid 129 through 131 removed outlier: 3.785A pdb=" N PHE J 130 " --> pdb=" O GLY J 175 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N GLY J 175 " --> pdb=" O PHE J 130 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N GLY J 93 " --> pdb=" O ASN J 180 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ALA J 184 " --> pdb=" O MET J 95 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLU J 186 " --> pdb=" O ILE J 97 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N GLU J 153 " --> pdb=" O GLY J 93 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N MET J 95 " --> pdb=" O ASP J 151 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N ASP J 151 " --> pdb=" O MET J 95 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ILE J 97 " --> pdb=" O VAL J 149 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N VAL J 149 " --> pdb=" O ILE J 97 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N ILE J 99 " --> pdb=" O LEU J 147 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N LEU J 147 " --> pdb=" O ILE J 99 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N PHE J 101 " --> pdb=" O PHE J 145 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N PHE J 145 " --> pdb=" O PHE J 101 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'J' and resid 111 through 113 removed outlier: 5.073A pdb=" N TYR J 112 " --> pdb=" O ILE J 196 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'K' and resid 2 through 10 removed outlier: 5.840A pdb=" N ALA K 22 " --> pdb=" O ARG K 50 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N HIS K 34 " --> pdb=" O TYR K 83 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N ALA K 81 " --> pdb=" O ILE K 36 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ARG K 4 " --> pdb=" O VAL K 80 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N LEU K 82 " --> pdb=" O ALA K 2 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N ALA K 2 " --> pdb=" O LEU K 82 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'K' and resid 135 through 140 removed outlier: 5.351A pdb=" N LEU K 147 " --> pdb=" O ASP K 100 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N ASP K 100 " --> pdb=" O LEU K 147 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N VAL K 149 " --> pdb=" O GLU K 98 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N GLU K 98 " --> pdb=" O VAL K 149 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N GLU K 186 " --> pdb=" O ILE K 97 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ILE K 99 " --> pdb=" O GLU K 186 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'K' and resid 111 through 113 removed outlier: 5.487A pdb=" N TYR K 112 " --> pdb=" O ILE K 196 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'K' and resid 129 through 131 1048 hydrogen bonds defined for protein. 3110 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: 6.13 Time building geometry restraints manager: 3.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 13617 1.03 - 1.23: 66 1.23 - 1.42: 5821 1.42 - 1.62: 8070 1.62 - 1.82: 170 Bond restraints: 27744 Sorted by residual: bond pdb=" C GLN C 66 " pdb=" O GLN C 66 " ideal model delta sigma weight residual 1.236 1.190 0.046 1.21e-02 6.83e+03 1.47e+01 bond pdb=" C ASP K 86 " pdb=" O ASP K 86 " ideal model delta sigma weight residual 1.232 1.184 0.047 1.32e-02 5.74e+03 1.29e+01 bond pdb=" C TYR E 185 " pdb=" N GLU E 186 " ideal model delta sigma weight residual 1.335 1.294 0.041 1.31e-02 5.83e+03 9.74e+00 bond pdb=" C GLU E 186 " pdb=" O GLU E 186 " ideal model delta sigma weight residual 1.237 1.201 0.035 1.17e-02 7.31e+03 9.11e+00 bond pdb=" C ASP C 65 " pdb=" O ASP C 65 " ideal model delta sigma weight residual 1.236 1.202 0.034 1.16e-02 7.43e+03 8.75e+00 ... (remaining 27739 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.64: 49294 1.64 - 3.28: 685 3.28 - 4.92: 79 4.92 - 6.57: 9 6.57 - 8.21: 1 Bond angle restraints: 50068 Sorted by residual: angle pdb=" N ASP C 80 " pdb=" CA ASP C 80 " pdb=" C ASP C 80 " ideal model delta sigma weight residual 111.36 105.92 5.44 1.09e+00 8.42e-01 2.49e+01 angle pdb=" CA ASP K 86 " pdb=" C ASP K 86 " pdb=" O ASP K 86 " ideal model delta sigma weight residual 121.39 116.01 5.38 1.12e+00 7.97e-01 2.31e+01 angle pdb=" CA HIS G 79 " pdb=" CB HIS G 79 " pdb=" CG HIS G 79 " ideal model delta sigma weight residual 113.80 118.27 -4.47 1.00e+00 1.00e+00 2.00e+01 angle pdb=" N ASP C 65 " pdb=" CA ASP C 65 " pdb=" C ASP C 65 " ideal model delta sigma weight residual 111.02 105.69 5.33 1.22e+00 6.72e-01 1.91e+01 angle pdb=" CA HIS G 79 " pdb=" C HIS G 79 " pdb=" O HIS G 79 " ideal model delta sigma weight residual 120.90 116.41 4.49 1.07e+00 8.73e-01 1.76e+01 ... (remaining 50063 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 11706 17.95 - 35.89: 914 35.89 - 53.84: 293 53.84 - 71.78: 78 71.78 - 89.73: 17 Dihedral angle restraints: 13008 sinusoidal: 7019 harmonic: 5989 Sorted by residual: dihedral pdb=" CA LYS G 56 " pdb=" C LYS G 56 " pdb=" N ASN G 57 " pdb=" CA ASN G 57 " ideal model delta harmonic sigma weight residual 180.00 163.66 16.34 0 5.00e+00 4.00e-02 1.07e+01 dihedral pdb=" CA PHE F 232 " pdb=" C PHE F 232 " pdb=" N PRO F 233 " pdb=" CA PRO F 233 " ideal model delta harmonic sigma weight residual -180.00 -163.86 -16.14 0 5.00e+00 4.00e-02 1.04e+01 dihedral pdb=" CA PHE G 232 " pdb=" C PHE G 232 " pdb=" N PRO G 233 " pdb=" CA PRO G 233 " ideal model delta harmonic sigma weight residual 180.00 -163.90 -16.10 0 5.00e+00 4.00e-02 1.04e+01 ... (remaining 13005 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 1457 0.030 - 0.061: 442 0.061 - 0.091: 130 0.091 - 0.121: 57 0.121 - 0.152: 8 Chirality restraints: 2094 Sorted by residual: chirality pdb=" CA ASP K 86 " pdb=" N ASP K 86 " pdb=" C ASP K 86 " pdb=" CB ASP K 86 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.77e-01 chirality pdb=" CA VAL J 56 " pdb=" N VAL J 56 " pdb=" C VAL J 56 " pdb=" CB VAL J 56 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 5.08e-01 chirality pdb=" CA ILE K 152 " pdb=" N ILE K 152 " pdb=" C ILE K 152 " pdb=" CB ILE K 152 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.45e-01 ... (remaining 2091 not shown) Planarity restraints: 4168 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 77 " -0.186 2.00e-02 2.50e+03 2.11e-01 6.67e+02 pdb=" CG ASN C 77 " -0.001 2.00e-02 2.50e+03 pdb=" OD1 ASN C 77 " 0.189 2.00e-02 2.50e+03 pdb=" ND2 ASN C 77 " -0.007 2.00e-02 2.50e+03 pdb="HD21 ASN C 77 " 0.316 2.00e-02 2.50e+03 pdb="HD22 ASN C 77 " -0.311 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN K 90 " 0.166 2.00e-02 2.50e+03 1.79e-01 4.81e+02 pdb=" CD GLN K 90 " -0.013 2.00e-02 2.50e+03 pdb=" OE1 GLN K 90 " -0.155 2.00e-02 2.50e+03 pdb=" NE2 GLN K 90 " -0.003 2.00e-02 2.50e+03 