Starting phenix.real_space_refine on Thu Aug 6 14:19:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9tyy_56447/08_2026/9tyy_56447.cif Found real_map, /net/cci-nas-00/data/ceres_data/9tyy_56447/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/9tyy_56447/08_2026/9tyy_56447.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9tyy_56447/08_2026/9tyy_56447.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9tyy_56447/08_2026/9tyy_56447.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9tyy_56447/08_2026/9tyy_56447.map" } 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-2.2rc3-6140/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, 34 Unusual residues: {' CA': 3, 'ATP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "J" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' CA': 2, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "K" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' CA': 2, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "L" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' CA': 2, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "M" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' CA': 2, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "N" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' CA': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.96, per 1000 atoms: 0.19 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: 1.11 Conformation dependent library (CDL) restraints added in 636.7 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: 0.47 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: 2.40 Time building geometry restraints manager: 1.52 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 2.510 nonbonded pdb=" OG1 THR M 134 " pdb="CA CA M 402 " model vdw 2.284 2.510 nonbonded pdb=" O2G ATP M 401 " pdb="CA CA M 402 " model vdw 2.307 2.510 nonbonded pdb=" O SER L 296 " pdb="CA CA L 403 " model vdw 2.312 2.510 nonbonded pdb=" OG1 THR L 134 " pdb="CA CA L 402 " model vdw 2.314 2.510 ... (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: 5.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.480 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 13.000 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:0.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.830 ------------------------------------------------------------------------------- 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 0.57215 / 0.31 (21155) hydrogen bonds : bond 0.15382 / 14.11 ( 799) hydrogen bonds : angle 7.12206 / 6.57 ( 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 : 0.360 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: 0.1346 time to fit residues: 24.6445 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 : 0.451 ------------------------------------------------------------------------------- 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 = 0.3407 r_free = 0.3407 target = 0.135695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.109753 restraints weight = 15270.323| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 1.35 r_work: 0.3029 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2892 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.0656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15612 Z= 0.137 Angle : 0.486 5.932 21155 Z= 0.263 Chirality : 0.039 0.132 2406 Planarity : 0.004 0.043 2658 Dihedral : 12.103 179.286 2565 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 2.20 % Allowed : 20.22 % 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: 0.09 (0.19), residues: 1890 helix: 0.75 (0.17), residues: 900 sheet: -1.09 (0.30), residues: 282 loop : -0.14 (0.23), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG J 306 TYR 0.018 0.001 TYR N 216 PHE 0.014 0.002 PHE J 126 HIS 0.003 0.000 HIS L 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.14 (15612) covalent geometry : angle 0.48633 / 0.26 (21155) hydrogen bonds : bond 0.03704 / 3.39 ( 799) hydrogen bonds : angle 5.31948 / 5.04 ( 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 120 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 86 time to evaluate : 0.575 Fit side-chains REVERT: B 1 MET cc_start: 0.8209 (mtm) cc_final: 0.7607 (mtp) REVERT: F 1 MET cc_start: 0.7705 (OUTLIER) cc_final: 0.7425 (mtt) REVERT: D 1 MET cc_start: 0.8249 (mtp) cc_final: 0.7342 (mtt) REVERT: I 150 ARG cc_start: 0.8177 (ttp80) cc_final: 0.7738 (mtp180) REVERT: K 187 ASP cc_start: 0.8233 (m-30) cc_final: 0.7873 (m-30) REVERT: L 306 ARG cc_start: 0.7053 (OUTLIER) cc_final: 0.6677 (ptt-90) REVERT: L 326 MET cc_start: 0.8627 (ttp) cc_final: 0.8316 (ttt) REVERT: N 109 LEU cc_start: 0.7932 (OUTLIER) cc_final: 0.7458 (mp) REVERT: N 145 GLN cc_start: 0.8764 (mt0) cc_final: 0.8409 (mp10) outliers start: 34 outliers final: 13 residues processed: 113 average time/residue: 0.1361 time to fit residues: 23.3196 Evaluate side-chains 98 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 82 time to evaluate : 0.564 ------------------------------------------------------------------------------- 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: 0.9980 chunk 133 optimal weight: 4.9990 chunk 163 optimal weight: 1.9990 chunk 188 optimal weight: 0.9990 chunk 53 optimal weight: 0.6980 chunk 78 optimal weight: 0.8980 chunk 4 optimal weight: 0.9980 chunk 56 optimal weight: 0.9990 chunk 40 optimal weight: 0.6980 chunk 118 optimal weight: 3.9990 chunk 90 optimal weight: 3.