Starting phenix.real_space_refine on Sun May 3 20:32:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9tyy_56447/05_2026/9tyy_56447.cif Found real_map, /net/cci-nas-00/data/ceres_data/9tyy_56447/05_2026/9tyy_56447.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9tyy_56447/05_2026/9tyy_56447.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9tyy_56447/05_2026/9tyy_56447.map" model { file = "/net/cci-nas-00/data/ceres_data/9tyy_56447/05_2026/9tyy_56447.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9tyy_56447/05_2026/9tyy_56447.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.013 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 12 9.91 5 P 36 5.49 5 S 84 5.16 5 C 9492 2.51 5 N 2736 2.21 5 O 3001 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 31 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/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: 3.40, per 1000 atoms: 0.22 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: 1.14 Conformation dependent library (CDL) restraints added in 569.3 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: 0.54 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: 2.61 Time building geometry restraints manager: 1.49 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: 20796 1.85 - 3.69: 294 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 - 0.025: 1378 0.025 - 0.050: 617 0.050 - 0.075: 237 0.075 - 0.100: 113 0.100 - 0.125: 61 Chirality restraints: 2406 Sorted by residual: 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 chirality pdb=" CA ARG L 130 " pdb=" N ARG L 130 " pdb=" C ARG L 130 " pdb=" CB ARG L 130 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.67e-01 chirality pdb=" CA ILE K 160 " pdb=" N ILE K 160 " pdb=" C ILE K 160 " pdb=" CB ILE K 160 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.63e-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: 5.480 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: 0.000 Extract box with map and model: 0.510 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.100 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.091 15612 Z= 0.164 Angle : 0.564 9.227 21155 Z= 0.298 Chirality : 0.038 0.125 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 covalent geometry : bond 0.00342 (15612) covalent geometry : angle 0.56417 (21155) hydrogen bonds : bond 0.15382 ( 799) hydrogen bonds : angle 7.12206 ( 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 : 0.538 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: 0.1532 time to fit residues: 27.8816 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 : 0.415 ------------------------------------------------------------------------------- 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: 4.9990 chunk 149 optimal weight: 4.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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** L 242 GLN ** M 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 200 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 = 0.3396 r_free = 0.3396 target = 0.134659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.108627 restraints weight = 15347.849| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 1.34 r_work: 0.3019 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2881 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.0853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15612 Z= 0.131 Angle : 0.469 5.767 21155 Z= 0.249 Chirality : 0.039 0.130 2406 Planarity : 0.004 0.043 2658 Dihedral : 12.070 179.038 2565 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % 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: 0.15 (0.19), residues: 1890 helix: 0.78 (0.17), residues: 900 sheet: -1.03 (0.30), residues: 282 loop : -0.10 (0.23), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG J 306 TYR 0.016 0.001 TYR N 216 PHE 0.012 0.002 PHE J 126 HIS 0.003 0.000 HIS L 93 Details of bonding type rmsd covalent geometry : bond 0.00290 (15612) covalent geometry : angle 0.46937 (21155) hydrogen bonds : bond 0.03300 ( 799) hydrogen bonds : angle 5.08916 ( 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 140 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 98 time to evaluate : 0.604 Fit side-chains revert: symmetry clash REVERT: B 1 MET cc_start: 0.8163 (mtm) cc_final: 0.7697 (mtp) REVERT: C 1 MET cc_start: 0.7826 (mtt) cc_final: 0.7624 (mtt) REVERT: D 1 MET cc_start: 0.8325 (mtp) cc_final: 0.7462 (mtt) REVERT: I 114 GLN cc_start: 0.8247 (OUTLIER) cc_final: 0.8019 (mt0) REVERT: I 150 ARG cc_start: 0.8191 (ttp80) cc_final: 0.7760 (mtp180) REVERT: L 187 ASP cc_start: 0.8419 (OUTLIER) cc_final: 0.8099 (m-30) REVERT: L 306 ARG cc_start: 0.7049 (OUTLIER) cc_final: 0.6686 (ptt-90) REVERT: L 326 MET cc_start: 0.8616 (ttp) cc_final: 0.8298 (ttt) REVERT: N 27 ARG cc_start: 0.7074 (mmm160) cc_final: 0.6811 (tpt90) REVERT: N 59 GLU cc_start: 0.7434 (mt-10) cc_final: 0.7186 (tt0) REVERT: N 109 LEU cc_start: 0.7950 (OUTLIER) cc_final: 0.7476 (mp) REVERT: N 145 GLN cc_start: 0.8780 (mt0) cc_final: 0.8428 (mp10) REVERT: N 154 GLU cc_start: 0.8417 (mt-10) cc_final: 0.7842 (tt0) outliers start: 42 outliers final: 15 residues processed: 132 average time/residue: 0.1442 time to fit residues: 28.0091 Evaluate side-chains 109 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 90 time to evaluate : 0.556 ------------------------------------------------------------------------------- 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 230 THR 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 90 THR Chi-restraints excluded: chain L residue 149 ASP Chi-restraints excluded: chain L residue 187 ASP Chi-restraints excluded: chain L residue 214 SER Chi-restraints excluded: chain L residue 306 ARG Chi-restraints excluded: chain M residue 99 ILE Chi-restraints excluded: chain M residue 112 LEU Chi-restraints excluded: chain 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 103 optimal weight: 0.7980 chunk 133 optimal weight: 6.9990 chunk 163 optimal weight: 4.9990 chunk 188 optimal weight: 0.7980 chunk 53 optimal weight: 0.9990 chunk 78 optimal weight: 3.9990 chunk 4 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 118 optimal weight: 3.9990 chunk 90 optimal weight: 3.