Starting phenix.real_space_refine on Fri Jul 3 18:57:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9tyy_56447/07_2026/9tyy_56447.cif Found real_map, /net/cci-nas-00/data/ceres_data/9tyy_56447/07_2026/9tyy_56447.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9tyy_56447/07_2026/9tyy_56447.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9tyy_56447/07_2026/9tyy_56447.map" model { file = "/net/cci-nas-00/data/ceres_data/9tyy_56447/07_2026/9tyy_56447.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9tyy_56447/07_2026/9tyy_56447.cif" } resolution = 3.2 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= 0.013 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 12 9.91 5 P 36 5.49 5 S 84 5.16 5 C 9492 2.51 5 N 2736 2.21 5 O 3001 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 31 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15361 Number of models: 1 Model: "" Number of chains: 19 Chain: "O" Number of atoms: 367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 367 Classifications: {'DNA': 18} Modifications used: {'p5*END': 1} Link IDs: {'rna3p': 17} Chain: "A" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 82 Unusual residues: {'ACE': 1} Classifications: {'peptide': 10, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'PTRANS': 1, 'TRANS': 8} Chain: "B" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 82 Unusual residues: {'ACE': 1} Classifications: {'peptide': 10, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'PTRANS': 1, 'TRANS': 8} Chain: "E" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 82 Unusual residues: {'ACE': 1} Classifications: {'peptide': 10, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'PTRANS': 1, 'TRANS': 8} Chain: "C" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 82 Unusual residues: {'ACE': 1} Classifications: {'peptide': 10, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'PTRANS': 1, 'TRANS': 8} Chain: "F" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 82 Unusual residues: {'ACE': 1} Classifications: {'peptide': 10, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'PTRANS': 1, 'TRANS': 8} Chain: "D" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 82 Unusual residues: {'ACE': 1} Classifications: {'peptide': 10, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'PTRANS': 1, 'TRANS': 8} Chain: "I" Number of atoms: 2384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2384 Classifications: {'peptide': 311} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 300} Chain breaks: 1 Chain: "J" Number of atoms: 2384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2384 Classifications: {'peptide': 311} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 300} Chain breaks: 1 Chain: "K" Number of atoms: 2384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2384 Classifications: {'peptide': 311} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 10, 'TRANS': 299} Chain breaks: 1 Chain: "L" Number of atoms: 2384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2384 Classifications: {'peptide': 311} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 10, 'TRANS': 299} Chain breaks: 1 Chain: "M" Number of atoms: 2384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2384 Classifications: {'peptide': 311} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 300} Chain breaks: 1 Chain: "N" Number of atoms: 2384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2384 Classifications: {'peptide': 311} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 10, 'TRANS': 299} Chain breaks: 1 Chain: "I" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 31 Ad-hoc single atom residues: {' CA': 3} Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain breaks: 3 Chain: "J" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 31 Ad-hoc single atom residues: {' CA': 2} Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain breaks: 2 Chain: "K" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 31 Ad-hoc single atom residues: {' CA': 2} Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain breaks: 2 Chain: "L" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 31 Ad-hoc single atom residues: {' CA': 2} Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain breaks: 2 Chain: "M" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 31 Ad-hoc single atom residues: {' CA': 2} Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain breaks: 2 Chain: "N" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 31 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain breaks: 1 Time building chain proxies: 3.50, per 1000 atoms: 0.23 Number of scatterers: 15361 At special positions: 0 Unit cell: (116.85, 113.43, 158.46, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 12 19.99 S 84 16.00 P 36 15.00 O 3001 8.00 N 2736 7.00 C 9492 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.91 Conformation dependent library (CDL) restraints added in 677.6 milliseconds 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3528 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 18 sheets defined 53.1% alpha, 15.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.50 Creating SS restraints... Processing helix chain 'C' and resid 2 through 10 Proline residue: C 7 - end of helix Processing helix chain 'F' and resid 2 through 6 Processing helix chain 'I' and resid 24 through 30 Processing helix chain 'I' and resid 34 through 44 Processing helix chain 'I' and resid 48 through 54 Processing helix chain 'I' and resid 56 through 62 removed outlier: 3.581A pdb=" N LEU I 60 " --> pdb=" O PRO I 56 " (cutoff:3.500A) Processing helix chain 'I' and resid 67 through 82 removed outlier: 3.575A pdb=" N LEU I 81 " --> pdb=" O GLU I 77 " (cutoff:3.500A) Processing helix chain 'I' and resid 89 through 96 Processing helix chain 'I' and resid 106 through 114 Processing helix chain 'I' and resid 132 through 145 removed outlier: 4.309A pdb=" N GLN I 145 " --> pdb=" O ALA I 141 " (cutoff:3.500A) Processing helix chain 'I' and resid 147 through 151 Processing helix chain 'I' and resid 167 through 179 removed outlier: 3.842A 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: 3.623A pdb=" N LEU I 204 " --> pdb=" O GLN I 200 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N TYR I 205 " --> pdb=" O THR I 201 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLN I 206 " --> pdb=" O GLN I 202 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ALA I 209 " --> pdb=" O TYR I 205 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLU I 213 " --> pdb=" O ALA I 209 " (cutoff:3.500A) Processing helix chain 'I' and resid 225 through 232 removed outlier: 3.550A pdb=" N THR I 230 " --> pdb=" O ALA I 226 " (cutoff:3.500A) Processing helix chain 'I' and resid 237 through 260 Processing helix chain 'I' and resid 288 through 296 removed outlier: 3.919A pdb=" N ILE I 292 " --> pdb=" O GLY I 288 " (cutoff:3.500A) Processing helix chain 'J' and resid 24 through 29 Processing helix chain 'J' and resid 34 through 44 Processing helix chain 'J' and resid 48 through 55 Processing helix chain 'J' and resid 56 through 63 removed outlier: 3.552A pdb=" N ILE J 63 " --> pdb=" O GLU J 59 " (cutoff:3.500A) Processing helix chain 'J' and resid 67 through 82 removed outlier: 3.782A pdb=" N LYS J 80 " --> pdb=" O ALA J 76 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU J 81 " --> pdb=" O GLU J 77 " (cutoff:3.500A) Processing helix chain 'J' and resid 89 through 98 removed outlier: 3.700A pdb=" N GLU J 98 " --> pdb=" O GLN J 94 " (cutoff:3.500A) Processing helix chain 'J' and resid 106 through 114 Processing helix chain 'J' and resid 132 through 144 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 179 removed outlier: 3.844A pdb=" N LEU J 171 " --> pdb=" O ARG J 167 " (cutoff:3.500A) Processing helix chain 'J' and resid 181 through 188 Processing helix chain 'J' and resid 196 through 214 removed outlier: 3.689A pdb=" N LEU J 204 " --> pdb=" O GLN J 200 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N TYR J 205 " --> pdb=" O THR J 201 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLN J 206 " --> pdb=" O GLN J 202 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA J 209 " --> pdb=" O TYR J 205 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLU J 213 " --> pdb=" O ALA J 209 " (cutoff:3.500A) Processing helix chain 'J' and resid 225 through 232 removed outlier: 3.622A pdb=" N THR J 230 " --> pdb=" O ALA J 226 " (cutoff:3.500A) Processing helix chain 'J' and resid 237 through 260 Processing helix chain 'J' and resid 288 through 296 removed outlier: 3.779A pdb=" N ILE J 292 " --> pdb=" O GLY J 288 " (cutoff:3.500A) Processing helix chain 'K' and resid 24 through 26 No H-bonds generated for 'chain 'K' and resid 24 through 26' Processing helix chain 'K' and resid 27 through 32 removed outlier: 3.643A pdb=" N CYS K 31 " --> pdb=" O ARG K 27 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLY K 32 " --> pdb=" O LEU K 28 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 27 through 32' Processing helix chain 'K' and resid 34 through 44 Processing helix chain 'K' and resid 48 through 55 Processing helix chain 'K' and resid 56 through 63 removed