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.3391 r_free = 0.3391 target = 0.134123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.107858 restraints weight = 15542.941| |-----------------------------------------------------------------------------| r_work (start): 0.3130 rms_B_bonded: 1.37 r_work: 0.2998 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2860 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 moved from start: 0.1012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15612 Z= 0.125 Angle : 0.440 5.761 21155 Z= 0.237 Chirality : 0.038 0.126 2406 Planarity : 0.003 0.040 2658 Dihedral : 12.035 179.197 2554 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 1.87 % Allowed : 20.22 % Favored : 77.91 % 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: 0.21 (0.19), residues: 1890 helix: 0.91 (0.17), residues: 894 sheet: -1.08 (0.30), residues: 282 loop : -0.15 (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 K 315 PHE 0.012 0.001 PHE N 248 HIS 0.002 0.000 HIS L 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.13 (15612) covalent geometry : angle 0.43997 / 0.24 (21155) hydrogen bonds : bond 0.03097 / 2.77 ( 799) hydrogen bonds : angle 4.81808 / 4.54 ( 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 125 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 96 time to evaluate : 0.601 Fit side-chains revert: symmetry clash REVERT: B 1 MET cc_start: 0.8263 (mtm) cc_final: 0.7710 (mtp) REVERT: D 1 MET cc_start: 0.8333 (mtp) cc_final: 0.7497 (mtt) REVERT: I 114 GLN cc_start: 0.8270 (OUTLIER) cc_final: 0.8022 (mt0) REVERT: I 150 ARG cc_start: 0.8204 (ttp80) cc_final: 0.7812 (mtp180) REVERT: K 187 ASP cc_start: 0.8194 (m-30) cc_final: 0.7842 (m-30) REVERT: L 306 ARG cc_start: 0.7066 (OUTLIER) cc_final: 0.6684 (ptt-90) REVERT: L 326 MET cc_start: 0.8613 (ttp) cc_final: 0.8305 (ttt) REVERT: N 27 ARG cc_start: 0.7056 (mmm160) cc_final: 0.6761 (tpt90) REVERT: N 59 GLU cc_start: 0.7470 (mt-10) cc_final: 0.7214 (tt0) REVERT: N 109 LEU cc_start: 0.7936 (OUTLIER) cc_final: 0.7423 (mp) REVERT: N 145 GLN cc_start: 0.8797 (mt0) cc_final: 0.8480 (mp10) REVERT: N 243 MET cc_start: 0.7668 (mtm) cc_final: 0.7258 (mtt) outliers start: 29 outliers final: 16 residues processed: 120 average time/residue: 0.1387 time to fit residues: 24.9055 Evaluate side-chains 111 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 92 time to evaluate : 0.575 ------------------------------------------------------------------------------- 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 158 MET 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 149 ASP Chi-restraints excluded: chain L residue 214 SER Chi-restraints excluded: chain L residue 306 ARG 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: 3.9990 chunk 95 optimal weight: 1.9990 chunk 131 optimal weight: 4.9990 chunk 162 optimal weight: 2.9990 chunk 75 optimal weight: 0.3980 chunk 119 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 5 optimal weight: 0.6980 chunk 20 optimal weight: 9.9990 chunk 188 optimal weight: 1.9990 chunk 130 optimal weight: 6.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- 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 = 0.3334 r_free = 0.3334 target = 0.129224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.102858 restraints weight = 15741.076| |-----------------------------------------------------------------------------| r_work (start): 0.3077 rms_B_bonded: 1.38 r_work: 0.2929 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2786 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8680 moved from start: 0.1334 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= 0.178 Angle : 0.476 6.102 21155 Z= 0.254 Chirality : 0.040 0.129 2406 Planarity : 0.004 0.046 2658 Dihedral : 12.149 179.421 2549 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 2.65 % Allowed : 19.57 % Favored : 77.78 % 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: 0.08 (0.19), residues: 1890 helix: 0.76 (0.17), residues: 900 sheet: -1.24 (0.31), residues: 