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 M 330 ASN ** N 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 200 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 = 0.3373 r_free = 0.3373 target = 0.132519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.106127 restraints weight = 15678.329| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 1.38 r_work: 0.2987 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2848 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.1279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15612 Z= 0.130 Angle : 0.439 5.807 21155 Z= 0.233 Chirality : 0.038 0.128 2406 Planarity : 0.003 0.039 2658 Dihedral : 11.955 178.903 2551 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 2.07 % Allowed : 19.90 % Favored : 78.04 % 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: 0.94 (0.17), residues: 894 sheet: -1.04 (0.31), residues: 282 loop : -0.09 (0.23), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG M 215 TYR 0.013 0.001 TYR N 315 PHE 0.011 0.001 PHE N 248 HIS 0.003 0.001 HIS L 93 Details of bonding type rmsd covalent geometry : bond 0.00291 (15612) covalent geometry : angle 0.43893 (21155) hydrogen bonds : bond 0.02943 ( 799) hydrogen bonds : angle 4.71288 ( 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 158 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 126 time to evaluate : 0.520 Fit side-chains REVERT: B 1 MET cc_start: 0.8276 (mtm) cc_final: 0.7821 (mtp) REVERT: D 1 MET cc_start: 0.8430 (mtp) cc_final: 0.7612 (mtt) REVERT: I 43 GLU cc_start: 0.8034 (mt-10) cc_final: 0.7676 (mt-10) REVERT: I 150 ARG cc_start: 0.8239 (ttp80) cc_final: 0.7855 (mtp180) REVERT: I 210 MET cc_start: 0.8468 (mtp) cc_final: 0.8226 (mtm) REVERT: I 308 GLU cc_start: 0.7730 (pt0) cc_final: 0.7117 (pm20) REVERT: J 39 LYS cc_start: 0.6065 (OUTLIER) cc_final: 0.5745 (mmmt) REVERT: K 77 GLU cc_start: 0.7908 (mm-30) cc_final: 0.7491 (mm-30) REVERT: K 98 GLU cc_start: 0.7836 (pt0) cc_final: 0.7542 (pt0) REVERT: K 114 GLN cc_start: 0.8653 (OUTLIER) cc_final: 0.8229 (mt0) REVERT: K 187 ASP cc_start: 0.8187 (m-30) cc_final: 0.7970 (m-30) REVERT: L 306 ARG cc_start: 0.7093 (OUTLIER) cc_final: 0.6708 (ptt-90) REVERT: L 326 MET cc_start: 0.8626 (ttp) cc_final: 0.8324 (ttt) REVERT: M 70 LYS cc_start: 0.7357 (tppp) cc_final: 0.7029 (ttpt) REVERT: M 107 LYS cc_start: 0.7582 (mtmm) cc_final: 0.6885 (mmtm) REVERT: M 108 GLU cc_start: 0.7266 (mm-30) cc_final: 0.6888 (mt-10) REVERT: M 235 ARG cc_start: 0.8094 (ttp80) cc_final: 0.7711 (tpt90) REVERT: N 27 ARG cc_start: 0.7055 (mmm160) cc_final: 0.6737 (tpt90) REVERT: N 59 GLU cc_start: 0.7451 (mt-10) cc_final: 0.7226 (tt0) REVERT: N 109 LEU cc_start: 0.7977 (OUTLIER) cc_final: 0.7476 (mp) REVERT: N 145 GLN cc_start: 0.8796 (mt0) cc_final: 0.8540 (mp10) REVERT: N 149 ASP cc_start: 0.7735 (OUTLIER) cc_final: 0.7517 (p0) REVERT: N 154 GLU cc_start: 0.8523 (mt-10) cc_final: 0.8004 (tt0) REVERT: N 243 MET cc_start: 0.7686 (mtm) cc_final: 0.7127 (mtt) REVERT: N 303 ARG cc_start: 0.8199 (ttp-110) cc_final: 0.7965 (ttp-110) outliers start: 32 outliers final: 13 residues processed: 154 average time/residue: 0.1452 time to fit residues: 32.4963 Evaluate side-chains 132 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 114 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 124 GLU Chi-restraints excluded: chain I residue 266 THR Chi-restraints excluded: chain I residue 326 MET Chi-restraints excluded: chain J residue 39 LYS Chi-restraints excluded: chain J residue 230 THR Chi-restraints excluded: chain K residue 88 THR Chi-restraints excluded: chain K residue 114 GLN Chi-restraints excluded: chain K residue 169 GLU Chi-restraints excluded: chain L residue 36 ASN Chi-restraints excluded: chain L residue 48 THR Chi-restraints excluded: chain L residue 99 ILE Chi-restraints excluded: chain L residue 148 ILE Chi-restraints excluded: chain L residue 306 ARG Chi-restraints excluded: chain M residue 99 ILE Chi-restraints excluded: chain M residue 332 ASP Chi-restraints excluded: chain N residue 99 ILE Chi-restraints excluded: chain N residue 109 LEU Chi-restraints excluded: chain N residue 149 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 89 optimal weight: 4.9990 chunk 95 optimal weight: 1.9990 chunk 131 optimal weight: 5.9990 chunk 162 optimal weight: 4.9990 chunk 75 optimal weight: 6.9990 chunk 119 optimal weight: 0.9980 chunk 71 optimal weight: 3.9990 chunk 5 optimal weight: 0.9990 chunk 20 optimal weight: 8.9990 chunk 188 optimal weight: 0.6980 chunk 130 optimal weight: 0.0010 overall best weight: 0.9390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** ** N 200 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 = 0.3361 r_free = 0.3361 target = 0.131432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.104237 restraints weight = 15660.227| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 1.46 r_work: 0.2971 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2828 