Starting phenix.real_space_refine on Fri Feb 6 21:25:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9svy_55291/02_2026/9svy_55291.cif Found real_map, /net/cci-nas-00/data/ceres_data/9svy_55291/02_2026/9svy_55291.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9svy_55291/02_2026/9svy_55291.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9svy_55291/02_2026/9svy_55291.map" model { file = "/net/cci-nas-00/data/ceres_data/9svy_55291/02_2026/9svy_55291.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9svy_55291/02_2026/9svy_55291.cif" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Ca 7 9.91 5 P 79 5.49 5 Mg 10 5.21 5 S 149 5.16 5 C 17159 2.51 5 N 4869 2.21 5 O 5431 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.05s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 27704 Number of models: 1 Model: "" Number of chains: 24 Chain: "B" Number of atoms: 2334 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2334 Classifications: {'peptide': 311} Link IDs: {'PTRANS': 7, 'TRANS': 303} Chain: "M" Number of atoms: 581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 581 Classifications: {'DNA': 29} Link IDs: {'rna3p': 28} Chain: "N" Number of atoms: 432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 432 Classifications: {'DNA': 21} Link IDs: {'rna3p': 20} Chain: "C" Number of atoms: 2532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2532 Classifications: {'peptide': 322} Link IDs: {'PTRANS': 11, 'TRANS': 310} Chain breaks: 1 Chain: "D" Number of atoms: 2586 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2586 Classifications: {'peptide': 336} Link IDs: {'PTRANS': 21, 'TRANS': 314} Chain breaks: 1 Chain: "A" Number of atoms: 1930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1930 Classifications: {'peptide': 239} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 232} Chain breaks: 1 Chain: "E" Number of atoms: 2435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2435 Classifications: {'peptide': 319} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 10, 'TRANS': 307} Chain: "F" Number of atoms: 2435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2435 Classifications: {'peptide': 319} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 10, 'TRANS': 307} Chain: "G" Number of atoms: 2435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2435 Classifications: {'peptide': 319} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 10, 'TRANS': 307} Chain: "H" Number of atoms: 2435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2435 Classifications: {'peptide': 319} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 10, 'TRANS': 307} Chain: "I" Number of atoms: 2435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2435 Classifications: {'peptide': 319} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 10, 'TRANS': 307} Chain: "J" Number of atoms: 2435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2435 Classifications: {'peptide': 319} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 10, 'TRANS': 307} Chain: "K" Number of atoms: 2376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2376 Classifications: {'peptide': 310} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 10, 'TRANS': 298} Chain breaks: 1 Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' CA': 1, ' MG': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' CA': 1, ' MG': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' CA': 1, ' MG': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "H" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' CA': 1, ' MG': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "I" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' CA': 1, ' MG': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "J" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' CA': 1, ' MG': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.69, per 1000 atoms: 0.24 Number of scatterers: 27704 At special positions: 0 Unit cell: (117.8, 131.1, 247.95, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Ca 7 19.99 S 149 16.00 P 79 15.00 Mg 10 11.99 O 5431 8.00 N 4869 7.00 C 17159 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.55 Conformation dependent library (CDL) restraints added in 1.2 seconds 6804 Ramachandran restraints generated. 3402 Oldfield, 0 Emsley, 3402 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6312 Finding SS restraints... Secondary structure from input PDB file: 177 helices and 30 sheets defined 51.6% alpha, 16.4% beta 20 base pairs and 27 stacking pairs defined. Time for finding SS restraints: 3.63 Creating SS restraints... Processing helix chain 'B' and resid 13 through 20 removed outlier: 3.528A pdb=" N ILE B 17 " --> pdb=" O THR B 13 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N GLN B 18 " --> pdb=" O GLU B 14 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 23 No H-bonds generated for 'chain 'B' and resid 21 through 23' Processing helix chain 'B' and resid 28 through 33 Processing helix chain 'B' and resid 38 through 43 Processing helix chain 'B' and resid 46 through 61 removed outlier: 3.508A pdb=" N ALA B 52 " --> pdb=" O LYS B 48 " (cutoff:3.500A) Processing helix chain 'B' and resid 68 through 79 removed outlier: 3.560A pdb=" N THR B 77 " --> pdb=" O GLU B 73 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N THR B 79 " --> pdb=" O LEU B 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 93 Processing helix chain 'B' and resid 112 through 128 removed outlier: 3.577A pdb=" N LEU B 128 " --> pdb=" O VAL B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 154 removed outlier: 3.754A pdb=" N LEU B 146 " --> pdb=" O THR B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 165 Processing helix chain 'B' and resid 174 through 192 Processing helix chain 'B' and resid 208 through 213 Processing helix chain 'B' and resid 221 through 240 Processing helix chain 'B' and resid 264 through 270 removed outlier: 4.056A pdb=" N TRP B 268 " --> pdb=" O LEU B 264 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N PHE B 270 " --> pdb=" O ARG B 266 " (cutoff:3.500A) Processing helix chain 'C' and resid 13 through 17 Processing helix chain 'C' and resid 20 through 31 Processing helix chain 'C' and resid 35 through 41 removed outlier: 3.649A pdb=" N GLU C 40 " --> pdb=" O GLU C 37 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL C 41 " --> pdb=" O LEU C 38 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 51 Processing helix chain 'C' and resid 53 through 67 removed outlier: 3.630A pdb=" N GLU C 67 " --> pdb=" O ILE C 63 " (cutoff:3.500A) Processing helix chain 'C' and resid 86 through 97 Processing helix chain 'C' and resid 104 through 111 Processing helix chain 'C' and resid 130 through 142 Processing helix chain 'C' and resid 143 through 144 No H-bonds generated for 'chain 'C' and resid 143 through 144' Processing helix chain 'C' and resid 145 through 149 Processing helix chain 'C' and resid 165 through 188 removed outlier: 3.505A pdb=" N VAL C 169 " --> pdb=" O MET C 165 " (cutoff:3.500A) Processing helix chain 'C' and resid 190 through 198 removed outlier: 3.638A pdb=" N LYS C 194 " --> pdb=" O GLU C 190 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ASP C 198 " --> pdb=" O LYS C 194 " (cutoff:3.500A) Processing helix chain 'C' and resid 200 through 206 Processing helix chain 'C' and resid 215 through 233 Proline residue: C 227 - end of helix Processing helix chain 'C' and resid 245 through 249 removed outlier: 3.512A pdb=" N ARG C 249 " --> pdb=" O PHE C 246 " (cutoff:3.500A) Processing helix chain 'C' and resid 254 through 276 Processing helix chain 'C' and resid 303 through 308 Processing helix chain 'D' and resid 2 through 6 Processing helix chain 'D' and resid 9 through 19 Processing helix chain 'D' and resid 23 through 30 removed outlier: 3.729A pdb=" N PHE D 30 " --> pdb=" O GLU D 26 " (cutoff:3.500A) Processing helix chain 'D' and resid 31 through 40 Processing helix chain 'D' and resid 42 through 59 Processing helix chain 'D' and resid 65 through 71 Processing helix chain 'D' and resid 86 through 94 Processing helix chain 'D' and resid 112 through 124 Processing helix chain 'D' and resid 125 through 126 No H-bonds generated for 'chain 'D' and resid 125 through 126' Processing helix chain 'D' and resid 127 through 131 Processing helix chain 'D' and resid 147 through 162 Proline residue: D 159 - end of helix Processing helix chain 'D' and resid 166 through 171 removed outlier: 3.895A pdb=" N LEU D 170 " --> pdb=" O PRO D 166 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N GLN D 171 " --> pdb=" O GLY D 167 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 166 through 171' Processing helix chain 'D' and resid 175 through 177 No H-bonds generated for 'chain 'D' and resid 175 through 177' Processing helix chain 'D' and resid 186 through 197 Processing helix chain 'D' and resid 197 through 204 removed outlier: 3.666A pdb=" N ARG D 204 " --> pdb=" O VAL D 200 " (cutoff:3.500A) Processing helix chain 'D' and resid 215 through 223 removed outlier: 4.070A pdb=" N PHE D 219 " --> pdb=" O VAL D 215 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N CYS D 221 " --> pdb=" O ALA D 217 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N GLU D 222 " --> pdb=" O PRO D 218 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N PHE D 223 " --> pdb=" O PHE D 219 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 250 removed outlier: 3.629A pdb=" N ARG D 231 " --> pdb=" O ALA D 227 " (cutoff:3.500A) Processing helix chain 'D' and resid 285 through 290 Processing helix chain 'A' and resid 23 through 28 removed outlier: 3.687A pdb=" N ILE A 27 " --> pdb=" O SER A 23 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLU A 28 " --> pdb=" O LEU A 24 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 23 through 28' Processing helix chain 'A' and resid 53 through 67 removed outlier: 3.666A pdb=" N LEU A 67 " --> pdb=" O ALA A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 72 Processing helix chain 'A' and resid 88 through 100 removed outlier: 3.508A pdb=" N LEU A 92 " --> pdb=" O ASP A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 113 Processing helix chain 'A' and resid 122 through 133 Processing helix chain 'A' and resid 133 through 140 Processing helix chain 'A' and resid 154 through 162 removed outlier: 3.552A pdb=" N GLY A 162 " --> pdb=" O ASP A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 187 Processing helix chain 'A' and resid 228 through 235 Processing helix chain 'E' and resid 26 through 32 removed outlier: 4.092A pdb=" N GLN E 30 " --> pdb=" O SER E 26 " (cutoff:3.500A) Processing helix chain 'E' and resid 34 through 44 removed outlier: 3.783A pdb=" N VAL E 38 " --> pdb=" O ASN E 34 " (cutoff:3.500A) Processing helix chain 'E' and resid 48 through 55 Processing helix chain 'E' and resid 56 through 62 removed outlier: 3.774A pdb=" N LEU E 60 " --> pdb=" O PRO E 56 " (cutoff:3.500A) Processing helix chain 'E' and resid 67 through 79 Processing helix chain 'E' and resid 89 through 94 Processing helix chain 'E' and resid 95 through 99 removed outlier: 4.094A pdb=" N GLU E 98 " --> pdb=" O ARG E 95 " (cutoff:3.500A) Processing helix chain 'E' and resid 106 through 114 Processing helix chain 'E' and resid 132 through 144 removed outlier: 3.574A pdb=" N VAL E 142 " --> pdb=" O HIS E 138 " (cutoff:3.500A) Processing helix chain 'E' and resid 167 through 178 removed outlier: 3.773A pdb=" N LEU E 171 " --> pdb=" O