outlier: 3.743A pdb=" N ILE K 63 " --> pdb=" O GLU K 59 " (cutoff:3.500A) Processing helix chain 'K' and resid 67 through 82 removed outlier: 3.576A pdb=" N LEU K 81 " --> pdb=" O GLU K 77 " (cutoff:3.500A) Processing helix chain 'K' and resid 89 through 98 removed outlier: 3.660A pdb=" N GLU K 98 " --> pdb=" O GLN K 94 " (cutoff:3.500A) Processing helix chain 'K' and resid 106 through 114 Processing helix chain 'K' and resid 132 through 144 Processing helix chain 'K' and resid 167 through 179 removed outlier: 3.636A pdb=" N LEU K 171 " --> pdb=" O ARG K 167 " (cutoff:3.500A) Processing helix chain 'K' and resid 181 through 188 Processing helix chain 'K' and resid 196 through 214 removed outlier: 3.636A pdb=" N LEU K 204 " --> pdb=" O GLN K 200 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N TYR K 205 " --> pdb=" O THR K 201 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLN K 206 " --> pdb=" O GLN K 202 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N VAL K 212 " --> pdb=" O SER K 208 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N GLU K 213 " --> pdb=" O ALA K 209 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N SER K 214 " --> pdb=" O MET K 210 " (cutoff:3.500A) Processing helix chain 'K' and resid 225 through 232 removed outlier: 4.007A pdb=" N THR K 230 " --> pdb=" O ALA K 226 " (cutoff:3.500A) Processing helix chain 'K' and resid 237 through 260 Processing helix chain 'K' and resid 288 through 296 removed outlier: 3.794A pdb=" N ILE K 292 " --> pdb=" O GLY K 288 " (cutoff:3.500A) Processing helix chain 'L' and resid 24 through 31 Processing helix chain 'L' and resid 34 through 44 Processing helix chain 'L' and resid 48 through 55 Processing helix chain 'L' and resid 56 through 63 Processing helix chain 'L' and resid 67 through 82 removed outlier: 3.519A pdb=" N LEU L 81 " --> pdb=" O GLU L 77 " (cutoff:3.500A) Processing helix chain 'L' and resid 89 through 98 Processing helix chain 'L' and resid 106 through 113 Processing helix chain 'L' and resid 132 through 144 Processing helix chain 'L' and resid 145 through 146 No H-bonds generated for 'chain 'L' and resid 145 through 146' Processing helix chain 'L' and resid 147 through 151 Processing helix chain 'L' and resid 167 through 179 removed outlier: 3.729A pdb=" N LEU L 171 " --> pdb=" O ARG L 167 " (cutoff:3.500A) Processing helix chain 'L' and resid 181 through 188 Processing helix chain 'L' and resid 196 through 214 removed outlier: 3.710A pdb=" N LEU L 204 " --> pdb=" O GLN L 200 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N TYR L 205 " --> pdb=" O THR L 201 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLN L 206 " --> pdb=" O GLN L 202 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ALA L 209 " --> pdb=" O TYR L 205 " (cutoff:3.500A) Processing helix chain 'L' and resid 225 through 232 removed outlier: 3.942A pdb=" N THR L 230 " --> pdb=" O ALA L 226 " (cutoff:3.500A) Processing helix chain 'L' and resid 237 through 260 Processing helix chain 'L' and resid 288 through 296 removed outlier: 3.728A pdb=" N ILE L 292 " --> pdb=" O GLY L 288 " (cutoff:3.500A) Processing helix chain 'M' and resid 24 through 31 Processing helix chain 'M' and resid 34 through 44 Processing helix chain 'M' and resid 48 through 55 Processing helix chain 'M' and resid 56 through 62 Processing helix chain 'M' and resid 67 through 82 removed outlier: 3.565A pdb=" N LEU M 81 " --> pdb=" O GLU M 77 " (cutoff:3.500A) Processing helix chain 'M' and resid 89 through 98 removed outlier: 3.699A pdb=" N GLU M 98 " --> pdb=" O GLN M 94 " (cutoff:3.500A) Processing helix chain 'M' and resid 106 through 114 Processing helix chain 'M' and resid 132 through 144 Processing helix chain 'M' and resid 145 through 146 No H-bonds generated for 'chain 'M' and resid 145 through 146' Processing helix chain 'M' and resid 147 through 151 Processing helix chain 'M' and resid 167 through 179 removed outlier: 3.697A pdb=" N LEU M 171 " --> pdb=" O ARG M 167 " (cutoff:3.500A) Processing helix chain 'M' and resid 181 through 188 Processing helix chain 'M' and resid 196 through 214 removed outlier: 3.811A pdb=" N LEU M 204 " --> pdb=" O GLN M 200 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N TYR M 205 " --> pdb=" O THR M 201 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLN M 206 " --> pdb=" O GLN M 202 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLU M 213 " --> pdb=" O ALA M 209 " (cutoff:3.500A) Processing helix chain 'M' and resid 225 through 232 removed outlier: 3.660A pdb=" N THR M 230 " --> pdb=" O ALA M 226 " (cutoff:3.500A) Processing helix chain 'M' and resid 237 through 260 Processing helix chain 'M' and resid 288 through 296 removed outlier: 3.744A pdb=" N ILE M 292 " --> pdb=" O GLY M 288 " (cutoff:3.500A) Processing helix chain 'N' and resid 24 through 30 Processing helix chain 'N' and resid 34 through 44 Processing helix chain 'N' and resid 48 through 55 Processing helix chain 'N' and resid 56 through 63 removed outlier: 3.699A pdb=" N ILE N 63 " --> pdb=" O GLU N 59 " (cutoff:3.500A) Processing helix chain 'N' and resid 67 through 82 Processing helix chain 'N' and resid 88 through 98 removed outlier: 3.603A pdb=" N GLU N 98 " --> pdb=" O GLN N 94 " (cutoff:3.500A) Processing helix chain 'N' and resid 106 through 113 Processing helix chain 'N' and resid 132 through 144 Processing helix chain 'N' and resid 145 through 146 No H-bonds generated for 'chain 'N' and resid 145 through 146' Processing helix chain 'N' and resid 147 through 151 Processing helix chain 'N' and resid 167 through 178 removed outlier: 3.668A pdb=" N LEU N 171 " --> pdb=" O ARG N 167 " (cutoff:3.500A) Processing helix chain 'N' and resid 181 through 188 Processing helix chain 'N' and resid 196 through 214 removed outlier: 3.712A pdb=" N LEU N 204 " --> pdb=" O GLN N 200 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N TYR N 205 " --> pdb=" O THR N 201 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLN N 206 " --> pdb=" O GLN N 202 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLU N 213 " --> pdb=" O ALA N 209 " (cutoff:3.500A) Processing helix chain 'N' and resid 225 through 232 removed outlier: 3.958A pdb=" N THR N 230 " --> pdb=" O ALA N 226 " (cutoff:3.500A) Processing helix chain 'N' and resid 237 through 260 Processing helix chain 'N' and resid 288 through 296 removed outlier: 3.708A pdb=" N ILE N 292 " --> pdb=" O GLY N 288 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'I' and resid 87 through 88 removed outlier: 3.718A pdb=" N GLY J 127 " --> pdb=" O ASN J 267 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N ARG J 299 " --> pdb=" O TYR J 315 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'I' and resid 101 through 102 Processing sheet with id=AA3, first strand: chain 'I' and resid 189 through 193 removed outlier: 5.649A pdb=" N LYS I 156 " --> pdb=" O TYR I 216 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU I 218 " --> pdb=" O LYS I 156 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLY I 127 " --> pdb=" O ASN I 267 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N ARG I 299 " --> pdb=" O TYR I 315 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'I' and resid 269 through 271 Processing sheet with id=AA5, first strand: chain 'J' and resid 87 through 88 removed outlier: 6.956A pdb=" N ALA K 157 " --> pdb=" O ALA K 190 " (cutoff:3.500A) removed outlier: 8.298A pdb=" N ALA K 192 " --> pdb=" O ALA K 157 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N TYR K 159 " --> pdb=" O ALA K 192 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N MET K 158 " --> pdb=" O ILE K 220 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N ASP K 222 " --> pdb=" O MET K 158 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ILE K 160 " --> pdb=" O ASP K 222 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N LEU K 219 " --> pdb=" O VAL K 264 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N THR K 266 " --> pdb=" O LEU K 219 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N VAL K 221 " --> pdb=" O THR K 266 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLY K 127 " --> pdb=" O ASN K 267 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N ARG K 299 " --> pdb=" O TYR K 315 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'J' and resid 101 through 102 Processing sheet with id=AA7, first strand: chain 'J' and resid 269 through 271 Processing sheet with id=AA8, first strand: chain 'K' and resid 87 through 88 removed outlier: 6.117A pdb=" N LEU L 219 " --> pdb=" O VAL L 264 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N THR L 266 " --> pdb=" O LEU L 219 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N VAL L 221 " --> pdb=" O THR L 266 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N GLY L 127 " --> pdb=" O ASN L 267 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N ARG L 299 " --> pdb=" O TYR L 315 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'K' and resid 101 through 102 Processing sheet with id=AB1, first strand: chain 'K' and resid 269 through 271 Processing sheet with id=AB2, first strand: chain 'L' and resid 87 through 88 removed outlier: 6.756A pdb=" N