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.1543 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= 0.128 Angle : 0.425 5.586 21155 Z= 0.227 Chirality : 0.038 0.130 2406 Planarity : 0.003 0.039 2658 Dihedral : 11.969 179.155 2551 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 2.52 % Allowed : 19.25 % 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: 0.36 (0.19), residues: 1890 helix: 1.02 (0.17), residues: 894 sheet: -1.08 (0.31), residues: 282 loop : -0.00 (0.23), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG J 306 TYR 0.012 0.001 TYR M 216 PHE 0.010 0.001 PHE N 248 HIS 0.003 0.000 HIS L 93 Details of bonding type rmsd covalent geometry : bond 0.00288 (15612) covalent geometry : angle 0.42477 (21155) hydrogen bonds : bond 0.02763 ( 799) hydrogen bonds : angle 4.56986 ( 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 175 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 136 time to evaluate : 0.610 Fit side-chains REVERT: A 1 MET cc_start: 0.7860 (mtm) cc_final: 0.7626 (mtp) REVERT: B 1 MET cc_start: 0.8285 (mtm) cc_final: 0.7878 (mtp) REVERT: D 1 MET cc_start: 0.8432 (mtp) cc_final: 0.7636 (mtt) REVERT: I 43 GLU cc_start: 0.8053 (mt-10) cc_final: 0.7691 (mt-10) REVERT: I 150 ARG cc_start: 0.8270 (ttp80) cc_final: 0.8056 (mtp180) REVERT: I 163 GLU cc_start: 0.7537 (OUTLIER) cc_final: 0.7334 (tt0) REVERT: I 176 GLU cc_start: 0.7526 (tm-30) cc_final: 0.6942 (tp30) REVERT: I 210 MET cc_start: 0.8425 (mtp) cc_final: 0.8150 (mtm) REVERT: I 308 GLU cc_start: 0.7731 (pt0) cc_final: 0.7098 (pm20) REVERT: J 39 LYS cc_start: 0.6057 (OUTLIER) cc_final: 0.5726 (mmmt) REVERT: J 258 GLU cc_start: 0.7693 (OUTLIER) cc_final: 0.7207 (tt0) REVERT: K 98 GLU cc_start: 0.7808 (pt0) cc_final: 0.7522 (pt0) REVERT: K 187 ASP cc_start: 0.8172 (m-30) cc_final: 0.7906 (m-30) REVERT: L 43 GLU cc_start: 0.8108 (mt-10) cc_final: 0.7421 (mp0) REVERT: L 98 GLU cc_start: 0.7471 (tt0) cc_final: 0.7086 (tt0) REVERT: L 187 ASP cc_start: 0.8470 (OUTLIER) cc_final: 0.8225 (m-30) REVERT: L 306 ARG cc_start: 0.7161 (OUTLIER) cc_final: 0.6711 (ptt-90) REVERT: L 308 GLU cc_start: 0.7748 (pt0) cc_final: 0.7417 (pm20) REVERT: L 326 MET cc_start: 0.8637 (ttp) cc_final: 0.8345 (ttt) REVERT: M 70 LYS cc_start: 0.7322 (tppp) cc_final: 0.6970 (ttpt) REVERT: M 107 LYS cc_start: 0.7532 (mtmm) cc_final: 0.6843 (mmtm) REVERT: M 108 GLU cc_start: 0.7251 (mm-30) cc_final: 0.6857 (mt-10) REVERT: M 118 GLU cc_start: 0.7994 (tt0) cc_final: 0.7437 (tt0) REVERT: M 235 ARG cc_start: 0.8143 (ttp80) cc_final: 0.7763 (tpt90) REVERT: N 27 ARG cc_start: 0.6995 (mmm160) cc_final: 0.6657 (tpt90) REVERT: N 59 GLU cc_start: 0.7469 (mt-10) cc_final: 0.7239 (tt0) REVERT: N 109 LEU cc_start: 0.7926 (OUTLIER) cc_final: 0.7423 (mp) REVERT: N 145 GLN cc_start: 0.8743 (OUTLIER) cc_final: 0.8540 (mp10) REVERT: N 149 ASP cc_start: 0.7776 (OUTLIER) cc_final: 0.7525 (p0) REVERT: N 154 GLU cc_start: 0.8523 (mt-10) cc_final: 0.8143 (tt0) REVERT: N 202 GLN cc_start: 0.7844 (mm-40) cc_final: 0.7189 (tm-30) REVERT: N 303 ARG cc_start: 0.8180 (ttp-110) cc_final: 0.7928 (ttp-110) outliers start: 39 outliers final: 17 residues processed: 167 average time/residue: 0.1401 time to fit residues: 35.0616 Evaluate side-chains 147 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 122 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 158 MET Chi-restraints excluded: chain I residue 163 GLU Chi-restraints excluded: chain I residue 233 SER Chi-restraints excluded: chain I residue 266 THR Chi-restraints excluded: chain I residue 326 MET Chi-restraints excluded: chain J residue 39 LYS 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 88 THR Chi-restraints excluded: chain K residue 99 ILE Chi-restraints excluded: chain K residue 161 ASP Chi-restraints excluded: chain K residue 169 GLU Chi-restraints excluded: chain L residue 36 ASN Chi-restraints excluded: chain L residue 99 ILE Chi-restraints excluded: chain L residue 149 ASP Chi-restraints excluded: chain L residue 187 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 N residue 109 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 51 optimal weight: 8.9990 chunk 169 optimal weight: 4.9990 chunk 124 optimal weight: 0.9980 chunk 48 optimal weight: 5.9990 chunk 187 optimal weight: 0.8980 chunk 183 optimal weight: 0.0470 chunk 90 optimal weight: 4.9990 chunk 175 optimal weight: 7.9990 chunk 34 optimal weight: 2.9990 chunk 163 optimal weight: 0.0070 chunk 103 optimal weight: 2.9990 overall best weight: 0.9898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 94 GLN ** N 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 200 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 = 0.3353 r_free = 0.3353 target = 0.130642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.102800 restraints weight = 15852.107| |-----------------------------------------------------------------------------| r_work (start): 0.3075 rms_B_bonded: 1.50 r_work: 0.2955 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.2812 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.1744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15612 Z= 0.131 Angle : 0.423 5.701 21155 Z= 0.226 Chirality : 0.038 0.137 2406 Planarity : 0.003 0.040 2658 Dihedral : 11.994 178.764 2549 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.39 % Allowed : 19.19 % Favored : 78.42 % 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: 0.40 (0.19), residues: 1890 helix: 1.01 (0.17), residues: 900 sheet: -1.12 (0.31), residues: 282 loop : 0.11 (0.23), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG J 306 TYR 0.011 