ARG E 167 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ARG E 177 " --> pdb=" O ALA E 173 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N TYR E 178 " --> pdb=" O VAL E 174 " (cutoff:3.500A) Processing helix chain 'E' and resid 181 through 188 Processing helix chain 'E' and resid 196 through 214 removed outlier: 4.122A pdb=" N LEU E 204 " --> pdb=" O GLN E 200 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N TYR E 205 " --> pdb=" O THR E 201 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N GLN E 206 " --> pdb=" O GLN E 202 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLU E 213 " --> pdb=" O ALA E 209 " (cutoff:3.500A) Processing helix chain 'E' and resid 227 through 232 removed outlier: 3.857A pdb=" N TYR E 232 " --> pdb=" O TYR E 228 " (cutoff:3.500A) Processing helix chain 'E' and resid 234 through 236 No H-bonds generated for 'chain 'E' and resid 234 through 236' Processing helix chain 'E' and resid 237 through 260 Processing helix chain 'E' and resid 288 through 296 removed outlier: 4.022A pdb=" N ILE E 292 " --> pdb=" O GLY E 288 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 32 Processing helix chain 'F' and resid 34 through 45 Processing helix chain 'F' and resid 48 through 54 Processing helix chain 'F' and resid 56 through 62 removed outlier: 3.633A pdb=" N LEU F 60 " --> pdb=" O PRO F 56 " (cutoff:3.500A) Processing helix chain 'F' and resid 67 through 82 Processing helix chain 'F' and resid 89 through 97 Processing helix chain 'F' and resid 106 through 114 Processing helix chain 'F' and resid 132 through 144 Processing helix chain 'F' and resid 145 through 146 No H-bonds generated for 'chain 'F' and resid 145 through 146' Processing helix chain 'F' and resid 147 through 151 Processing helix chain 'F' and resid 167 through 178 removed outlier: 3.987A pdb=" N LEU F 171 " --> pdb=" O ARG F 167 " (cutoff:3.500A) Processing helix chain 'F' and resid 181 through 188 Processing helix chain 'F' and resid 196 through 214 removed outlier: 4.034A pdb=" N LEU F 204 " --> pdb=" O GLN F 200 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N TYR F 205 " --> pdb=" O THR F 201 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N GLN F 206 " --> pdb=" O GLN F 202 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N VAL F 212 " --> pdb=" O SER F 208 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N GLU F 213 " --> pdb=" O ALA F 209 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N SER F 214 " --> pdb=" O MET F 210 " (cutoff:3.500A) Processing helix chain 'F' and resid 227 through 232 removed outlier: 3.687A pdb=" N TYR F 232 " --> pdb=" O TYR F 228 " (cutoff:3.500A) Processing helix chain 'F' and resid 234 through 236 No H-bonds generated for 'chain 'F' and resid 234 through 236' Processing helix chain 'F' and resid 237 through 260 Processing helix chain 'F' and resid 289 through 296 Processing helix chain 'G' and resid 26 through 32 removed outlier: 3.886A pdb=" N GLN G 30 " --> pdb=" O SER G 26 " (cutoff:3.500A) Processing helix chain 'G' and resid 34 through 45 Processing helix chain 'G' and resid 48 through 54 Processing helix chain 'G' and resid 56 through 62 removed outlier: 3.536A pdb=" N ASN G 62 " --> pdb=" O LYS G 58 " (cutoff:3.500A) Processing helix chain 'G' and resid 67 through 82 Processing helix chain 'G' and resid 89 through 97 Processing helix chain 'G' and resid 106 through 113 Processing helix chain 'G' and resid 132 through 144 Processing helix chain 'G' and resid 145 through 146 No H-bonds generated for 'chain 'G' and resid 145 through 146' Processing helix chain 'G' and resid 147 through 151 Processing helix chain 'G' and resid 167 through 179 removed outlier: 3.828A pdb=" N LEU G 171 " --> pdb=" O ARG G 167 " (cutoff:3.500A) Processing helix chain 'G' and resid 181 through 188 Processing helix chain 'G' and resid 196 through 214 removed outlier: 4.063A pdb=" N LEU G 204 " --> pdb=" O GLN G 200 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N TYR G 205 " --> pdb=" O THR G 201 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLN G 206 " --> pdb=" O GLN G 202 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N VAL G 212 " --> pdb=" O SER G 208 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N GLU G 213 " --> pdb=" O ALA G 209 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N SER G 214 " --> pdb=" O MET G 210 " (cutoff:3.500A) Processing helix chain 'G' and resid 227 through 232 removed outlier: 3.565A pdb=" N TYR G 232 " --> pdb=" O TYR G 228 " (cutoff:3.500A) Processing helix chain 'G' and resid 234 through 236 No H-bonds generated for 'chain 'G' and resid 234 through 236' Processing helix chain 'G' and resid 237 through 260 Processing helix chain 'G' and resid 288 through 296 removed outlier: 3.906A pdb=" N ILE G 292 " --> pdb=" O GLY G 288 " (cutoff:3.500A) Processing helix chain 'H' and resid 26 through 32 removed outlier: 3.918A pdb=" N GLN H 30 " --> pdb=" O SER H 26 " (cutoff:3.500A) Processing helix chain 'H' and resid 34 through 45 Processing helix chain 'H' and resid 48 through 54 Processing helix chain 'H' and resid 56 through 62 removed outlier: 3.548A pdb=" N ASN H 62 " --> pdb=" O LYS H 58 " (cutoff:3.500A) Processing helix chain 'H' and resid 67 through 82 removed outlier: 3.725A pdb=" N LYS H 80 " --> pdb=" O ALA H 76 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N LEU H 81 " --> pdb=" O GLU H 77 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N VAL H 82 " --> pdb=" O ALA H 78 " (cutoff:3.500A) Processing helix chain 'H' and resid 89 through 97 Processing helix chain 'H' and resid 106 through 114 Processing helix chain 'H' and resid 133 through 144 Processing helix chain 'H' and resid 145 through 146 No H-bonds generated for 'chain 'H' and resid 145 through 146' Processing helix chain 'H' and resid 147 through 151 Processing helix chain 'H' and resid 167 through 178 removed outlier: 3.819A pdb=" N LEU H 171 " --> pdb=" O ARG H 167 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ARG H 177 " --> pdb=" O ALA H 173 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N TYR H 178 " --> pdb=" O VAL H 174 " (cutoff:3.500A) Processing helix chain 'H' and resid 181 through 187 Processing helix chain 'H' and resid 196 through 211 removed outlier: 4.086A pdb=" N LEU H 204 " --> pdb=" O GLN H 200 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N TYR H 205 " --> pdb=" O THR H 201 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N GLN H 206 " --> pdb=" O GLN H 202 " (cutoff:3.500A) Processing helix chain 'H' and resid 227 through 232 removed outlier: 3.757A pdb=" N TYR H 232 " --> pdb=" O TYR H 228 " (cutoff:3.500A) Processing helix chain 'H' and resid 234 through 236 No H-bonds generated for 'chain 'H' and resid 234 through 236' Processing helix chain 'H' and resid 237 through 260 Processing helix chain 'H' and resid 288 through 296 removed outlier: 4.065A pdb=" N ILE H 292 " --> pdb=" O GLY H 288 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA H 293 " --> pdb=" O GLY H 289 " (cutoff:3.500A) Processing helix chain 'I' and resid 26 through 31 removed outlier: 3.777A pdb=" N GLN I 30 " --> pdb=" O SER I 26 " (cutoff:3.500A) Processing helix chain 'I' and resid 34 through 44 Processing helix chain 'I' and resid 48 through 55 Processing helix chain 'I' and resid 56 through 62 removed outlier: 3.654A pdb=" N LEU I 60 " --> pdb=" O PRO I 56 " (cutoff:3.500A) Processing helix chain 'I' and resid 67 through 82 Processing helix chain 'I' and resid 89 through 97 Processing helix chain 'I' and resid 106 through 114 Processing helix chain 'I' and resid 132 through 144 Processing helix chain 'I' and resid 145 through 146 No H-bonds generated for 'chain 'I' and resid 145 through 146' Processing helix chain 'I' and resid 147 through 151 Processing helix chain 'I' and resid 167 through 178 removed outlier: 3.816A pdb=" N LEU I 171 " --> pdb=" O ARG I 167 " (cutoff:3.500A) Processing helix chain 'I' and resid 181 through 188 Processing helix chain 'I' and resid 196 through 214 removed outlier: 4.064A pdb=" N LEU I 204 " --> pdb=" O GLN I 200 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N TYR I 205 " --> pdb=" O THR I 201 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N GLN I 206 " --> pdb=" O GLN I 202 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N VAL I 212 " --> pdb=" O SER I 208 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N GLU I 213 " --> pdb=" O ALA I 209 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N SER I 214 " --> pdb=" O MET I 210 " (cutoff:3.500A) Processing helix chain 'I' and resid 227 through 232 removed outlier: 3.852A pdb=" N TYR I 232 " --> pdb=" O TYR I 228 " (cutoff:3.500A) Processing helix chain 'I' and resid 234 through 236 No H-bonds generated for 'chain 'I' and resid 234 through 236' Processing helix chain 'I' and resid 237 through 260 Processing helix chain 'I' and resid 288 through 296 removed outlier: 4.208A pdb=" N ILE I 292 " --> pdb=" O GLY I 288 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA I 293 " --> pdb=" O GLY I 289 " (cutoff:3.500A) Processing helix chain 'J' and resid 24 through 32 removed outlier: 3.602A pdb=" N GLN J 30 " --> pdb=" O ARG J 27 " (cutoff:3.500A) Processing helix chain 'J' and resid 34 through 45 Processing helix chain 'J' and resid 48 through 54 removed outlier: 3.557A pdb=" N VAL J 52 " --> pdb=" O THR J 48 " (cutoff:3.500A) Processing helix chain 'J' and resid 56 through 62 removed outlier: 3.596A pdb=" N LEU J 60 " --> pdb=" O PRO J 56 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ASN J 62 " --> pdb=" O LYS J 58 " (cutoff:3.500A) Processing helix chain 'J' and resid 67 through 82 removed outlier: 3.627A pdb=" N LYS J 80 " --> pdb=" O ALA J 76 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N LEU J 81 " --> pdb=" O GLU J 77 " (cutoff:3.500A) Processing helix chain 'J' and resid 89 through 96 Processing helix chain 'J' and resid 97 through 99 No H-bonds generated for 'chain 'J' and resid 97 through 99' Processing helix chain 'J' and resid 106 through 113 Processing helix chain 'J' and resid 132 through 144 removed outlier: 3.566A pdb=" N VAL J 142 " --> pdb=" O HIS J 138 " (cutoff:3.500A) Processing helix chain 'J' and resid 145 through 146 No H-bonds generated for 'chain 'J' and resid 145 through 146' Processing helix chain 'J' and resid 147 through 151 Processing helix chain 'J' and resid 167 through 178 removed outlier: 3.903A pdb=" N LEU J 171 " --> pdb=" O ARG J 167 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ARG J 177 " --> pdb=" O ALA J 173 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N TYR J 178 " --> pdb=" O VAL J 174 " (cutoff:3.500A) Processing helix chain 'J' and resid 181 through 188 Processing helix chain 'J' and resid 196 through 214 removed outlier: 4.013A pdb=" N LEU J 204 " --> pdb=" O GLN J 200 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N TYR J 205 " --> pdb=" O THR J 201 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLN J 206 " --> pdb=" O GLN J 202 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ALA J 209 " --> pdb=" O TYR J 205 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N VAL J 212 " --> pdb=" O SER J 208 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N GLU J 213 " --> pdb=" O ALA J 209 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N SER J 214 " --> pdb=" O MET J 210 " (cutoff:3.500A) Processing helix chain 'J' and resid 227 through 232 removed outlier: 3.743A pdb=" N TYR J 