282 loop : -0.09 (0.23), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG J 235 TYR 0.016 0.001 TYR N 315 PHE 0.014 0.002 PHE N 248 HIS 0.003 0.001 HIS I 294 Details of bonding type rmsd/Z covalent geometry : bond 0.00405 / 0.18 (15612) covalent geometry : angle 0.47587 / 0.25 (21155) hydrogen bonds : bond 0.03152 / 2.78 ( 799) hydrogen bonds : angle 4.83393 / 4.51 ( 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 182 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 141 time to evaluate : 0.584 Fit side-chains revert: symmetry clash REVERT: B 1 MET cc_start: 0.8309 (mtm) cc_final: 0.7824 (mtp) REVERT: D 1 MET cc_start: 0.8495 (mtp) cc_final: 0.7633 (mtt) REVERT: I 43 GLU cc_start: 0.8038 (mt-10) cc_final: 0.7687 (mt-10) REVERT: I 308 GLU cc_start: 0.7768 (pt0) cc_final: 0.7093 (pm20) REVERT: J 258 GLU cc_start: 0.7784 (OUTLIER) cc_final: 0.7347 (tt0) REVERT: K 114 GLN cc_start: 0.8690 (OUTLIER) cc_final: 0.8283 (mt0) REVERT: L 43 GLU cc_start: 0.8068 (mt-10) cc_final: 0.7457 (mp0) REVERT: L 98 GLU cc_start: 0.7519 (tt0) cc_final: 0.7124 (tt0) REVERT: L 306 ARG cc_start: 0.7231 (OUTLIER) cc_final: 0.6837 (ptt-90) REVERT: L 308 GLU cc_start: 0.7840 (pt0) cc_final: 0.7485 (pm20) REVERT: L 326 MET cc_start: 0.8661 (ttp) cc_final: 0.8354 (ttt) REVERT: M 108 GLU cc_start: 0.7288 (mm-30) cc_final: 0.6901 (mt-10) REVERT: M 118 GLU cc_start: 0.7970 (tt0) cc_final: 0.7536 (tt0) REVERT: M 235 ARG cc_start: 0.8207 (ttp80) cc_final: 0.7778 (tpt90) REVERT: N 23 GLN cc_start: 0.7998 (tt0) cc_final: 0.7705 (mt0) REVERT: N 27 ARG cc_start: 0.7086 (mmm160) cc_final: 0.6717 (tpt90) REVERT: N 40 LYS cc_start: 0.7047 (OUTLIER) cc_final: 0.6808 (ttpt) REVERT: N 59 GLU cc_start: 0.7494 (mt-10) cc_final: 0.7263 (tt0) REVERT: N 109 LEU cc_start: 0.8005 (OUTLIER) cc_final: 0.7457 (mp) REVERT: N 145 GLN cc_start: 0.8802 (mt0) cc_final: 0.8495 (mp10) REVERT: N 202 GLN cc_start: 0.7911 (mm-40) cc_final: 0.7308 (tm-30) REVERT: N 243 MET cc_start: 0.7712 (mtm) cc_final: 0.7160 (mtt) outliers start: 41 outliers final: 25 residues processed: 176 average time/residue: 0.1385 time to fit residues: 36.0974 Evaluate side-chains 154 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 124 time to evaluate : 0.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain I residue 99 ILE Chi-restraints excluded: chain I residue 112 LEU Chi-restraints excluded: chain I residue 158 MET 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 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 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 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: 3.9990 chunk 169 optimal weight: 4.9990 chunk 124 optimal weight: 0.9990 chunk 48 optimal weight: 5.9990 chunk 187 optimal weight: 0.5980 chunk 183 optimal weight: 3.9990 chunk 90 optimal weight: 6.9990 chunk 175 optimal weight: 6.9990 chunk 34 optimal weight: 6.9990 chunk 163 optimal weight: 6.9990 chunk 103 optimal weight: 0.9980 overall best weight: 2.1186 ------------------------------------------------------------------------------- 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** ** 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 = 0.3307 r_free = 0.3307 target = 0.126972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.100236 restraints weight = 15977.977| |-----------------------------------------------------------------------------| r_work (start): 0.3043 rms_B_bonded: 1.42 r_work: 0.2894 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2751 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.2751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8710 moved from start: 0.1589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 15612 Z= 0.219 Angle : 0.490 6.072 21155 Z= 0.263 Chirality : 0.041 0.132 2406 Planarity : 0.004 0.041 2658 Dihedral : 12.265 178.544 2549 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 3.23 % Allowed : 19.51 % 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: -0.08 (0.19), residues: 1890 helix: 0.60 (0.17), residues: 900 sheet: -1.42 (0.31), residues: 282 loop : -0.07 (0.23), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG J 306 TYR 0.017 0.002 TYR N 315 PHE 0.014 0.002 PHE N 248 HIS 0.003 0.001 HIS L 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00512 / 0.22 (15612) covalent geometry : angle 0.48978 / 0.26 (21155) hydrogen bonds : bond 0.03249 / 2.84 ( 799) hydrogen bonds : angle 4.90821 / 4.55 ( 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 180 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 130 time to evaluate : 0.621 Fit side-chains revert: symmetry clash REVERT: B 1 MET cc_start: 0.8331 (mtm) cc_final: 0.7853 (mtp) REVERT: I 27 ARG cc_start: 0.6323 (tpt-90) cc_final: 0.6095 (mtp180) REVERT: I 43 GLU cc_start: 0.8051 (mt-10) cc_final: 0.7708 (mt-10) REVERT: I 308 GLU cc_start: 0.7774 (pt0) cc_final: 0.7113 (pm20) REVERT: J 258 GLU cc_start: 0.7854 (OUTLIER) cc_final: 0.7458 (tt0) REVERT: K 114 GLN cc_start: 0.8712 (OUTLIER) cc_final: 0.8300 (mt0) REVERT: L 43 GLU cc_start: 0.8103 (mt-10) cc_final: 0.7472 (mp0) REVERT: L 96 ARG cc_start: 0.8139 (mmm160) cc_final: 0.7917 (mtp85) REVERT: L 98 GLU cc_start: 0.7521 (tt0) cc_final: 0.7135 (tt0) REVERT: L 306 ARG cc_start: 0.7335 (OUTLIER) cc_final: 0.6913 (ptt-90) REVERT: L 326 MET cc_start: 0.8652 (ttp) cc_final: 0.8339 (ttt) REVERT: M 108 GLU cc_start: 0.7312 (mm-30) cc_final: 0.6915 (mt-10) REVERT: M 118 GLU cc_start: 0.8033 (tt0) cc_final: 0.7618 (tt0) REVERT: M 235 ARG cc_start: 0.8325 (ttp80) cc_final: 0.7879 (tpt90) REVERT: N 27 ARG cc_start: 0.7138 (mmm160) cc_final: 0.6767 (tpt90) REVERT: N 40 LYS cc_start: 0.7075 (OUTLIER) cc_final: 0.6804 (ttpt) REVERT: N 109 LEU cc_start: 0.8093 (OUTLIER) cc_final: 0.7504 (mp) REVERT: N 118 GLU cc_start: 0.7770 (tt0) cc_final: 0.7320 (tt0) REVERT: N 145 GLN cc_start: 0.8834 (OUTLIER) cc_final: 0.8555 (mp10) REVERT: N 202 GLN cc_start: 0.7904 (mm-40) cc_final: 0.7362 (tm-30) REVERT: N 243 MET cc_start: 0.7770 (mtm) cc_final: 0.7209 (mtt) outliers start: 50 outliers final: 28 residues processed: 170 average time/residue: 0.1453 time to fit residues: 36.3208 Evaluate side-chains 160 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 126 time to evaluate : 0.556 ------------------------------------------------------------------------------- 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 233 SER Chi-restraints excluded: chain I residue 270 VAL Chi-restraints excluded: chain I residue 326 MET Chi-restraints excluded: chain J residue 163 GLU 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 K residue 230 THR 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 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 233 SER 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: 6.9990 chunk 15 optimal weight: 5.9990 chunk 73 optimal weight: 0.7980 chunk 125 optimal weight: 0.0570 chunk 96 optimal weight: 3.9990 chunk 111 optimal weight: 0.8980 chunk 52 optimal weight: 4.9990 chunk 148 optimal weight: 1.9990 chunk 88 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 81 optimal weight: 0.9980 overall best weight: 0.9500 ------------------------------------------------------------------------------- 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 = 0.3337 r_free = 0.3337 target = 0.129416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.102946 restraints weight = 15636.273| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 1.39 r_work: 0.2935 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2792 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.2792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8676 moved from start: 0.1655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15612 Z= 0.132 Angle : 0.433 5.499 21155 Z= 0.234 Chirality : 0.038 0.140 2406 Planarity : 0.003 0.042 2658 Dihedral : 12.155 178.920 2549 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 2.52 % Allowed : 20.16 % Favored : 77.33 % 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: 0.82 (0.17), residues: 900 sheet: -1.32 (0.31), residues: 282 loop : 0.00 (0.23), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG J 306 TYR 0.010 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 0.00294 / 0.13 (15612) covalent geometry : angle 0.43280 / 0.23 (21155) hydrogen bonds : bond 0.02869 / 2.53 ( 799) hydrogen bonds : angle 4.69293 / 4.35 ( 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 162 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 123 time to evaluate : 0.583 Fit side-chains REVERT: B 1 MET cc_start: 0.8253 (mtm) cc_final: 0.7830 (mtp) REVERT: I 27 ARG cc_start: 0.6306 (tpt-90) cc_final: 0.6103 (mtp180) REVERT: I 43 GLU cc_start: 0.8047 (mt-10) cc_final: 0.7691 (mt-10) REVERT: I 308 GLU cc_start: 0.7754 (pt0) cc_final: 0.7112 (pm20) REVERT: J 258 GLU cc_start: 0.7789 (OUTLIER) cc_final: 0.7349 (tt0) REVERT: K 114 GLN cc_start: 0.8692 (OUTLIER) cc_final: 0.8266 (mt0) REVERT: L 43 GLU cc_start: 0.8102 (mt-10) cc_final: 0.7404 (mp0) REVERT: L 98 GLU cc_start: 0.7476 (tt0) cc_final: 0.7023 (tt0) REVERT: L 108 GLU cc_start: 0.7711 (mt-10) cc_final: 0.7241 (tt0) REVERT: L 306 ARG cc_start: 0.7260 (OUTLIER) cc_final: 0.6827 (ptt-90) REVERT: L 326 MET cc_start: 0.8656 (ttp) cc_final: 0.8398 (ttt) REVERT: M 108 GLU cc_start: 0.7283 (mm-30) cc_final: 0.6895 (mt-10) REVERT: M 118 GLU cc_start: 0.8038 (tt0) cc_final: 0.7617 (tt0) REVERT: M 235 ARG cc_start: 0.8287 (ttp80) cc_final: 0.7911 (tpt90) REVERT: N 27 ARG cc_start: 