0.001 TYR M 216 PHE 0.009 0.001 PHE M 327 HIS 0.003 0.000 HIS L 93 Details of bonding type rmsd covalent geometry : bond 0.00296 (15612) covalent geometry : angle 0.42282 (21155) hydrogen bonds : bond 0.02762 ( 799) hydrogen bonds : angle 4.50480 ( 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 179 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 142 time to evaluate : 0.564 Fit side-chains REVERT: B 1 MET cc_start: 0.8273 (mtm) cc_final: 0.7886 (mtp) REVERT: D 1 MET cc_start: 0.8448 (mtp) cc_final: 0.7663 (mtt) REVERT: I 43 GLU cc_start: 0.8008 (mt-10) cc_final: 0.7640 (mt-10) REVERT: I 176 GLU cc_start: 0.7538 (tm-30) cc_final: 0.6904 (tp30) REVERT: I 210 MET cc_start: 0.8396 (mtp) cc_final: 0.8135 (mtm) REVERT: I 308 GLU cc_start: 0.7747 (pt0) cc_final: 0.7106 (pm20) REVERT: J 258 GLU cc_start: 0.7735 (OUTLIER) cc_final: 0.7277 (tt0) REVERT: K 114 GLN cc_start: 0.8617 (OUTLIER) cc_final: 0.8182 (mt0) REVERT: K 187 ASP cc_start: 0.8179 (m-30) cc_final: 0.7787 (m-30) REVERT: L 43 GLU cc_start: 0.8101 (mt-10) cc_final: 0.7394 (mp0) REVERT: L 98 GLU cc_start: 0.7471 (tt0) cc_final: 0.7076 (tt0) REVERT: L 108 GLU cc_start: 0.7588 (mt-10) cc_final: 0.7106 (tt0) REVERT: L 187 ASP cc_start: 0.8463 (OUTLIER) cc_final: 0.8237 (m-30) REVERT: L 306 ARG cc_start: 0.7168 (OUTLIER) cc_final: 0.6720 (ptt-90) REVERT: L 308 GLU cc_start: 0.7747 (pt0) cc_final: 0.7403 (pm20) REVERT: L 326 MET cc_start: 0.8627 (ttp) cc_final: 0.8349 (ttt) REVERT: M 70 LYS cc_start: 0.7278 (tppp) cc_final: 0.6914 (ttpt) REVERT: M 107 LYS cc_start: 0.7501 (mtmm) cc_final: 0.6813 (mmtm) REVERT: M 108 GLU cc_start: 0.7210 (mm-30) cc_final: 0.6816 (mt-10) REVERT: M 235 ARG cc_start: 0.8202 (ttp80) cc_final: 0.7822 (tpt90) REVERT: N 40 LYS cc_start: 0.6977 (OUTLIER) cc_final: 0.6760 (ttpt) REVERT: N 59 GLU cc_start: 0.7480 (mt-10) cc_final: 0.7218 (tt0) REVERT: N 109 LEU cc_start: 0.7932 (OUTLIER) cc_final: 0.7390 (mp) REVERT: N 145 GLN cc_start: 0.8730 (OUTLIER) cc_final: 0.8527 (mp10) REVERT: N 149 ASP cc_start: 0.7801 (OUTLIER) cc_final: 0.7518 (p0) REVERT: N 154 GLU cc_start: 0.8504 (mt-10) cc_final: 0.8143 (tt0) REVERT: N 202 GLN cc_start: 0.7847 (mm-40) cc_final: 0.7234 (tm-30) REVERT: N 284 LYS cc_start: 0.8375 (mttm) cc_final: 0.7888 (mtmm) REVERT: N 303 ARG cc_start: 0.8161 (ttp-110) cc_final: 0.7946 (ttp-110) outliers start: 37 outliers final: 18 residues processed: 167 average time/residue: 0.1415 time to fit residues: 34.3269 Evaluate side-chains 162 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 136 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 88 THR Chi-restraints excluded: chain K residue 99 ILE Chi-restraints excluded: chain K residue 114 GLN Chi-restraints excluded: chain K residue 161 ASP Chi-restraints excluded: chain K residue 169 GLU Chi-restraints excluded: chain L residue 36 ASN Chi-restraints excluded: chain L residue 99 ILE Chi-restraints excluded: chain L residue 187 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 332 ASP Chi-restraints excluded: chain N residue 40 LYS 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 16 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 73 optimal weight: 0.1980 chunk 125 optimal weight: 0.7980 chunk 96 optimal weight: 0.5980 chunk 111 optimal weight: 4.9990 chunk 52 optimal weight: 0.9980 chunk 148 optimal weight: 6.9990 chunk 88 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 94 GLN ** N 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 200 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 = 0.3354 r_free = 0.3354 target = 0.130778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.103028 restraints weight = 15701.631| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 1.49 r_work: 0.2956 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2813 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.1853 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= 0.126 Angle : 0.418 5.527 21155 Z= 0.223 Chirality : 0.038 0.130 2406 Planarity : 0.003 0.040 2658 Dihedral : 12.016 179.217 2549 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.52 % Allowed : 19.32 % Favored : 78.17 % 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: 0.46 (0.19), residues: 1890 helix: 1.05 (0.17), residues: 900 sheet: -1.14 (0.32), residues: 282 loop : 0.16 (0.23), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 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 covalent geometry : bond 0.00283 (15612) covalent geometry : angle 0.41806 (21155) hydrogen bonds : bond 0.02686 ( 799) hydrogen bonds : angle 4.46712 ( 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 182 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 143 time to evaluate : 0.584 Fit side-chains REVERT: B 1 MET cc_start: 0.8239 (mtm) cc_final: 0.7871 (mtp) REVERT: D 1 MET cc_start: 0.8438 (mtp) cc_final: 0.7702 (mtt) REVERT: I 43 GLU cc_start: 0.8017 (mt-10) cc_final: 0.7646 (mt-10) REVERT: I 176 GLU cc_start: 0.7526 (tm-30) cc_final: 0.6890 (tp30) REVERT: I 210 MET cc_start: 0.8374 (mtp) cc_final: 0.8106 (mtm) REVERT: I 308 GLU cc_start: 0.7728 (pt0) cc_final: 0.7098 (pm20) REVERT: J 258 GLU cc_start: 0.7741 (OUTLIER) cc_final: 0.7286 (tt0) REVERT: K 98 GLU cc_start: 0.7804 (pt0) cc_final: 0.7507 (pt0) REVERT: K 187 ASP cc_start: 0.8166 (m-30) cc_final: 0.7785 (m-30) REVERT: L 43 GLU cc_start: 0.8115 (mt-10) cc_final: 0.7402 (mp0) REVERT: L 98 GLU cc_start: 0.7437 (tt0) cc_final: 0.7014 (tt0) REVERT: L 108 GLU cc_start: 0.7578 (mt-10) cc_final: 0.7109 (tt0) REVERT: L 187 ASP cc_start: 0.8445 (OUTLIER) cc_final: 0.8217 (m-30) REVERT: L 306 ARG cc_start: 