ALA M 157 " --> pdb=" O ALA M 190 " (cutoff:3.500A) removed outlier: 8.094A pdb=" N ALA M 192 " --> pdb=" O ALA M 157 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N TYR M 159 " --> pdb=" O ALA M 192 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N LEU M 219 " --> pdb=" O VAL M 264 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N THR M 266 " --> pdb=" O LEU M 219 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N VAL M 221 " --> pdb=" O THR M 266 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLY M 127 " --> pdb=" O ASN M 267 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ARG M 299 " --> pdb=" O TYR M 315 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 101 through 102 Processing sheet with id=AB4, first strand: chain 'L' and resid 269 through 271 Processing sheet with id=AB5, first strand: chain 'M' and resid 87 through 88 removed outlier: 6.348A pdb=" N MET N 158 " --> pdb=" O ILE N 220 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N ASP N 222 " --> pdb=" O MET N 158 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N ILE N 160 " --> pdb=" O ASP N 222 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N LEU N 219 " --> pdb=" O VAL N 264 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N THR N 266 " --> pdb=" O LEU N 219 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N VAL N 221 " --> pdb=" O THR N 266 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N ARG N 299 " --> pdb=" O TYR N 315 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'M' and resid 101 through 102 Processing sheet with id=AB7, first strand: chain 'M' and resid 269 through 271 Processing sheet with id=AB8, first strand: chain 'N' and resid 101 through 102 Processing sheet with id=AB9, first strand: chain 'N' and resid 269 through 271 799 hydrogen bonds defined for protein. 2217 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.83 Time building geometry restraints manager: 1.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4152 1.33 - 1.45: 2551 1.45 - 1.57: 8706 1.57 - 1.69: 65 1.69 - 1.81: 138 Bond restraints: 15612 Sorted by residual: bond pdb=" C ACE F 0 " pdb=" N MET F 1 " ideal model delta sigma weight residual 1.329 1.420 -0.091 2.00e-02 2.50e+03 2.07e+01 bond pdb=" C ACE C 0 " pdb=" N MET C 1 " ideal model delta sigma weight residual 1.329 1.419 -0.090 2.00e-02 2.50e+03 2.03e+01 bond pdb=" C ACE A 0 " pdb=" N MET A 1 " ideal model delta sigma weight residual 1.329 1.419 -0.090 2.00e-02 2.50e+03 2.01e+01 bond pdb=" C ACE B 0 " pdb=" N MET B 1 " ideal model delta sigma weight residual 1.329 1.419 -0.090 2.00e-02 2.50e+03 2.01e+01 bond pdb=" C ACE D 0 " pdb=" N MET D 1 " ideal model delta sigma weight residual 1.329 1.418 -0.089 2.00e-02 2.50e+03 2.00e+01 ... (remaining 15607 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.85: 20783 1.85 - 3.69: 307 3.69 - 5.54: 57 5.54 - 7.38: 2 7.38 - 9.23: 6 Bond angle restraints: 21155 Sorted by residual: angle pdb=" CB LYS I 64 " pdb=" CG LYS I 64 " pdb=" CD LYS I 64 " ideal model delta sigma weight residual 111.30 120.53 -9.23 2.30e+00 1.89e-01 1.61e+01 angle pdb=" CG MET A 1 " pdb=" SD MET A 1 " pdb=" CE MET A 1 " ideal model delta sigma weight residual 100.90 109.17 -8.27 2.20e+00 2.07e-01 1.41e+01 angle pdb=" CG MET D 1 " pdb=" SD MET D 1 " pdb=" CE MET D 1 " ideal model delta sigma weight residual 100.90 109.17 -8.27 2.20e+00 2.07e-01 1.41e+01 angle pdb=" CG MET B 1 " pdb=" SD MET B 1 " pdb=" CE MET B 1 " ideal model delta sigma weight residual 100.90 109.11 -8.21 2.20e+00 2.07e-01 1.39e+01 angle pdb=" CG MET F 1 " pdb=" SD MET F 1 " pdb=" CE MET F 1 " ideal model delta sigma weight residual 100.90 108.77 -7.87 2.20e+00 2.07e-01 1.28e+01 ... (remaining 21150 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.96: 9193 35.96 - 71.91: 420 71.91 - 107.87: 7 107.87 - 143.83: 0 143.83 - 179.79: 1 Dihedral angle restraints: 9621 sinusoidal: 4125 harmonic: 5496 Sorted by residual: dihedral pdb=" CH3 ACE F 0 " pdb=" C ACE F 0 " pdb=" N MET F 1 " pdb=" CA MET F 1 " ideal model delta sinusoidal sigma weight residual -180.00 -0.21 -179.79 1 5.00e+00 4.00e-02 7.68e+02 dihedral pdb=" CA ASP L 149 " pdb=" CB ASP L 149 " pdb=" CG ASP L 149 " pdb=" OD1 ASP L 149 " ideal model delta sinusoidal sigma weight residual -30.00 -89.33 59.33 1 2.00e+01 2.50e-03 1.18e+01 dihedral pdb=" CG ARG K 170 " pdb=" CD ARG K 170 " pdb=" NE ARG K 170 " pdb=" CZ ARG K 170 " ideal model delta sinusoidal sigma weight residual 180.00 135.15 44.85 2 1.50e+01 4.44e-03 1.06e+01 ... (remaining 9618 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 1362 0.026 - 0.051: 634 0.051 - 0.077: 228 0.077 - 0.102: 128 0.102 - 0.128: 54 Chirality restraints: 2406 Sorted by residual: chirality pdb=" C3' DC O 6 " pdb=" C4' DC O 6 " pdb=" O3' DC O 6 " pdb=" C2' DC O 6 " both_signs ideal model delta sigma weight residual False -2.73 -2.60 -0.13 2.00e-01 2.50e+01 4.09e-01 chirality pdb=" P DA O 1 " pdb=" OP1 DA O 1 " pdb=" OP2 DA O 1 " pdb=" O5' DA O 1 " both_signs ideal model delta sigma weight residual True 2.34 -2.46 -0.13 2.00e-01 2.50e+01 4.09e-01 chirality pdb=" CA ILE M 160 " pdb=" N ILE M 160 " pdb=" C ILE M 160 " pdb=" CB ILE M 160 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.93e-01 ... (remaining 2403 not shown) Planarity restraints: 2658 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL J 82 " 0.032 5.00e-02 4.00e+02 4.93e-02 3.89e+00 pdb=" N PRO J 83 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO J 83 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO J 83 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG I 130 " -0.009 2.00e-02 2.50e+03 1.70e-02 2.88e+00 pdb=" C ARG I 130 " 0.029 2.00e-02 2.50e+03 pdb=" O ARG I 130 " -0.011 2.00e-02 2.50e+03 pdb=" N THR I 131 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG N 130 " -0.008 2.00e-02 2.50e+03 1.57e-02 2.45e+00 pdb=" C ARG N 130 " 0.027 2.00e-02 2.50e+03 pdb=" O ARG N 130 " -0.010 2.00e-02 2.50e+03 pdb=" N THR N 131 " -0.009 2.00e-02 2.50e+03 ... (remaining 2655 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 3592 2.80 - 3.32: 14465 3.32 - 3.85: 26706 3.85 - 4.37: 33388 4.37 - 4.90: 56355 Nonbonded interactions: 134506 Sorted by model distance: nonbonded pdb="CA CA L 403 " pdb=" O1G ATP M 401 " model vdw 2.269 3.250 nonbonded pdb=" OG1 THR M 134 " pdb="CA CA M 402 " model vdw 2.284 3.250 nonbonded pdb=" O2G ATP M 401 " pdb="CA CA M 402 " model vdw 2.307 3.250 nonbonded pdb=" O SER L 296 " pdb="CA CA L 403 " model vdw 2.312 3.250 nonbonded pdb=" OG1 THR L 134 " pdb="CA CA L 402 " model vdw 2.314 3.250 ... (remaining 134501 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = (chain 'I' and resid 21 through 402) selection = (chain 'J' and resid 21 through 402) selection = (chain 'K' and resid 21 through 402) selection = (chain 'L' and resid 21 through 402) selection = (chain 'M' and resid 21 through 402) selection = chain 'N' } 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: 5.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.530 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 14.230 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.091 15612 Z= 0.198 Angle : 0.572 9.227 21155 Z= 0.314 Chirality : 0.039 0.128 2406 Planarity : 0.004 0.061 2658 Dihedral : 17.772 179.786 6093 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 1.03 % Allowed : 20.74 % Favored : 78.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.16 % 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: -0.22 (0.19), residues: 1890 helix: 0.56 (0.17), residues: 912 sheet: -0.00 (0.36), residues: 216 loop : -0.97 (0.21), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 3 TYR 0.014 0.001 TYR K 315 PHE 0.016 0.002 PHE L 126 HIS 0.002 0.000 HIS I 138 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.20 (15612) covalent geometry : angle 0.57189 / 0.31 (21155) hydrogen bonds : bond 0.15382 / 14.09 ( 799) hydrogen bonds : angle 7.12206 / 6.56 ( 2217) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 117 time to evaluate : 0.384 Fit side-chains REVERT: B 1 MET cc_start: 0.8421 (OUTLIER) cc_final: 0.7910 (mtt) REVERT: D 1 MET cc_start: 0.8430 (mtp) cc_final: 0.7659 (mtp) REVERT: L 326 MET cc_start: 0.8444 (ttp) cc_final: 0.8184 (ttt) REVERT: N 40 LYS cc_start: 0.7655 (OUTLIER) cc_final: 0.7284 (ttpt) outliers start: 16 outliers final: 5 residues processed: 127 average time/residue: 0.1348 time to fit residues: 24.4578 Evaluate side-chains 107 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 100 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain M residue 90 THR Chi-restraints excluded: chain M residue 99 ILE Chi-restraints excluded: chain N residue 40 LYS Chi-restraints excluded: chain N residue 99 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 98 optimal weight: 0.6980 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 4.