0.7095 (mmm160) cc_final: 0.6720 (tpt90) REVERT: N 40 LYS cc_start: 0.7014 (OUTLIER) cc_final: 0.6761 (ttpt) REVERT: N 109 LEU cc_start: 0.8026 (OUTLIER) cc_final: 0.7511 (mp) REVERT: N 145 GLN cc_start: 0.8808 (OUTLIER) cc_final: 0.8559 (mp10) outliers start: 39 outliers final: 26 residues processed: 153 average time/residue: 0.1361 time to fit residues: 31.2495 Evaluate side-chains 153 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 121 time to evaluate : 0.576 ------------------------------------------------------------------------------- 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 112 LEU Chi-restraints excluded: chain I residue 125 MET Chi-restraints excluded: chain I residue 158 MET Chi-restraints excluded: chain I residue 233 SER 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 116 optimal weight: 0.8980 chunk 34 optimal weight: 5.9990 chunk 68 optimal weight: 1.9990 chunk 1 optimal weight: 0.1980 chunk 5 optimal weight: 0.0770 chunk 144 optimal weight: 2.9990 chunk 165 optimal weight: 0.8980 chunk 49 optimal weight: 0.5980 chunk 184 optimal weight: 2.9990 chunk 189 optimal weight: 4.9990 chunk 103 optimal weight: 3.9990 overall best weight: 0.5338 ------------------------------------------------------------------------------- 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** L 242 GLN ** 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 = 0.3361 r_free = 0.3361 target = 0.131486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.103143 restraints weight = 15411.520| |-----------------------------------------------------------------------------| r_work (start): 0.3077 rms_B_bonded: 1.55 r_work: 0.2954 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2807 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8608 moved from start: 0.1706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 15612 Z= 0.109 Angle : 0.419 5.337 21155 Z= 0.228 Chirality : 0.038 0.159 2406 Planarity : 0.003 0.042 2658 Dihedral : 12.080 178.750 2549 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.71 % Allowed : 19.96 % Favored : 77.33 % 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: 0.34 (0.19), residues: 1890 helix: 0.98 (0.17), residues: 900 sheet: -1.23 (0.32), residues: 282 loop : 0.08 (0.23), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 2 TYR 0.008 0.001 TYR L 178 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 0.00234 / 0.11 (15612) covalent geometry : angle 0.41912 / 0.23 (21155) hydrogen bonds : bond 0.02676 / 2.39 ( 799) hydrogen bonds : angle 4.55063 / 4.21 ( 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 182 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 140 time to evaluate : 0.573 Fit side-chains REVERT: B 1 MET cc_start: 0.8216 (mtm) cc_final: 0.7784 (mtp) REVERT: I 43 GLU cc_start: 0.8027 (mt-10) cc_final: 0.7650 (mt-10) REVERT: I 176 GLU cc_start: 0.7484 (tm-30) cc_final: 0.6906 (tp30) REVERT: I 308 GLU cc_start: 0.7701 (pt0) cc_final: 0.7053 (pm20) REVERT: J 258 GLU cc_start: 0.7669 (OUTLIER) cc_final: 0.7207 (tt0) REVERT: K 42 GLU cc_start: 0.7938 (mt-10) cc_final: 0.7731 (mt-10) REVERT: K 98 GLU cc_start: 0.7851 (pt0) cc_final: 0.7546 (pt0) REVERT: K 114 GLN cc_start: 0.8587 (OUTLIER) cc_final: 0.8161 (mt0) REVERT: L 43 GLU cc_start: 0.8060 (mt-10) cc_final: 0.7342 (mp0) REVERT: L 98 GLU cc_start: 0.7408 (tt0) cc_final: 0.6952 (tt0) REVERT: L 108 GLU cc_start: 0.7634 (mt-10) cc_final: 0.7166 (tt0) REVERT: L 306 ARG cc_start: 0.7168 (OUTLIER) cc_final: 0.6689 (ptt-90) REVERT: L 308 GLU cc_start: 0.7735 (pt0) cc_final: 0.7366 (pm20) REVERT: L 326 MET cc_start: 0.8643 (ttp) cc_final: 0.8375 (ttt) REVERT: M 27 ARG cc_start: 0.7416 (tpt90) cc_final: 0.7061 (tpt90) REVERT: M 70 LYS cc_start: 0.7293 (tppp) cc_final: 0.6918 (ttpt) REVERT: M 107 LYS cc_start: 0.7421 (mtmm) cc_final: 0.6727 (mmtm) REVERT: M 108 GLU cc_start: 0.7204 (mm-30) cc_final: 0.6794 (mt-10) REVERT: M 118 GLU cc_start: 0.8018 (tt0) cc_final: 0.7570 (tt0) REVERT: M 235 ARG cc_start: 0.8206 (ttp80) cc_final: 0.7830 (tpt90) REVERT: N 27 ARG cc_start: 0.6942 (mmm160) cc_final: 0.6570 (tpt90) REVERT: N 40 LYS cc_start: 0.6917 (OUTLIER) cc_final: 0.6684 (ttpt) REVERT: N 145 GLN cc_start: 0.8708 (OUTLIER) cc_final: 0.8463 (mp10) REVERT: N 154 GLU cc_start: 0.8467 (mt-10) cc_final: 0.8075 (tt0) REVERT: N 202 GLN cc_start: 0.7818 (mm-40) cc_final: 0.7167 (tm-30) REVERT: N 284 LYS cc_start: 0.8369 (mttm) cc_final: 0.7864 (mtmm) outliers start: 42 outliers final: 29 residues processed: 171 average time/residue: 0.1434 time to fit residues: 35.8855 Evaluate side-chains 165 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 131 time to evaluate : 0.665 ------------------------------------------------------------------------------- 