pdb="HE21 GLN K 90 " 0.268 2.00e-02 2.50e+03 pdb="HE22 GLN K 90 " -0.262 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN J 190 " -0.031 2.00e-02 2.50e+03 5.16e-02 3.99e+01 pdb=" CG ASN J 190 " 0.064 2.00e-02 2.50e+03 pdb=" OD1 ASN J 190 " 0.001 2.00e-02 2.50e+03 pdb=" ND2 ASN J 190 " -0.088 2.00e-02 2.50e+03 pdb="HD21 ASN J 190 " -0.004 2.00e-02 2.50e+03 pdb="HD22 ASN J 190 " 0.057 2.00e-02 2.50e+03 ... (remaining 4165 not shown) Histogram of nonbonded interaction distances: 1.55 - 2.16: 959 2.16 - 2.77: 52481 2.77 - 3.38: 75442 3.38 - 3.99: 89376 3.99 - 4.60: 143770 Nonbonded interactions: 362028 Sorted by model distance: nonbonded pdb=" OE1 GLU H 139 " pdb=" H GLU H 139 " model vdw 1.550 2.450 nonbonded pdb=" OE1 GLN E 76 " pdb=" H GLN E 76 " model vdw 1.552 2.450 nonbonded pdb=" OE1 GLU E 240 " pdb=" H GLU E 240 " model vdw 1.570 2.450 nonbonded pdb=" OE1 GLU H 240 " pdb=" H GLU H 240 " model vdw 1.572 2.450 nonbonded pdb=" O LEU K 16 " pdb=" HG SER K 19 " model vdw 1.602 2.450 ... (remaining 362023 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 19 through 44 or resid 47 through 58 or resid 61 through 8 \ 2)) selection = (chain 'C' and (resid 19 or (resid 20 and (name N or name CA or name C or name O \ or name CB or name CG or name CD or name OE1 or name NE2)) or (resid 21 and (na \ me N or name CA or name C or name O or name CB or name CG or name CD1 or name CD \ 2 or name HA or name HB2 or name HB3 or name HG or name HD11 or name HD12 or nam \ e HD13 or name HD21 or name HD22 or name HD23)) or resid 22 through 44 or resid \ 47 through 58 or resid 61 through 82)) } ncs_group { reference = (chain 'B' and ((resid 191 and (name N or name CA or name C or name O or name CB \ )) or (resid 192 and (name N or name CA or name C or name O or name CB or name \ CG or name CD1 or name CD2)) or (resid 193 and (name N or name CA or name C or n \ ame O or name CB or name OG )) or (resid 194 and (name N or name CA or name C or \ name O or name CB or name CG or name CD or name OE1 or name OE2)) or (resid 195 \ and (name N or name CA or name C or name O or name CB or name CG1 or name CG2 o \ r name CD1)) or (resid 196 and (name N or name CA or name C or name O or name CB \ or name CG or name CD or name OE1 or name OE2 or name HA or name HB2 or name HB \ 3 or name HG2 or name HG3)) or resid 197 through 258)) selection = chain 'D' } ncs_group { reference = (chain 'E' and (resid 0 through 24 or (resid 35 and (name N or name CA or name C \ or name O or name CB or name OG or name HA or name HB2 or name HB3 or name HG ) \ ) or resid 36 through 71 or (resid 72 and (name N or name CA or name C or name O \ or name CB or name CG or name ND1 or name CD2 or name CE1 or name NE2 or name H \ or name HA or name HB2 or name HB3 or name HD2 or name HE1 or name HE2)) or res \ id 73 through 270 or resid 273 through 287)) selection = (chain 'F' and (resid 0 through 24 or (resid 35 and (name N or name CA or name C \ or name O or name CB or name OG or name HA or name HB2 or name HB3 or name HG ) \ ) or resid 36 through 270 or resid 273 through 287)) selection = (chain 'G' and (resid 0 through 24 or (resid 35 and (name N or name CA or name C \ or name O or name CB or name OG or name HA or name HB2 or name HB3 or name HG ) \ ) or resid 36 through 270 or resid 273 through 287)) selection = (chain 'H' and (resid 0 through 24 or resid 35 through 270 or resid 273 through \ 287)) } ncs_group { reference = chain 'J' selection = chain 'K' } 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=0.20 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.190 Extract box with map and model: 0.430 Check model and map are aligned: 0.100 Set scattering table: 0.040 Process input model: 28.100 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.050 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:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 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 : 0.004 0.048 14089 Z= 0.234 Angle : 0.590 8.206 18928 Z= 0.367 Chirality : 0.036 0.152 2094 Planarity : 0.004 0.074 2450 Dihedral : 15.878 89.725 5294 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.37 % Favored : 97.51 % Rotamer: Outliers : 0.74 % Allowed : 15.70 % Favored : 83.56 % 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: 1.50 (0.20), residues: 1737 helix: 1.86 (0.14), residues: 1267 sheet: -0.73 (0.43), residues: 120 loop : -1.59 (0.29), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 30 TYR 0.019 0.001 TYR E 228 PHE 0.020 0.002 PHE J 140 TRP 0.009 0.001 TRP F 275 HIS 0.005 0.001 HIS B 213 Details of bonding type rmsd covalent geometry : bond 0.00448 (14089) covalent geometry : angle 0.58989 (18928) hydrogen bonds : bond 0.14796 ( 1048) hydrogen bonds : angle 5.81165 ( 3110) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 228 time to evaluate : 0.917 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 MET cc_start: 0.7776 (ttm) cc_final: 0.7510 (mtp) REVERT: C 77 ASN cc_start: 0.7397 (OUTLIER) cc_final: 0.6379 (m110) REVERT: C 78 LEU cc_start: 0.8402 (tp) cc_final: 0.8053 (tp) REVERT: C 80 ASP cc_start: 0.8175 (t70) cc_final: 0.7921 (t70) outliers start: 11 outliers final: 3 residues processed: 233 average time/residue: 0.2886 time to fit residues: 96.6750 Evaluate side-chains 220 residues out of total 1475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 216 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 72 LYS Chi-restraints excluded: chain C residue 77 ASN Chi-restraints excluded: chain K residue 38 ARG Chi-restraints excluded: chain K residue 141 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.5980 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 5.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 239 HIS J 194 ASN K 141 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.145496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.110468 restraints weight = 101379.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.112917 restraints weight = 93325.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.114854 restraints weight = 45374.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.115828 restraints weight = 29586.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.119590 restraints weight = 23979.366| |-----------------------------------------------------------------------------| r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3479 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3479 r_free = 0.3479 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3478 r_free = 0.3478 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3478 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.0858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14089 Z= 0.160 Angle : 0.499 5.273 18928 Z= 0.288 Chirality : 0.034 0.153 2094 Planarity : 0.003 0.045 2450 Dihedral : 4.428 71.928 1889 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.12 % Allowed : 1.97 % Favored : 97.92 % Rotamer: Outliers : 1.68 % Allowed : 15.36 % Favored : 82.