232 " --> pdb=" O TYR J 228 " (cutoff:3.500A) Processing helix chain 'J' and resid 234 through 236 No H-bonds generated for 'chain 'J' and resid 234 through 236' Processing helix chain 'J' and resid 237 through 260 Processing helix chain 'J' and resid 289 through 296 removed outlier: 3.515A pdb=" N ALA J 293 " --> pdb=" O GLY J 289 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA J 295 " --> pdb=" O ILE J 291 " (cutoff:3.500A) Processing helix chain 'K' and resid 26 through 32 removed outlier: 4.333A pdb=" N GLN K 30 " --> pdb=" O SER K 26 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N CYS K 31 " --> pdb=" O ARG K 27 " (cutoff:3.500A) Processing helix chain 'K' and resid 34 through 45 Processing helix chain 'K' and resid 48 through 54 Processing helix chain 'K' and resid 56 through 63 removed outlier: 3.810A pdb=" N LEU K 60 " --> pdb=" O PRO K 56 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ASN K 62 " --> pdb=" O LYS K 58 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ILE K 63 " --> pdb=" O GLU K 59 " (cutoff:3.500A) Processing helix chain 'K' and resid 67 through 82 removed outlier: 3.699A pdb=" N LYS K 80 " --> pdb=" O ALA K 76 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LEU K 81 " --> pdb=" O GLU K 77 " (cutoff:3.500A) Processing helix chain 'K' and resid 89 through 97 Processing helix chain 'K' and resid 106 through 114 Processing helix chain 'K' and resid 132 through 144 removed outlier: 3.651A pdb=" N VAL K 142 " --> pdb=" O HIS K 138 " (cutoff:3.500A) Processing helix chain 'K' and resid 145 through 146 No H-bonds generated for 'chain 'K' and resid 145 through 146' Processing helix chain 'K' and resid 147 through 151 Processing helix chain 'K' and resid 167 through 178 removed outlier: 3.934A pdb=" N LEU K 171 " --> pdb=" O ARG K 167 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU K 172 " --> pdb=" O PRO K 168 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ARG K 177 " --> pdb=" O ALA K 173 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N TYR K 178 " --> pdb=" O VAL K 174 " (cutoff:3.500A) Processing helix chain 'K' and resid 181 through 188 Processing helix chain 'K' and resid 196 through 214 removed outlier: 4.000A pdb=" N LEU K 204 " --> pdb=" O GLN K 200 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N TYR K 205 " --> pdb=" O THR K 201 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLN K 206 " --> pdb=" O GLN K 202 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALA K 209 " --> pdb=" O TYR K 205 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N VAL K 212 " --> pdb=" O SER K 208 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N GLU K 213 " --> pdb=" O ALA K 209 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N SER K 214 " --> pdb=" O MET K 210 " (cutoff:3.500A) Processing helix chain 'K' and resid 227 through 232 removed outlier: 3.619A pdb=" N ASP K 231 " --> pdb=" O LEU K 227 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N TYR K 232 " --> pdb=" O TYR K 228 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 227 through 232' Processing helix chain 'K' and resid 237 through 260 Processing helix chain 'K' and resid 288 through 296 removed outlier: 4.163A pdb=" N ILE K 292 " --> pdb=" O GLY K 288 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ALA K 293 " --> pdb=" O GLY K 289 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 66 through 67 removed outlier: 3.507A pdb=" N LEU A 117 " --> pdb=" O VAL B 66 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N PHE A 116 " --> pdb=" O VAL A 78 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N GLU A 77 " --> pdb=" O LEU A 143 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N ASP A 42 " --> pdb=" O LEU A 191 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N ALA A 193 " --> pdb=" O ASP A 42 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N LEU A 44 " --> pdb=" O ALA A 193 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N ILE A 43 " --> pdb=" O HIS A 237 " (cutoff:3.500A) removed outlier: 8.440A pdb=" N MET A 239 " --> pdb=" O ILE A 43 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N GLU A 45 " --> pdb=" O MET A 239 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N PHE A 241 " --> pdb=" O GLU A 45 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N HIS A 47 " --> pdb=" O PHE A 241 " (cutoff:3.500A) removed outlier: 8.683A pdb=" N LYS A 243 " --> pdb=" O HIS A 47 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ARG A 238 " --> pdb=" O ARG A 258 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ARG A 258 " --> pdb=" O ARG A 238 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N PHE A 270 " --> pdb=" O PHE A 253 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 81 through 82 Processing sheet with id=AA3, first strand: chain 'B' and resid 167 through 171 removed outlier: 6.871A pdb=" N ASN B 131 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N VAL B 202 " --> pdb=" O ASN B 131 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N LYS B 201 " --> pdb=" O ALA B 244 " (cutoff:3.500A) removed outlier: 8.051A pdb=" N VAL B 246 " --> pdb=" O LYS B 201 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N VAL B 203 " --> pdb=" O VAL B 246 " (cutoff:3.500A) removed outlier: 8.548A pdb=" N THR B 248 " --> pdb=" O VAL B 203 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N VAL B 205 " --> pdb=" O THR B 248 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N THR B 103 " --> pdb=" O VAL B 247 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N ASN B 249 " --> pdb=" O THR B 103 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N ILE B 105 " --> pdb=" O ASN B 249 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N ARG B 275 " --> pdb=" O ALA B 296 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 251 through 253 Processing sheet with id=AA5, first strand: chain 'C' and resid 345 through 347 removed outlier: 3.504A pdb=" N GLN C 340 " --> pdb=" O ARG C 347 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ARG C 322 " --> pdb=" O PHE C 339 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ARG C 312 " --> pdb=" O TYR C 327 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N THR C 121 " --> pdb=" O LEU C 282 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ALA C 279 " --> pdb=" O ARG C 237 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR C 283 " --> pdb=" O VAL C 241 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N GLU C 154 " --> pdb=" O LEU C 238 " (cutoff:3.500A) removed outlier: 8.355A pdb=" N ILE C 240 " --> pdb=" O GLU C 154 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N VAL C 156 " --> pdb=" O ILE C 240 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N ASP C 242 " --> pdb=" O VAL C 156 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N ILE C 158 " --> pdb=" O ASP C 242 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N LEU D 63 " --> pdb=" O TYR C 210 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 286 through 291 Processing sheet with id=AA7, first strand: chain 'D' and resid 81 through 82 Processing sheet with id=AA8, first strand: chain 'D' and resid 337 through 339 removed outlier: 4.295A pdb=" N ARG D 313 " --> pdb=" O TYR D 330 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N ARG D 295 " --> pdb=" O LEU D 318 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ILE D 102 " --> pdb=" O VAL D 294 " (cutoff:3.500A) removed outlier: 7.954A pdb=" N LEU D 296 " --> pdb=" O ILE D 102 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N GLU D 104 " --> pdb=" O LEU D 296 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N ALA D 298 " --> pdb=" O GLU D 104 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N ALA D 106 " --> pdb=" O ALA D 298 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N ARG D 300 " --> pdb=" O ALA D 106 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N THR D 103 " --> pdb=" O CYS D 255 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N ASN D 257 " --> pdb=" O THR D 103 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N LEU D 105 " --> pdb=" O ASN D 257 " (cutoff:3.500A) removed outlier: 8.702A pdb=" N LEU D 254 " --> pdb=" O ARG D 208 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N VAL D 210 " --> pdb=" O LEU D 254 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N ILE D 256 " --> pdb=" O VAL D 210 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N ILE D 212 " --> pdb=" O ILE D 256 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N GLY D 136 " --> pdb=" O ALA D 207 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N LEU D 209 " --> pdb=" O GLY D 136 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N ALA D 137 " --> pdb=" O PHE D 180 " (cutoff:3.500A) removed outlier: 7.992A pdb=" N GLU D 182 " --> pdb=" O ALA D 137 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N TYR D 139 " --> pdb=" O GLU D 182 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N THR E 87 " --> pdb=" O ILE D 181 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 259 through 261 Processing sheet with id=AB1, first strand: chain 'E' and resid 101 through 102 Processing sheet with id=AB2, first strand: chain 'E' and resid 333 through 335 removed outlier: 6.431A pdb=" N ARG E 299 " --> pdb=" O TYR E 315 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ILE E 122 " --> pdb=" O THR E 298 " (cutoff:3.500A) removed outlier: 8.178A pdb=" N LEU E 300 " --> pdb=" O ILE E 122 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N GLU E 124 " --> pdb=" O LEU E 300 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N LEU E 302 " --> pdb=" O GLU E 124 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N PHE E 126 " --> pdb=" O LEU E 302 " (cutoff:3.500A) removed outlier: 9.012A pdb=" N LYS E 304 " --> pdb=" O PHE E 126 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N THR E 123 " --> pdb=" O ILE E 265 " (cutoff:3.500A) removed outlier: 7.818A pdb=" N ASN E 267 " --> pdb=" O THR E 123 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N MET E 125 " --> pdb=" O ASN E 267 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N ALA E 217 " --> pdb=" O ALA E 262 " (cutoff:3.500A) removed outlier: 8.105A pdb=" N VAL E 264 " --> pdb=" O ALA E 217 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N LEU E 219 " --> pdb=" O VAL E 264 " (cutoff:3.500A) removed outlier: 8.350A pdb=" N THR E 266 " --> pdb=" O LEU E 219 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N VAL E 221 " --> pdb=" O THR E 266 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N LYS E 156 " --> pdb=" O TYR E 216 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU E 218 " --> pdb=" O LYS E 156 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 269 through 271 Processing sheet with id=AB4, first strand: chain 'F' and resid 101 through 102 Processing sheet with id=AB5, first strand: chain 'F' and resid 333 through 335 removed outlier: 3.560A pdb=" N GLY F 333 " --> pdb=" O ASN F 330 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N ARG F 299 " --> pdb=" O TYR F 315 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N ILE F 122 " --> pdb=" O THR F 298 " (cutoff:3.500A) removed outlier: 8.311A pdb=" N LEU F 300 " --> pdb=" O ILE F 122 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N GLU F 124 " --> pdb=" O LEU F 300 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N LEU F 302 " --> pdb=" O GLU F 124 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N PHE F 126 " --> pdb=" O LEU F 302 " (cutoff:3.500A) removed outlier: 8.922A pdb=" N LYS F 304 " --> pdb=" O PHE F 126 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N LYS F 156 " --> pdb=" O LEU F 218 " (cutoff:3.500A) removed outlier: 8.277A pdb=" N ILE F 220 " --> pdb=" O LYS F 156 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N MET F 158 " --> pdb=" O ILE F 220 " (cutoff:3.500A) removed outlier: 7.759A pdb=" N ASP F 222 " --> pdb=" O MET F 158 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N ILE F 160 " --> pdb=" O ASP F 222 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 269 through 271 Processing sheet with id=AB7, first strand: chain 'G' and resid 101 through 102 Processing sheet with id=AB8, first strand: chain 'G' and resid 333 through 335 removed outlier: 3.688A pdb=" N GLY G 333 " --> pdb=" O ASN G 330 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N ARG G 299 " --> pdb=" O TYR G 315 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ILE G 122 " --> pdb=" O THR G 298 " (cutoff:3.500A) removed outlier: 8.291A pdb=" N LEU G 300 " --> pdb=" O ILE G 122 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N GLU G 124 " --> pdb=" O LEU G 300 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N LEU G 302 " --> pdb=" O GLU G 124 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N PHE G 126 " --> pdb=" O LEU G 302 " (cutoff:3.500A) removed outlier: 8.725A pdb=" N LYS G 304 " --> pdb=" O PHE G 126 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N THR G 123 " --> pdb=" O ILE G 265 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N LYS G 156 " --> pdb=" O LEU G 218 " (cutoff:3.500A) removed outlier: 8.501A pdb=" N ILE G 220 " --> pdb=" O LYS G 156 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N MET G 158 " --> pdb=" O ILE G 220 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N ASP G 222 " --> pdb=" O MET G 158 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ILE G 160 " --> pdb=" O ASP G 222 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 269 through 271 Processing sheet with id=AC1, first strand: chain 'H' and resid 101 through 102 Processing sheet with id=AC2, first strand: chain 'H' and resid 333 through 335 removed outlier: 6.298A pdb=" N ARG H 299 " --> pdb=" O TYR H 315 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N THR H 123 " --> pdb=" O ILE H 265 " (cutoff:3.500A) removed outlier: 5.628A pdb=" N LYS H 156 " --> pdb=" O TYR H 216 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LEU H 218 " --> pdb=" O LYS H 156 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'H' and resid 269 through 271 Processing sheet with id=AC4, first strand: chain 'I' and resid 101 through 102 Processing sheet with id=AC5, first strand: chain 'I' and resid 333 through 335 removed outlier: 3.525A pdb=" N ALA I 328 " --> pdb=" O GLY I 335 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N ARG I 299 " --> pdb=" O TYR I 315 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N ILE I 122 " --> pdb=" O THR I 298 " (cutoff:3.500A) removed outlier: 8.313A pdb=" N LEU I 300 " --> pdb=" O ILE I 122 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N GLU I 124 " --> pdb=" O LEU I 300 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N LEU I 302 " --> pdb=" O GLU I 124 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N PHE I 126 " --> pdb=" O LEU I 302 " (cutoff:3.500A) removed outlier: 8.742A pdb=" N LYS I 304 " --> pdb=" O PHE I 126 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N THR I 123 " --> pdb=" O ILE I 265 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N ASN I 267 " --> pdb=" O THR I 123 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N MET I 125 " --> pdb=" O ASN I 267 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N LYS I 156 " --> pdb=" O TYR I 216 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU I 218 " --> pdb=" O LYS I 156 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 269 through 271 Processing sheet with id=AC7, first strand: chain 'J' and resid 101 through 102 Processing sheet with id=AC8, first strand: chain 'J' and resid 333 through 335 removed outlier: 6.144A pdb=" N ARG J 299 " --> pdb=" O TYR J 315 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N THR J 298 " --> pdb=" O ILE J 122 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N THR J 123 " --> pdb=" O ILE J 265 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA J 262 " --> pdb=" O ALA J 217 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N LYS J 156 " --> pdb=" O TYR J 216 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU J 218 " --> pdb=" O LYS J 156 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'J' and resid 269 through 271 Processing sheet with id=AD1, first strand: chain 'K' and resid 101 through 102 Processing sheet with id=AD2, first strand: chain 'K' and resid 189 through 193 removed outlier: 5.671A pdb=" N LYS K 156 " --> pdb=" O TYR K 216 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N LEU K 218 " --> pdb=" O LYS K 156 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ALA K 262 " --> pdb=" O ALA K 217 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLY K 127 " --> pdb=" O ASN K 267 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ILE K 122 " --> pdb=" O THR K 298 " (cutoff:3.500A) removed outlier: 8.138A pdb=" N LEU K 300 " --> pdb=" O ILE K 122 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N GLU K 124 " --> pdb=" O LEU K 300 " (cutoff:3.500A) removed outlier: 7.873A pdb=" N LEU K 302 " --> pdb=" O GLU K 124 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N PHE K 126 " --> pdb=" O LEU K 302 " (cutoff:3.500A) removed outlier: 8.706A pdb=" N LYS K 304 " --> pdb=" O PHE K 126 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N TYR K 301 " --> pdb=" O ILE K 314 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N ILE K 314 " --> pdb=" O TYR K 301 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N ARG K 303 " --> pdb=" O CYS K 312 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N CYS K 312 " --> pdb=" O ARG K 303 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'K' and resid 269 through 271 1286 hydrogen bonds defined for protein. 3636 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 47 hydrogen bonds 94 hydrogen bond angles 0 basepair planarities 20 basepair parallelities 27 stacking parallelities Total time for adding SS restraints: 5.52 Time building geometry restraints manager: 3.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 8100 1.33 - 1.45: 4188 1.45 - 1.57: 15565 1.57 - 1.69: 146 1.69 - 1.81: 232 Bond restraints: 28231 Sorted by residual: bond pdb=" C GLY B 218 " pdb=" O GLY B 218 " ideal model delta sigma weight residual 1.236 1.244 -0.008 5.30e-03 3.56e+04 2.21e+00 bond pdb=" C GLU E 91 " pdb=" N PHE E 92 " ideal model delta sigma weight residual 1.331 1.314 0.017 1.38e-02 5.25e+03 1.53e+00 bond pdb=" C4 ADP C 401 " pdb=" C5 ADP C 401 " ideal model delta sigma weight residual 1.490 1.469 0.021 2.00e-02 2.50e+03 1.14e+00 bond pdb=" CA VAL H 82 " pdb=" C VAL H 82 " ideal model delta sigma weight residual 1.522 1.530 -0.007 7.10e-03 1.98e+04 1.08e+00 bond pdb=" C1' ATP D 401 " pdb=" O4' ATP D 401 " ideal model delta sigma weight residual 1.416 1.403 0.013 1.30e-02 5.92e+03 1.01e+00 ... (remaining 28226 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.09: 38079 2.09 - 4.18: 291 4.18 - 6.27: 34 6.27 - 8.36: 1 8.36 - 10.45: 2 Bond angle restraints: 38407 Sorted by residual: angle pdb=" N VAL C 151 " pdb=" CA VAL C 151 " pdb=" C VAL C 151 " ideal model delta sigma weight residual 113.42 109.20 4.22 1.17e+00 7.31e-01 1.30e+01 angle pdb=" OP1 DC M 8 " pdb=" P DC M 8 " pdb=" OP2 DC M 8 " ideal model delta sigma weight residual 120.00 109.55 10.45 3.00e+00 1.11e-01 1.21e+01 angle pdb=" C PHE F 129 " pdb=" N ARG F 130 " pdb=" CA ARG F 130 " ideal model delta sigma weight residual 121.54 127.53 -5.99 1.91e+00 2.74e-01 9.84e+00 angle pdb=" C PHE G 129 " pdb=" N ARG G 130 " pdb=" CA ARG G 130 " ideal model delta sigma weight residual 121.54 127.42 -5.88 1.91e+00 2.74e-01 9.48e+00 angle pdb=" C4' DG M 15 " pdb=" O4' DG M 15 " pdb=" C1' DG M 15 " ideal model delta sigma weight residual 109.70 105.10 4.60 1.50e+00 4.44e-01 9.41e+00 ... (remaining 38402 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.25: 16263 28.25 - 56.49: 816 56.49 - 84.74: 83 84.74 - 112.99: 17 112.99 - 141.24: 1 Dihedral angle restraints: 17180 sinusoidal: 7361 harmonic: 9819 Sorted by residual: dihedral pdb=" C4' DC M 5 " pdb=" C3' DC M 5 " pdb=" O3' DC M 5 " pdb=" P DC M 6 " ideal model delta sinusoidal sigma weight residual 220.00 78.76 141.24 1 3.50e+01 8.16e-04 1.39e+01 dihedral pdb=" CA TYR H 232 " pdb=" C TYR H 232 " pdb=" N SER H 233 " pdb=" CA SER H 233 " ideal model delta harmonic sigma weight residual -180.00 -162.00 -18.00 0 5.00e+00 4.00e-02 1.30e+01 dihedral pdb=" CA GLY B 112 " pdb=" C GLY B 112 " pdb=" N LYS B 113 " pdb=" CA LYS B 113 " ideal model delta harmonic sigma weight residual -180.00 -162.06 -17.94 0 5.00e+00 4.00e-02 1.29e+01 ... (remaining 17177 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 4102 0.077 - 0.154: 307 0.154 - 0.231: 0 0.231 - 0.309: 0 0.309 - 0.386: 1 Chirality restraints: 4410 Sorted by residual: chirality pdb=" P DC M 8 " pdb=" OP1 DC M 8 " pdb=" OP2 DC M 8 " pdb=" O5' DC M 8 " both_signs ideal model delta sigma weight residual True 2.35 -2.73 -0.39 2.00e-01 2.50e+01 3.72e+00 chirality pdb=" CA ARG F 130 " pdb=" N ARG F 130 " pdb=" C ARG F 130 " pdb=" CB ARG F 130 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.55e-01 chirality pdb=" CA ARG E 130 " pdb=" N ARG E 130 " pdb=" C ARG E 130 " pdb=" CB ARG E 130 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.46e-01 ... (remaining 4407 not shown) Planarity restraints: 4759 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DG M 15 " -0.024 2.00e-02 2.50e+03 1.09e-02 3.55e+00 pdb=" N9 DG M 15 " 0.027 2.00e-02 2.50e+03 pdb=" C8 DG M 15 " 0.002 2.00e-02 2.50e+03 pdb=" N7 DG M 15 " -0.002 2.00e-02 2.50e+03 pdb=" C5 DG M 15 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DG M 15 " 0.001 2.00e-02 2.50e+03 pdb=" O6 DG M 15 " -0.007 2.00e-02 2.50e+03 pdb=" N1 DG M 15 " -0.003 2.00e-02 2.50e+03 pdb=" C2 DG M 15 " 0.001 2.00e-02 2.50e+03 pdb=" N2 DG M 15 " 0.002 2.00e-02 2.50e+03 pdb=" N3 DG M 15 " 0.003 2.00e-02 2.50e+03 pdb=" C4 DG M 15 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG M 21 " -0.021 2.00e-02 2.50e+03 9.53e-03 2.72e+00 pdb=" N9 DG M 21 " 0.025 2.00e-02 2.50e+03 pdb=" C8 DG M 21 " 0.001 2.00e-02 2.50e+03 pdb=" N7 DG M 21 " -0.002 2.00e-02 2.50e+03 pdb=" C5 DG M 21 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DG M 21 " 0.001 2.00e-02 2.50e+03 pdb=" O6 DG M 21 " -0.006 2.00e-02 2.50e+03 pdb=" N1 DG M 21 " -0.003 2.00e-02 2.50e+03 pdb=" C2 DG M 21 " 0.001 2.00e-02 2.50e+03 pdb=" N2 DG M 21 " 0.001 2.00e-02 2.50e+03 pdb=" N3 DG M 21 " 0.002 2.00e-02 2.50e+03 pdb=" C4 DG M 21 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA M 12 " -0.020 2.00e-02 2.50e+03 9.64e-03 2.56e+00 pdb=" N9 DA M 12 " 0.024 2.00e-02 2.50e+03 pdb=" C8 DA M 12 " 0.001 2.00e-02 2.50e+03 pdb=" N7 DA M 12 " -0.001 2.00e-02 2.50e+03 pdb=" C5 DA M 12 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DA M 12 " -0.001 2.00e-02 2.50e+03 pdb=" N6 DA M 12 " -0.005 2.00e-02 2.50e+03 pdb=" N1 DA M 12 " -0.001 2.00e-02 2.50e+03 pdb=" C2 DA M 12 " 0.001 2.00e-02 2.50e+03 pdb=" N3 DA M 12 " 0.003 2.00e-02 2.50e+03 pdb=" C4 DA M 12 " 0.002 2.00e-02 