Starting phenix.real_space_refine on Sat Aug 23 06:28:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8pvf_17964/08_2025/8pvf_17964.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pvf_17964/08_2025/8pvf_17964.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8pvf_17964/08_2025/8pvf_17964.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pvf_17964/08_2025/8pvf_17964.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8pvf_17964/08_2025/8pvf_17964.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pvf_17964/08_2025/8pvf_17964.map" } resolution = 2.9 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= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 8 5.49 5 S 72 5.16 5 C 6372 2.51 5 N 1704 2.21 5 O 1984 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10140 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2491 Classifications: {'peptide': 337} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 15, 'TRANS': 321} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: B, C, D Time building chain proxies: 1.59, per 1000 atoms: 0.16 Number of scatterers: 10140 At special positions: 0 Unit cell: (95.0895, 84.9915, 96.7725, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 72 16.00 P 8 15.00 O 1984 8.00 N 1704 7.00 C 6372 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.62 Conformation dependent library (CDL) restraints added in 258.8 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2440 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 12 sheets defined 36.5% alpha, 30.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'A' and resid 26 through 38 removed outlier: 3.519A pdb=" N GLU A 38 " --> pdb=" O ARG A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 63 Processing helix chain 'A' and resid 95 through 99 Processing helix chain 'A' and resid 100 through 105 Processing helix chain 'A' and resid 118 through 123 Processing helix chain 'A' and resid 124 through 127 Processing helix chain 'A' and resid 151 through 155 Processing helix chain 'A' and resid 167 through 184 Proline residue: A 175 - end of helix Processing helix chain 'A' and resid 230 through 239 removed outlier: 3.787A pdb=" N GLY A 236 " --> pdb=" O ALA A 232 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LYS A 237 " --> pdb=" O LYS A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 243 Processing helix chain 'A' and resid 272 through 285 Processing helix chain 'A' and resid 300 through 305 Processing helix chain 'A' and resid 316 through 318 No H-bonds generated for 'chain 'A' and resid 316 through 318' Processing helix chain 'A' and resid 335 through 352 Processing helix chain 'B' and resid 26 through 38 removed outlier: 3.519A pdb=" N GLU B 38 " --> pdb=" O ARG B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 63 Processing helix chain 'B' and resid 95 through 99 Processing helix chain 'B' and resid 100 through 105 Processing helix chain 'B' and resid 118 through 123 Processing helix chain 'B' and resid 124 through 127 Processing helix chain 'B' and resid 151 through 155 Processing helix chain 'B' and resid 167 through 184 Proline residue: B 175 - end of helix Processing helix chain 'B' and resid 230 through 239 removed outlier: 3.787A pdb=" N GLY B 236 " --> pdb=" O ALA B 232 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LYS B 237 " --> pdb=" O LYS B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 240 through 243 Processing helix chain 'B' and resid 272 through 285 Processing helix chain 'B' and resid 300 through 305 Processing helix chain 'B' and resid 316 through 318 No H-bonds generated for 'chain 'B' and resid 316 through 318' Processing helix chain 'B' and resid 335 through 352 Processing helix chain 'C' and resid 26 through 38 removed outlier: 3.519A pdb=" N GLU C 38 " --> pdb=" O ARG C 34 " (cutoff:3.500A) Processing helix chain 'C' and resid 53 through 63 Processing helix chain 'C' and resid 95 through 99 Processing helix chain 'C' and resid 100 through 105 Processing helix chain 'C' and resid 118 through 123 Processing helix chain 'C' and resid 124 through 127 Processing helix chain 'C' and resid 151 through 155 Processing helix chain 'C' and resid 167 through 184 Proline residue: C 175 - end of helix Processing helix chain 'C' and resid 230 through 239 removed outlier: 3.787A pdb=" N GLY C 236 " --> pdb=" O ALA C 232 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LYS C 237 " --> pdb=" O LYS C 233 " (cutoff:3.500A) Processing helix chain 'C' and resid 240 through 243 Processing helix chain 'C' and resid 272 through 285 Processing helix chain 'C' and resid 300 through 305 Processing helix chain 'C' and resid 316 through 