0.7154 (OUTLIER) cc_final: 0.6653 (ttp80) REVERT: L 308 GLU cc_start: 0.7752 (pt0) cc_final: 0.7401 (pm20) REVERT: L 326 MET cc_start: 0.8630 (ttp) cc_final: 0.8347 (ttt) REVERT: M 27 ARG cc_start: 0.7147 (mmm160) cc_final: 0.6869 (tpt90) REVERT: M 70 LYS cc_start: 0.7310 (tppp) cc_final: 0.6936 (ttpt) REVERT: M 108 GLU cc_start: 0.7201 (mm-30) cc_final: 0.6814 (mt-10) REVERT: M 118 GLU cc_start: 0.8025 (tt0) cc_final: 0.7497 (tt0) REVERT: M 235 ARG cc_start: 0.8222 (ttp80) cc_final: 0.7844 (tpt90) REVERT: N 59 GLU cc_start: 0.7453 (mt-10) cc_final: 0.7197 (tt0) REVERT: N 149 ASP cc_start: 0.7780 (OUTLIER) cc_final: 0.7505 (p0) REVERT: N 154 GLU cc_start: 0.8468 (mt-10) cc_final: 0.8123 (tt0) REVERT: N 202 GLN cc_start: 0.7832 (mm-40) cc_final: 0.7219 (tm-30) REVERT: N 303 ARG cc_start: 0.8155 (ttp-110) cc_final: 0.7927 (ttp-110) outliers start: 39 outliers final: 25 residues processed: 173 average time/residue: 0.1520 time to fit residues: 37.8458 Evaluate side-chains 165 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 136 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 112 LEU Chi-restraints excluded: chain I residue 124 GLU 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 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 88 THR Chi-restraints excluded: chain K residue 99 ILE Chi-restraints excluded: chain K residue 161 ASP Chi-restraints excluded: chain K residue 169 GLU Chi-restraints excluded: chain L residue 36 ASN Chi-restraints excluded: chain L residue 99 ILE Chi-restraints excluded: chain L residue 149 ASP Chi-restraints excluded: chain L residue 187 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 99 ILE Chi-restraints excluded: chain N residue 112 LEU Chi-restraints excluded: chain N residue 149 ASP Chi-restraints excluded: chain N residue 187 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 116 optimal weight: 1.9990 chunk 34 optimal weight: 5.9990 chunk 68 optimal weight: 7.9990 chunk 1 optimal weight: 6.9990 chunk 5 optimal weight: 0.3980 chunk 144 optimal weight: 3.9990 chunk 165 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 184 optimal weight: 1.9990 chunk 189 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 overall best weight: 1.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 94 GLN N 145 GLN ** N 200 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 = 0.3323 r_free = 0.3323 target = 0.128229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.101761 restraints weight = 15701.562| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 1.38 r_work: 0.2920 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2777 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.1982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 15612 Z= 0.170 Angle : 0.448 5.802 21155 Z= 0.238 Chirality : 0.039 0.154 2406 Planarity : 0.003 0.040 2658 Dihedral : 12.165 178.818 2549 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 2.58 % Allowed : 19.25 % Favored : 78.17 % 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: 0.30 (0.19), residues: 1890 helix: 0.95 (0.17), residues: 900 sheet: -1.35 (0.31), residues: 288 loop : 0.14 (0.23), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG J 306 TYR 0.013 0.001 TYR N 315 PHE 0.011 0.001 PHE N 248 HIS 0.003 0.000 HIS L 93 Details of bonding type rmsd covalent geometry : bond 0.00395 (15612) covalent geometry : angle 0.44816 (21155) hydrogen bonds : bond 0.02906 ( 799) hydrogen bonds : angle 4.58042 ( 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 195 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 155 time to evaluate : 0.599 Fit side-chains REVERT: B 1 MET cc_start: 0.8290 (mtm) cc_final: 0.7900 (mtt) REVERT: D 1 MET cc_start: 0.8506 (mtp) cc_final: 0.7703 (mtt) REVERT: I 43 GLU cc_start: 0.8040 (mt-10) cc_final: 0.7671 (mt-10) REVERT: I 176 GLU cc_start: 0.7541 (tm-30) cc_final: 0.6909 (tp30) REVERT: I 210 MET cc_start: 0.8420 (mtp) cc_final: 0.8171 (mtm) REVERT: I 308 GLU cc_start: 0.7764 (pt0) cc_final: 0.7125 (pm20) REVERT: J 39 LYS cc_start: 0.6251 (OUTLIER) cc_final: 0.5828 (mmmt) REVERT: J 59 GLU cc_start: 0.7468 (tt0) cc_final: 0.7178 (tt0) REVERT: J 77 GLU cc_start: 0.7559 (tm-30) cc_final: 0.7129 (tm-30) REVERT: J 108 GLU cc_start: 0.7111 (mm-30) cc_final: 0.6674 (mt-10) REVERT: J 128 GLU cc_start: 0.7897 (pt0) cc_final: 0.7656 (pt0) REVERT: J 258 GLU cc_start: 0.7841 (OUTLIER) cc_final: 0.7447 (tt0) REVERT: K 98 GLU cc_start: 0.7871 (pt0) cc_final: 0.7570 (pt0) REVERT: K 114 GLN cc_start: 0.8674 (OUTLIER) cc_final: 0.8241 (mt0) REVERT: K 326 MET cc_start: 0.8596 (ttm) cc_final: 0.8300 (tpp) REVERT: L 43 GLU cc_start: 0.8166 (mt-10) cc_final: 0.7451 (mp0) REVERT: L 98 GLU cc_start: 0.7454 (tt0) cc_final: 0.7000 (tt0) REVERT: L 108 GLU cc_start: 0.7635 (mt-10) cc_final: 0.7183 (tt0) REVERT: L 187 ASP cc_start: 0.8466 (OUTLIER) cc_final: 0.8238 (m-30) REVERT: L 306 ARG cc_start: 0.7288 (OUTLIER) cc_final: 0.6778 (ttp80) REVERT: L 326 MET cc_start: 0.8632 (ttp) cc_final: 0.8336 (ttt) REVERT: M 27 ARG cc_start: 0.7237 (mmm160) cc_final: 0.6876 (tpt90) REVERT: M 70 LYS cc_start: 0.7393 (tppp) cc_final: 0.6973 (ttpt) REVERT: M 108 GLU cc_start: 0.7244 (mm-30) cc_final: 0.6857 (mt-10) REVERT: M 118 GLU cc_start: 0.8059 (tt0) cc_final: 0.7565 (tt0) REVERT: M 235 ARG cc_start: 0.8332 (ttp80) cc_final: 0.7938 (tpt90) REVERT: N 59 GLU cc_start: 0.7503 (mt-10) cc_final: 0.7251 (tt0) REVERT: N 154 GLU cc_start: 0.8473 (mt-10) cc_final: 0.8148 (tt0) REVERT: N 202 GLN cc_start: 0.7826 (mm-40) cc_final: 0.7281 (tm-30) outliers start: 40 outliers final: 26 residues processed: 184 average