2.50e+03 ... (remaining 4756 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 174 2.54 - 3.13: 20006 3.13 - 3.72: 41032 3.72 - 4.31: 58658 4.31 - 4.90: 99696 Nonbonded interactions: 219566 Sorted by model distance: nonbonded pdb=" O1G ATP F 401 " pdb="MG MG F 403 " model vdw 1.954 2.170 nonbonded pdb=" O2G ATP D 401 " pdb="MG MG D 402 " model vdw 1.975 2.170 nonbonded pdb=" O1B ADP C 401 " pdb="MG MG C 402 " model vdw 1.982 2.170 nonbonded pdb=" O2G ATP I 401 " pdb="MG MG I 403 " model vdw 2.013 2.170 nonbonded pdb=" OG1 THR J 134 " pdb="MG MG J 403 " model vdw 2.016 2.170 ... (remaining 219561 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 'E' and (resid 21 through 273 or resid 283 through 339)) selection = (chain 'F' and (resid 21 through 273 or resid 283 through 339)) selection = (chain 'G' and (resid 21 through 273 or resid 283 through 339)) selection = (chain 'H' and (resid 21 through 273 or resid 283 through 339)) selection = (chain 'I' and (resid 21 through 273 or resid 283 through 339)) selection = (chain 'J' and (resid 21 through 273 or resid 283 through 339)) selection = (chain 'K' and resid 21 through 339) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.480 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 28.820 Find NCS groups from input model: 0.710 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 28231 Z= 0.117 Angle : 0.465 10.450 38407 Z= 0.249 Chirality : 0.039 0.386 4410 Planarity : 0.003 0.059 4759 Dihedral : 15.830 141.237 10868 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.15), residues: 3402 helix: 0.98 (0.14), residues: 1535 sheet: 1.40 (0.23), residues: 594 loop : -1.12 (0.17), residues: 1273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 96 TYR 0.009 0.001 TYR C 216 PHE 0.023 0.001 PHE F 129 TRP 0.003 0.001 TRP A 231 HIS 0.012 0.001 HIS D 148 Details of bonding type rmsd covalent geometry : bond 0.00254 (28231) covalent geometry : angle 0.46525 (38407) hydrogen bonds : bond 0.17577 ( 1333) hydrogen bonds : angle 6.21764 ( 3730) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6804 Ramachandran restraints generated. 3402 Oldfield, 0 Emsley, 3402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6804 Ramachandran restraints generated. 3402 Oldfield, 0 Emsley, 3402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 2797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 290 time to evaluate : 1.058 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 72 TYR cc_start: 0.6917 (t80) cc_final: 0.6558 (t80) REVERT: B 314 TRP cc_start: 0.4639 (m-90) cc_final: 0.4382 (t60) REVERT: C 165 MET cc_start: 0.9205 (mmt) cc_final: 0.8934 (mmt) REVERT: D 22 LYS cc_start: 0.9007 (mmmt) cc_final: 0.8661 (mmmm) REVERT: F 72 ASP cc_start: 0.8634 (m-30) cc_final: 0.8318 (m-30) REVERT: F 202 GLN cc_start: 0.8626 (tp-100) cc_final: 0.8097 (tm-30) REVERT: F 233 SER cc_start: 0.8812 (m) cc_final: 0.8425 (p) REVERT: G 72 ASP cc_start: 0.8579 (m-30) cc_final: 0.8196 (m-30) REVERT: I 247 ARG cc_start: 0.8460 (ttm110) cc_final: 0.8131 (mtm110) REVERT: I 306 ARG cc_start: 0.7877 (tmm160) cc_final: 0.7613 (tmm160) REVERT: K 57 LYS cc_start: 0.9168 (ttpt) cc_final: 0.8854 (ttpp) REVERT: K 285 LYS cc_start: 0.7771 (mmpt) cc_final: 0.6867 (pttp) outliers start: 0 outliers final: 0 residues processed: 290 average time/residue: 0.9689 time to fit residues: 312.6591 Evaluate side-chains 199 residues out of total 2797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 199 time to evaluate : 1.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 197 optimal weight: 0.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 0.7980 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 0.9980 chunk 155 optimal weight: 7.9990 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 4.9990 chunk 298 optimal weight: 4.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 203 ASN C 275 ASN ** D 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 101 GLN K 330 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.126466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.079532 restraints weight = 48749.821| |-----------------------------------------------------------------------------| r_work (start): 0.3086 rms_B_bonded: 2.69 r_work: 0.2964 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2851 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.0978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 28231 Z= 0.166 Angle : 0.541 7.852 38407 Z= 0.287 Chirality : 0.041 0.172 4410 Planarity : 0.004 0.053 4759 Dihedral : 12.857 141.463 4596 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 0.93 % Allowed : 10.15 % Favored : 88.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.15), residues: 3402 helix: 1.18 (0.14), residues: 1516 sheet: 1.33 (0.22), residues: 594 loop : -1.00 (0.17), residues: 1292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 160 TYR 0.014 0.001 TYR K 191 PHE 0.019 0.001 PHE A 137 TRP 0.007 0.001 TRP A 231 HIS 0.015 0.001 HIS D 148 Details of bonding type rmsd covalent geometry : bond 0.00381 (28231) covalent geometry : angle 0.54130 (38407) hydrogen bonds : bond 0.04517 ( 1333) hydrogen bonds : angle 4.64324 ( 3730) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6804 Ramachandran restraints generated. 3402 Oldfield, 0 Emsley, 3402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6804 Ramachandran restraints generated. 3402 Oldfield, 0 Emsley, 3402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 2797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 215 time to evaluate : 1.030 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 55 ARG cc_start: 0.7846 (ttp80) cc_final: 0.7532 (ttp80) REVERT: B 72 TYR cc_start: 0.7131 (t80) cc_final: 0.6869 (t80) REVERT: C 165 MET cc_start: 0.9051 (mmt) cc_final: 0.8705 (mmt) REVERT: D 22 LYS cc_start: 0.8878 (mmmt) cc_final: 0.8676 (mmmm) REVERT: D 158 GLN cc_start: 0.9233 (tp40) cc_final: 0.8264 (tp-100) REVERT: A 238 ARG cc_start: 0.7885 (ttm110) cc_final: 0.7386 (mtt90) REVERT: E 338 LYS cc_start: 0.7792 (OUTLIER) cc_final: 0.7495 (mttt) REVERT: F 72 ASP cc_start: 0.8664 (m-30) cc_final: 0.8287 (m-30) REVERT: F 202 GLN cc_start: 0.8647 (tp-100) cc_final: 0.8114 (tm-30) REVERT: F 233 SER cc_start: 0.8853 (m) cc_final: 0.8464 (p) REVERT: G 36 ASN cc_start: 0.8686 (m110) cc_final: 0.8468 (m110) REVERT: G 39 LYS cc_start: 0.8827 (mmmm) cc_final: 0.8593 (mmmt) REVERT: G 72 ASP cc_start: 0.8583 (m-30) cc_final: 0.8208 (m-30) REVERT: H 163 GLU cc_start: 0.9095 (OUTLIER) cc_final: 0.8215 (mt-10) REVERT: I 247 ARG cc_start: 0.8316 (ttm110) cc_final: 0.8009 (mtm110) REVERT: I 306 ARG cc_start: 0.7701 (tmm160) cc_final: 0.7429 (tmm160) REVERT: J 278 MET cc_start: 0.2630 (pmm) cc_final: 0.2327 (pmm) REVERT: J 326 MET cc_start: 0.8920 (tpp) cc_final: 0.8610 (mmm) outliers start: 26 outliers final: 10 residues processed: 230 average time/residue: 0.8552 time to fit residues: 221.8102 Evaluate side-chains 199 residues out of total 2797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 187 time to evaluate : 1.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 119 CYS Chi-restraints excluded: chain D residue 4 ASP Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 181 GLU Chi-restraints excluded: chain E residue 243 MET Chi-restraints excluded: chain E residue 338 LYS Chi-restraints excluded: chain H residue 163 GLU Chi-restraints excluded: chain H residue 230 THR Chi-restraints excluded: chain J residue 273 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 97 optimal weight: 4.9990 chunk 17 optimal weight: 5.9990 chunk 296 optimal weight: 0.7980 chunk 286 optimal weight: 0.8980 chunk 337 optimal weight: 9.9990 chunk 13 optimal weight: 9.9990 chunk 72 optimal weight: 7.9990 chunk 16 optimal weight: 4.9990 chunk 33 optimal weight: 7.9990 chunk 22 optimal weight: 10.0000 chunk 124 optimal weight: 20.0000 overall best weight: 3.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 275 ASN ** D 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 36 ASN E 272 GLN J 62 ASN K 330 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.124499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.077830 restraints weight = 48954.901| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 2.65 r_work: 0.2926 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2813 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.1309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.053 28231 Z= 0.308 Angle : 0.618 8.122 38407 Z= 0.328 Chirality : 0.046 0.164 4410 Planarity : 0.005 0.100 4759 Dihedral : 13.069 142.382 4596 Min Nonbonded Distance : 1.831 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.50 % Favored : 96.47 % Rotamer: Outliers : 2.15 % Allowed : 11.58 % Favored : 86.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.15), residues: 3402 helix: 0.97 (0.14), residues: 1515 sheet: 1.20 (0.22), residues: 590 loop : -1.23 (0.16), residues: 1297 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 292 TYR 0.020 0.002 TYR I 159 PHE 0.014 0.002 PHE A 80 TRP 0.009 0.001 TRP B 314 HIS 0.007 0.001 HIS D 148 Details of bonding type rmsd covalent geometry : bond 0.00747 (28231) covalent geometry : angle 0.61805 (38407) hydrogen bonds : bond 0.05770 ( 1333) hydrogen bonds : angle 4.74777 ( 3730) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6804 Ramachandran restraints generated. 3402 Oldfield, 0 Emsley, 3402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6804 Ramachandran restraints generated. 3402 Oldfield, 0 Emsley, 3402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 2797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 197 time to evaluate : 1.113 Fit side-chains revert: symmetry clash REVERT: B 16 MET cc_start: 0.4285 (OUTLIER) cc_final: 0.3594 (tmt) REVERT: C 165 MET cc_start: 0.9062 (mmt) cc_final: 0.8744 (mmt) REVERT: C 269 MET cc_start: 0.8656 (mmm) cc_final: 0.8418 (mmm) REVERT: A 99 ARG cc_start: 0.6901 (OUTLIER) cc_final: 0.6126 (tmm160) REVERT: A 199 MET cc_start: 0.8231 (OUTLIER) cc_final: 0.7964 (mtm) REVERT: A 238 ARG cc_start: 0.7860 (ttm110) cc_final: 0.7465 (mtt90) REVERT: E 96 ARG cc_start: 0.7071 (tmm160) cc_final: 0.6783 (tmm160) REVERT: E 254 ARG cc_start: 0.8318 (OUTLIER) cc_final: 0.7967 (mtp180) REVERT: E 338 LYS cc_start: 0.7882 (OUTLIER) cc_final: 0.7606 (mttt) REVERT: F 72 ASP cc_start: 0.8714 (m-30) cc_final: 0.8330 (m-30) REVERT: F 202 GLN cc_start: 0.8749 (tp-100) cc_final: 0.8163 (tm-30) REVERT: F 233 SER cc_start: 0.8942 (m) cc_final: 0.8511 (p) REVERT: G 36 ASN cc_start: 0.8675 (m110) cc_final: 0.8417 (m110) REVERT: G 72 ASP cc_start: 0.8632 (m-30) cc_final: 0.8266 (m-30) REVERT: H 163 GLU cc_start: 0.9160 (OUTLIER) cc_final: 0.8305 (mt-10) REVERT: I 247 ARG cc_start: 0.8340 (ttm110) cc_final: 0.8042 (mtm110) REVERT: I 306 ARG cc_start: 0.7736 (tmm160) cc_final: 0.7510 (tmm160) REVERT: J 278 MET cc_start: 0.2489 (pmm) cc_final: 0.2120 (pmm) REVERT: K 191 TYR cc_start: 0.7674 (t80) cc_final: 0.7453 (t80) REVERT: K 285 LYS cc_start: 0.6351 (mmpt) cc_final: 0.5798 (mtmp) outliers start: 60 outliers final: 22 residues processed: 234 average time/residue: 0.8582 time to fit residues: 226.4767 Evaluate side-chains 216 residues out of total 2797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 188 time to evaluate : 0.