318 No H-bonds generated for 'chain 'C' and resid 316 through 318' Processing helix chain 'C' and resid 335 through 352 Processing helix chain 'D' and resid 26 through 38 removed outlier: 3.519A pdb=" N GLU D 38 " --> pdb=" O ARG D 34 " (cutoff:3.500A) Processing helix chain 'D' and resid 53 through 63 Processing helix chain 'D' and resid 95 through 99 Processing helix chain 'D' and resid 100 through 105 Processing helix chain 'D' and resid 118 through 123 Processing helix chain 'D' and resid 124 through 127 Processing helix chain 'D' and resid 151 through 155 Processing helix chain 'D' and resid 167 through 184 Proline residue: D 175 - end of helix Processing helix chain 'D' and resid 230 through 239 removed outlier: 3.787A pdb=" N GLY D 236 " --> pdb=" O ALA D 232 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LYS D 237 " --> pdb=" O LYS D 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 240 through 243 Processing helix chain 'D' and resid 272 through 285 Processing helix chain 'D' and resid 300 through 305 Processing helix chain 'D' and resid 316 through 318 No H-bonds generated for 'chain 'D' and resid 316 through 318' Processing helix chain 'D' and resid 335 through 352 Processing sheet with id=1, first strand: chain 'A' and resid 74 through 76 removed outlier: 10.094A pdb=" N VAL A 87 " --> pdb=" O THR A 43 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N VAL A 45 " --> pdb=" O VAL A 87 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N LEU A 20 " --> pdb=" O VAL A 45 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N ILE A 47 " --> pdb=" O LEU A 20 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N ILE A 22 " --> pdb=" O ILE A 47 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N THR A 19 " --> pdb=" O ILE A 108 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N CYS A 110 " --> pdb=" O THR A 19 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N GLY A 21 " --> pdb=" O CYS A 110 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N VAL A 109 " --> pdb=" O ILE A 134 " (cutoff:3.500A) Processing sheet with id=2, first strand: chain 'A' and resid 225 through 228 removed outlier: 9.310A pdb=" N THR A 247 " --> pdb=" O VAL A 187 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N GLY A 189 " --> pdb=" O THR A 247 " (cutoff:3.500A) removed outlier: 8.597A pdb=" N MET A 249 " --> pdb=" O GLY A 189 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N MET A 191 " --> pdb=" O MET A 249 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N ILE A 251 " --> pdb=" O MET A 191 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N THR A 193 " --> pdb=" O ILE A 251 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N LYS A 266 " --> pdb=" O VAL A 187 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N GLY A 189 " --> pdb=" O THR A 264 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N THR A 264 " --> pdb=" O GLY A 189 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N MET A 191 " --> pdb=" O ASP A 262 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ASP A 262 " --> pdb=" O MET A 191 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N THR A 193 " --> pdb=" O VAL A 260 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N VAL A 260 " --> pdb=" O THR A 193 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N ILE A 329 " --> pdb=" O ASP A 314 " (cutoff:3.500A) Processing sheet with id=3, first strand: chain 'A' and resid 225 through 228 removed outlier: 9.310A pdb=" N THR A 247 " --> pdb=" O VAL A 187 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N GLY A 189 " --> pdb=" O THR A 247 " (cutoff:3.500A) removed outlier: 8.597A pdb=" N MET A 249 " --> pdb=" O GLY A 189 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N MET A 191 " --> pdb=" O MET A 249 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N ILE A 251 " --> pdb=" O MET A 191 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N THR A 193 " --> pdb=" O ILE A 251 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N LYS A 266 " --> pdb=" O VAL A 187 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N GLY A 189 " --> pdb=" O THR A 264 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N THR A 264 " --> pdb=" O GLY A 189 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N MET A 191 " --> pdb=" O ASP A 262 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ASP A 262 " --> pdb=" O MET A 191 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N THR A 193 " --> pdb=" O VAL A 260 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N VAL A 260 " --> pdb=" O THR A 193 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N PHE A 325 " --> pdb=" O