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** J 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 242 GLN ** M 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 200 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.136223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.108944 restraints weight = 15308.083| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 1.46 r_work: 0.3037 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2897 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.0708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15612 Z= 0.136 Angle : 0.488 5.907 21155 Z= 0.263 Chirality : 0.039 0.132 2406 Planarity : 0.004 0.042 2658 Dihedral : 12.077 179.043 2565 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.20 % Allowed : 20.16 % Favored : 77.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.16 % 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: 0.07 (0.19), residues: 1890 helix: 0.73 (0.17), residues: 900 sheet: -1.11 (0.30), residues: 282 loop : -0.13 (0.23), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG J 306 TYR 0.018 0.001 TYR N 216 PHE 0.014 0.002 PHE M 327 HIS 0.003 0.001 HIS L 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.14 (15612) covalent geometry : angle 0.48836 / 0.26 (21155) hydrogen bonds : bond 0.03521 / 3.20 ( 799) hydrogen bonds : angle 5.25779 / 4.98 ( 2217) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 90 time to evaluate : 0.577 Fit side-chains REVERT: B 1 MET cc_start: 0.8195 (mtm) cc_final: 0.7589 (mtp) REVERT: F 1 MET cc_start: 0.7699 (OUTLIER) cc_final: 0.7435 (mtt) REVERT: D 1 MET cc_start: 0.8251 (mtp) cc_final: 0.7320 (mtt) REVERT: I 150 ARG cc_start: 0.8165 (ttp80) cc_final: 0.7706 (mtp180) REVERT: K 187 ASP cc_start: 0.8236 (m-30) cc_final: 0.7876 (m-30) REVERT: L 306 ARG cc_start: 0.7055 (OUTLIER) cc_final: 0.6653 (ptt-90) REVERT: L 326 MET cc_start: 0.8663 (ttp) cc_final: 0.8348 (ttt) REVERT: N 27 ARG cc_start: 0.7058 (mmm160) cc_final: 0.6757 (tpt90) REVERT: N 109 LEU cc_start: 0.7877 (OUTLIER) cc_final: 0.7401 (mp) REVERT: N 145 GLN cc_start: 0.8756 (mt0) cc_final: 0.8400 (mp10) outliers start: 34 outliers final: 13 residues processed: 116 average time/residue: 0.1495 time to fit residues: 25.4292 Evaluate side-chains 100 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 84 time to evaluate : 0.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain I residue 99 ILE Chi-restraints excluded: chain I residue 266 THR Chi-restraints excluded: chain I residue 326 MET Chi-restraints excluded: chain J residue 230 THR Chi-restraints excluded: chain K residue 88 THR Chi-restraints excluded: chain K residue 148 ILE Chi-restraints excluded: chain K residue 169 GLU Chi-restraints excluded: chain K residue 251 MET Chi-restraints excluded: chain L residue 36 ASN Chi-restraints excluded: chain L residue 90 THR Chi-restraints excluded: chain L residue 149 ASP Chi-restraints excluded: chain L residue 306 ARG Chi-restraints excluded: chain M residue 99 ILE Chi-restraints excluded: chain N residue 99 ILE Chi-restraints excluded: chain N residue 109 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 103 optimal weight: 1.9990 chunk 133 optimal weight: 4.9990 chunk 163 optimal weight: 0.9990 chunk 188 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 78 optimal weight: 0.9990 chunk 4 optimal weight: 0.7980 chunk 56 optimal weight: 0.9990 chunk 40 optimal weight: 0.9980 chunk 118 optimal weight: 3.9990 chunk 90 optimal weight: 3.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 242 GLN ** J 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 330 ASN ** N 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 294 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.134069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.107871 restraints weight = 15600.841| |-----------------------------------------------------------------------------| r_work (start): 0.3143 rms_B_bonded: 1.37 r_work: 0.3001 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2860 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.1039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15612 Z= 0.133 Angle : 0.446 5.818 21155 Z= 0.240 Chirality : 0.039 0.127 2406 Planarity : 0.004 0.040 2658 Dihedral : 12.023 179.268 2554 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 1.87 % Allowed : 20.28 % Favored : 77.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.16 % 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: 0.16 (0.19), residues: 1890 helix: 0.86 (0.17), residues: 894 sheet: -1.09 (0.31), residues: 282 loop : -0.14 (0.23), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG J 215 TYR 0.013 0.001 TYR N 315 PHE 0.013 0.001 PHE N 248 HIS 0.003 0.000 HIS I 294 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 (15612) covalent geometry : angle 0.44554 / 0.24 (21155) hydrogen bonds : bond 0.03154 / 2.80 ( 799) hydrogen bonds : angle 4.85152 / 4.56 ( 2217) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 105 time to evaluate : 0.506 Fit side-chains revert: symmetry clash REVERT: B 1 MET cc_start: 0.8270 (mtm) cc_final: 0.7717 (mtp) REVERT: D 1 MET cc_start: 0.8350 (mtp) cc_final: 0.7494 (mtt) REVERT: I 114 GLN cc_start: 0.8280 (OUTLIER) cc_final: 0.8035 (mt0) REVERT: I 150 ARG cc_start: 0.8217 (ttp80) cc_final: 0.7843 (mtp180) REVERT: L 306 ARG cc_start: 0.7078 (OUTLIER) cc_final: 0.6732 (ptt-90) REVERT: L 326 MET cc_start: 0.8666 (ttp) cc_final: 0.8359 (ttt) REVERT: M 235 ARG cc_start: 0.8049 (ttp80) cc_final: 0.7672 (tpt90) REVERT: N 27 ARG cc_start: 0.7091 (mmm160) cc_final: 0.6796 (tpt90) REVERT: N 59 GLU cc_start: 0.7496 (mt-10) cc_final: 0.7239 (tt0) REVERT: N 109 LEU cc_start: 0.7971 (OUTLIER) cc_final: 0.7467 (mp) REVERT: N 145 GLN cc_start: 0.8815 (mt0) cc_final: 0.8478 (mp10) REVERT: N 154 GLU cc_start: 0.8502 (mt-10) cc_final: 0.7817 (tt0) REVERT: N 243 MET cc_start: 0.7698 (mtm) cc_final: 0.7295 (mtt) outliers start: 29 outliers final: 15 residues processed: 129 average time/residue: 0.1476 time to fit residues: 27.8426 Evaluate side-chains 116 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 98 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 99 ILE Chi-restraints excluded: chain I residue 114 GLN Chi-restraints excluded: chain I residue 233 SER Chi-restraints excluded: chain I residue 266 THR Chi-restraints excluded: chain I residue 326 MET Chi-restraints excluded: chain J residue 230 THR Chi-restraints excluded: chain K residue 88 THR Chi-restraints excluded: chain K residue 148 ILE Chi-restraints excluded: chain K residue 169 GLU Chi-restraints excluded: chain L residue 48 THR Chi-restraints excluded: chain L residue 99 ILE Chi-restraints excluded: chain L residue 148 ILE Chi-restraints excluded: chain L residue 214 SER Chi-restraints excluded: chain L residue 306 ARG Chi-restraints excluded: chain M residue 99 ILE Chi-restraints excluded: chain N residue 99 ILE Chi-restraints excluded: chain N residue 109 LEU Chi-restraints excluded: chain N residue 149 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 89 optimal weight: 4.9990 chunk 95 optimal weight: 4.9990 chunk 131 optimal weight: 4.9990 chunk 162 optimal weight: 3.9990 chunk 75 optimal weight: 0.5980 chunk 119 optimal weight: 2.9990 chunk 71 optimal weight: 4.9990 chunk 5 optimal weight: 0.9980 chunk 20 optimal weight: 9.9990 chunk 188 optimal weight: 0.8980 chunk 130 optimal weight: 6.9990 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** J 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 290 ASN ** N 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.127936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.100943 restraints weight = 15864.337| |-----------------------------------------------------------------------------| r_work (start): 0.3003 rms_B_bonded: 1.44 r_work: 0.2852 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2709 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.2709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8691 moved from start: 0.1476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 15612 Z= 0.209 Angle : 0.502 6.269 21155 Z= 0.268 Chirality : 0.041 0.133 2406 Planarity : 0.004 0.050 2658 Dihedral : 12.217 178.770 2551 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 3.04 % Allowed : 19.38 % Favored : 77.