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 MET Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 119 CYS Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 284 LEU Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 99 ARG Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 199 MET Chi-restraints excluded: chain E residue 243 MET Chi-restraints excluded: chain E residue 254 ARG Chi-restraints excluded: chain E residue 257 ASP Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 338 LYS Chi-restraints excluded: chain F residue 28 LEU Chi-restraints excluded: chain G residue 273 VAL Chi-restraints excluded: chain H residue 163 GLU Chi-restraints excluded: chain H residue 230 THR Chi-restraints excluded: chain I residue 31 CYS Chi-restraints excluded: chain J residue 273 VAL Chi-restraints excluded: chain K residue 52 VAL Chi-restraints excluded: chain K residue 125 MET Chi-restraints excluded: chain K residue 230 THR Chi-restraints excluded: chain K residue 244 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 140 optimal weight: 3.9990 chunk 280 optimal weight: 0.7980 chunk 20 optimal weight: 10.0000 chunk 49 optimal weight: 1.9990 chunk 239 optimal weight: 0.7980 chunk 158 optimal weight: 1.9990 chunk 247 optimal weight: 2.9990 chunk 179 optimal weight: 1.9990 chunk 25 optimal weight: 10.0000 chunk 320 optimal weight: 7.9990 chunk 3 optimal weight: 5.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 62 ASN F 272 GLN 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 = 0.125969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.078724 restraints weight = 48359.193| |-----------------------------------------------------------------------------| r_work (start): 0.3082 rms_B_bonded: 2.68 r_work: 0.2963 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2850 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.1323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 28231 Z= 0.155 Angle : 0.533 8.817 38407 Z= 0.279 Chirality : 0.041 0.156 4410 Planarity : 0.004 0.044 4759 Dihedral : 12.967 142.165 4596 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.65 % Favored : 97.33 % Rotamer: Outliers : 1.61 % Allowed : 13.19 % Favored : 85.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.15), residues: 3402 helix: 1.16 (0.14), residues: 1519 sheet: 1.15 (0.22), residues: 595 loop : -1.18 (0.17), residues: 1288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG J 247 TYR 0.023 0.001 TYR B 72 PHE 0.014 0.001 PHE A 80 TRP 0.009 0.001 TRP B 314 HIS 0.008 0.001 HIS D 148 Details of bonding type rmsd covalent geometry : bond 0.00364 (28231) covalent geometry : angle 0.53281 (38407) hydrogen bonds : bond 0.04092 ( 1333) hydrogen bonds : angle 4.38386 ( 3730) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6804 Ramachandran restraints generated. 3402 Oldfield, 0 Emsley, 3402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6804 Ramachandran restraints generated. 3402 Oldfield, 0 Emsley, 3402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 2797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 199 time to evaluate : 1.050 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 16 MET cc_start: 0.4277 (OUTLIER) cc_final: 0.3629 (tmt) REVERT: C 95 HIS cc_start: 0.8226 (m-70) cc_final: 0.7839 (m-70) REVERT: C 165 MET cc_start: 0.9027 (mmt) cc_final: 0.8719 (mmt) REVERT: A 199 MET cc_start: 0.8238 (OUTLIER) cc_final: 0.8015 (mtm) REVERT: E 96 ARG cc_start: 0.7170 (tmm160) cc_final: 0.6881 (tmm160) REVERT: E 306 ARG cc_start: 0.7713 (ttp-110) cc_final: 0.7381 (tmm160) REVERT: E 338 LYS cc_start: 0.7819 (OUTLIER) cc_final: 0.7554 (mttt) REVERT: F 72 ASP cc_start: 0.8698 (m-30) cc_final: 0.8311 (m-30) REVERT: F 202 GLN cc_start: 0.8716 (tp-100) cc_final: 0.8123 (tm-30) REVERT: F 233 SER cc_start: 0.8843 (m) cc_final: 0.8436 (p) REVERT: G 36 ASN cc_start: 0.8694 (m110) cc_final: 0.8468 (m110) REVERT: G 39 LYS cc_start: 0.8859 (mmmm) cc_final: 0.8598 (mmmt) REVERT: G 72 ASP cc_start: 0.8597 (m-30) cc_final: 0.8222 (m-30) REVERT: G 306 ARG cc_start: 0.8239 (tmm160) cc_final: 0.8023 (ttp-110) REVERT: H 163 GLU cc_start: 0.9142 (OUTLIER) cc_final: 0.8277 (mt-10) REVERT: I 247 ARG cc_start: 0.8334 (ttm110) cc_final: 0.8049 (mtm110) REVERT: I 306 ARG cc_start: 0.7661 (tmm160) cc_final: 0.7454 (tmm160) REVERT: J 278 MET cc_start: 0.2512 (pmm) cc_final: 0.2151 (pmm) REVERT: K 285 LYS cc_start: 0.6205 (mmpt) cc_final: 0.5683 (mtmp) REVERT: K 330 ASN cc_start: 0.5099 (m110) cc_final: 0.4853 (m110) outliers start: 45 outliers final: 13 residues processed: 230 average time/residue: 0.8427 time to fit residues: 219.6705 Evaluate side-chains 208 residues out of total 2797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 191 time to evaluate : 0.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 MET Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 119 CYS Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 199 MET Chi-restraints excluded: chain E residue 243 MET Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 338 LYS Chi-restraints excluded: chain F residue 28 LEU Chi-restraints excluded: chain G residue 266 THR Chi-restraints excluded: chain H residue 163 GLU Chi-restraints excluded: chain H residue 230 THR Chi-restraints excluded: chain I residue 31 CYS Chi-restraints excluded: chain K residue 244 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 191 optimal weight: 1.9990 chunk 233 optimal weight: 7.9990 chunk 283 optimal weight: 4.9990 chunk 326 optimal weight: 10.0000 chunk 245 optimal weight: 0.6980 chunk 135 optimal weight: 3.9990 chunk 155 optimal weight: 5.9990 chunk 24 optimal weight: 5.9990 chunk 116 optimal weight: 0.9990 chunk 192 optimal weight: 1.9990 chunk 108 optimal weight: 5.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 62 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.125441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.078143 restraints weight = 48536.633| |-----------------------------------------------------------------------------| r_work (start): 0.3075 rms_B_bonded: 2.67 r_work: 0.2954 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2842 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.1423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 28231 Z= 0.184 Angle : 0.547 9.305 38407 Z= 0.286 Chirality : 0.041 0.156 4410 Planarity : 0.004 0.057 4759 Dihedral : 12.953 142.056 4596 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.15 % Favored : 96.83 % Rotamer: Outliers : 1.86 % Allowed : 14.19 % Favored : 83.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.15), residues: 3402 helix: 1.16 (0.14), residues: 1521 sheet: 1.21 (0.21), residues: 590 loop : -1.22 (0.17), residues: 1291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 292 TYR 0.024 0.001 TYR B 72 PHE 0.013 0.001 PHE A 80 TRP 0.005 0.001 TRP B 314 HIS 0.010 0.001 HIS D 148 Details of bonding type rmsd covalent geometry : bond 0.00438 (28231) covalent geometry : angle 0.54677 (38407) hydrogen bonds : bond 0.04311 ( 1333) hydrogen bonds : angle 4.35074 ( 3730) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6804 Ramachandran restraints generated. 3402 Oldfield, 0 Emsley, 3402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6804 Ramachandran restraints generated. 3402 Oldfield, 0 Emsley, 3402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 2797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 204 time to evaluate : 1.031 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 16 MET cc_start: 0.4258 (OUTLIER) cc_final: 0.3599 (tmt) REVERT: B 235 LYS cc_start: 0.7735 (mtmp) cc_final: 0.7417 (mtmm) REVERT: C 95 HIS cc_start: 0.8225 (m-70) cc_final: 0.7842 (m-70) REVERT: C 165 MET cc_start: 0.9032 (mmt) cc_final: 0.8734 (mmt) REVERT: E 338 LYS cc_start: 0.7878 (OUTLIER) cc_final: 0.7605 (mttt) REVERT: F 72 ASP cc_start: 0.8700 (m-30) cc_final: 0.8316 (m-30) REVERT: F 202 GLN cc_start: 0.8717 (tp-100) cc_final: 0.8129 (tm-30) REVERT: F 233 SER cc_start: 0.8866 (m) cc_final: 0.8461 (p) REVERT: G 36 ASN cc_start: 0.8693 (m110) cc_final: 0.8448 (m110) REVERT: G 39 LYS cc_start: 0.8855 (mmmm) cc_final: 0.8578 (mmmt) REVERT: G 72 ASP cc_start: 0.8607 (m-30) cc_final: 0.8230 (m-30) REVERT: G 306 ARG cc_start: 0.8202 (tmm160) cc_final: 0.7981 (ttp-110) REVERT: H 163 GLU cc_start: 0.9130 (OUTLIER) cc_final: 0.8325 (mt-10) REVERT: I 247 ARG cc_start: 0.8365 (ttm110) cc_final: 0.8098 (mtm110) REVERT: I 306 ARG cc_start: 0.7690 (tmm160) cc_final: 0.7460 (tmm160) REVERT: J 278 MET cc_start: 0.2565 (pmm) cc_final: 0.2146 (pmm) REVERT: K 285 LYS cc_start: 0.6212 (mmpt) cc_final: 0.5697 (mtmp) outliers start: 52 outliers final: 26 residues processed: 241 average time/residue: 0.8035 time to fit residues: 220.0597 Evaluate side-chains 221 residues out of total 2797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 192 time to evaluate : 1.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 MET Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 119 CYS Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 284 LEU Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain E residue 243 MET Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 338 LYS Chi-restraints excluded: chain F residue 28 LEU Chi-restraints excluded: chain F residue 103 THR Chi-restraints excluded: chain G residue 266 THR Chi-restraints excluded: chain G residue 273 VAL Chi-restraints excluded: chain H residue 109 LEU Chi-restraints excluded: chain H residue 125 MET Chi-restraints excluded: chain H residue 163 GLU Chi-restraints excluded: chain H residue 230 THR Chi-restraints excluded: chain H residue 257 ASP Chi-restraints excluded: chain I residue 31 CYS Chi-restraints excluded: chain I residue 61 ILE Chi-restraints excluded: chain I residue 266 THR Chi-restraints excluded: chain J residue 273 VAL Chi-restraints excluded: chain K residue 230 THR Chi-restraints excluded: chain K residue 244 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 298 optimal weight: 1.9990 chunk 251 optimal weight: 0.0370 chunk 182 optimal weight: 2.9990 chunk 36 optimal weight: 5.9990 chunk 149 optimal weight: 0.3980 chunk 133 optimal weight: 0.8980 chunk 196 optimal weight: 0.8980 chunk 255 optimal weight: 4.9990 chunk 303 optimal weight: 10.0000 chunk 246 optimal weight: 3.9990 chunk 170 optimal weight: 0.8980 overall best weight: 0.6258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 233 HIS ** D 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 62 ASN K 330 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.128470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.081947 restraints weight = 48424.772| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 2.68 r_work: 0.2996 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2884 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.1512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 28231 Z= 0.107 Angle : 0.522 10.174 38407 Z= 0.269 Chirality : 0.039 0.184 4410 Planarity : 0.003 0.055 4759 Dihedral : 12.819 141.355 4596 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.23 % Favored : 97.74 % Rotamer: Outliers : 1.43 % Allowed : 15.05 % Favored : 83.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.15), residues: 3402 helix: 1.33 (0.14), residues: 1523 sheet: 1.18 (0.22), residues: 606 loop : -1.07 (0.17), residues: 1273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG D 160 TYR 0.024 0.001 TYR B 72 PHE 0.012 0.001 PHE A 80 TRP 0.006 0.001 TRP B 314 HIS 0.011 0.001 HIS D 148 Details of bonding type rmsd covalent geometry : bond 0.00235 (28231) covalent geometry : angle 0.52189 (38407) hydrogen bonds : bond 0.03055 ( 1333) hydrogen bonds : angle 4.08978 ( 3730) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6804 Ramachandran restraints generated. 