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.46 (0.20), residues: 1737 helix: 2.53 (0.14), residues: 1283 sheet: -0.53 (0.45), residues: 120 loop : -1.24 (0.32), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 47 TYR 0.013 0.001 TYR E 228 PHE 0.016 0.001 PHE G 232 TRP 0.008 0.001 TRP F 275 HIS 0.004 0.001 HIS G 251 Details of bonding type rmsd covalent geometry : bond 0.00327 (14089) covalent geometry : angle 0.49942 (18928) hydrogen bonds : bond 0.07514 ( 1048) hydrogen bonds : angle 4.44404 ( 3110) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 218 time to evaluate : 0.647 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 LYS cc_start: 0.9171 (tptt) cc_final: 0.8928 (tptt) REVERT: A 75 GLU cc_start: 0.8749 (tm-30) cc_final: 0.8470 (tm-30) REVERT: B 253 LYS cc_start: 0.6562 (OUTLIER) cc_final: 0.6253 (mmtm) REVERT: C 80 ASP cc_start: 0.8146 (t70) cc_final: 0.7876 (t70) REVERT: H 39 GLU cc_start: 0.8534 (OUTLIER) cc_final: 0.8083 (mm-30) REVERT: E 84 CYS cc_start: 0.8271 (m) cc_final: 0.8051 (m) REVERT: K 51 THR cc_start: 0.6316 (OUTLIER) cc_final: 0.6020 (t) outliers start: 25 outliers final: 15 residues processed: 233 average time/residue: 0.2889 time to fit residues: 97.0634 Evaluate side-chains 231 residues out of total 1475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 213 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 253 LYS Chi-restraints excluded: chain C residue 20 GLN Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 55 GLU Chi-restraints excluded: chain C residue 72 LYS Chi-restraints excluded: chain D residue 229 MET Chi-restraints excluded: chain H residue 39 GLU Chi-restraints excluded: chain E residue 213 HIS Chi-restraints excluded: chain E residue 286 THR Chi-restraints excluded: chain G residue 132 GLU Chi-restraints excluded: chain G residue 133 THR Chi-restraints excluded: chain G residue 213 HIS Chi-restraints excluded: chain J residue 11 CYS Chi-restraints excluded: chain J residue 42 ASN Chi-restraints excluded: chain J residue 201 THR Chi-restraints excluded: chain K residue 38 ARG Chi-restraints excluded: chain K residue 51 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 127 optimal weight: 1.9990 chunk 94 optimal weight: 3.9990 chunk 158 optimal weight: 7.9990 chunk 52 optimal weight: 4.9990 chunk 43 optimal weight: 0.7980 chunk 86 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 25 optimal weight: 5.9990 chunk 126 optimal weight: 0.6980 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 239 HIS ** J 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.145776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.109803 restraints weight = 98859.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.112803 restraints weight = 81384.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.113873 restraints weight = 47981.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.115734 restraints weight = 28787.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.116514 restraints weight = 23560.487| |-----------------------------------------------------------------------------| r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3449 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3449 r_free = 0.3449 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3449 r_free = 0.3449 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3449 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.1273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14089 Z= 0.154 Angle : 0.472 5.151 18928 Z= 0.272 Chirality : 0.033 0.145 2094 Planarity : 0.003 0.030 2450 Dihedral : 3.970 57.668 1885 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.49 % Favored : 97.40 % Rotamer: Outliers : 1.48 % Allowed : 16.37 % Favored : 82.14 % 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: 2.86 (0.20), residues: 1737 helix: 2.83 (0.14), residues: 1288 sheet: -0.38 (0.47), residues: 120 loop : -1.19 (0.32), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 47 TYR 0.010 0.001 TYR E 228 PHE 0.021 0.001 PHE K 85 TRP 0.007 0.001 TRP F 275 HIS 0.004 0.001 HIS B 213 Details of bonding type rmsd covalent geometry : bond 0.00315 (14089) covalent geometry : angle 0.47178 (18928) hydrogen bonds : bond 0.07084 ( 1048) hydrogen bonds : angle 4.15136 ( 3110) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 219 time to evaluate : 0.784 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 LYS cc_start: 0.9166 (tptt) cc_final: 0.8899 (tptt) REVERT: A 75 GLU cc_start: 0.8737 (tm-30) cc_final: 0.8482 (tm-30) REVERT: H 39 GLU cc_start: 0.8565 (OUTLIER) cc_final: 0.8096 (mm-30) REVERT: E 84 CYS cc_start: 0.8284 (m) cc_final: 0.8070 (m) REVERT: E 211 LEU cc_start: 0.8805 (OUTLIER) cc_final: 0.8386 (mp) REVERT: E 255 ASN cc_start: 0.7581 (m-40) cc_final: 0.7328 (t0) REVERT: G 213 HIS cc_start: 0.8688 (OUTLIER) cc_final: 0.7354 (m-70) REVERT: J 103 GLN cc_start: 0.6735 (pm20) cc_final: 0.6069 (pp30) REVERT: J 185 PHE cc_start: 0.6893 (m-10) cc_final: 0.6560 (m-80) REVERT: K 51 THR cc_start: 0.6377 (OUTLIER) cc_final: 0.6071 (t) REVERT: K 79 GLU cc_start: 0.7111 (mm-30) cc_final: 0.6871 (mm-30) outliers start: 22 outliers final: 16 residues processed: 231 average time/residue: 0.2849 time to fit residues: 95.5057 Evaluate side-chains 231 residues out of total 1475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 211 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain C residue 20 GLN Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 55 GLU Chi-restraints excluded: chain C residue 72 LYS Chi-restraints excluded: chain D residue 229 MET Chi-restraints excluded: chain D residue 248 VAL Chi-restraints excluded: chain H residue 39 GLU Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain E residue 211 LEU Chi-restraints excluded: chain E residue 213 HIS Chi-restraints excluded: chain E residue 286 THR Chi-restraints excluded: chain F residue 182 ILE Chi-restraints excluded: chain G residue 132 GLU Chi-restraints excluded: chain G residue 213 HIS Chi-restraints excluded: chain J residue 42 ASN Chi-restraints excluded: chain J residue 201 THR Chi-restraints excluded: chain K residue 38 ARG Chi-restraints excluded: chain K residue 51 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 3 optimal weight: 1.9990 chunk 55 optimal weight: 5.9990 chunk 153 optimal weight: 0.7980 chunk 64 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 163 optimal weight: 9.9990 chunk 98 optimal weight: 1.9990 chunk 97 optimal weight: 0.5980 chunk 41 optimal weight: 0.9990 chunk 51 optimal weight: 0.9990 chunk 129 optimal weight: 1.