time/residue: 0.1563 time to fit residues: 41.1963 Evaluate side-chains 181 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 150 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 99 ILE 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 39 LYS Chi-restraints excluded: chain J residue 125 MET Chi-restraints excluded: chain J residue 161 ASP Chi-restraints excluded: chain J residue 230 THR Chi-restraints excluded: chain J residue 258 GLU Chi-restraints excluded: chain K residue 48 THR Chi-restraints excluded: chain K residue 99 ILE Chi-restraints excluded: chain K residue 114 GLN Chi-restraints excluded: chain K residue 169 GLU Chi-restraints excluded: chain L residue 36 ASN Chi-restraints excluded: chain L residue 99 ILE Chi-restraints excluded: chain L residue 187 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 187 ASP Chi-restraints excluded: chain M residue 266 THR Chi-restraints excluded: chain M residue 332 ASP Chi-restraints excluded: chain N residue 99 ILE Chi-restraints excluded: chain N residue 112 LEU Chi-restraints excluded: chain N residue 149 ASP Chi-restraints excluded: chain N residue 187 ASP Chi-restraints excluded: chain N residue 251 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 177 optimal weight: 5.9990 chunk 179 optimal weight: 6.9990 chunk 107 optimal weight: 0.9990 chunk 127 optimal weight: 5.9990 chunk 120 optimal weight: 3.9990 chunk 32 optimal weight: 4.9990 chunk 111 optimal weight: 0.6980 chunk 37 optimal weight: 5.9990 chunk 52 optimal weight: 5.9990 chunk 38 optimal weight: 3.9990 chunk 189 optimal weight: 0.7980 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 94 GLN N 145 GLN ** N 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.125125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.098446 restraints weight = 16096.305| |-----------------------------------------------------------------------------| r_work (start): 0.3023 rms_B_bonded: 1.42 r_work: 0.2877 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.2735 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.2735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.2226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 15612 Z= 0.225 Angle : 0.498 6.083 21155 Z= 0.265 Chirality : 0.041 0.148 2406 Planarity : 0.004 0.040 2658 Dihedral : 12.519 178.617 2549 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.58 % Allowed : 19.57 % Favored : 77.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.19), residues: 1890 helix: 0.66 (0.17), residues: 900 sheet: -1.51 (0.31), residues: 282 loop : 0.06 (0.23), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG J 306 TYR 0.017 0.002 TYR N 315 PHE 0.012 0.001 PHE N 248 HIS 0.003 0.001 HIS K 294 Details of bonding type rmsd covalent geometry : bond 0.00528 (15612) covalent geometry : angle 0.49757 (21155) hydrogen bonds : bond 0.03278 ( 799) hydrogen bonds : angle 4.85713 ( 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 194 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 154 time to evaluate : 0.578 Fit side-chains REVERT: A 1 MET cc_start: 0.7854 (OUTLIER) cc_final: 0.7647 (mtp) REVERT: B 1 MET cc_start: 0.8345 (mtm) cc_final: 0.7996 (mtt) REVERT: D 1 MET cc_start: 0.8486 (mtp) cc_final: 0.7702 (mtt) REVERT: I 43 GLU cc_start: 0.8055 (mt-10) cc_final: 0.7681 (mt-10) REVERT: I 210 MET cc_start: 0.8439 (mtp) cc_final: 0.8212 (mtm) REVERT: I 308 GLU cc_start: 0.7770 (pt0) cc_final: 0.7144 (pm20) REVERT: J 39 LYS cc_start: 0.6264 (OUTLIER) cc_final: 0.5868 (mmmt) REVERT: J 59 GLU cc_start: 0.7479 (tt0) cc_final: 0.7111 (tt0) REVERT: J 108 GLU cc_start: 0.7167 (mm-30) cc_final: 0.6725 (mt-10) REVERT: J 128 GLU cc_start: 0.7916 (pt0) cc_final: 0.7653 (pt0) REVERT: J 202 GLN cc_start: 0.7536 (mt0) cc_final: 0.7002 (tt0) REVERT: J 258 GLU cc_start: 0.7964 (OUTLIER) cc_final: 0.7706 (tt0) REVERT: K 114 GLN cc_start: 0.8707 (OUTLIER) cc_final: 0.8282 (mt0) REVERT: K 202 GLN cc_start: 0.7549 (mt0) cc_final: 0.7098 (tt0) REVERT: K 303 ARG cc_start: 0.8385 (ttp80) cc_final: 0.8133 (ttp-110) REVERT: L 43 GLU cc_start: 0.8124 (mt-10) cc_final: 0.7410 (mp0) REVERT: L 98 GLU cc_start: 0.7486 (tt0) cc_final: 0.7047 (tt0) REVERT: L 306 ARG cc_start: 0.7391 (OUTLIER) cc_final: 0.7154 (tpt170) REVERT: M 70 LYS cc_start: 0.7476 (tppp) cc_final: 0.6999 (ttpt) REVERT: M 108 GLU cc_start: 0.7315 (mm-30) cc_final: 0.6904 (mt-10) REVERT: M 118 GLU cc_start: 0.8104 (tt0) cc_final: 0.7762 (tt0) REVERT: M 235 ARG cc_start: 0.8446 (ttp80) cc_final: 0.8016 (tpt90) REVERT: N 59 GLU cc_start: 0.7567 (mt-10) cc_final: 0.7361 (tt0) REVERT: N 118 GLU cc_start: 0.7822 (tt0) cc_final: 0.7378 (tt0) REVERT: N 154 GLU cc_start: 0.8501 (mt-10) cc_final: 0.8193 (tt0) REVERT: N 202 GLN cc_start: 0.7851 (mm-40) cc_final: 0.7295 (tm-30) outliers start: 40 outliers final: 30 residues processed: 183 average time/residue: 0.1586 time to fit residues: 41.1498 Evaluate side-chains 183 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 148 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A 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 125 MET Chi-restraints excluded: chain I residue 230 THR 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 39 LYS 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 169 GLU Chi-restraints excluded: chain K residue 230 THR Chi-restraints excluded: chain L residue 36 ASN 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 266 THR 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 233 SER Chi-restraints excluded: chain M residue 266 THR Chi-restraints excluded: chain M residue 332 ASP Chi-restraints