3402 Oldfield, 0 Emsley, 3402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6804 Ramachandran restraints generated. 3402 Oldfield, 0 Emsley, 3402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 2797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 208 time to evaluate : 1.056 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 16 MET cc_start: 0.4110 (OUTLIER) cc_final: 0.3428 (tmt) REVERT: B 55 ARG cc_start: 0.8328 (tmm-80) cc_final: 0.7973 (ttp80) REVERT: B 64 PHE cc_start: 0.7538 (t80) cc_final: 0.7334 (t80) REVERT: C 95 HIS cc_start: 0.8245 (m-70) cc_final: 0.7969 (m-70) REVERT: C 165 MET cc_start: 0.9002 (mmt) cc_final: 0.8690 (mmt) REVERT: E 91 GLU cc_start: 0.8041 (mp0) cc_final: 0.7721 (mp0) REVERT: E 96 ARG cc_start: 0.7208 (tmm160) cc_final: 0.6946 (tmm160) REVERT: E 306 ARG cc_start: 0.8028 (tmm160) cc_final: 0.7744 (tmm160) REVERT: E 338 LYS cc_start: 0.7891 (OUTLIER) cc_final: 0.7619 (mttt) REVERT: F 27 ARG cc_start: 0.7976 (mmm-85) cc_final: 0.7771 (mmm160) REVERT: F 72 ASP cc_start: 0.8669 (m-30) cc_final: 0.8287 (m-30) REVERT: F 202 GLN cc_start: 0.8634 (tp-100) cc_final: 0.8089 (tm-30) REVERT: F 233 SER cc_start: 0.8784 (m) cc_final: 0.8419 (p) REVERT: G 36 ASN cc_start: 0.8699 (m110) cc_final: 0.8470 (m110) REVERT: G 72 ASP cc_start: 0.8572 (m-30) cc_final: 0.8212 (m-30) REVERT: G 306 ARG cc_start: 0.8263 (tmm160) cc_final: 0.8032 (ttp-110) REVERT: H 163 GLU cc_start: 0.9168 (OUTLIER) cc_final: 0.8321 (mt-10) REVERT: H 230 THR cc_start: 0.9410 (OUTLIER) cc_final: 0.9172 (p) REVERT: I 247 ARG cc_start: 0.8330 (ttm110) cc_final: 0.8064 (mtm110) REVERT: I 306 ARG cc_start: 0.7649 (tmm160) cc_final: 0.7421 (tmm160) REVERT: J 278 MET cc_start: 0.2251 (pmm) cc_final: 0.1939 (pmm) REVERT: K 285 LYS cc_start: 0.6158 (mmpt) cc_final: 0.5654 (mtmp) outliers start: 40 outliers final: 20 residues processed: 236 average time/residue: 0.7674 time to fit residues: 207.2177 Evaluate side-chains 221 residues out of total 2797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 197 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 MET Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 119 CYS Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain D residue 8 LEU Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain E residue 243 MET Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 338 LYS Chi-restraints excluded: chain F residue 103 THR Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 125 MET Chi-restraints excluded: chain H residue 163 GLU Chi-restraints excluded: chain H residue 185 VAL Chi-restraints excluded: chain H residue 230 THR Chi-restraints excluded: chain I residue 31 CYS Chi-restraints excluded: chain I residue 36 ASN Chi-restraints excluded: chain I residue 99 ILE Chi-restraints excluded: chain K residue 244 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 339 optimal weight: 3.9990 chunk 247 optimal weight: 3.9990 chunk 292 optimal weight: 6.9990 chunk 185 optimal weight: 0.8980 chunk 190 optimal weight: 0.9990 chunk 195 optimal weight: 1.9990 chunk 242 optimal weight: 3.9990 chunk 156 optimal weight: 4.9990 chunk 275 optimal weight: 3.9990 chunk 157 optimal weight: 4.9990 chunk 29 optimal weight: 8.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 62 ASN K 242 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.124857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.077519 restraints weight = 48259.592| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 2.67 r_work: 0.2944 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2832 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.1555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 28231 Z= 0.215 Angle : 0.581 10.639 38407 Z= 0.301 Chirality : 0.042 0.163 4410 Planarity : 0.004 0.068 4759 Dihedral : 12.911 141.561 4596 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.41 % Favored : 96.56 % Rotamer: Outliers : 1.64 % Allowed : 15.77 % Favored : 82.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.15), residues: 3402 helix: 1.22 (0.14), residues: 1521 sheet: 1.21 (0.21), residues: 590 loop : -1.17 (0.17), residues: 1291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 160 TYR 0.028 0.001 TYR B 72 PHE 0.012 0.001 PHE K 129 TRP 0.011 0.001 TRP B 314 HIS 0.016 0.001 HIS D 148 Details of bonding type rmsd covalent geometry : bond 0.00516 (28231) covalent geometry : angle 0.58072 (38407) hydrogen bonds : bond 0.04564 ( 1333) hydrogen bonds : angle 4.31793 ( 3730) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6804 Ramachandran restraints generated. 3402 Oldfield, 0 Emsley, 3402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6804 Ramachandran restraints generated. 3402 Oldfield, 0 Emsley, 3402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 2797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 201 time to evaluate : 1.023 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 16 MET cc_start: 0.4225 (OUTLIER) cc_final: 0.3558 (tmt) REVERT: B 64 PHE cc_start: 0.7534 (t80) cc_final: 0.7317 (t80) REVERT: C 95 HIS cc_start: 0.8247 (m-70) cc_final: 0.7960 (m-70) REVERT: C 165 MET cc_start: 0.9038 (mmt) cc_final: 0.8735 (mmt) REVERT: E 306 ARG cc_start: 0.7908 (tmm160) cc_final: 0.7673 (tmm160) REVERT: E 338 LYS cc_start: 0.7898 (OUTLIER) cc_final: 0.7625 (mttt) REVERT: F 72 ASP cc_start: 0.8696 (m-30) cc_final: 0.8276 (m-30) REVERT: F 202 GLN cc_start: 0.8711 (tp-100) cc_final: 0.8121 (tm-30) REVERT: F 233 SER cc_start: 0.8861 (m) cc_final: 0.8453 (p) REVERT: G 36 ASN cc_start: 0.8676 (m110) cc_final: 0.8434 (m110) REVERT: G 72 ASP cc_start: 0.8600 (m-30) cc_final: 0.8232 (m-30) REVERT: G 306 ARG cc_start: 0.8210 (tmm160) cc_final: 0.7975 (ttp-110) REVERT: H 163 GLU cc_start: 0.9134 (OUTLIER) cc_final: 0.8345 (mt-10) REVERT: I 247 ARG cc_start: 0.8356 (ttm110) cc_final: 0.8088 (mtm110) REVERT: I 306 ARG cc_start: 0.7694 (tmm160) cc_final: 0.7474 (tmm160) REVERT: J 278 MET cc_start: 0.1873 (pmm) cc_final: 0.1565 (pmm) REVERT: K 285 LYS cc_start: 0.6254 (mmpt) cc_final: 0.5742 (mtmp) outliers start: 46 outliers final: 25 residues processed: 232 average time/residue: 0.7846 time to fit residues: 207.3792 Evaluate side-chains 225 residues out of total 2797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 197 time to evaluate : 1.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 MET Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 119 CYS Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain D residue 8 LEU Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 277 ASP Chi-restraints excluded: chain D residue 284 LEU Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain E residue 243 MET Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 338 LYS Chi-restraints excluded: chain F residue 99 ILE Chi-restraints excluded: chain F residue 103 THR Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 109 LEU Chi-restraints excluded: chain H residue 163 GLU Chi-restraints excluded: chain H residue 185 VAL Chi-restraints excluded: chain H residue 230 THR Chi-restraints excluded: chain H residue 266 THR Chi-restraints excluded: chain I residue 31 CYS Chi-restraints excluded: chain I residue 36 ASN Chi-restraints excluded: chain I residue 61 ILE Chi-restraints excluded: chain I residue 99 ILE Chi-restraints excluded: chain J residue 99 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 219 optimal weight: 0.2980 chunk 90 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 150 optimal weight: 3.9990 chunk 75 optimal weight: 5.9990 chunk 10 optimal weight: 5.9990 chunk 130 optimal weight: 4.9990 chunk 304 optimal weight: 6.9990 chunk 104 optimal weight: 8.9990 chunk 298 optimal weight: 0.8980 overall best weight: 2.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 62 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.125158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.077943 restraints weight = 48452.143| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 2.66 r_work: 0.2948 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2836 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.1584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 28231 Z= 0.205 Angle : 0.586 11.109 38407 Z= 0.302 Chirality : 0.042 0.165 4410 Planarity : 0.004 0.062 4759 Dihedral : 12.959 141.755 4596 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.94 % Favored : 97.00 % Rotamer: Outliers : 1.54 % Allowed : 16.09 % Favored : 82.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.15), residues: 3402 helix: 1.17 (0.14), residues: 1520 sheet: 1.11 (0.21), residues: 589 loop : -1.20 (0.17), residues: 1293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG F 27 TYR 0.029 0.001 TYR B 72 PHE 0.013 0.001 PHE F 126 TRP 0.010 0.001 TRP B 314 HIS 0.021 0.001 HIS D 148 Details of bonding type rmsd covalent geometry : bond 0.00493 (28231) covalent geometry : angle 0.58614 (38407) hydrogen bonds : bond 0.04432 ( 1333) hydrogen bonds : angle 4.30841 ( 3730) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6804 Ramachandran restraints generated. 3402 Oldfield, 0 Emsley, 3402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6804 Ramachandran restraints generated. 3402 Oldfield, 0 Emsley, 3402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 2797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 202 time to evaluate : 0.822 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 16 MET cc_start: 0.4218 (OUTLIER) cc_final: 0.3560 (tmt) REVERT: B 64 PHE cc_start: 0.7481 (t80) cc_final: 0.7218 (t80) REVERT: C 95 HIS cc_start: 0.8247 (m-70) cc_final: 0.7859 (m-70) REVERT: C 165 MET cc_start: 0.9042 (mmt) cc_final: 0.8739 (mmt) REVERT: A 143 LEU cc_start: 0.4667 (mt) cc_final: 0.4013 (tt) REVERT: E 306 ARG cc_start: 0.7926 (tmm160) cc_final: 0.7669 (tmm160) REVERT: E 338 LYS cc_start: 0.7866 (OUTLIER) cc_final: 0.7658 (mttt) REVERT: F 72 ASP cc_start: 0.8702 (m-30) cc_final: 0.8298 (m-30) REVERT: F 202 GLN cc_start: 0.8733 (tp-100) cc_final: 0.8171 (tm-30) REVERT: F 233 SER cc_start: 0.8862 (m) cc_final: 0.8463 (p) REVERT: G 36 ASN cc_start: 0.8678 (m110) cc_final: 0.8438 (m110) REVERT: G 39 LYS cc_start: 0.8841 (mmmm) cc_final: 0.8599 (mmmt) REVERT: G 72 ASP cc_start: 0.8606 (m-30) cc_final: 0.8230 (m-30) REVERT: G 306 ARG cc_start: 0.8218 (tmm160) cc_final: 0.7989 (ttp-110) REVERT: H 43 GLU cc_start: 0.7937 (pp20) cc_final: 0.7720 (pp20) REVERT: H 163 GLU cc_start: 0.9135 (OUTLIER) cc_final: 0.8336 (mt-10) REVERT: I 247 ARG cc_start: 0.8342 (ttm110) cc_final: 0.8081 (mtm110) REVERT: I 306 ARG cc_start: 0.7702 (tmm160) cc_final: 0.7492 (tmm160) REVERT: J 278 MET cc_start: 0.1968 (pmm) cc_final: 0.1550 (pmm) REVERT: K 285 LYS cc_start: 0.6173 (mmpt) cc_final: 0.5667 (mtmp) outliers start: 43 outliers final: 30 residues processed: 233 average time/residue: 0.7917 time to fit residues: 210.2795 Evaluate side-chains 229 residues out of total 2797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 196 time to evaluate : 1.