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 239 HIS G 123 HIS ** J 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 194 ASN ** K 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.146211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.102642 restraints weight = 111435.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.104813 restraints weight = 51540.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.105902 restraints weight = 34956.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.107251 restraints weight = 29619.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.106998 restraints weight = 25452.510| |-----------------------------------------------------------------------------| r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3324 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3324 r_free = 0.3324 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3324 r_free = 0.3324 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3324 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.1563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14089 Z= 0.138 Angle : 0.450 5.153 18928 Z= 0.257 Chirality : 0.033 0.138 2094 Planarity : 0.003 0.039 2450 Dihedral : 3.793 51.116 1885 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.37 % Favored : 97.57 % Rotamer: Outliers : 2.02 % Allowed : 16.58 % Favored : 81.40 % 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: 3.10 (0.20), residues: 1737 helix: 3.01 (0.14), residues: 1289 sheet: -0.33 (0.49), residues: 120 loop : -1.15 (0.32), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 116 TYR 0.009 0.001 TYR G 259 PHE 0.013 0.001 PHE G 232 TRP 0.006 0.001 TRP F 275 HIS 0.003 0.001 HIS E 251 Details of bonding type rmsd covalent geometry : bond 0.00277 (14089) covalent geometry : angle 0.44986 (18928) hydrogen bonds : bond 0.06657 ( 1048) hydrogen bonds : angle 3.93975 ( 3110) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 224 time to evaluate : 0.907 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 253 LYS cc_start: 0.6534 (OUTLIER) cc_final: 0.6327 (mmtm) REVERT: H 39 GLU cc_start: 0.8561 (OUTLIER) cc_final: 0.8165 (mm-30) REVERT: E 84 CYS cc_start: 0.8387 (m) cc_final: 0.8110 (m) REVERT: E 211 LEU cc_start: 0.8907 (OUTLIER) cc_final: 0.8539 (mp) REVERT: E 255 ASN cc_start: 0.7644 (m-40) cc_final: 0.7443 (t0) REVERT: E 281 LEU cc_start: 0.8941 (OUTLIER) cc_final: 0.8740 (mm) REVERT: G 213 HIS cc_start: 0.8899 (OUTLIER) cc_final: 0.7589 (m-70) REVERT: J 103 GLN cc_start: 0.6642 (pm20) cc_final: 0.6061 (pp30) REVERT: J 185 PHE cc_start: 0.6696 (m-10) cc_final: 0.6260 (m-80) REVERT: K 51 THR cc_start: 0.6640 (OUTLIER) cc_final: 0.6400 (t) REVERT: K 127 ASN cc_start: 0.8250 (t0) cc_final: 0.7921 (m-40) outliers start: 29 outliers final: 23 residues processed: 241 average time/residue: 0.2823 time to fit residues: 98.9363 Evaluate side-chains 238 residues out of total 1475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 209 time to evaluate : 0.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 253 LYS Chi-restraints excluded: chain C residue 20 GLN Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 49 MET Chi-restraints excluded: chain C residue 55 GLU Chi-restraints excluded: chain C residue 72 LYS Chi-restraints excluded: chain D residue 213 HIS Chi-restraints excluded: chain D residue 229 MET Chi-restraints excluded: chain D residue 248 VAL Chi-restraints excluded: chain H residue 39 GLU Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain E residue 211 LEU Chi-restraints excluded: chain E residue 213 HIS Chi-restraints excluded: chain E residue 281 LEU Chi-restraints excluded: chain E residue 286 THR Chi-restraints excluded: chain F residue 182 ILE Chi-restraints excluded: chain F residue 241 CYS Chi-restraints excluded: chain G residue 132 GLU Chi-restraints excluded: chain G residue 152 TYR Chi-restraints excluded: chain G residue 213 HIS Chi-restraints excluded: chain J residue 30 GLN Chi-restraints excluded: chain J residue 42 ASN Chi-restraints excluded: chain J residue 113 ASP Chi-restraints excluded: chain J residue 201 THR Chi-restraints excluded: chain K residue 38 ARG Chi-restraints excluded: chain K residue 51 THR Chi-restraints excluded: chain K residue 143 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 166 optimal weight: 7.9990 chunk 154 optimal weight: 9.9990 chunk 102 optimal weight: 0.0030 chunk 68 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 87 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 chunk 131 optimal weight: 1.9990 chunk 170 optimal weight: 10.0000 chunk 18 optimal weight: 10.0000 chunk 47 optimal weight: 2.9990 overall best weight: 1.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 239 HIS ** J 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 141 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.143764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.107930 restraints weight = 97865.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.110639 restraints weight = 85949.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.112076 restraints weight = 46430.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.113251 restraints weight = 29592.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.115783 restraints weight = 24696.004| |-----------------------------------------------------------------------------| r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3434 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3434 r_free = 0.3434 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3434 r_free = 0.3434 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3434 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.1715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 14089 Z= 0.186 Angle : 0.486 5.098 18928 Z= 0.280 Chirality : 0.034 0.135 2094 Planarity : 0.003 0.032 2450 Dihedral : 3.737 43.283 1885 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.72 % Favored : 97.22 % Rotamer: Outliers : 2.36 % Allowed : 17.25 % Favored : 80.39 % 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: 2.94 (0.20), residues: 1737 helix: 2.88 (0.13), residues: 1288 sheet: -0.50 (0.48), residues: 120 loop : -1.10 (0.32), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 116 TYR 0.010 0.001 TYR G 259 PHE 0.013 0.001 PHE G 232 TRP 0.007 0.001 TRP G 275 HIS 0.005 0.001 HIS E 251 Details of bonding type rmsd covalent geometry : bond 0.00406 (14089) covalent geometry : angle 0.48593 (18928) hydrogen bonds : bond 0.07338 ( 1048) hydrogen bonds : angle 4.09195 ( 3110) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 211 time to evaluate : 0.758 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 199 HIS cc_start: 0.7541 (OUTLIER) cc_final: 0.6932 (t70) REVERT: B 253 LYS cc_start: 0.6454 (OUTLIER) cc_final: 0.6176 (mmtm) REVERT: H 39 GLU cc_start: 0.8616 (OUTLIER) cc_final: 0.8059 (mm-30) REVERT: E 84 CYS cc_start: 0.8392 (m) cc_final: 0.8150 (m) REVERT: E 211 LEU cc_start: 0.8815 (OUTLIER) cc_final: 0.8482 (mp) REVERT: E 281 LEU cc_start: 0.8828 (OUTLIER) cc_final: 0.8621 (mm) REVERT: G 213 HIS cc_start: 0.8687 (OUTLIER) cc_final: 0.7362 (m-70) REVERT: J 103 GLN cc_start: 0.6844 (pm20) cc_final: 0.6261 (pp30) REVERT: J 185 PHE cc_start: 0.6866 (m-10) cc_final: 0.6515 (m-80) REVERT: K 51 THR cc_start: 0.6562 (OUTLIER) cc_final: 0.6263 (t) REVERT: K 100 ASP cc_start: 0.7621 (m-30) cc_final: 0.7226 (m-30) outliers start: 34 outliers final: 23 residues processed: 229 average time/residue: 0.2940 time to fit residues: 96.4067 Evaluate side-chains 235 residues out of total 1475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 205 time to evaluate : 0.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 199 HIS Chi-restraints excluded: chain B residue 213 HIS Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 253 LYS Chi-restraints excluded: chain C residue 20 GLN Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 49 MET Chi-restraints excluded: chain C residue 55 GLU Chi-restraints excluded: chain C residue 72 LYS Chi-restraints excluded: chain D residue 213 HIS Chi-restraints excluded: chain D residue 229 MET Chi-restraints excluded: chain D residue 248 VAL Chi-restraints excluded: chain H residue 39 GLU Chi-restraints excluded: chain E residue 108 ILE Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain E residue 211 LEU Chi-restraints excluded: chain E residue 213 HIS Chi-restraints excluded: chain E residue 281 LEU Chi-restraints excluded: chain E residue 286 THR Chi-restraints excluded: chain F residue 182 ILE Chi-restraints excluded: chain G residue 152 TYR Chi-restraints excluded: chain G residue 213 HIS Chi-restraints excluded: chain J residue 30 GLN Chi-restraints excluded: chain J residue 42 ASN Chi-restraints excluded: chain J residue 113 ASP Chi-restraints excluded: chain J residue 201 THR Chi-restraints excluded: chain K residue 38 ARG Chi-restraints excluded: chain K residue 51 THR Chi-restraints excluded: chain K residue 143 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 159 optimal weight: 7.9990 chunk 151 optimal weight: 7.9990 chunk 137 optimal weight: 0.7980 chunk 78 optimal weight: 0.0000 chunk 38 optimal weight: 2.9990 chunk 140 optimal weight: 8.9990 chunk 71 optimal weight: 0.9980 chunk 29 optimal weight: 4.9990 chunk 48 optimal weight: 0.7980 chunk 129 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 239 HIS ** J 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 141 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.146295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.111066 restraints weight = 103347.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.113873 restraints weight = 88755.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.115591 restraints weight = 45082.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.116909 restraints weight = 28776.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.120455 restraints weight = 23788.098| |-----------------------------------------------------------------------------| r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3486 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3486 r_free = 0.3486 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3486 r_free = 0.3486 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3486 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.1916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 14089 Z= 0.128 Angle : 0.444 5.123 18928 Z= 0.250 Chirality : 0.033 0.136 2094 Planarity : 0.003 0.030 2450 Dihedral : 3.597 37.372 1885 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.31 % Favored : 97.63 % Rotamer: Outliers : 2.22 % Allowed : 17.72 % Favored : 80.05 % 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: 3.21 (0.20), residues: 1737 helix: 3.10 (0.14), residues: 1295 sheet: -0.49 (0.49), residues: 120 loop : -1.12 (0.33), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 116 TYR 0.008 0.001 TYR G 259 PHE 0.013 0.001 PHE G 232 TRP 0.006 0.001 TRP G 275 HIS 0.004 0.001 HIS B 213 Details of bonding type rmsd covalent geometry : bond 0.00250 (14089) covalent geometry : angle 0.44444 (18928) hydrogen bonds : bond 0.06327 ( 1048) hydrogen bonds : angle 3.77670 ( 3110) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 217 time to evaluate : 0.990 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 199 HIS cc_start: 0.7299 (OUTLIER) cc_final: 0.6748 (t70) REVERT: H 39 GLU cc_start: 0.8549 (OUTLIER) cc_final: 0.8003 (mm-30) REVERT: E 80 ASP cc_start: 0.7693 (m-30) cc_final: 0.7165 (m-30) REVERT: E 211 LEU cc_start: 0.8770 (OUTLIER) cc_final: 0.8331 (mp) REVERT: E 281 LEU cc_start: 0.8848 (OUTLIER) cc_final: 0.8616 (mm) REVERT: G 213 HIS cc_start: 0.8652 (OUTLIER) cc_final: 0.7325 (m-70) REVERT: J 103 GLN cc_start: 0.6826 (pm20) cc_final: 0.6270 (pp30) REVERT: J 185 PHE cc_start: 0.6804 (m-10) cc_final: 0.6359 (m-80) REVERT: K 51 THR cc_start: 0.6520 (OUTLIER) cc_final: 0.6214 (t) REVERT: K 100 ASP cc_start: 0.7646 (m-30) cc_final: 0.7246 (m-30) outliers start: 32 outliers final: 20 residues processed: 237 average time/residue: 0.2766 time to fit residues: 95.4247 Evaluate side-chains 235 residues out of total 1475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 209 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 199 HIS Chi-restraints excluded: chain B residue 213 HIS Chi-restraints excluded: chain C residue 20 GLN Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 49 MET Chi-restraints excluded: chain C residue 55 GLU Chi-restraints excluded: chain D residue 213 HIS Chi-restraints excluded: chain D residue 229 MET Chi-restraints excluded: chain D residue 248 VAL Chi-restraints excluded: chain H residue 39 GLU Chi-restraints excluded: chain E residue 23 ASN Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain E residue 211 LEU Chi-restraints excluded: chain E residue 213 HIS Chi-restraints excluded: chain E residue 281 LEU Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 130 ILE Chi-restraints excluded: chain F residue 241 CYS Chi-restraints excluded: chain G residue 132 GLU Chi-restraints excluded: chain G residue 152 TYR Chi-restraints excluded: chain G residue 213 HIS Chi-restraints excluded: chain J residue 42 ASN Chi-restraints excluded: chain J residue 201 THR Chi-restraints excluded: chain K residue 51 THR Chi-restraints excluded: chain K residue 143 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 89 optimal weight: 0.8980 chunk 36 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 159 optimal weight: 6.9990 chunk 166 optimal weight: 8.9990 chunk 62 optimal weight: 0.6980 chunk 131 optimal weight: 1.9990 chunk 15 optimal weight: 0.4980 chunk 50 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 151 optimal weight: 7.