excluded: chain N residue 99 ILE Chi-restraints excluded: chain N residue 112 LEU Chi-restraints excluded: chain N residue 187 ASP Chi-restraints excluded: chain N residue 251 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 70 optimal weight: 1.9990 chunk 58 optimal weight: 0.7980 chunk 131 optimal weight: 0.9980 chunk 180 optimal weight: 0.9980 chunk 21 optimal weight: 0.7980 chunk 171 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 4 optimal weight: 0.8980 chunk 135 optimal weight: 1.9990 chunk 106 optimal weight: 5.9990 chunk 36 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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** L 242 GLN ** M 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 145 GLN ** N 200 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 = 0.3320 r_free = 0.3320 target = 0.127772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.099926 restraints weight = 15819.932| |-----------------------------------------------------------------------------| r_work (start): 0.3053 rms_B_bonded: 1.50 r_work: 0.2927 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2785 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.2183 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= 0.126 Angle : 0.426 5.370 21155 Z= 0.229 Chirality : 0.038 0.139 2406 Planarity : 0.003 0.041 2658 Dihedral : 12.129 178.713 2549 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.07 % Allowed : 20.28 % 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: 0.28 (0.19), residues: 1890 helix: 0.91 (0.17), residues: 900 sheet: -1.42 (0.31), residues: 282 loop : 0.16 (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 M 216 PHE 0.010 0.001 PHE M 327 HIS 0.003 0.000 HIS L 93 Details of bonding type rmsd covalent geometry : bond 0.00282 (15612) covalent geometry : angle 0.42636 (21155) hydrogen bonds : bond 0.02727 ( 799) hydrogen bonds : angle 4.53319 ( 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 185 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 153 time to evaluate : 0.634 Fit side-chains REVERT: B 1 MET cc_start: 0.8260 (mtm) cc_final: 0.7943 (mtt) REVERT: D 1 MET cc_start: 0.8480 (mtp) cc_final: 0.7683 (mtt) REVERT: I 43 GLU cc_start: 0.8028 (mt-10) cc_final: 0.7651 (mt-10) REVERT: I 176 GLU cc_start: 0.7545 (tm-30) cc_final: 0.6912 (tp30) REVERT: I 210 MET cc_start: 0.8375 (mtp) cc_final: 0.8133 (mtm) REVERT: I 308 GLU cc_start: 0.7721 (pt0) cc_final: 0.7066 (pm20) REVERT: J 59 GLU cc_start: 0.7270 (tt0) cc_final: 0.6985 (tt0) REVERT: J 108 GLU cc_start: 0.7051 (mm-30) cc_final: 0.6566 (mt-10) REVERT: J 128 GLU cc_start: 0.7843 (pt0) cc_final: 0.7610 (pt0) REVERT: J 202 GLN cc_start: 0.7359 (mt0) cc_final: 0.6834 (tt0) REVERT: J 258 GLU cc_start: 0.7793 (OUTLIER) cc_final: 0.7429 (tt0) REVERT: K 98 GLU cc_start: 0.7860 (pt0) cc_final: 0.7638 (pt0) REVERT: K 114 GLN cc_start: 0.8535 (OUTLIER) cc_final: 0.8095 (mt0) REVERT: K 303 ARG cc_start: 0.8311 (ttp80) cc_final: 0.8086 (ttp-110) REVERT: K 326 MET cc_start: 0.8528 (ttm) cc_final: 0.8319 (tpp) REVERT: L 43 GLU cc_start: 0.8070 (mt-10) cc_final: 0.7354 (mp0) REVERT: L 98 GLU cc_start: 0.7360 (tt0) cc_final: 0.6939 (tt0) REVERT: M 27 ARG cc_start: 0.7349 (mmm160) cc_final: 0.6938 (tpt90) REVERT: M 70 LYS cc_start: 0.7429 (tppp) cc_final: 0.6949 (ttpt) REVERT: M 108 GLU cc_start: 0.7151 (mm-30) cc_final: 0.6730 (mt-10) REVERT: M 118 GLU cc_start: 0.8057 (tt0) cc_final: 0.7546 (tt0) REVERT: M 235 ARG cc_start: 0.8322 (ttp80) cc_final: 0.7929 (tpt90) REVERT: N 59 GLU cc_start: 0.7455 (mt-10) cc_final: 0.7207 (tt0) REVERT: N 154 GLU cc_start: 0.8405 (mt-10) cc_final: 0.8078 (tt0) REVERT: N 202 GLN cc_start: 0.7749 (mm-40) cc_final: 0.7181 (tm-30) REVERT: N 235 ARG cc_start: 0.8006 (tmt-80) cc_final: 0.7761 (tpt90) outliers start: 32 outliers final: 22 residues processed: 179 average time/residue: 0.1526 time to fit residues: 39.2031 Evaluate side-chains 174 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 150 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 99 ILE Chi-restraints excluded: chain I residue 112 LEU Chi-restraints excluded: chain I residue 230 THR Chi-restraints excluded: chain I residue 233 SER Chi-restraints excluded: chain I residue 326 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 169 GLU Chi-restraints excluded: chain L residue 36 ASN Chi-restraints excluded: chain L residue 90 THR Chi-restraints excluded: chain L residue 99 ILE Chi-restraints excluded: chain L residue 149 ASP Chi-restraints excluded: chain L residue 214 SER Chi-restraints excluded: chain L residue 266 THR Chi-restraints excluded: chain M residue 99 ILE Chi-restraints excluded: chain M residue 125 MET Chi-restraints excluded: chain M residue 149 ASP Chi-restraints excluded: chain M residue 266 THR Chi-restraints excluded: chain N residue 112 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 8 optimal weight: 3.9990 chunk 15 optimal weight: 0.0010 chunk 34 optimal weight: 5.9990 chunk 111 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 3 optimal weight: 0.9990 chunk 1 optimal weight: 5.9990 chunk 50 optimal weight: 0.9990 chunk 65 optimal weight: 0.0670 chunk 92 optimal weight: 0.8980 overall best weight: 0.5928 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 200 GLN L 145 GLN ** M 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 145 GLN ** N 200 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 = 0.3361 r_free = 0.3361 target = 0.131197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.105240 restraints weight = 15749.471| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 