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.16 % 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: -0.06 (0.19), residues: 1890 helix: 0.65 (0.17), residues: 894 sheet: -1.37 (0.31), residues: 282 loop : -0.13 (0.23), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG J 235 TYR 0.018 0.002 TYR N 315 PHE 0.015 0.002 PHE N 248 HIS 0.003 0.001 HIS L 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00478 / 0.21 (15612) covalent geometry : angle 0.50227 / 0.27 (21155) hydrogen bonds : bond 0.03300 / 2.89 ( 799) hydrogen bonds : angle 4.92271 / 4.58 ( 2217) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 140 time to evaluate : 0.551 Fit side-chains revert: symmetry clash REVERT: B 1 MET cc_start: 0.8314 (mtm) cc_final: 0.7840 (mtp) REVERT: D 1 MET cc_start: 0.8478 (OUTLIER) cc_final: 0.7658 (mtt) REVERT: I 43 GLU cc_start: 0.8043 (mt-10) cc_final: 0.7658 (mt-10) REVERT: I 163 GLU cc_start: 0.7064 (OUTLIER) cc_final: 0.6709 (tt0) REVERT: I 308 GLU cc_start: 0.7759 (pt0) cc_final: 0.7084 (pm20) REVERT: J 258 GLU cc_start: 0.7793 (OUTLIER) cc_final: 0.7390 (tt0) REVERT: K 98 GLU cc_start: 0.7953 (pt0) cc_final: 0.7619 (pt0) REVERT: K 114 GLN cc_start: 0.8680 (OUTLIER) cc_final: 0.8263 (mt0) REVERT: L 43 GLU cc_start: 0.8072 (mt-10) cc_final: 0.7452 (mp0) REVERT: L 96 ARG cc_start: 0.8112 (mmm160) cc_final: 0.7887 (mtp85) REVERT: L 98 GLU cc_start: 0.7522 (tt0) cc_final: 0.7161 (tt0) REVERT: L 306 ARG cc_start: 0.7263 (OUTLIER) cc_final: 0.6869 (ptt-90) REVERT: L 326 MET cc_start: 0.8674 (ttp) cc_final: 0.8362 (ttt) REVERT: M 108 GLU cc_start: 0.7297 (mm-30) cc_final: 0.6893 (mt-10) REVERT: M 118 GLU cc_start: 0.8028 (tt0) cc_final: 0.7634 (tt0) REVERT: M 235 ARG cc_start: 0.8271 (ttp80) cc_final: 0.7814 (tpt90) REVERT: N 40 LYS cc_start: 0.7055 (OUTLIER) cc_final: 0.6818 (ttpt) REVERT: N 59 GLU cc_start: 0.7523 (mt-10) cc_final: 0.7314 (tt0) REVERT: N 109 LEU cc_start: 0.8030 (OUTLIER) cc_final: 0.7452 (mp) REVERT: N 118 GLU cc_start: 0.7723 (tt0) cc_final: 0.7256 (tt0) REVERT: N 145 GLN cc_start: 0.8794 (mt0) cc_final: 0.8462 (mp10) REVERT: N 202 GLN cc_start: 0.7914 (mm-40) cc_final: 0.7319 (tm-30) REVERT: N 243 MET cc_start: 0.7732 (mtm) cc_final: 0.7170 (mtt) outliers start: 47 outliers final: 26 residues processed: 179 average time/residue: 0.1401 time to fit residues: 36.5191 Evaluate side-chains 161 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 128 time to evaluate : 0.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain I residue 99 ILE Chi-restraints excluded: chain I residue 112 LEU Chi-restraints excluded: chain I residue 163 GLU Chi-restraints excluded: chain I residue 233 SER Chi-restraints excluded: chain I residue 326 MET Chi-restraints excluded: chain J residue 99 ILE Chi-restraints excluded: chain J residue 230 THR Chi-restraints excluded: chain J residue 258 GLU Chi-restraints excluded: chain K residue 48 THR Chi-restraints excluded: chain K residue 88 THR Chi-restraints excluded: chain K residue 99 ILE Chi-restraints excluded: chain K residue 114 GLN Chi-restraints excluded: chain K residue 148 ILE Chi-restraints excluded: chain K residue 169 GLU Chi-restraints excluded: chain L residue 48 THR Chi-restraints excluded: chain L residue 90 THR Chi-restraints excluded: chain L residue 99 ILE Chi-restraints excluded: chain L residue 148 ILE Chi-restraints excluded: chain L residue 149 ASP Chi-restraints excluded: chain L residue 214 SER Chi-restraints excluded: chain L residue 306 ARG Chi-restraints excluded: chain M residue 99 ILE Chi-restraints excluded: chain M residue 112 LEU Chi-restraints excluded: chain M residue 233 SER Chi-restraints excluded: chain M residue 266 THR Chi-restraints excluded: chain N residue 40 LYS Chi-restraints excluded: chain N residue 99 ILE Chi-restraints excluded: chain N residue 109 LEU Chi-restraints excluded: chain N residue 149 ASP Chi-restraints excluded: chain N residue 187 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 51 optimal weight: 6.9990 chunk 169 optimal weight: 0.4980 chunk 124 optimal weight: 0.9990 chunk 48 optimal weight: 4.9990 chunk 187 optimal weight: 0.9990 chunk 183 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 chunk 175 optimal weight: 5.9990 chunk 34 optimal weight: 5.9990 chunk 163 optimal weight: 5.9990 chunk 103 optimal weight: 1.9990 overall best weight: 1.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** J 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.129303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.101284 restraints weight = 15848.358| |-----------------------------------------------------------------------------| r_work (start): 0.3066 rms_B_bonded: 1.50 r_work: 0.2945 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2803 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8663 moved from start: 0.1599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 15612 Z= 0.155 Angle : 0.451 5.598 21155 Z= 0.244 Chirality : 0.039 0.131 2406 Planarity : 0.003 0.041 2658 Dihedral : 12.166 178.815 2551 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 2.71 % Allowed : 20.03 % Favored : 77.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.16 % 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: 0.05 (0.19), residues: 1890 helix: 0.71 (0.17), residues: 900 sheet: -1.33 (0.31), residues: 282 loop : -0.03 (0.23), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG J 306 TYR 0.012 0.001 TYR N 315 PHE 0.010 0.001 PHE N 248 HIS 0.003 0.000 HIS L 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.16 (15612) covalent geometry : angle 0.45113 / 0.24 (21155) hydrogen bonds : bond 0.03016 / 2.66 ( 799) hydrogen bonds : angle 4.77765 / 4.43 ( 2217) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 130 time to evaluate : 0.555 Fit side-chains revert: symmetry clash REVERT: B 1 MET cc_start: 0.8284 (mtm) cc_final: 0.7851 (mtp) REVERT: D 1 MET cc_start: 0.8495 (mtp) cc_final: 0.8243 (mtm) REVERT: I 27 ARG cc_start: 0.6268 (tpt-90) cc_final: 0.6068 (mtp180) REVERT: I 43 GLU cc_start: 0.8036 (mt-10) cc_final: 0.7657 (mt-10) REVERT: I 163 GLU cc_start: 0.7047 (OUTLIER) cc_final: 0.6688 (tt0) REVERT: I 308 GLU cc_start: 0.7745 (pt0) cc_final: 0.7087 (pm20) REVERT: J 258 GLU cc_start: 0.7750 (OUTLIER) cc_final: 0.7356 (tt0) REVERT: K 98 GLU cc_start: 0.7933 (pt0) cc_final: 0.7623 (pt0) REVERT: K 114 GLN cc_start: 0.8667 (OUTLIER) cc_final: 0.8242 (mt0) REVERT: L 43 GLU cc_start: 0.8079 (mt-10) cc_final: 0.7439 (mp0) REVERT: L 98 GLU cc_start: 0.7475 (tt0) cc_final: 0.7029 (tt0) REVERT: L 108 GLU cc_start: 0.7674 (mt-10) cc_final: 0.7208 (tt0) REVERT: L 306 ARG cc_start: 0.7206 (OUTLIER) cc_final: 0.6833 (ptt-90) REVERT: L 326 MET cc_start: 0.8650 (ttp) cc_final: 0.8392 (ttt) REVERT: M 108 GLU cc_start: 0.7262 (mm-30) cc_final: 0.6861 (mt-10) REVERT: M 118 GLU cc_start: 0.8008 (tt0) cc_final: 0.7583 (tt0) REVERT: M 235 ARG cc_start: 0.8262 (ttp80) cc_final: 0.7848 (tpt90) REVERT: N 40 LYS cc_start: 0.7051 (OUTLIER) cc_final: 0.6791 (ttpt) REVERT: N 109 LEU cc_start: 0.8009 (OUTLIER) cc_final: 0.7438 (mp) REVERT: N 145 GLN cc_start: 0.8819 (OUTLIER) cc_final: 0.8547 (mp10) REVERT: N 243 MET cc_start: 0.7679 (mtm) cc_final: 0.7111 (mtt) outliers start: 42 outliers final: 22 residues processed: 163 average time/residue: 0.1473 time to fit residues: 35.1497 Evaluate side-chains 153 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 124 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain I residue 158 MET Chi-restraints excluded: chain I residue 163 GLU Chi-restraints excluded: chain I residue 233 SER Chi-restraints excluded: chain I residue 270 VAL Chi-restraints excluded: chain I residue 326 MET Chi-restraints excluded: chain J residue 230 THR Chi-restraints excluded: chain J residue 258 GLU Chi-restraints excluded: chain K residue 88 THR Chi-restraints excluded: chain K residue 99 ILE Chi-restraints excluded: chain K residue 114 GLN Chi-restraints excluded: chain K residue 148 ILE Chi-restraints excluded: chain K residue 169 GLU Chi-restraints excluded: chain L residue 48 THR Chi-restraints excluded: chain L residue 99 ILE Chi-restraints excluded: chain L residue 149 ASP Chi-restraints excluded: chain L residue 214 SER Chi-restraints excluded: chain L residue 306 ARG Chi-restraints excluded: chain M residue 99 ILE Chi-restraints excluded: chain M residue 125 MET Chi-restraints excluded: chain M residue 266 THR Chi-restraints excluded: chain M residue 332 ASP Chi-restraints excluded: chain N residue 40 LYS Chi-restraints excluded: chain N residue 99 ILE Chi-restraints excluded: chain N residue 109 LEU Chi-restraints excluded: chain N residue 112 LEU Chi-restraints excluded: chain N residue 145 GLN Chi-restraints excluded: chain N residue 149 ASP Chi-restraints excluded: chain N residue 187 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 16 optimal weight: 0.7980 chunk 15 optimal weight: 0.9980 chunk 73 optimal weight: 6.9990 chunk 125 optimal weight: 0.9990 chunk 96 optimal weight: 4.9990 chunk 111 optimal weight: 2.9990 chunk 52 optimal weight: 0.2980 chunk 148 optimal weight: 2.9990 chunk 88 optimal weight: 0.0470 chunk 56 optimal weight: 0.8980 chunk 81 optimal weight: 1.9990 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 242 GLN ** J 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.132131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.104337 restraints weight = 15539.109| |-----------------------------------------------------------------------------| r_work (start): 0.3107 rms_B_bonded: 1.48 r_work: 0.2988 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2843 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.1654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 15612 Z= 0.108 Angle : 0.417 5.282 21155 Z= 0.226 Chirality : 0.038 0.138 2406 Planarity : 0.003 0.045 2658 Dihedral : 12.074 178.938 2551 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.71 % Allowed : 20.22 % Favored : 77.