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 112 LEU Chi-restraints excluded: chain I residue 158 MET 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 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 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 36 ASN Chi-restraints excluded: chain L residue 48 THR 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 177 optimal weight: 2.9990 chunk 179 optimal weight: 8.9990 chunk 107 optimal weight: 0.6980 chunk 127 optimal weight: 5.9990 chunk 120 optimal weight: 3.9990 chunk 32 optimal weight: 0.5980 chunk 111 optimal weight: 0.9980 chunk 37 optimal weight: 6.9990 chunk 52 optimal weight: 0.8980 chunk 38 optimal weight: 4.9990 chunk 189 optimal weight: 4.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... J 145 GLN ** 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 = 0.3336 r_free = 0.3336 target = 0.129418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.102829 restraints weight = 15785.302| |-----------------------------------------------------------------------------| r_work (start): 0.3075 rms_B_bonded: 1.42 r_work: 0.2926 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2783 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8676 moved from start: 0.1803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 15612 Z= 0.153 Angle : 0.441 5.753 21155 Z= 0.237 Chirality : 0.039 0.128 2406 Planarity : 0.003 0.042 2658 Dihedral : 12.149 178.656 2549 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.65 % Allowed : 19.96 % Favored : 77.39 % 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: 0.26 (0.19), residues: 1890 helix: 0.92 (0.17), residues: 900 sheet: -1.34 (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 0.012 0.001 TYR N 315 PHE 0.012 0.001 PHE K 327 HIS 0.003 0.000 HIS L 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.15 (15612) covalent geometry : angle 0.44077 / 0.24 (21155) hydrogen bonds : bond 0.02859 / 2.53 ( 799) hydrogen bonds : angle 4.59353 / 4.24 ( 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 179 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 138 time to evaluate : 0.596 Fit side-chains REVERT: B 1 MET cc_start: 0.8284 (mtm) cc_final: 0.7863 (mtp) REVERT: I 43 GLU cc_start: 0.8060 (mt-10) cc_final: 0.7693 (mt-10) REVERT: I 176 GLU cc_start: 0.7532 (tm-30) cc_final: 0.6969 (tp30) REVERT: I 308 GLU cc_start: 0.7746 (pt0) cc_final: 0.7128 (pm20) REVERT: J 258 GLU cc_start: 0.7779 (OUTLIER) cc_final: 0.7334 (tt0) REVERT: K 114 GLN cc_start: 0.8669 (OUTLIER) cc_final: 0.8245 (mt0) REVERT: L 43 GLU cc_start: 0.8113 (mt-10) cc_final: 0.7403 (mp0) REVERT: L 98 GLU cc_start: 0.7470 (tt0) cc_final: 0.7027 (tt0) REVERT: L 306 ARG cc_start: 0.7260 (OUTLIER) cc_final: 0.6836 (ptt-90) REVERT: L 326 MET cc_start: 0.8659 (ttp) cc_final: 0.8376 (ttt) REVERT: M 27 ARG cc_start: 0.7476 (tpt90) cc_final: 0.7168 (tpt90) REVERT: M 70 LYS cc_start: 0.7368 (tppp) cc_final: 0.6979 (ttpt) REVERT: M 108 GLU cc_start: 0.7287 (mm-30) cc_final: 0.6902 (mt-10) REVERT: M 118 GLU cc_start: 0.8040 (tt0) cc_final: 0.7619 (tt0) REVERT: M 235 ARG cc_start: 0.8318 (ttp80) cc_final: 0.7927 (tpt90) REVERT: N 40 LYS cc_start: 0.7039 (OUTLIER) cc_final: 0.6792 (ttpt) REVERT: N 118 GLU cc_start: 0.7795 (tt0) cc_final: 0.7314 (tt0) REVERT: N 145 GLN cc_start: 0.8786 (OUTLIER) cc_final: 0.8524 (mp10) REVERT: N 154 GLU cc_start: 0.8521 (mt-10) cc_final: 0.8142 (tt0) REVERT: N 202 GLN cc_start: 0.7836 (mm-40) cc_final: 0.7253 (tm-30) outliers start: 41 outliers final: 31 residues processed: 168 average time/residue: 0.1443 time to fit residues: 35.2806 Evaluate side-chains 172 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 136 time to evaluate : 0.555 ------------------------------------------------------------------------------- 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 112 LEU Chi-restraints excluded: chain I residue 158 MET 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 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 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 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 70 optimal weight: 6.9990 chunk 58 optimal weight: 2.9990 chunk 131 optimal weight: 5.9990 chunk 180 optimal weight: 4.9990 chunk 21 optimal weight: 4.9990 chunk 171 optimal weight: 4.9990 chunk 33 optimal weight: 0.8980 chunk 4 optimal weight: 0.9990 chunk 135 optimal weight: 0.0170 chunk 106 optimal weight: 5.9990 chunk 36 optimal weight: 4.9990 overall best weight: 1.9824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 242 GLN ** 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 = 0.3297 r_free = 0.3297 target = 0.126211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.099087 