LEU A 321 " (cutoff:3.500A) Processing sheet with id=4, first strand: chain 'B' and resid 74 through 76 removed outlier: 10.094A pdb=" N VAL B 87 " --> pdb=" O THR B 43 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N VAL B 45 " --> pdb=" O VAL B 87 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N LEU B 20 " --> pdb=" O VAL B 45 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N ILE B 47 " --> pdb=" O LEU B 20 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N ILE B 22 " --> pdb=" O ILE B 47 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N THR B 19 " --> pdb=" O ILE B 108 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N CYS B 110 " --> pdb=" O THR B 19 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N GLY B 21 " --> pdb=" O CYS B 110 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N VAL B 109 " --> pdb=" O ILE B 134 " (cutoff:3.500A) Processing sheet with id=5, first strand: chain 'B' and resid 225 through 228 removed outlier: 9.310A pdb=" N THR B 247 " --> pdb=" O VAL B 187 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N GLY B 189 " --> pdb=" O THR B 247 " (cutoff:3.500A) removed outlier: 8.597A pdb=" N MET B 249 " --> pdb=" O GLY B 189 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N MET B 191 " --> pdb=" O MET B 249 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N ILE B 251 " --> pdb=" O MET B 191 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N THR B 193 " --> pdb=" O ILE B 251 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N LYS B 266 " --> pdb=" O VAL B 187 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N GLY B 189 " --> pdb=" O THR B 264 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N THR B 264 " --> pdb=" O GLY B 189 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N MET B 191 " --> pdb=" O ASP B 262 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ASP B 262 " --> pdb=" O MET B 191 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N THR B 193 " --> pdb=" O VAL B 260 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N VAL B 260 " --> pdb=" O THR B 193 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N ILE B 329 " --> pdb=" O ASP B 314 " (cutoff:3.500A) Processing sheet with id=6, first strand: chain 'B' and resid 225 through 228 removed outlier: 9.310A pdb=" N THR B 247 " --> pdb=" O VAL B 187 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N GLY B 189 " --> pdb=" O THR B 247 " (cutoff:3.500A) removed outlier: 8.597A pdb=" N MET B 249 " --> pdb=" O GLY B 189 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N MET B 191 " --> pdb=" O MET B 249 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N ILE B 251 " --> pdb=" O MET B 191 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N THR B 193 " --> pdb=" O ILE B 251 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N LYS B 266 " --> pdb=" O VAL B 187 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N GLY B 189 " --> pdb=" O THR B 264 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N THR B 264 " --> pdb=" O GLY B 189 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N MET B 191 " --> pdb=" O ASP B 262 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ASP B 262 " --> pdb=" O MET B 191 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N THR B 193 " --> pdb=" O VAL B 260 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N VAL B 260 " --> pdb=" O THR B 193 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N PHE B 325 " --> pdb=" O LEU B 321 " (cutoff:3.500A) Processing sheet with id=7, first strand: chain 'C' and resid 74 through 76 removed outlier: 10.094A pdb=" N VAL C 87 " --> pdb=" O THR C 43 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N VAL C 45 " --> pdb=" O VAL C 87 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N LEU C 20 " --> pdb=" O VAL C 45 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N ILE C 47 " --> pdb=" O LEU C 20 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N ILE C 22 " --> pdb=" O ILE C 47 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N THR C 19 " --> pdb=" O ILE C 108 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N CYS C 110 " --> pdb=" O THR C 19 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N GLY C 21 " --> pdb=" O CYS C 110 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N VAL C 109 " --> pdb=" O ILE C 134 " (cutoff:3.500A) Processing sheet with id=8, first strand: chain 'C' and resid 225 through 228 removed outlier: 9.310A pdb=" N THR C 247 " --> pdb=" O VAL C 187 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N GLY C 189 " --> pdb=" O THR C 247 " (cutoff:3.500A) removed outlier: 8.597A pdb=" N