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.16 % 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: 0.31 (0.19), residues: 1890 helix: 0.95 (0.17), residues: 900 sheet: -1.23 (0.31), residues: 282 loop : 0.06 (0.23), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG J 306 TYR 0.008 0.001 TYR L 178 PHE 0.008 0.001 PHE M 327 HIS 0.003 0.000 HIS L 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.11 (15612) covalent geometry : angle 0.41696 / 0.23 (21155) hydrogen bonds : bond 0.02672 / 2.37 ( 799) hydrogen bonds : angle 4.52068 / 4.19 ( 2217) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 130 time to evaluate : 0.612 Fit side-chains REVERT: B 1 MET cc_start: 0.8234 (mtm) cc_final: 0.7824 (mtp) REVERT: D 1 MET cc_start: 0.8499 (OUTLIER) cc_final: 0.7689 (mtt) REVERT: I 43 GLU cc_start: 0.8013 (mt-10) cc_final: 0.7612 (mt-10) REVERT: I 163 GLU cc_start: 0.6946 (OUTLIER) cc_final: 0.6593 (tt0) REVERT: I 176 GLU cc_start: 0.7501 (tm-30) cc_final: 0.6941 (tp30) REVERT: I 308 GLU cc_start: 0.7699 (pt0) cc_final: 0.7057 (pm20) REVERT: J 258 GLU cc_start: 0.7695 (OUTLIER) cc_final: 0.7231 (tt0) REVERT: K 114 GLN cc_start: 0.8615 (OUTLIER) cc_final: 0.8167 (mt0) REVERT: L 43 GLU cc_start: 0.8073 (mt-10) cc_final: 0.7378 (mp0) REVERT: L 98 GLU cc_start: 0.7464 (tt0) cc_final: 0.7047 (tt0) REVERT: L 108 GLU cc_start: 0.7659 (mt-10) cc_final: 0.7203 (tt0) REVERT: L 211 MET cc_start: 0.8832 (mtm) cc_final: 0.8604 (mtp) REVERT: L 306 ARG cc_start: 0.7154 (OUTLIER) cc_final: 0.6726 (ptt-90) REVERT: L 308 GLU cc_start: 0.7752 (pt0) cc_final: 0.7408 (pm20) REVERT: L 326 MET cc_start: 0.8659 (ttp) cc_final: 0.8402 (ttt) REVERT: M 70 LYS cc_start: 0.7355 (tppp) cc_final: 0.6981 (ttpt) REVERT: M 107 LYS cc_start: 0.7482 (mtmm) cc_final: 0.6786 (mmtm) REVERT: M 108 GLU cc_start: 0.7220 (mm-30) cc_final: 0.6821 (mt-10) REVERT: M 118 GLU cc_start: 0.7988 (tt0) cc_final: 0.7558 (tt0) REVERT: M 235 ARG cc_start: 0.8195 (ttp80) cc_final: 0.7845 (tpt90) REVERT: N 40 LYS cc_start: 0.6941 (OUTLIER) cc_final: 0.6698 (ttpt) REVERT: N 145 GLN cc_start: 0.8757 (OUTLIER) cc_final: 0.8507 (mp10) REVERT: N 154 GLU cc_start: 0.8474 (mt-10) cc_final: 0.8104 (tt0) REVERT: N 202 GLN cc_start: 0.7843 (mm-40) cc_final: 0.7210 (tm-30) outliers start: 42 outliers final: 26 residues processed: 162 average time/residue: 0.1352 time to fit residues: 32.9275 Evaluate side-chains 162 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 129 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain I residue 99 ILE Chi-restraints excluded: chain I residue 158 MET Chi-restraints excluded: chain I residue 163 GLU Chi-restraints excluded: chain I residue 233 SER Chi-restraints excluded: chain I residue 270 VAL Chi-restraints excluded: chain I residue 326 MET Chi-restraints excluded: chain J residue 230 THR Chi-restraints excluded: chain J residue 258 GLU Chi-restraints excluded: chain K residue 48 THR Chi-restraints excluded: chain K residue 88 THR Chi-restraints excluded: chain K residue 99 ILE Chi-restraints excluded: chain K residue 114 GLN Chi-restraints excluded: chain K residue 148 ILE Chi-restraints excluded: chain K residue 149 ASP Chi-restraints excluded: chain K residue 169 GLU Chi-restraints excluded: chain L residue 48 THR Chi-restraints excluded: chain L residue 90 THR Chi-restraints excluded: chain L residue 99 ILE Chi-restraints excluded: chain L residue 149 ASP Chi-restraints excluded: chain L residue 214 SER Chi-restraints excluded: chain L residue 306 ARG Chi-restraints excluded: chain M residue 99 ILE Chi-restraints excluded: chain M residue 125 MET Chi-restraints excluded: chain M residue 266 THR Chi-restraints excluded: chain M residue 332 ASP Chi-restraints excluded: chain N residue 40 LYS Chi-restraints excluded: chain N residue 60 LEU Chi-restraints excluded: chain N residue 99 ILE Chi-restraints excluded: chain N residue 112 LEU Chi-restraints excluded: chain N residue 145 GLN Chi-restraints excluded: chain N residue 149 ASP Chi-restraints excluded: chain N residue 187 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 116 optimal weight: 4.9990 chunk 34 optimal weight: 5.9990 chunk 68 optimal weight: 3.9990 chunk 1 optimal weight: 0.9990 chunk 5 optimal weight: 0.8980 chunk 144 optimal weight: 4.9990 chunk 165 optimal weight: 0.1980 chunk 49 optimal weight: 0.7980 chunk 184 optimal weight: 1.9990 chunk 189 optimal weight: 0.0570 chunk 103 optimal weight: 3.9990 overall best weight: 0.5900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** J 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 200 GLN ** L 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.132582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.104969 restraints weight = 15403.917| |-----------------------------------------------------------------------------| r_work (start): 0.3103 rms_B_bonded: 1.47 r_work: 0.2984 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2844 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.1723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 15612 Z= 0.108 Angle : 0.415 5.342 21155 Z= 0.224 Chirality : 0.038 0.128 2406 Planarity : 0.003 0.042 2658 Dihedral : 12.058 178.439 2551 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.78 % Allowed : 19.96 % Favored : 77.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.16 % 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: 0.41 (0.19), residues: 1890 helix: 1.06 (0.17), residues: 900 sheet: -1.20 (0.32), residues: 282 loop : 0.09 (0.23), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG J 306 TYR 0.007 0.001 TYR N 315 PHE 0.009 0.001 PHE M 327 HIS 0.003 0.000 HIS L 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.11 (15612) covalent geometry : angle 0.41486 / 0.22 (21155) hydrogen bonds : bond 0.02642 / 2.35 ( 799) hydrogen bonds : angle 4.47371 / 4.14 ( 2217) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 137 time to evaluate : 0.535 Fit side-chains REVERT: B 1 MET cc_start: 0.8239 (mtm) cc_final: 0.7841 (mtp) REVERT: D 1 MET cc_start: 0.8478 (mtp) cc_final: 0.7708 (mtt) REVERT: I 43 GLU cc_start: 0.8009 (mt-10) cc_final: 0.7636 (mt-10) REVERT: I 163 GLU cc_start: 0.6929 (OUTLIER) cc_final: 0.6578 (tt0) REVERT: I 176 GLU cc_start: 0.7494 (tm-30) cc_final: 0.6934 (tp30) REVERT: I 308 GLU cc_start: 0.7715 (pt0) cc_final: 0.7086 (pm20) REVERT: J 258 GLU cc_start: 0.7689 (OUTLIER) cc_final: 0.7205 (tt0) REVERT: K 42 GLU cc_start: 0.8018 (mt-10) cc_final: 0.7784 (mt-10) REVERT: K 98 GLU cc_start: 0.7845 (pt0) cc_final: 0.7557 (pt0) REVERT: K 114 GLN cc_start: 0.8605 (OUTLIER) cc_final: 0.8148 (mt0) REVERT: L 43 GLU cc_start: 0.8069 (mt-10) cc_final: 0.7364 (mp0) REVERT: L 98 GLU cc_start: 0.7430 (tt0) cc_final: 0.7040 (tt0) REVERT: L 108 GLU cc_start: 0.7635 (mt-10) cc_final: 0.7172 (tt0) REVERT: L 211 MET cc_start: 0.8849 (mtm) cc_final: 0.8589 (mtp) REVERT: L 306 ARG cc_start: 0.7135 (OUTLIER) cc_final: 0.6715 (ptt-90) REVERT: L 308 GLU cc_start: 0.7717 (pt0) cc_final: 0.7394 (pm20) REVERT: L 326 MET cc_start: 0.8650 (ttp) cc_final: 0.8358 (ttt) REVERT: M 70 LYS cc_start: 0.7360 (tppp) cc_final: 0.6987 (ttpt) REVERT: M 107 LYS cc_start: 0.7476 (mtmm) cc_final: 0.6780 (mmtm) REVERT: M 108 GLU cc_start: 0.7208 (mm-30) cc_final: 0.6818 (mt-10) REVERT: M 118 GLU cc_start: 0.7993 (tt0) cc_final: 0.7568 (tt0) REVERT: M 235 ARG cc_start: 0.8191 (ttp80) cc_final: 0.7848 (tpt90) REVERT: N 40 LYS cc_start: 0.6990 (OUTLIER) cc_final: 0.6744 (ttpt) REVERT: N 145 GLN cc_start: 0.8732 (OUTLIER) cc_final: 0.8483 (mp10) REVERT: N 154 GLU cc_start: 0.8482 (mt-10) cc_final: 0.8116 (tt0) REVERT: N 202 GLN cc_start: 0.7807 (mm-40) cc_final: 0.7189 (tm-30) REVERT: N 284 LYS cc_start: 0.8341 (mttm) cc_final: 0.7867 (mtmm) outliers start: 43 outliers final: 27 residues processed: 169 average time/residue: 0.1472 time to fit residues: 36.0448 Evaluate side-chains 163 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 130 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain I residue 163 GLU Chi-restraints excluded: chain I residue 233 SER Chi-restraints excluded: chain I residue 270 VAL Chi-restraints excluded: chain I residue 326 MET Chi-restraints excluded: chain J residue 125 MET Chi-restraints excluded: chain J residue 161 ASP Chi-restraints excluded: chain J residue 230 THR Chi-restraints excluded: chain J residue 258 GLU Chi-restraints excluded: chain K residue 48 THR Chi-restraints excluded: chain K residue 88 THR Chi-restraints excluded: chain K residue 99 ILE Chi-restraints excluded: chain K residue 114 GLN Chi-restraints excluded: chain K residue 148 ILE Chi-restraints excluded: chain K residue 149 ASP Chi-restraints excluded: chain K residue 169 GLU Chi-restraints excluded: chain L residue 36 ASN Chi-restraints excluded: chain L residue 48 THR Chi-restraints excluded: chain L residue 90 THR Chi-restraints excluded: chain L residue 99 ILE Chi-restraints excluded: chain L residue 149 ASP Chi-restraints excluded: chain L residue 214 SER Chi-restraints excluded: chain L residue 306 ARG Chi-restraints excluded: chain M residue 99 ILE Chi-restraints excluded: chain M residue 125 MET Chi-restraints excluded: chain M residue 149 ASP Chi-restraints excluded: chain M residue 332 ASP Chi-restraints excluded: chain N residue 40 LYS Chi-restraints excluded: chain N residue 60 LEU Chi-restraints excluded: chain N residue 99 ILE Chi-restraints excluded: chain N residue 145 GLN Chi-restraints excluded: chain N residue 149 ASP Chi-restraints excluded: chain N residue 187 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 177 optimal weight: 3.9990 chunk 179 optimal weight: 4.9990 chunk 107 optimal weight: 0.7980 chunk 127 optimal weight: 1.9990 chunk 120 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 111 optimal weight: 2.9990 chunk 37 optimal weight: 5.9990 chunk 52 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 189 optimal weight: 4.