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 MET Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 119 CYS Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain D residue 8 LEU Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 277 ASP Chi-restraints excluded: chain D residue 284 LEU Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain E residue 243 MET Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 338 LYS Chi-restraints excluded: chain F residue 99 ILE Chi-restraints excluded: chain F residue 103 THR Chi-restraints excluded: chain G residue 266 THR Chi-restraints excluded: chain G residue 273 VAL Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 109 LEU Chi-restraints excluded: chain H residue 163 GLU Chi-restraints excluded: chain H residue 185 VAL Chi-restraints excluded: chain H residue 230 THR Chi-restraints excluded: chain H residue 266 THR Chi-restraints excluded: chain I residue 31 CYS Chi-restraints excluded: chain I residue 36 ASN Chi-restraints excluded: chain I residue 61 ILE Chi-restraints excluded: chain I residue 99 ILE Chi-restraints excluded: chain I residue 266 THR Chi-restraints excluded: chain J residue 99 ILE Chi-restraints excluded: chain J residue 273 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 239 optimal weight: 2.9990 chunk 159 optimal weight: 3.9990 chunk 248 optimal weight: 1.9990 chunk 47 optimal weight: 8.9990 chunk 208 optimal weight: 0.7980 chunk 241 optimal weight: 0.9980 chunk 46 optimal weight: 0.9990 chunk 212 optimal weight: 0.9990 chunk 247 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 216 optimal weight: 0.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 62 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.126491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.079673 restraints weight = 48110.588| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 2.67 r_work: 0.2991 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2880 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.1631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 28231 Z= 0.123 Angle : 0.549 13.758 38407 Z= 0.280 Chirality : 0.040 0.178 4410 Planarity : 0.004 0.046 4759 Dihedral : 12.851 141.304 4596 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.35 % Favored : 97.59 % Rotamer: Outliers : 1.25 % Allowed : 16.62 % Favored : 82.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.15), residues: 3402 helix: 1.31 (0.14), residues: 1519 sheet: 1.14 (0.22), residues: 596 loop : -1.09 (0.17), residues: 1287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG J 247 TYR 0.027 0.001 TYR A 187 PHE 0.011 0.001 PHE A 80 TRP 0.006 0.001 TRP C 317 HIS 0.020 0.001 HIS D 148 Details of bonding type rmsd covalent geometry : bond 0.00280 (28231) covalent geometry : angle 0.54938 (38407) hydrogen bonds : bond 0.03347 ( 1333) hydrogen bonds : angle 4.10350 ( 3730) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6804 Ramachandran restraints generated. 3402 Oldfield, 0 Emsley, 3402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6804 Ramachandran restraints generated. 3402 Oldfield, 0 Emsley, 3402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 2797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 201 time to evaluate : 1.156 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 64 PHE cc_start: 0.7483 (t80) cc_final: 0.7240 (t80) REVERT: B 235 LYS cc_start: 0.7560 (mtmp) cc_final: 0.7171 (mtmm) REVERT: C 95 HIS cc_start: 0.8332 (m-70) cc_final: 0.8029 (m-70) REVERT: C 118 MET cc_start: 0.8826 (mtt) cc_final: 0.8615 (mpt) REVERT: C 165 MET cc_start: 0.9018 (mmt) cc_final: 0.8704 (mmt) REVERT: E 91 GLU cc_start: 0.8105 (mp0) cc_final: 0.7751 (mp0) REVERT: E 306 ARG cc_start: 0.7982 (tmm160) cc_final: 0.7749 (tmm160) REVERT: F 72 ASP cc_start: 0.8682 (m-30) cc_final: 0.8283 (m-30) REVERT: F 202 GLN cc_start: 0.8667 (tp-100) cc_final: 0.8108 (tm-30) REVERT: F 233 SER cc_start: 0.8803 (m) cc_final: 0.8433 (p) REVERT: G 39 LYS cc_start: 0.8822 (mmmm) cc_final: 0.8333 (mppt) REVERT: G 72 ASP cc_start: 0.8577 (m-30) cc_final: 0.8219 (m-30) REVERT: G 306 ARG cc_start: 0.8263 (tmm160) cc_final: 0.8028 (ttp-110) REVERT: H 163 GLU cc_start: 0.9151 (OUTLIER) cc_final: 0.8355 (mt-10) REVERT: I 247 ARG cc_start: 0.8312 (ttm110) cc_final: 0.8053 (mtm110) REVERT: I 306 ARG cc_start: 0.7690 (tmm160) cc_final: 0.7485 (tmm160) REVERT: J 278 MET cc_start: 0.1981 (pmm) cc_final: 0.1648 (pmm) REVERT: J 326 MET cc_start: 0.9062 (OUTLIER) cc_final: 0.8543 (tpp) REVERT: K 285 LYS cc_start: 0.6191 (mmpt) cc_final: 0.5674 (mtmp) outliers start: 35 outliers final: 25 residues processed: 224 average time/residue: 0.8494 time to fit residues: 216.2197 Evaluate side-chains 223 residues out of total 2797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 196 time to evaluate : 1.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 119 CYS Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain D residue 8 LEU Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 284 LEU Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain E residue 243 MET Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain F residue 103 THR Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 163 GLU Chi-restraints excluded: chain H residue 185 VAL Chi-restraints excluded: chain H residue 230 THR Chi-restraints excluded: chain H residue 257 ASP Chi-restraints excluded: chain H residue 266 THR Chi-restraints excluded: chain I residue 31 CYS Chi-restraints excluded: chain I residue 36 ASN Chi-restraints excluded: chain I residue 61 ILE Chi-restraints excluded: chain I residue 99 ILE Chi-restraints excluded: chain I residue 266 THR Chi-restraints excluded: chain J residue 99 ILE Chi-restraints excluded: chain J residue 326 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 254 optimal weight: 0.5980 chunk 167 optimal weight: 3.9990 chunk 28 optimal weight: 0.5980 chunk 59 optimal weight: 4.9990 chunk 241 optimal weight: 7.9990 chunk 36 optimal weight: 1.9990 chunk 202 optimal weight: 2.9990 chunk 61 optimal weight: 5.9990 chunk 160 optimal weight: 2.9990 chunk 127 optimal weight: 8.9990 chunk 273 optimal weight: 0.0980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 62 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.127441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.080914 restraints weight = 48288.814| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 2.66 r_work: 0.2981 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2869 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.1643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 28231 Z= 0.141 Angle : 0.564 13.019 38407 Z= 0.288 Chirality : 0.040 0.169 4410 Planarity : 0.004 0.052 4759 Dihedral : 12.825 141.052 4596 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.65 % Favored : 97.30 % Rotamer: Outliers : 1.07 % Allowed : 16.95 % Favored : 81.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.60 (0.15), residues: 3402 helix: 1.32 (0.14), residues: 1519 sheet: 1.14 (0.22), residues: 595 loop : -1.08 (0.17), residues: 1288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG J 247 TYR 0.033 0.001 TYR A 187 PHE 0.011 0.001 PHE F 126 TRP 0.006 0.001 TRP B 314 HIS 0.033 0.001 HIS D 148 Details of bonding type rmsd covalent geometry : bond 0.00330 (28231) covalent geometry : angle 0.56394 (38407) hydrogen bonds : bond 0.03612 ( 1333) hydrogen bonds : angle 4.11830 ( 3730) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6804 Ramachandran restraints generated. 3402 Oldfield, 0 Emsley, 3402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6804 Ramachandran restraints generated. 3402 Oldfield, 0 Emsley, 3402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 2797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 200 time to evaluate : 0.939 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 55 ARG cc_start: 0.8259 (tmm-80) cc_final: 0.8053 (ttp80) REVERT: B 64 PHE cc_start: 0.7455 (t80) cc_final: 0.7190 (t80) REVERT: C 95 HIS cc_start: 0.8309 (m-70) cc_final: 0.8038 (m-70) REVERT: C 118 MET cc_start: 0.8831 (mtt) cc_final: 0.8593 (mpt) REVERT: C 165 MET cc_start: 0.9022 (mmt) cc_final: 0.8720 (mmt) REVERT: E 91 GLU cc_start: 0.8084 (mp0) cc_final: 0.7759 (mp0) REVERT: E 306 ARG cc_start: 0.8039 (tmm160) cc_final: 0.7798 (tmm160) REVERT: F 72 ASP cc_start: 0.8678 (m-30) cc_final: 0.8263 (m-30) REVERT: F 202 GLN cc_start: 0.8674 (tp-100) cc_final: 0.8116 (tm-30) REVERT: F 233 SER cc_start: 0.8814 (m) cc_final: 0.8440 (p) REVERT: G 39 LYS cc_start: 0.8844 (mmmm) cc_final: 0.8345 (mppt) REVERT: G 72 ASP cc_start: 0.8580 (m-30) cc_final: 0.8218 (m-30) REVERT: G 306 ARG cc_start: 0.8268 (tmm160) cc_final: 0.8031 (ttp-110) REVERT: H 163 GLU cc_start: 0.9149 (OUTLIER) cc_final: 0.8342 (mt-10) REVERT: I 247 ARG cc_start: 0.8319 (ttm110) cc_final: 0.8063 (mtm110) REVERT: I 306 ARG cc_start: 0.7700 (tmm160) cc_final: 0.7496 (tmm160) REVERT: J 278 MET cc_start: 0.1967 (pmm) cc_final: 0.1638 (pmm) REVERT: K 285 LYS cc_start: 0.6214 (mmpt) cc_final: 0.5682 (mtmp) outliers start: 30 outliers final: 24 residues processed: 224 average time/residue: 0.8244 time to fit residues: 209.6112 Evaluate side-chains 221 residues out of total 2797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 196 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 119 CYS Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain D residue 8 LEU Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 284 LEU Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain E residue 243 MET Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain F residue 103 THR Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 163 GLU Chi-restraints excluded: chain H residue 185 VAL Chi-restraints excluded: chain H residue 230 THR Chi-restraints excluded: chain H residue 257 ASP Chi-restraints excluded: chain H residue 266 THR Chi-restraints excluded: chain I residue 31 CYS Chi-restraints excluded: chain I residue 61 ILE Chi-restraints excluded: chain I residue 99 ILE Chi-restraints excluded: chain I residue 266 THR Chi-restraints excluded: chain J residue 99 ILE Chi-restraints excluded: chain K residue 244 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 118 optimal weight: 7.9990 chunk 175 optimal weight: 0.8980 chunk 224 optimal weight: 3.9990 chunk 209 optimal weight: 4.9990 chunk 79 optimal weight: 3.9990 chunk 331 optimal weight: 6.9990 chunk 262 optimal weight: 0.9990 chunk 133 optimal weight: 3.9990 chunk 296 optimal weight: 0.9980 chunk 77 optimal weight: 5.9990 chunk 300 optimal weight: 0.8980 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 62 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.126930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.080362 restraints weight = 48034.968| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 2.65 r_work: 0.2974 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2863 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.1667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 28231 Z= 0.159 Angle : 0.572 12.929 38407 Z= 0.293 Chirality : 0.041 0.171 4410 Planarity : 0.004 0.051 4759 Dihedral : 12.853 141.055 4596 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.79 % Favored : 97.15 % Rotamer: Outliers : 1.14 % Allowed : 17.13 % Favored : 81.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.15), residues: 3402 helix: 1.28 (0.14), residues: 1519 sheet: 1.14 (0.22), residues: 592 loop : -1.08 (0.17), residues: 1291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG J 247 TYR 0.058 0.001 TYR A 187 PHE 0.012 0.001 PHE F 126 TRP 0.007 0.001 TRP B 314 HIS 0.035 0.001 HIS D 148 Details of bonding type rmsd covalent geometry : bond 0.00377 (28231) covalent geometry : angle 0.57163 (38407) hydrogen bonds : bond 0.03852 ( 1333) hydrogen bonds : angle 4.16045 ( 3730) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13273.27 seconds wall clock time: 225 minutes 26.77 seconds (13526.77 seconds total)