MET C 249 " --> pdb=" O GLY C 189 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N MET C 191 " --> pdb=" O MET C 249 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N ILE C 251 " --> pdb=" O MET C 191 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N THR C 193 " --> pdb=" O ILE C 251 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N LYS C 266 " --> pdb=" O VAL C 187 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N GLY C 189 " --> pdb=" O THR C 264 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N THR C 264 " --> pdb=" O GLY C 189 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N MET C 191 " --> pdb=" O ASP C 262 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ASP C 262 " --> pdb=" O MET C 191 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N THR C 193 " --> pdb=" O VAL C 260 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N VAL C 260 " --> pdb=" O THR C 193 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N ILE C 329 " --> pdb=" O ASP C 314 " (cutoff:3.500A) Processing sheet with id=9, first strand: chain 'C' and resid 225 through 228 removed outlier: 9.310A pdb=" N THR C 247 " --> pdb=" O VAL C 187 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N GLY C 189 " --> pdb=" O THR C 247 " (cutoff:3.500A) removed outlier: 8.597A pdb=" N MET C 249 " --> pdb=" O GLY C 189 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N MET C 191 " --> pdb=" O MET C 249 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N ILE C 251 " --> pdb=" O MET C 191 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N THR C 193 " --> pdb=" O ILE C 251 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N LYS C 266 " --> pdb=" O VAL C 187 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N GLY C 189 " --> pdb=" O THR C 264 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N THR C 264 " --> pdb=" O GLY C 189 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N MET C 191 " --> pdb=" O ASP C 262 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ASP C 262 " --> pdb=" O MET C 191 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N THR C 193 " --> pdb=" O VAL C 260 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N VAL C 260 " --> pdb=" O THR C 193 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N PHE C 325 " --> pdb=" O LEU C 321 " (cutoff:3.500A) Processing sheet with id=10, first strand: chain 'D' and resid 74 through 76 removed outlier: 10.094A pdb=" N VAL D 87 " --> pdb=" O THR D 43 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N VAL D 45 " --> pdb=" O VAL D 87 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N LEU D 20 " --> pdb=" O VAL D 45 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N ILE D 47 " --> pdb=" O LEU D 20 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N ILE D 22 " --> pdb=" O ILE D 47 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N THR D 19 " --> pdb=" O ILE D 108 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N CYS D 110 " --> pdb=" O THR D 19 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N GLY D 21 " --> pdb=" O CYS D 110 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N VAL D 109 " --> pdb=" O ILE D 134 " (cutoff:3.500A) Processing sheet with id=11, first strand: chain 'D' and resid 225 through 228 removed outlier: 9.310A pdb=" N THR D 247 " --> pdb=" O VAL D 187 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N GLY D 189 " --> pdb=" O THR D 247 " (cutoff:3.500A) removed outlier: 8.597A pdb=" N MET D 249 " --> pdb=" O GLY D 189 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N MET D 191 " --> pdb=" O MET D 249 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N ILE D 251 " --> pdb=" O MET D 191 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N THR D 193 " --> pdb=" O ILE D 251 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N LYS D 266 " --> pdb=" O VAL D 187 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N GLY D 189 " --> pdb=" O THR D 264 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N THR D 264 " --> pdb=" O GLY D 189 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N MET D 191 " --> pdb=" O ASP D 262 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ASP D 262 " --> pdb=" O MET D 191 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N THR D 193 " --> pdb=" O VAL D 260 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N VAL D 260 " --> pdb=" O THR D 193 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N ILE D 329 " --> pdb=" O ASP D 314 " (cutoff:3.500A) Processing sheet with id=12, first strand: chain 'D' and resid 225 through 228 removed outlier: 9.310A pdb=" N THR D 247 " --> pdb=" O VAL D 187 