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 242 GLN J 145 GLN ** J 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 94 GLN ** N 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.126644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.098456 restraints weight = 16022.819| |-----------------------------------------------------------------------------| r_work (start): 0.3013 rms_B_bonded: 1.51 r_work: 0.2892 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2749 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8684 moved from start: 0.1922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 15612 Z= 0.241 Angle : 0.501 6.254 21155 Z= 0.267 Chirality : 0.041 0.131 2406 Planarity : 0.004 0.042 2658 Dihedral : 12.326 178.620 2551 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.97 % Allowed : 20.03 % Favored : 77.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.16 % 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: 0.01 (0.19), residues: 1890 helix: 0.69 (0.17), residues: 900 sheet: -1.55 (0.31), residues: 282 loop : 0.02 (0.23), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG J 306 TYR 0.017 0.002 TYR N 315 PHE 0.014 0.002 PHE K 327 HIS 0.003 0.001 HIS L 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00574 / 0.24 (15612) covalent geometry : angle 0.50131 / 0.27 (21155) hydrogen bonds : bond 0.03217 / 2.81 ( 799) hydrogen bonds : angle 4.80707 / 4.42 ( 2217) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 154 time to evaluate : 0.580 Fit side-chains REVERT: B 1 MET cc_start: 0.8326 (mtm) cc_final: 0.7892 (mtp) REVERT: I 43 GLU cc_start: 0.8034 (mt-10) cc_final: 0.7663 (mt-10) REVERT: I 163 GLU cc_start: 0.7132 (OUTLIER) cc_final: 0.6779 (tt0) REVERT: I 308 GLU cc_start: 0.7738 (pt0) cc_final: 0.7088 (pm20) REVERT: J 39 LYS cc_start: 0.6131 (OUTLIER) cc_final: 0.5742 (mmmt) REVERT: J 59 GLU cc_start: 0.7580 (tt0) cc_final: 0.7312 (tt0) REVERT: J 77 GLU cc_start: 0.7577 (tm-30) cc_final: 0.7144 (tm-30) REVERT: J 108 GLU cc_start: 0.7069 (mm-30) cc_final: 0.6827 (mm-30) REVERT: J 128 GLU cc_start: 0.7964 (pt0) cc_final: 0.7685 (pt0) REVERT: J 258 GLU cc_start: 0.7837 (OUTLIER) cc_final: 0.7476 (tt0) REVERT: K 114 GLN cc_start: 0.8698 (OUTLIER) cc_final: 0.8281 (mt0) REVERT: K 303 ARG cc_start: 0.8344 (ttp80) cc_final: 0.8104 (ttp-110) REVERT: L 43 GLU cc_start: 0.8078 (mt-10) cc_final: 0.7354 (mp0) REVERT: L 96 ARG cc_start: 0.8158 (mmm160) cc_final: 0.7949 (mtp85) REVERT: L 98 GLU cc_start: 0.7436 (tt0) cc_final: 0.6920 (tt0) REVERT: L 108 GLU cc_start: 0.7686 (mt-10) cc_final: 0.7218 (tt0) REVERT: L 306 ARG cc_start: 0.7307 (OUTLIER) cc_final: 0.6884 (ptt-90) REVERT: L 326 MET cc_start: 0.8668 (ttp) cc_final: 0.8418 (ttt) REVERT: M 70 LYS cc_start: 0.7352 (tppp) cc_final: 0.6943 (ttpt) REVERT: M 108 GLU cc_start: 0.7268 (mm-30) cc_final: 0.6862 (mt-10) REVERT: M 118 GLU cc_start: 0.8106 (tt0) cc_final: 0.7685 (tt0) REVERT: M 235 ARG cc_start: 0.8375 (ttp80) cc_final: 0.7924 (tpt90) REVERT: N 40 LYS cc_start: 0.6993 (OUTLIER) cc_final: 0.6752 (ttpt) REVERT: N 118 GLU cc_start: 0.7826 (tt0) cc_final: 0.7364 (tt0) REVERT: N 145 GLN cc_start: 0.8796 (mt0) cc_final: 0.8463 (mp10) REVERT: N 154 GLU cc_start: 0.8502 (mt-10) cc_final: 0.8132 (tt0) REVERT: N 202 GLN cc_start: 0.7866 (mm-40) cc_final: 0.7340 (tm-30) outliers start: 46 outliers final: 34 residues processed: 188 average time/residue: 0.1467 time to fit residues: 39.6753 Evaluate side-chains 186 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 146 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain I residue 99 ILE Chi-restraints excluded: chain I residue 163 GLU Chi-restraints excluded: chain I residue 233 SER Chi-restraints excluded: chain I residue 266 THR Chi-restraints excluded: chain I residue 270 VAL Chi-restraints excluded: chain I residue 326 MET Chi-restraints excluded: chain J residue 39 LYS Chi-restraints excluded: chain J residue 84 MET Chi-restraints excluded: chain J residue 125 MET Chi-restraints excluded: chain J residue 161 ASP Chi-restraints excluded: chain J residue 230 THR Chi-restraints excluded: chain J residue 258 GLU Chi-restraints excluded: chain J residue 266 THR Chi-restraints excluded: chain K residue 48 THR Chi-restraints excluded: chain K residue 88 THR Chi-restraints excluded: chain K residue 99 ILE Chi-restraints excluded: chain K residue 114 GLN Chi-restraints excluded: chain K residue 148 ILE Chi-restraints excluded: chain K residue 149 ASP Chi-restraints excluded: chain K residue 169 GLU Chi-restraints excluded: chain K residue 230 THR Chi-restraints excluded: chain L residue 36 ASN Chi-restraints excluded: chain L residue 48 THR Chi-restraints excluded: chain L residue 90 THR Chi-restraints excluded: chain L residue 99 ILE Chi-restraints excluded: chain L residue 214 SER Chi-restraints excluded: chain L residue 306 ARG Chi-restraints excluded: chain M residue 99 ILE Chi-restraints excluded: chain M residue 149 ASP Chi-restraints excluded: chain M residue 187 ASP Chi-restraints excluded: chain M residue 266 THR Chi-restraints excluded: chain M residue 332 ASP Chi-restraints excluded: chain N residue 40 LYS Chi-restraints excluded: chain N residue 99 ILE Chi-restraints excluded: chain N residue 109 LEU Chi-restraints excluded: chain N residue 112 LEU Chi-restraints excluded: chain N residue 149 ASP Chi-restraints excluded: chain N residue 187 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 70 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 chunk 131 optimal weight: 2.9990 chunk 180 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 chunk 171 optimal weight: 0.8980 chunk 33 optimal weight: 0.5980 chunk 4 optimal weight: 0.9990 chunk 135 optimal weight: 2.9990 chunk 106 optimal weight: 5.9990 chunk 36 optimal weight: 2.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... J 94 GLN ** J 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 202 GLN ** L 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.130018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.102109 restraints weight = 15654.742| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 1.48 r_work: 0.2953 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2811 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8645 moved from start: 0.1954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15612 Z= 0.123 Angle : 0.432 5.354 21155 Z= 0.234 Chirality : 0.038 0.149 2406 Planarity : 0.003 0.044 2658 Dihedral : 12.185 179.002 2551 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.52 % Allowed : 20.48 % Favored : 77.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.16 % 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: 0.23 (0.19), residues: 1890 helix: 0.89 (0.17), residues: 900 sheet: -1.40 (0.31), residues: 282 loop : 0.08 (0.23), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG J 306 TYR 0.009 0.001 TYR J 315 PHE 0.008 0.001 PHE M 327 HIS 0.003 0.000 HIS L 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 (15612) covalent geometry : angle 0.43194 / 0.23 (21155) hydrogen bonds : bond 0.02797 / 2.46 ( 799) hydrogen bonds : angle 4.60110 / 4.22 ( 2217) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 145 time to evaluate : 0.571 Fit side-chains REVERT: B 1 MET cc_start: 0.8239 (mtm) cc_final: 0.7875 (mtt) REVERT: I 43 GLU cc_start: 0.8026 (mt-10) cc_final: 0.7652 (mt-10) REVERT: I 163 GLU cc_start: 0.7061 (OUTLIER) cc_final: 0.6726 (tt0) REVERT: I 176 GLU cc_start: 0.7520 (tm-30) cc_final: 0.6961 (tp30) REVERT: I 308 GLU cc_start: 0.7730 (pt0) cc_final: 0.7107 (pm20) REVERT: J 39 LYS cc_start: 0.6107 (OUTLIER) cc_final: 0.5752 (mmmt) REVERT: J 258 GLU cc_start: 0.7757 (OUTLIER) cc_final: 0.7338 (tt0) REVERT: K 42 GLU cc_start: 0.8068 (mt-10) cc_final: 0.7834 (mt-10) REVERT: K 114 GLN cc_start: 0.8642 (OUTLIER) cc_final: 0.8201 (mt0) REVERT: K 326 MET cc_start: 0.8587 (ttm) cc_final: 0.8332 (tpp) REVERT: L 43 GLU cc_start: 0.8087 (mt-10) cc_final: 0.7368 (mp0) REVERT: L 98 GLU cc_start: 0.7409 (tt0) cc_final: 0.6992 (tt0) REVERT: L 108 GLU cc_start: 0.7663 (mt-10) cc_final: 0.7211 (tt0) REVERT: L 235 ARG cc_start: 0.8028 (tpt-90) cc_final: 0.7811 (tpt90) REVERT: L 306 ARG cc_start: 0.7205 (OUTLIER) cc_final: 0.6746 (ttp80) REVERT: L 326 MET cc_start: 0.8656 (ttp) cc_final: 0.8424 (ttt) REVERT: M 70 LYS cc_start: 0.7371 (tppp) cc_final: 0.6952 (ttpt) REVERT: M 108 GLU cc_start: 0.7230 (mm-30) cc_final: 0.6829 (mt-10) REVERT: M 118 GLU cc_start: 0.8045 (tt0) cc_final: 0.7632 (tt0) REVERT: M 235 ARG cc_start: 0.8332 (ttp80) cc_final: 0.7934 (tpt90) REVERT: N 40 LYS cc_start: 0.7069 (OUTLIER) cc_final: 0.6816 (ttpt) REVERT: N 118 GLU cc_start: 0.7818 (tt0) cc_final: 0.7359 (tt0) REVERT: N 145 GLN cc_start: 0.8769 (OUTLIER) cc_final: 0.8485 (mp10) REVERT: N 154 GLU cc_start: 0.8458 (mt-10) cc_final: 0.8114 (tt0) REVERT: N 202 GLN cc_start: 0.7823 (mm-40) cc_final: 0.7251 (tm-30) outliers start: 39 outliers final: 28 residues processed: 174 average time/residue: 0.1321 time to fit residues: 33.7225 Evaluate side-chains 177 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 142 time to evaluate : 0.