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 239 HIS J 124 GLN ** J 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 141 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.147457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.112182 restraints weight = 92311.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.113808 restraints weight = 72507.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.114863 restraints weight = 52432.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.117741 restraints weight = 28898.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.117964 restraints weight = 21934.595| |-----------------------------------------------------------------------------| r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3468 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3468 r_free = 0.3468 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3468 r_free = 0.3468 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3468 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.2072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 14089 Z= 0.135 Angle : 0.459 6.129 18928 Z= 0.258 Chirality : 0.033 0.134 2094 Planarity : 0.003 0.033 2450 Dihedral : 3.383 17.433 1877 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.43 % Favored : 97.51 % Rotamer: Outliers : 2.29 % Allowed : 17.99 % Favored : 79.72 % 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: 3.24 (0.20), residues: 1737 helix: 3.10 (0.13), residues: 1293 sheet: -0.48 (0.50), residues: 120 loop : -1.05 (0.33), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 116 TYR 0.008 0.001 TYR G 259 PHE 0.013 0.001 PHE G 232 TRP 0.007 0.001 TRP G 275 HIS 0.004 0.001 HIS E 213 Details of bonding type rmsd covalent geometry : bond 0.00274 (14089) covalent geometry : angle 0.45938 (18928) hydrogen bonds : bond 0.06381 ( 1048) hydrogen bonds : angle 3.77416 ( 3110) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 207 time to evaluate : 0.817 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 199 HIS cc_start: 0.7291 (OUTLIER) cc_final: 0.6741 (t70) REVERT: C 20 GLN cc_start: 0.7760 (OUTLIER) cc_final: 0.7401 (mt0) REVERT: H 39 GLU cc_start: 0.8524 (OUTLIER) cc_final: 0.7954 (mm-30) REVERT: E 211 LEU cc_start: 0.8874 (OUTLIER) cc_final: 0.8441 (mp) REVERT: E 281 LEU cc_start: 0.8888 (OUTLIER) cc_final: 0.8660 (mm) REVERT: J 103 GLN cc_start: 0.6900 (pm20) cc_final: 0.6318 (pp30) REVERT: J 185 PHE cc_start: 0.6750 (m-10) cc_final: 0.6349 (m-80) REVERT: K 51 THR cc_start: 0.6411 (OUTLIER) cc_final: 0.6101 (t) REVERT: K 100 ASP cc_start: 0.7639 (m-30) cc_final: 0.7255 (m-30) outliers start: 33 outliers final: 23 residues processed: 227 average time/residue: 0.2645 time to fit residues: 88.0820 Evaluate side-chains 233 residues out of total 1475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 204 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 199 HIS Chi-restraints excluded: chain B residue 213 HIS Chi-restraints excluded: chain C residue 20 GLN Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 49 MET Chi-restraints excluded: chain C residue 55 GLU Chi-restraints excluded: chain D residue 213 HIS Chi-restraints excluded: chain D residue 229 MET Chi-restraints excluded: chain H residue 39 GLU Chi-restraints excluded: chain E residue 23 ASN Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain E residue 211 LEU Chi-restraints excluded: chain E residue 213 HIS Chi-restraints excluded: chain E residue 281 LEU Chi-restraints excluded: chain E residue 286 THR Chi-restraints excluded: chain F residue 9 GLU Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 130 ILE Chi-restraints excluded: chain F residue 182 ILE Chi-restraints excluded: chain F residue 241 CYS Chi-restraints excluded: chain G residue 132 GLU Chi-restraints excluded: chain G residue 152 TYR Chi-restraints excluded: chain G residue 213 HIS Chi-restraints excluded: chain J residue 42 ASN Chi-restraints excluded: chain J residue 96 THR Chi-restraints excluded: chain J residue 113 ASP Chi-restraints excluded: chain J residue 201 THR Chi-restraints excluded: chain K residue 51 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 145 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 15 optimal weight: 0.9980 chunk 91 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 103 optimal weight: 0.7980 chunk 80 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 153 optimal weight: 5.9990 chunk 39 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 239 HIS ** J 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 141 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.144573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.109104 restraints weight = 99532.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.112284 restraints weight = 85164.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.113805 restraints weight = 42327.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.114789 restraints weight = 27569.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.117523 restraints weight = 23292.386| |-----------------------------------------------------------------------------| r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3448 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3448 r_free = 0.3448 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3448 r_free = 0.3448 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3448 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.2107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 14089 Z= 0.164 Angle : 0.476 5.054 18928 Z= 0.271 Chirality : 0.034 0.134 2094 Planarity : 0.003 0.037 2450 Dihedral : 3.436 17.735 1877 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.55 % Favored : 97.40 % Rotamer: Outliers : 2.22 % Allowed : 17.86 % Favored : 79.