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N GLY D 189 " --> pdb=" O THR D 247 " (cutoff:3.500A) removed outlier: 8.597A pdb=" N MET D 249 " --> pdb=" O GLY D 189 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N MET D 191 " --> pdb=" O MET D 249 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N ILE D 251 " --> pdb=" O MET D 191 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N THR D 193 " --> pdb=" O ILE D 251 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N LYS D 266 " --> pdb=" O VAL D 187 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N GLY D 189 " --> pdb=" O THR D 264 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N THR D 264 " --> pdb=" O GLY D 189 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N MET D 191 " --> pdb=" O ASP D 262 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ASP D 262 " --> pdb=" O MET D 191 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N THR D 193 " --> pdb=" O VAL D 260 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N VAL D 260 " --> pdb=" O THR D 193 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N PHE D 325 " --> pdb=" O LEU D 321 " (cutoff:3.500A) 452 hydrogen bonds defined for protein. 1176 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: 1.77 Time building geometry restraints manager: 0.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2212 1.34 - 1.46: 2900 1.46 - 1.58: 5096 1.58 - 1.70: 16 1.70 - 1.82: 108 Bond restraints: 10332 Sorted by residual: bond pdb=" C1D NAD B 401 " pdb=" O4D NAD B 401 " ideal model delta sigma weight residual 1.376 1.433 -0.057 2.00e-02 2.50e+03 8.26e+00 bond pdb=" C1D NAD A 401 " pdb=" O4D NAD A 401 " ideal model delta sigma weight residual 1.376 1.433 -0.057 2.00e-02 2.50e+03 8.26e+00 bond pdb=" C1D NAD D 401 " pdb=" O4D NAD D 401 " ideal model delta sigma weight residual 1.376 1.433 -0.057 2.00e-02 2.50e+03 8.26e+00 bond pdb=" C1D NAD C 401 " pdb=" O4D NAD C 401 " ideal model delta sigma weight residual 1.376 1.433 -0.057 2.00e-02 2.50e+03 8.26e+00 bond pdb=" C ALA D 137 " pdb=" N PRO D 138 " ideal model delta sigma weight residual 1.329 1.362 -0.033 1.18e-02 7.18e+03 7.74e+00 ... (remaining 10327 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.96: 10508 1.96 - 3.92: 3048 3.92 - 5.88: 428 5.88 - 7.84: 68 7.84 - 9.80: 12 Bond angle restraints: 14064 Sorted by residual: angle pdb=" CA ASP C 95 " pdb=" CB ASP C 95 " pdb=" CG ASP C 95 " ideal model delta sigma weight residual 112.60 119.09 -6.49 1.00e+00 1.00e+00 4.21e+01 angle pdb=" CA ASP D 95 " pdb=" CB ASP D 95 " pdb=" CG ASP D 95 " ideal model delta sigma weight residual 112.60 119.09 -6.49 1.00e+00 1.00e+00 4.21e+01 angle pdb=" CA ASP B 95 " pdb=" CB ASP B 95 " pdb=" CG ASP B 95 " ideal model delta sigma weight residual 112.60 119.07 -6.47 1.00e+00 1.00e+00 4.18e+01 angle pdb=" CA ASP A 95 " pdb=" CB ASP A 95 " pdb=" CG ASP A 95 " ideal model delta sigma weight residual 112.60 119.07 -6.47 1.00e+00 1.00e+00 4.18e+01 angle pdb=" C ASP A 262 " pdb=" CA ASP A 262 " pdb=" CB ASP A 262 " ideal model delta sigma weight residual 111.17 120.97 -9.80 1.54e+00 4.22e-01 4.05e+01 ... (remaining 14059 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.41: 5468 15.41 - 30.81: 676 30.81 - 46.21: 92 46.21 - 61.61: 44 61.61 - 77.01: 24 Dihedral angle restraints: 6304 sinusoidal: 2476 harmonic: 3828 Sorted by residual: dihedral pdb=" CA MET B 191 " pdb=" C MET B 191 " pdb=" N THR B 192 " pdb=" CA THR B 192 " ideal model delta harmonic sigma weight residual 180.00 155.00 25.00 0 5.00e+00 4.00e-02 2.50e+01 dihedral pdb=" CA MET C 191 " pdb=" C MET C 191 " pdb=" N THR C 192 " pdb=" CA THR C 192 " ideal model delta harmonic sigma weight residual 180.00 155.00 25.00 0 5.00e+00 4.00e-02 2.50e+01 dihedral pdb=" CA MET A 191 " pdb=" C MET A 191 " pdb=" N THR A 192 " pdb=" CA THR A 192 " ideal model delta harmonic sigma weight residual 180.00 155.00 25.00 0 5.00e+00 4.00e-02 2.50e+01 ... (remaining 6301 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 826 0.062 - 0.124: 510 0.124 - 0.186: 260 0.186 - 0.248: 36 0.248 - 0.310: 8 Chirality restraints: 1640 Sorted by residual: chirality pdb=" CB ILE C 108 " pdb=" CA ILE C 108 " pdb=" CG1 ILE C 108 " pdb=" CG2 ILE C 108 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.31 2.00e-01 2.50e+01 2.41e+00 chirality pdb=" CB ILE A 108 " pdb=" CA ILE A 108 " pdb=" CG1 ILE A 108 " pdb=" CG2 ILE A 108 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.31 2.00e-01 2.50e+01 2.41e+00 chirality pdb=" CB ILE D 108 " pdb=" CA ILE D 108 " pdb=" CG1 ILE D 108 " pdb=" CG2 ILE D 108 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.31 2.00e-01 2.50e+01 