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain I residue 163 GLU Chi-restraints excluded: chain I residue 270 VAL Chi-restraints excluded: chain I residue 326 MET Chi-restraints excluded: chain J residue 39 LYS Chi-restraints excluded: chain J residue 125 MET Chi-restraints excluded: chain J residue 161 ASP Chi-restraints excluded: chain J residue 230 THR Chi-restraints excluded: chain J residue 258 GLU Chi-restraints excluded: chain K residue 48 THR Chi-restraints excluded: chain K residue 88 THR Chi-restraints excluded: chain K residue 99 ILE Chi-restraints excluded: chain K residue 114 GLN Chi-restraints excluded: chain K residue 148 ILE Chi-restraints excluded: chain K residue 149 ASP Chi-restraints excluded: chain K residue 169 GLU Chi-restraints excluded: chain L residue 36 ASN Chi-restraints excluded: chain L residue 48 THR Chi-restraints excluded: chain L residue 99 ILE Chi-restraints excluded: chain L residue 214 SER Chi-restraints excluded: chain L residue 306 ARG Chi-restraints excluded: chain M residue 99 ILE Chi-restraints excluded: chain M residue 125 MET Chi-restraints excluded: chain M residue 149 ASP Chi-restraints excluded: chain M residue 187 ASP Chi-restraints excluded: chain M residue 266 THR Chi-restraints excluded: chain M residue 332 ASP Chi-restraints excluded: chain N residue 40 LYS Chi-restraints excluded: chain N residue 60 LEU Chi-restraints excluded: chain N residue 99 ILE Chi-restraints excluded: chain N residue 112 LEU Chi-restraints excluded: chain N residue 145 GLN Chi-restraints excluded: chain N residue 149 ASP Chi-restraints excluded: chain N residue 187 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 8 optimal weight: 5.9990 chunk 15 optimal weight: 3.9990 chunk 34 optimal weight: 5.9990 chunk 111 optimal weight: 0.7980 chunk 29 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 3 optimal weight: 0.3980 chunk 1 optimal weight: 4.9990 chunk 50 optimal weight: 0.6980 chunk 65 optimal weight: 0.0270 chunk 92 optimal weight: 0.8980 overall best weight: 0.5638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 242 GLN ** J 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 202 GLN ** L 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.131616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.103894 restraints weight = 15723.277| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 1.48 r_work: 0.2975 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2829 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.1963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 15612 Z= 0.108 Angle : 0.415 5.421 21155 Z= 0.225 Chirality : 0.038 0.142 2406 Planarity : 0.003 0.043 2658 Dihedral : 12.101 179.123 2551 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.26 % Allowed : 20.48 % Favored : 77.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.16 % 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: 0.41 (0.20), residues: 1890 helix: 1.05 (0.17), residues: 900 sheet: -1.30 (0.32), residues: 282 loop : 0.14 (0.23), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG J 306 TYR 0.008 0.001 TYR L 301 PHE 0.009 0.001 PHE M 327 HIS 0.003 0.000 HIS L 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.11 (15612) covalent geometry : angle 0.41493 / 0.22 (21155) hydrogen bonds : bond 0.02625 / 2.32 ( 799) hydrogen bonds : angle 4.43987 / 4.08 ( 2217) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 138 time to evaluate : 0.569 Fit side-chains REVERT: B 1 MET cc_start: 0.8247 (mtm) cc_final: 0.7893 (mtt) REVERT: D 1 MET cc_start: 0.8414 (mtm) cc_final: 0.7925 (mtp) REVERT: I 43 GLU cc_start: 0.8011 (mt-10) cc_final: 0.7638 (mt-10) REVERT: I 163 GLU cc_start: 0.7008 (OUTLIER) cc_final: 0.6682 (tt0) REVERT: I 176 GLU cc_start: 0.7519 (tm-30) cc_final: 0.6908 (tp30) REVERT: I 308 GLU cc_start: 0.7718 (pt0) cc_final: 0.7093 (pm20) REVERT: J 258 GLU cc_start: 0.7700 (OUTLIER) cc_final: 0.7249 (tt0) REVERT: K 42 GLU cc_start: 0.8018 (mt-10) cc_final: 0.7778 (mt-10) REVERT: K 114 GLN cc_start: 0.8595 (OUTLIER) cc_final: 0.8135 (mt0) REVERT: K 326 MET cc_start: 0.8561 (ttm) cc_final: 0.8339 (tpp) REVERT: L 43 GLU cc_start: 0.8085 (mt-10) cc_final: 0.7358 (mp0) REVERT: L 98 GLU cc_start: 0.7421 (tt0) cc_final: 0.6991 (tt0) REVERT: L 108 GLU cc_start: 0.7637 (mt-10) cc_final: 0.7184 (tt0) REVERT: L 235 ARG cc_start: 0.7914 (tpt-90) cc_final: 0.7596 (tpt90) REVERT: L 306 ARG cc_start: 0.7201 (OUTLIER) cc_final: 0.6726 (ttp80) REVERT: L 326 MET cc_start: 0.8671 (ttp) cc_final: 0.8381 (ttt) REVERT: M 27 ARG cc_start: 0.7315 (tpt90) cc_final: 0.6850 (tmt170) REVERT: M 70 LYS cc_start: 0.7336 (tppp) cc_final: 0.6918 (ttpt) REVERT: M 108 GLU cc_start: 0.7217 (mm-30) cc_final: 0.6814 (mt-10) REVERT: M 118 GLU cc_start: 0.8023 (tt0) cc_final: 0.7494 (tt0) REVERT: M 235 ARG cc_start: 0.8299 (ttp80) cc_final: 0.7923 (tpt90) REVERT: N 40 LYS cc_start: 0.6994 (OUTLIER) cc_final: 0.6748 (ttpt) REVERT: N 118 GLU cc_start: 0.7818 (tt0) cc_final: 0.7328 (tt0) REVERT: N 145 GLN cc_start: 0.8711 (OUTLIER) cc_final: 0.8425 (mp10) REVERT: N 149 ASP cc_start: 0.7702 (OUTLIER) cc_final: 0.7468 (p0) REVERT: N 154 GLU cc_start: 0.8458 (mt-10) cc_final: 0.8123 (tt0) REVERT: N 202 GLN cc_start: 0.7775 (mm-40) cc_final: 0.7209 (tm-30) REVERT: N 303 ARG cc_start: 0.8231 (ttp-110) cc_final: 0.7989 (ttp-110) outliers start: 35 outliers final: 25 residues processed: 166 average time/residue: 0.1384 time to fit residues: 33.5187 Evaluate side-chains 167 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 135 time to evaluate : 0.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain I residue 99 ILE Chi-restraints excluded: chain I residue 163 GLU Chi-restraints excluded: chain I residue 270 VAL Chi-restraints excluded: chain I residue 326 MET Chi-restraints excluded: chain J residue 125 MET Chi-restraints excluded: chain J residue 161 ASP Chi-restraints excluded: chain J residue 230 THR Chi-restraints excluded: chain J residue 258 GLU Chi-restraints excluded: chain J residue 266 THR Chi-restraints excluded: chain K residue 48 THR Chi-restraints excluded: chain K residue 99 ILE Chi-restraints excluded: chain K residue 114 GLN Chi-restraints excluded: chain K residue 148 ILE Chi-restraints excluded: chain K residue 149 ASP Chi-restraints excluded: chain K residue 169 GLU Chi-restraints excluded: chain L residue 36 ASN Chi-restraints excluded: chain L residue 48 THR Chi-restraints excluded: chain L residue 90 THR Chi-restraints excluded: chain L residue 214 SER Chi-restraints excluded: chain L residue 306 ARG Chi-restraints excluded: chain M residue 99 ILE Chi-restraints excluded: chain M residue 125 MET Chi-restraints excluded: chain M residue 149 ASP Chi-restraints excluded: chain M residue 266 THR Chi-restraints excluded: chain N residue 40 LYS Chi-restraints excluded: chain N residue 60 LEU Chi-restraints excluded: chain N residue 112 LEU Chi-restraints excluded: chain N residue 145 GLN Chi-restraints excluded: chain N residue 149 ASP Chi-restraints excluded: chain N residue 187 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 87 optimal weight: 0.9980 chunk 5 optimal weight: 3.9990 chunk 27 optimal weight: 5.9990 chunk 3 optimal weight: 0.0050 chunk 156 optimal weight: 0.9990 chunk 0 optimal weight: 7.9990 chunk 79 optimal weight: 1.9990 chunk 129 optimal weight: 0.6980 chunk 2 optimal weight: 2.9990 chunk 81 optimal weight: 0.9980 chunk 115 optimal weight: 2.9990 overall best weight: 0.7396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** J 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 135 GLN ** N 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.131542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.105410 restraints weight = 15694.146| |-----------------------------------------------------------------------------| r_work (start): 0.3117 rms_B_bonded: 1.33 r_work: 0.2976 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2835 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 moved from start: 0.2002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15612 Z= 0.114 Angle : 0.415 5.496 21155 Z= 0.224 Chirality : 0.038 0.140 2406 Planarity : 0.003 0.042 2658 Dihedral : 12.096 179.089 2549 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.20 % Allowed : 20.54 % Favored : 77.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.16 % 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: 0.45 (0.20), residues: 1890 helix: 1.07 (0.17), residues: 900 sheet: -1.29 (0.32), residues: 282 loop : 0.19 (0.23), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG J 306 TYR 0.008 0.001 TYR N 315 PHE 0.009 0.001 PHE M 327 HIS 0.003 0.000 HIS L 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.11 (15612) covalent geometry : angle 0.41486 / 0.22 (21155) hydrogen bonds : bond 0.02618 / 2.31 ( 799) hydrogen bonds : angle 4.41430 / 4.05 ( 2217) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4383.25 seconds wall clock time: 76 minutes 0.99 seconds (4560.99 seconds total)