restraints weight = 15891.943| |-----------------------------------------------------------------------------| r_work (start): 0.3027 rms_B_bonded: 1.44 r_work: 0.2883 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2740 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8719 moved from start: 0.1996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 15612 Z= 0.212 Angle : 0.496 7.156 21155 Z= 0.265 Chirality : 0.041 0.138 2406 Planarity : 0.004 0.042 2658 Dihedral : 12.358 178.436 2549 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.52 % Allowed : 20.09 % Favored : 77.39 % 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: -1.64 (0.30), residues: 288 loop : 0.06 (0.23), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG J 306 TYR 0.016 0.002 TYR N 315 PHE 0.012 0.001 PHE N 248 HIS 0.003 0.001 HIS L 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00495 / 0.21 (15612) covalent geometry : angle 0.49563 / 0.26 (21155) hydrogen bonds : bond 0.03187 / 2.81 ( 799) hydrogen bonds : angle 4.81778 / 4.43 ( 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 192 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 153 time to evaluate : 0.514 Fit side-chains REVERT: B 1 MET cc_start: 0.8328 (mtm) cc_final: 0.7949 (mtt) REVERT: I 43 GLU cc_start: 0.8053 (mt-10) cc_final: 0.7700 (mt-10) REVERT: I 308 GLU cc_start: 0.7792 (pt0) cc_final: 0.7169 (pm20) REVERT: J 59 GLU cc_start: 0.7662 (tt0) cc_final: 0.7323 (tt0) REVERT: J 77 GLU cc_start: 0.7630 (tm-30) cc_final: 0.7186 (tm-30) REVERT: J 108 GLU cc_start: 0.7109 (mm-30) cc_final: 0.6875 (mm-30) REVERT: J 128 GLU cc_start: 0.7987 (pt0) cc_final: 0.7717 (pt0) REVERT: J 258 GLU cc_start: 0.7900 (OUTLIER) cc_final: 0.7555 (tt0) REVERT: K 42 GLU cc_start: 0.8092 (mt-10) cc_final: 0.7884 (mt-10) REVERT: K 114 GLN cc_start: 0.8723 (OUTLIER) cc_final: 0.8308 (mt0) REVERT: K 303 ARG cc_start: 0.8345 (ttp80) cc_final: 0.8110 (ttp-110) REVERT: L 43 GLU cc_start: 0.8109 (mt-10) cc_final: 0.7384 (mp0) REVERT: L 96 ARG cc_start: 0.8200 (mmm160) cc_final: 0.7996 (mtp85) REVERT: L 98 GLU cc_start: 0.7492 (tt0) cc_final: 0.7068 (tt0) REVERT: L 108 GLU cc_start: 0.7751 (mt-10) cc_final: 0.7274 (tt0) REVERT: L 306 ARG cc_start: 0.7365 (OUTLIER) cc_final: 0.6867 (ttp80) REVERT: L 326 MET cc_start: 0.8660 (ttp) cc_final: 0.8412 (ttt) REVERT: M 27 ARG cc_start: 0.7509 (tpt90) cc_final: 0.7164 (tpt90) REVERT: M 70 LYS cc_start: 0.7419 (tppp) cc_final: 0.6997 (ttpt) REVERT: M 108 GLU cc_start: 0.7308 (mm-30) cc_final: 0.6910 (mt-10) REVERT: M 118 GLU cc_start: 0.8077 (tt0) cc_final: 0.7679 (tt0) REVERT: M 235 ARG cc_start: 0.8434 (ttp80) cc_final: 0.8006 (tpt90) REVERT: N 40 LYS cc_start: 0.7049 (OUTLIER) cc_final: 0.6790 (ttpt) REVERT: N 109 LEU cc_start: 0.8085 (OUTLIER) cc_final: 0.7596 (mp) REVERT: N 118 GLU cc_start: 0.7879 (tt0) cc_final: 0.7425 (tt0) REVERT: N 145 GLN cc_start: 0.8818 (OUTLIER) cc_final: 0.8508 (mp10) REVERT: N 154 GLU cc_start: 0.8505 (mt-10) cc_final: 0.8151 (tt0) REVERT: N 202 GLN cc_start: 0.7870 (mm-40) cc_final: 0.7385 (tm-30) outliers start: 39 outliers final: 31 residues processed: 180 average time/residue: 0.1344 time to fit residues: 34.6281 Evaluate side-chains 184 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 147 time to evaluate : 0.575 ------------------------------------------------------------------------------- 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 112 LEU Chi-restraints excluded: chain I residue 158 MET 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 84 MET Chi-restraints excluded: chain J residue 125 MET 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 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 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 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=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: 4.9990 chunk 111 optimal weight: 0.8980 chunk 29 optimal weight: 0.7980 chunk 0 optimal weight: 8.9990 chunk 3 optimal weight: 0.9990 chunk 1 optimal weight: 0.0370 chunk 50 optimal weight: 0.9980 chunk 65 optimal weight: 0.0870 chunk 92 optimal weight: 2.9990 overall best weight: 0.5636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 242 GLN J 94 GLN ** J 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 202 GLN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.129955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.102027 restraints weight = 15723.874| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 1.49 r_work: 0.2941 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2799 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8637 moved from start: 0.1984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 15612 Z= 0.114 Angle : 