2.41e+00 ... (remaining 1637 not shown) Planarity restraints: 1792 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 252 " 0.172 9.50e-02 1.11e+02 8.18e-02 1.31e+01 pdb=" NE ARG C 252 " -0.028 2.00e-02 2.50e+03 pdb=" CZ ARG C 252 " 0.051 2.00e-02 2.50e+03 pdb=" NH1 ARG C 252 " -0.019 2.00e-02 2.50e+03 pdb=" NH2 ARG C 252 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 252 " 0.172 9.50e-02 1.11e+02 8.18e-02 1.31e+01 pdb=" NE ARG D 252 " -0.028 2.00e-02 2.50e+03 pdb=" CZ ARG D 252 " 0.051 2.00e-02 2.50e+03 pdb=" NH1 ARG D 252 " -0.019 2.00e-02 2.50e+03 pdb=" NH2 ARG D 252 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 252 " -0.172 9.50e-02 1.11e+02 8.18e-02 1.31e+01 pdb=" NE ARG B 252 " 0.028 2.00e-02 2.50e+03 pdb=" CZ ARG B 252 " -0.051 2.00e-02 2.50e+03 pdb=" NH1 ARG B 252 " 0.019 2.00e-02 2.50e+03 pdb=" NH2 ARG B 252 " 0.011 2.00e-02 2.50e+03 ... (remaining 1789 not shown) Histogram of nonbonded interaction distances: 2.41 - 2.91: 3824 2.91 - 3.41: 9600 3.41 - 3.91: 18864 3.91 - 4.40: 22038 4.40 - 4.90: 35102 Nonbonded interactions: 89428 Sorted by model distance: nonbonded pdb=" O ALA A 137 " pdb=" OG SER A 164 " model vdw 2.413 3.040 nonbonded pdb=" O ALA B 137 " pdb=" OG SER B 164 " model vdw 2.413 3.040 nonbonded pdb=" O ALA C 137 " pdb=" OG SER C 164 " model vdw 2.413 3.040 nonbonded pdb=" O ALA D 137 " pdb=" OG SER D 164 " model vdw 2.413 3.040 nonbonded pdb=" O SER B 136 " pdb=" OG SER B 136 " model vdw 2.493 3.040 ... (remaining 89423 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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: 1.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.060 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.010 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:7.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 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 : 0.010 0.057 10332 Z= 0.651 Angle : 1.803 9.801 14064 Z= 1.192 Chirality : 0.091 0.310 1640 Planarity : 0.011 0.091 1792 Dihedral : 14.887 77.012 3864 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 0.60 Ramachandran Plot: Outliers : 0.30 % Allowed : 4.18 % Favored : 95.52 % Rotamer: Outliers : 1.12 % Allowed : 7.43 % Favored : 91.45 % Cbeta Deviations : 0.33 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.16 (0.21), residues: 1340 helix: -0.96 (0.22), residues: 352 sheet: -1.41 (0.28), residues: 272 loop : -0.23 (0.23), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.053 0.008 ARG C 252 TYR 0.040 0.008 TYR B 146 PHE 0.026 0.007 PHE D 304 TRP 0.032 0.008 TRP B 101 HIS 0.008 0.004 HIS A 125 Details of bonding type rmsd covalent geometry : bond 0.01023 (10332) covalent geometry : angle 1.80274 (14064) hydrogen bonds : bond 0.17967 ( 400) hydrogen bonds : angle 7.29457 ( 1176) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 304 time to evaluate : 0.357 Fit side-chains REVERT: A 37 MET cc_start: 0.7451 (mmt) cc_final: 0.7128 (mpm) REVERT: A 43 THR cc_start: 0.7608 (t) cc_final: 0.7330 (m) REVERT: A 55 GLU cc_start: 0.6945 (mp0) cc_final: 0.6592 (mp0) REVERT: A 71 ASN cc_start: 0.7216 (t0) cc_final: 0.6593 (m-40) REVERT: A 75 GLU cc_start: 0.7628 (pt0) cc_final: 0.7360 (pt0) REVERT: A 89 LYS cc_start: 0.7003 (mtpt) cc_final: 0.6682 (mtpt) REVERT: A 120 GLU cc_start: 0.7692 (tt0) cc_final: 0.7109 (mp0) REVERT: A 131 LYS cc_start: 0.7686 (mmtp) cc_final: 0.7183 (mttm) REVERT: A 159 LYS cc_start: 0.6956 (mmtt) cc_final: 0.6564 (ttmm) REVERT: A 160 PHE cc_start: 0.7491 (m-80) cc_final: 0.7260 (m-80) REVERT: A 183 LYS cc_start: 0.7221 (tptt) cc_final: 0.6942 (tptm) REVERT: A 247 THR cc_start: 0.8509 (t) cc_final: 0.8162 (p) REVERT: A 252 ARG cc_start: 0.7537 (mtt180) cc_final: 0.7030 (mpp80) REVERT: A 282 GLU cc_start: 0.6790 (tt0) cc_final: 0.6441 (mt-10) REVERT: A 289 LYS cc_start: 0.7953 (ttpt) cc_final: 0.7449 (ttmm) REVERT: A 308 LYS cc_start: 0.7991 (mttp) cc_final: 0.7762 (mttp) REVERT: A 327 LYS cc_start: 0.8054 (ttmm) cc_final: 0.7766 (tppp) REVERT: B 37 MET cc_start: 0.7451 (mmt) cc_final: 0.7128 (mpm) REVERT: B 43 THR cc_start: 0.7606 (t) cc_final: 0.7330 (m) REVERT: B 55 GLU cc_start: 0.6947 (mp0) cc_final: 0.6594 (mp0) REVERT: B 71 ASN cc_start: 0.7218 (t0) cc_final: 0.6593 (m-40) REVERT: B 75 GLU cc_start: 0.7630 (pt0) cc_final: 0.7361 (pt0) REVERT: B 89 LYS cc_start: 0.7004 (mtpt) cc_final: 0.6683 (mtpt) REVERT: B 120 GLU cc_start: 0.7693 (tt0) cc_final: 0.7109 (mp0) REVERT: B 131 LYS cc_start: 0.7684 (mmtp) cc_final: 0.7180 (mttm) REVERT: B 159 LYS cc_start: 0.6956 (mmtt) cc_final: 0.6565 (ttmm) REVERT: B 160 PHE cc_start: 0.7491 (m-80) cc_final: 0.7261 (m-80) REVERT: B 183 LYS cc_start: 0.7219 (tptt) cc_final: 