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.10 (0.20), residues: 1737 helix: 3.00 (0.13), residues: 1293 sheet: -0.74 (0.50), residues: 110 loop : -1.00 (0.33), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG K 38 TYR 0.009 0.001 TYR G 259 PHE 0.012 0.001 PHE G 232 TRP 0.007 0.001 TRP G 275 HIS 0.004 0.001 HIS B 213 Details of bonding type rmsd covalent geometry : bond 0.00353 (14089) covalent geometry : angle 0.47641 (18928) hydrogen bonds : bond 0.06850 ( 1048) hydrogen bonds : angle 3.90413 ( 3110) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 208 time to evaluate : 0.784 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 199 HIS cc_start: 0.7409 (OUTLIER) cc_final: 0.6819 (t70) REVERT: C 66 GLN cc_start: 0.8429 (tm-30) cc_final: 0.8003 (tm-30) REVERT: H 39 GLU cc_start: 0.8576 (OUTLIER) cc_final: 0.7999 (mm-30) REVERT: E 84 CYS cc_start: 0.8401 (m) cc_final: 0.8197 (m) REVERT: E 211 LEU cc_start: 0.8823 (OUTLIER) cc_final: 0.8436 (mp) REVERT: E 281 LEU cc_start: 0.8827 (OUTLIER) cc_final: 0.8601 (mm) REVERT: J 103 GLN cc_start: 0.6913 (pm20) cc_final: 0.6348 (pp30) REVERT: J 185 PHE cc_start: 0.6785 (m-10) cc_final: 0.6317 (m-80) REVERT: K 51 THR cc_start: 0.6528 (OUTLIER) cc_final: 0.6238 (t) REVERT: K 143 LYS cc_start: 0.5474 (OUTLIER) cc_final: 0.4882 (tptt) REVERT: K 150 LYS cc_start: 0.6284 (mtmm) cc_final: 0.5265 (tmmt) outliers start: 32 outliers final: 24 residues processed: 227 average time/residue: 0.2653 time to fit residues: 88.9340 Evaluate side-chains 233 residues out of total 1475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 203 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 199 HIS Chi-restraints excluded: chain B residue 213 HIS Chi-restraints excluded: chain C residue 20 GLN Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 49 MET Chi-restraints excluded: chain C residue 55 GLU Chi-restraints excluded: chain D residue 213 HIS Chi-restraints excluded: chain D residue 229 MET Chi-restraints excluded: chain D residue 248 VAL Chi-restraints excluded: chain H residue 39 GLU Chi-restraints excluded: chain E residue 23 ASN Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain E residue 211 LEU Chi-restraints excluded: chain E residue 213 HIS Chi-restraints excluded: chain E residue 281 LEU Chi-restraints excluded: chain E residue 286 THR Chi-restraints excluded: chain F residue 51 MET Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 130 ILE Chi-restraints excluded: chain F residue 182 ILE Chi-restraints excluded: chain F residue 241 CYS Chi-restraints excluded: chain G residue 132 GLU Chi-restraints excluded: chain G residue 152 TYR Chi-restraints excluded: chain G residue 213 HIS Chi-restraints excluded: chain J residue 42 ASN Chi-restraints excluded: chain J residue 113 ASP Chi-restraints excluded: chain J residue 201 THR Chi-restraints excluded: chain K residue 51 THR Chi-restraints excluded: chain K residue 143 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 67 optimal weight: 1.9990 chunk 6 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 135 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 120 optimal weight: 1.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 199 HIS ** J 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 141 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.143132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.101523 restraints weight = 110590.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.101950 restraints weight = 46991.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.103394 restraints weight = 38410.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.103990 restraints weight = 29887.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.104227 restraints weight = 27270.143| |-----------------------------------------------------------------------------| r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3283 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3283 r_free = 0.3283 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3283 r_free = 0.3283 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3283 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.2226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 14089 Z= 0.195 Angle : 0.505 5.233 18928 Z= 0.289 Chirality : 0.034 0.128 2094 Planarity : 0.003 0.033 2450 Dihedral : 3.541 18.145 1877 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.60 % Favored : 97.34 % Rotamer: Outliers : 2.29 % Allowed : 17.72 % Favored : 79.99 % 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: 2.85 (0.20), residues: 1737 helix: 2.82 (0.13), residues: 1293 sheet: -0.86 (0.50), residues: 110 loop : -1.07 (0.32), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 116 TYR 0.011 0.001 TYR G 259 PHE 0.013 0.001 PHE F 232 TRP 0.007 0.001 TRP G 275 HIS 0.005 0.001 HIS B 213 Details of bonding type rmsd covalent geometry : bond 0.00428 (14089) covalent geometry : angle 0.50492 (18928) hydrogen bonds : bond 0.07481 ( 1048) hydrogen bonds : angle 4.08763 ( 3110) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 207 time to evaluate : 0.805 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 66 GLN cc_start: 0.8407 (tm-30) cc_final: 0.7961 (tm-30) REVERT: D 246 ARG cc_start: 0.8146 (ttm-80) cc_final: 0.7891 (ttp80) REVERT: H 39 GLU cc_start: 0.8503 (OUTLIER) cc_final: 0.8046 (mm-30) REVERT: E 84 CYS cc_start: 0.8509 (m) cc_final: 0.8250 (m) REVERT: E 211 LEU cc_start: 0.8896 (OUTLIER) cc_final: 0.8567 (mp) REVERT: E 281 LEU cc_start: 0.8926 (OUTLIER) cc_final: 0.8690 (mm) REVERT: G 84 CYS cc_start: 0.8651 (m) cc_final: 0.8380 (m) REVERT: J 103 GLN cc_start: 0.6890 (pm20) cc_final: 0.6196 (pp30) REVERT: J 185 PHE cc_start: 0.6693 (m-10) cc_final: 0.6067 (m-80) REVERT: K 51 THR cc_start: 0.6715 (OUTLIER) cc_final: 0.6514 (t) REVERT: K 143 LYS cc_start: 0.5550 (OUTLIER) cc_final: 0.5058 (tptt) REVERT: K 150 LYS cc_start: 0.6582 (mtmm) cc_final: 0.5549 (tmmt) outliers start: 33 outliers final: 22 residues processed: 228 average time/residue: 0.2891 time to fit residues: 95.4676 Evaluate side-chains 234 residues out of total 1475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 207 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 213 HIS Chi-restraints excluded: chain C residue 20 GLN Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 49 MET Chi-restraints excluded: chain C residue 55 GLU Chi-restraints excluded: chain D residue 213 HIS Chi-restraints excluded: chain D residue 229 MET Chi-restraints excluded: chain D residue 248 VAL Chi-restraints excluded: chain H residue 39 GLU Chi-restraints excluded: chain E residue 108 ILE Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain E residue 211 LEU Chi-restraints excluded: chain E residue 213 HIS Chi-restraints excluded: chain E residue 281 LEU Chi-restraints excluded: chain E residue 286 THR Chi-restraints excluded: chain F residue 51 MET Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 130 ILE Chi-restraints excluded: chain F residue 241 CYS Chi-restraints excluded: chain G residue 152 TYR Chi-restraints excluded: chain G residue 213 HIS Chi-restraints excluded: chain J residue 30 GLN Chi-restraints excluded: chain J residue 113 ASP Chi-restraints excluded: chain J residue 201 THR Chi-restraints excluded: chain K residue 51 THR Chi-restraints excluded: chain K residue 143 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 81 optimal weight: 6.9990 chunk 53 optimal weight: 4.9990 chunk 145 optimal weight: 0.9980 chunk 92 optimal weight: 0.8980 chunk 110 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 157 optimal weight: 7.9990 chunk 123 optimal weight: 1.9990 chunk 159 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.144018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.099686 restraints weight = 100791.