0.428 5.207 21155 Z= 0.232 Chirality : 0.038 0.136 2406 Planarity : 0.003 0.044 2658 Dihedral : 12.161 179.323 2549 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.26 % Allowed : 20.09 % 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: 0.27 (0.19), residues: 1890 helix: 0.93 (0.17), residues: 900 sheet: -1.40 (0.32), residues: 282 loop : 0.12 (0.23), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 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 0.00243 / 0.11 (15612) covalent geometry : angle 0.42770 / 0.23 (21155) hydrogen bonds : bond 0.02763 / 2.46 ( 799) hydrogen bonds : angle 4.54749 / 4.18 ( 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 177 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 142 time to evaluate : 0.505 Fit side-chains REVERT: B 1 MET cc_start: 0.8260 (mtm) cc_final: 0.7908 (mtt) REVERT: I 43 GLU cc_start: 0.8021 (mt-10) cc_final: 0.7649 (mt-10) REVERT: I 176 GLU cc_start: 0.7516 (tm-30) cc_final: 0.6907 (tp30) REVERT: I 308 GLU cc_start: 0.7754 (pt0) cc_final: 0.7128 (pm20) REVERT: J 258 GLU cc_start: 0.7768 (OUTLIER) cc_final: 0.7346 (tt0) REVERT: K 42 GLU cc_start: 0.7994 (mt-10) cc_final: 0.7763 (mt-10) REVERT: K 98 GLU cc_start: 0.7867 (pt0) cc_final: 0.7560 (pt0) REVERT: K 114 GLN cc_start: 0.8610 (OUTLIER) cc_final: 0.8164 (mt0) REVERT: K 326 MET cc_start: 0.8548 (ttm) cc_final: 0.8344 (tpp) REVERT: L 43 GLU cc_start: 0.8079 (mt-10) cc_final: 0.7352 (mp0) REVERT: L 98 GLU cc_start: 0.7417 (tt0) cc_final: 0.6990 (tt0) REVERT: L 108 GLU cc_start: 0.7645 (mt-10) cc_final: 0.7181 (tt0) REVERT: L 306 ARG cc_start: 0.7215 (OUTLIER) cc_final: 0.6712 (ttp80) REVERT: L 326 MET cc_start: 0.8626 (ttp) cc_final: 0.8381 (ttt) REVERT: M 108 GLU cc_start: 0.7224 (mm-30) cc_final: 0.6826 (mt-10) REVERT: M 118 GLU cc_start: 0.8009 (tt0) cc_final: 0.7486 (tt0) REVERT: M 235 ARG cc_start: 0.8346 (ttp80) cc_final: 0.7967 (tpt90) REVERT: N 40 LYS cc_start: 0.7025 (OUTLIER) cc_final: 0.6774 (ttpt) REVERT: N 118 GLU cc_start: 0.7832 (tt0) cc_final: 0.7357 (tt0) REVERT: N 145 GLN cc_start: 0.8731 (OUTLIER) cc_final: 0.8478 (mp10) REVERT: N 149 ASP cc_start: 0.7733 (OUTLIER) cc_final: 0.7483 (p0) REVERT: N 154 GLU cc_start: 0.8468 (mt-10) cc_final: 0.8120 (tt0) REVERT: N 202 GLN cc_start: 0.7788 (mm-40) cc_final: 0.7223 (tm-30) outliers start: 35 outliers final: 27 residues processed: 166 average time/residue: 0.1355 time to fit residues: 32.9530 Evaluate side-chains 173 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 140 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain I residue 112 LEU Chi-restraints excluded: chain I residue 158 MET 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 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 169 GLU Chi-restraints excluded: chain L residue 36 ASN Chi-restraints excluded: chain L residue 48 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 163 GLU 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 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: 0.5980 chunk 5 optimal weight: 0.4980 chunk 27 optimal weight: 0.9980 chunk 3 optimal weight: 0.4980 chunk 156 optimal weight: 0.9980 chunk 0 optimal weight: 7.9990 chunk 79 optimal weight: 4.9990 chunk 129 optimal weight: 0.9980 chunk 2 optimal weight: 0.8980 chunk 81 optimal weight: 0.9980 chunk 115 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** J 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 202 GLN ** 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 = 0.3346 r_free = 0.3346 target = 0.130299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.101953 restraints weight = 15616.457| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 1.55 r_work: 0.2943 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2798 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.2798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 0.2007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15612 Z= 0.117 Angle : 0.425 5.489 21155 Z= 0.229 Chirality : 0.038 0.143 2406 Planarity : 0.003 0.042 2658 Dihedral : 12.115 179.017 2547 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.33 % Allowed : 20.09 % 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: 0.34 (0.20), residues: 1890 helix: 0.98 (0.17), residues: 900 sheet: -1.41 (0.31), residues: 288 loop : 0.19 (0.24), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG J 306 TYR 0.009 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 0.00257 / 0.12 (15612) covalent geometry : angle 0.42481 / 0.23 (21155) hydrogen bonds : bond 0.02705 / 2.40 ( 799) hydrogen bonds : angle 4.45805 / 4.10 ( 2217) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4449.83 seconds wall clock time: 77 minutes 1.23 seconds (4621.23 seconds total)