1.35 r_work: 0.2967 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2828 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.2189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 15612 Z= 0.105 Angle : 0.413 5.268 21155 Z= 0.221 Chirality : 0.038 0.134 2406 Planarity : 0.003 0.041 2658 Dihedral : 11.942 178.878 2549 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.74 % Allowed : 20.61 % 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: 0.47 (0.20), residues: 1890 helix: 1.08 (0.17), residues: 900 sheet: -1.39 (0.32), residues: 270 loop : 0.24 (0.23), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG J 235 TYR 0.011 0.001 TYR M 216 PHE 0.009 0.001 PHE M 327 HIS 0.003 0.000 HIS L 93 Details of bonding type rmsd covalent geometry : bond 0.00231 (15612) covalent geometry : angle 0.41282 (21155) hydrogen bonds : bond 0.02576 ( 799) hydrogen bonds : angle 4.38110 ( 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 174 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 147 time to evaluate : 0.622 Fit side-chains REVERT: B 1 MET cc_start: 0.8256 (mtm) cc_final: 0.7967 (mtt) REVERT: D 1 MET cc_start: 0.8500 (mtp) cc_final: 0.7815 (mtt) REVERT: I 43 GLU cc_start: 0.8026 (mt-10) cc_final: 0.7658 (mt-10) REVERT: I 176 GLU cc_start: 0.7554 (tm-30) cc_final: 0.6918 (tp30) REVERT: I 210 MET cc_start: 0.8407 (mtp) cc_final: 0.8125 (mtm) REVERT: I 308 GLU cc_start: 0.7741 (pt0) cc_final: 0.7156 (pm20) REVERT: J 202 GLN cc_start: 0.7401 (mt0) cc_final: 0.6888 (tt0) REVERT: J 235 ARG cc_start: 0.8031 (tpt90) cc_final: 0.7787 (tpt-90) REVERT: J 258 GLU cc_start: 0.7783 (OUTLIER) cc_final: 0.7303 (tt0) REVERT: K 114 GLN cc_start: 0.8587 (OUTLIER) cc_final: 0.8151 (mt0) REVERT: K 187 ASP cc_start: 0.8186 (m-30) cc_final: 0.7892 (m-30) REVERT: L 43 GLU cc_start: 0.8098 (mt-10) cc_final: 0.7398 (mp0) REVERT: L 98 GLU cc_start: 0.7439 (tt0) cc_final: 0.7058 (tt0) REVERT: L 308 GLU cc_start: 0.7763 (pt0) cc_final: 0.7458 (pm20) REVERT: M 27 ARG cc_start: 0.7431 (mmm160) cc_final: 0.6996 (tpt90) REVERT: M 70 LYS cc_start: 0.7446 (tppp) cc_final: 0.6992 (ttpt) REVERT: M 108 GLU cc_start: 0.7191 (mm-30) cc_final: 0.6816 (mt-10) REVERT: M 118 GLU cc_start: 0.7970 (tt0) cc_final: 0.7516 (tt0) REVERT: M 235 ARG cc_start: 0.8342 (ttp80) cc_final: 0.7999 (tpt90) REVERT: N 59 GLU cc_start: 0.7490 (mt-10) cc_final: 0.7255 (tt0) REVERT: N 154 GLU cc_start: 0.8442 (mt-10) cc_final: 0.8171 (tt0) REVERT: N 202 GLN cc_start: 0.7685 (mm-40) cc_final: 0.7218 (tm-30) REVERT: N 235 ARG cc_start: 0.8089 (tmt-80) cc_final: 0.7849 (tpt90) REVERT: N 303 ARG cc_start: 0.8224 (ttp-110) cc_final: 0.7977 (ttp-110) outliers start: 27 outliers final: 23 residues processed: 169 average time/residue: 0.1343 time to fit residues: 33.7362 Evaluate side-chains 167 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 142 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 99 ILE Chi-restraints excluded: chain I residue 112 LEU Chi-restraints excluded: chain I residue 125 MET Chi-restraints excluded: chain I residue 230 THR Chi-restraints excluded: chain I residue 233 SER Chi-restraints excluded: chain I residue 326 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 169 GLU Chi-restraints excluded: chain L residue 36 ASN Chi-restraints excluded: chain L residue 90 THR Chi-restraints excluded: chain L residue 99 ILE Chi-restraints excluded: chain L residue 149 ASP Chi-restraints excluded: chain L residue 214 SER Chi-restraints excluded: chain L residue 266 THR Chi-restraints excluded: chain M residue 99 ILE Chi-restraints excluded: chain M residue 125 MET Chi-restraints excluded: chain M residue 149 ASP Chi-restraints excluded: chain M residue 266 THR Chi-restraints excluded: chain N residue 112 LEU Chi-restraints excluded: chain N residue 330 ASN 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: 1.9990 chunk 27 optimal weight: 4.9990 chunk 3 optimal weight: 0.4980 chunk 156 optimal weight: 0.0270 chunk 0 optimal weight: 0.9980 chunk 79 optimal weight: 4.9990 chunk 129 optimal weight: 0.5980 chunk 2 optimal weight: 7.9990 chunk 81 optimal weight: 0.8980 chunk 115 optimal weight: 3.9990 overall best weight: 0.5238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 145 GLN ** N 200 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 = 0.3376 r_free = 0.3376 target = 0.132443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.105722 restraints weight = 15576.946| |-----------------------------------------------------------------------------| r_work (start): 0.3118 rms_B_bonded: 1.41 r_work: 0.2976 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2833 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.2239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 15612 Z= 0.099 Angle : 0.405 5.494 21155 Z= 0.217 Chirality : 0.038 0.133 2406 Planarity : 0.003 0.041 2658 Dihedral : 11.855 178.864 2549 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.87 % Allowed : 20.41 % Favored : 77.71 % 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: 0.59 (0.20), residues: 1890 helix: 1.17 (0.18), residues: 900 sheet: -1.28 (0.33), residues: 270 loop : 0.27 (0.23), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG J 306 TYR 0.010 0.001 TYR M 216 PHE 0.009 0.001 PHE M 327 HIS 0.003 0.000 HIS K 93 Details of bonding type rmsd covalent geometry : bond 0.00215 (15612) covalent geometry : angle 0.40488 (21155) hydrogen bonds : bond 0.02478 ( 799) hydrogen bonds : angle 4.30616 ( 2217) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4544.86 seconds wall clock time: 79 minutes 1.70 seconds (4741.70 seconds total)