0.6940 (tptm) REVERT: B 247 THR cc_start: 0.8509 (t) cc_final: 0.8161 (p) REVERT: B 252 ARG cc_start: 0.7538 (mtt180) cc_final: 0.7030 (mpp80) REVERT: B 282 GLU cc_start: 0.6790 (tt0) cc_final: 0.6441 (mt-10) REVERT: B 289 LYS cc_start: 0.7955 (ttpt) cc_final: 0.7451 (ttmm) REVERT: B 308 LYS cc_start: 0.7991 (mttp) cc_final: 0.7760 (mttp) REVERT: B 327 LYS cc_start: 0.8056 (ttmm) cc_final: 0.7767 (tppp) REVERT: C 37 MET cc_start: 0.7452 (mmt) cc_final: 0.7128 (mpm) REVERT: C 43 THR cc_start: 0.7609 (t) cc_final: 0.7332 (m) REVERT: C 55 GLU cc_start: 0.6947 (mp0) cc_final: 0.6594 (mp0) REVERT: C 71 ASN cc_start: 0.7217 (t0) cc_final: 0.6592 (m-40) REVERT: C 75 GLU cc_start: 0.7630 (pt0) cc_final: 0.7360 (pt0) REVERT: C 89 LYS cc_start: 0.7005 (mtpt) cc_final: 0.6683 (mtpt) REVERT: C 120 GLU cc_start: 0.7693 (tt0) cc_final: 0.7109 (mp0) REVERT: C 131 LYS cc_start: 0.7685 (mmtp) cc_final: 0.7182 (mttm) REVERT: C 159 LYS cc_start: 0.6956 (mmtt) cc_final: 0.6563 (ttmm) REVERT: C 160 PHE cc_start: 0.7492 (m-80) cc_final: 0.7260 (m-80) REVERT: C 183 LYS cc_start: 0.7221 (tptt) cc_final: 0.6941 (tptm) REVERT: C 247 THR cc_start: 0.8508 (t) cc_final: 0.8162 (p) REVERT: C 252 ARG cc_start: 0.7537 (mtt180) cc_final: 0.7029 (mpp80) REVERT: C 282 GLU cc_start: 0.6792 (tt0) cc_final: 0.6442 (mt-10) REVERT: C 289 LYS cc_start: 0.7954 (ttpt) cc_final: 0.7450 (ttmm) REVERT: C 308 LYS cc_start: 0.7993 (mttp) cc_final: 0.7762 (mttp) REVERT: C 327 LYS cc_start: 0.8057 (ttmm) cc_final: 0.7769 (tppp) REVERT: D 37 MET cc_start: 0.7451 (mmt) cc_final: 0.7127 (mpm) REVERT: D 43 THR cc_start: 0.7607 (t) cc_final: 0.7330 (m) REVERT: D 55 GLU cc_start: 0.6947 (mp0) cc_final: 0.6593 (mp0) REVERT: D 71 ASN cc_start: 0.7218 (t0) cc_final: 0.6594 (m-40) REVERT: D 75 GLU cc_start: 0.7629 (pt0) cc_final: 0.7359 (pt0) REVERT: D 89 LYS cc_start: 0.7003 (mtpt) cc_final: 0.6681 (mtpt) REVERT: D 120 GLU cc_start: 0.7694 (tt0) cc_final: 0.7109 (mp0) REVERT: D 131 LYS cc_start: 0.7685 (mmtp) cc_final: 0.7182 (mttm) REVERT: D 159 LYS cc_start: 0.6957 (mmtt) cc_final: 0.6563 (ttmm) REVERT: D 160 PHE cc_start: 0.7492 (m-80) cc_final: 0.7261 (m-80) REVERT: D 183 LYS cc_start: 0.7223 (tptt) cc_final: 0.6944 (tptm) REVERT: D 247 THR cc_start: 0.8509 (t) cc_final: 0.8163 (p) REVERT: D 252 ARG cc_start: 0.7539 (mtt180) cc_final: 0.7030 (mpp80) REVERT: D 282 GLU cc_start: 0.6790 (tt0) cc_final: 0.6439 (mt-10) REVERT: D 289 LYS cc_start: 0.7953 (ttpt) cc_final: 0.7449 (ttmm) REVERT: D 308 LYS cc_start: 0.7992 (mttp) cc_final: 0.7762 (mttp) REVERT: D 327 LYS cc_start: 0.8051 (ttmm) cc_final: 0.7766 (tppp) outliers start: 12 outliers final: 8 residues processed: 308 average time/residue: 0.5660 time to fit residues: 185.1505 Evaluate side-chains 232 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 224 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 ASP Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain B residue 95 ASP Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain C residue 95 ASP Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain D residue 95 ASP Chi-restraints excluded: chain D residue 261 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 98 optimal weight: 0.5980 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 2.9990 chunk 55 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 92 GLN A 107 GLN A 195 HIS ** B 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 92 GLN B 107 GLN B 195 HIS B 201 GLN ** C 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 92 GLN C 107 GLN C 195 HIS ** D 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 92 GLN D 107 GLN D 195 HIS D 201 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.107684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.094273 restraints weight = 12331.866| |-----------------------------------------------------------------------------| r_work (start): 0.2976 rms_B_bonded: 1.35 r_work: 0.2889 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.2763 rms_B_bonded: 3.03 restraints_weight: 0.2500 r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.2072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10332 Z= 0.123 Angle : 0.549 5.989 14064 Z= 0.290 Chirality : 0.046 0.156 1640 Planarity : 0.004 0.035 1792 Dihedral : 9.107 78.592 1656 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.30 % Allowed : 2.99 % Favored : 96.72 % Rotamer: Outliers : 1.86 % Allowed : 11.52 % Favored : 86.