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.102448 restraints weight = 45146.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.104052 restraints weight = 29269.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.104895 restraints weight = 27489.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.104568 restraints weight = 23789.309| |-----------------------------------------------------------------------------| r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3298 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3298 r_free = 0.3298 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3298 r_free = 0.3298 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3298 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.2258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 14089 Z= 0.166 Angle : 0.486 5.129 18928 Z= 0.276 Chirality : 0.034 0.140 2094 Planarity : 0.003 0.056 2450 Dihedral : 3.533 18.088 1877 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.55 % Favored : 97.40 % Rotamer: Outliers : 2.02 % Allowed : 17.65 % Favored : 80.32 % 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: 2.93 (0.20), residues: 1737 helix: 2.88 (0.13), residues: 1293 sheet: -0.83 (0.50), residues: 110 loop : -1.06 (0.32), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG F 19 TYR 0.009 0.001 TYR G 259 PHE 0.012 0.001 PHE G 232 TRP 0.008 0.001 TRP G 275 HIS 0.005 0.001 HIS B 213 Details of bonding type rmsd covalent geometry : bond 0.00354 (14089) covalent geometry : angle 0.48633 (18928) hydrogen bonds : bond 0.07078 ( 1048) hydrogen bonds : angle 3.97143 ( 3110) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 208 time to evaluate : 0.774 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 217 MET cc_start: 0.4992 (mmp) cc_final: 0.4633 (mmp) REVERT: C 66 GLN cc_start: 0.8400 (tm-30) cc_final: 0.7938 (tm-30) REVERT: H 39 GLU cc_start: 0.8548 (OUTLIER) cc_final: 0.8019 (mm-30) REVERT: E 84 CYS cc_start: 0.8466 (m) cc_final: 0.8226 (m) REVERT: E 211 LEU cc_start: 0.8877 (OUTLIER) cc_final: 0.8561 (mp) REVERT: E 281 LEU cc_start: 0.8964 (OUTLIER) cc_final: 0.8739 (mm) REVERT: G 84 CYS cc_start: 0.8629 (m) cc_final: 0.8363 (m) REVERT: J 103 GLN cc_start: 0.6946 (pm20) cc_final: 0.6268 (pp30) REVERT: J 185 PHE cc_start: 0.6746 (m-10) cc_final: 0.6132 (m-80) REVERT: K 51 THR cc_start: 0.6669 (OUTLIER) cc_final: 0.6458 (t) REVERT: K 143 LYS cc_start: 0.5580 (OUTLIER) cc_final: 0.5029 (tptt) REVERT: K 150 LYS cc_start: 0.6468 (mtmm) cc_final: 0.5663 (tmmt) outliers start: 29 outliers final: 21 residues processed: 227 average time/residue: 0.2784 time to fit residues: 92.4263 Evaluate side-chains 231 residues out of total 1475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 205 time to evaluate : 0.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 213 HIS Chi-restraints excluded: chain C residue 20 GLN Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 49 MET Chi-restraints excluded: chain C residue 55 GLU Chi-restraints excluded: chain D residue 213 HIS Chi-restraints excluded: chain D residue 229 MET Chi-restraints excluded: chain D residue 248 VAL Chi-restraints excluded: chain H residue 39 GLU Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain E residue 211 LEU Chi-restraints excluded: chain E residue 213 HIS Chi-restraints excluded: chain E residue 281 LEU Chi-restraints excluded: chain E residue 286 THR Chi-restraints excluded: chain F residue 51 MET Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 130 ILE Chi-restraints excluded: chain F residue 241 CYS Chi-restraints excluded: chain G residue 152 TYR Chi-restraints excluded: chain G residue 213 HIS Chi-restraints excluded: chain J residue 42 ASN Chi-restraints excluded: chain J residue 113 ASP Chi-restraints excluded: chain J residue 201 THR Chi-restraints excluded: chain K residue 51 THR Chi-restraints excluded: chain K residue 143 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 76 optimal weight: 0.9980 chunk 75 optimal weight: 0.5980 chunk 54 optimal weight: 1.9990 chunk 119 optimal weight: 1.9990 chunk 144 optimal weight: 4.9990 chunk 150 optimal weight: 0.3980 chunk 162 optimal weight: 20.0000 chunk 89 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 113 optimal weight: 0.6980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 141 ASN ** K 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.146049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.110723 restraints weight = 95013.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.111829 restraints weight = 78734.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.113178 restraints weight = 54300.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.115881 restraints weight = 30913.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.116353 restraints weight = 23256.936| |-----------------------------------------------------------------------------| r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3454 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3454 r_free = 0.3454 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3454 r_free = 0.3454 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3454 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.2378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 14089 Z= 0.131 Angle : 0.463 5.190 18928 Z= 0.259 Chirality : 0.033 0.142 2094 Planarity : 0.003 0.057 2450 Dihedral : 3.461 17.687 1877 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.31 % Favored : 97.63 % Rotamer: Outliers : 1.82 % Allowed : 18.13 % Favored : 80.05 % 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: 3.20 (0.20), residues: 1737 helix: 3.09 (0.14), residues: 1293 sheet: -0.84 (0.51), residues: 110 loop : -0.96 (0.33), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 246 TYR 0.009 0.001 TYR E 259 PHE 0.012 0.001 PHE G 232 TRP 0.011 0.001 TRP G 275 HIS 0.005 0.001 HIS B 213 Details of bonding type rmsd covalent geometry : bond 0.00262 (14089) covalent geometry : angle 0.46303 (18928) hydrogen bonds : bond 0.06375 ( 1048) hydrogen bonds : angle 3.74642 ( 3110) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4609.28 seconds wall clock time: 79 minutes 15.90 seconds (4755.90 seconds total)