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.05 (0.23), residues: 1340 helix: 0.63 (0.26), residues: 396 sheet: -1.29 (0.28), residues: 292 loop : 0.54 (0.26), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG D 39 TYR 0.010 0.001 TYR B 146 PHE 0.013 0.002 PHE C 304 TRP 0.003 0.001 TRP A 331 HIS 0.005 0.001 HIS B 67 Details of bonding type rmsd covalent geometry : bond 0.00285 (10332) covalent geometry : angle 0.54940 (14064) hydrogen bonds : bond 0.03459 ( 400) hydrogen bonds : angle 4.91542 ( 1176) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 228 time to evaluate : 0.235 Fit side-chains REVERT: A 71 ASN cc_start: 0.7658 (t0) cc_final: 0.7174 (m-40) REVERT: A 120 GLU cc_start: 0.7989 (tt0) cc_final: 0.7670 (mp0) REVERT: A 131 LYS cc_start: 0.8259 (mmtp) cc_final: 0.7772 (mttm) REVERT: A 289 LYS cc_start: 0.8261 (ttpt) cc_final: 0.7817 (ttmm) REVERT: B 71 ASN cc_start: 0.7647 (t0) cc_final: 0.7163 (m-40) REVERT: B 120 GLU cc_start: 0.7984 (tt0) cc_final: 0.7669 (mp0) REVERT: B 131 LYS cc_start: 0.8260 (mmtp) cc_final: 0.7772 (mttm) REVERT: B 289 LYS cc_start: 0.8270 (ttpt) cc_final: 0.7821 (ttmm) REVERT: C 71 ASN cc_start: 0.7641 (t0) cc_final: 0.7157 (m-40) REVERT: C 120 GLU cc_start: 0.7981 (tt0) cc_final: 0.7673 (mp0) REVERT: C 131 LYS cc_start: 0.8255 (mmtp) cc_final: 0.7768 (mttm) REVERT: C 289 LYS cc_start: 0.8248 (ttpt) cc_final: 0.7813 (ttmm) REVERT: D 71 ASN cc_start: 0.7657 (t0) cc_final: 0.7170 (m-40) REVERT: D 120 GLU cc_start: 0.7973 (tt0) cc_final: 0.7663 (mp0) REVERT: D 131 LYS cc_start: 0.8262 (mmtp) cc_final: 0.7770 (mttm) REVERT: D 289 LYS cc_start: 0.8264 (ttpt) cc_final: 0.7823 (ttmm) outliers start: 20 outliers final: 8 residues processed: 244 average time/residue: 0.5620 time to fit residues: 146.5721 Evaluate side-chains 176 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 168 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 342 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 63 optimal weight: 4.9990 chunk 29 optimal weight: 5.9990 chunk 52 optimal weight: 0.7980 chunk 98 optimal weight: 3.9990 chunk 78 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 7 optimal weight: 4.9990 chunk 107 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 117 optimal weight: 6.9990 chunk 45 optimal weight: 0.6980 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 ASN A 107 GLN A 195 HIS ** A 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 340 ASN B 48 ASN B 107 GLN B 195 HIS ** B 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN C 48 ASN C 107 GLN C 195 HIS ** C 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 340 ASN D 48 ASN D 107 GLN D 195 HIS ** D 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 340 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.110612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.097627 restraints weight = 12358.936| |-----------------------------------------------------------------------------| r_work (start): 0.2974 rms_B_bonded: 1.33 r_work: 0.2890 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.2768 rms_B_bonded: 2.96 restraints_weight: 0.2500 r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.2648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 10332 Z= 0.159 Angle : 0.547 6.749 14064 Z= 0.285 Chirality : 0.048 0.143 1640 Planarity : 0.004 0.035 1792 Dihedral : 8.914 82.188 1644 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.30 % Allowed : 2.99 % Favored : 96.72 % Rotamer: Outliers : 5.58 % Allowed : 15.61 % Favored : 78.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.23 (0.24), residues: 1340 helix: 0.75 (0.26), residues: 396 sheet: -0.99 (0.31), residues: 280 loop : 0.51 (0.26), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG D 39 TYR 0.013 0.002 TYR D 146 PHE 0.012 0.002 PHE A 304 TRP 0.004 0.001 TRP C 101 HIS 0.006 0.002 HIS A 125 Details of bonding type rmsd covalent geometry : bond 0.00374 (10332) covalent geometry : angle 0.54663 (14064) hydrogen bonds : bond 0.03373 ( 400) hydrogen bonds : angle 4.69596 ( 1176) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 178 time to evaluate : 0.239 Fit side-chains REVERT: A 71 ASN cc_start: 0.7704 (t0) cc_final: 0.7219 (m-40) REVERT: A 120 GLU cc_start: 0.7904 (tt0) cc_final: 0.7603 (mp0) REVERT: A 131 LYS cc_start: 0.8216 (mmtp) cc_final: 0.7734 (mttm) REVERT: A 274 GLU cc_start: 0.7863 (tp30) cc_final: 0.7583 (mm-30) REVERT: A 289 LYS cc_start: 0.8223 (ttpt) cc_final: 0.7874 (ttmm) REVERT: A 308 LYS cc_start: 0.8871 (OUTLIER) cc_final: 0.8453 (mttp) REVERT: A 319 ILE cc_start: 0.8546 (OUTLIER) cc_final: 0.8170 (tp) REVERT: B 71 ASN cc_start: 0.7707 (t0) cc_final: 0.7222 (m-40) REVERT: B 120 GLU cc_start: 0.7907 (tt0) cc_final: 0.7599 (mp0) REVERT: B 131 LYS cc_start: 0.8217 (mmtp) cc_final: 0.7735 (mttm) REVERT: B 274 GLU cc_start: 0.7870 (tp30) cc_final: 0.7587 (mm-30) REVERT: B 289 LYS cc_start: 0.8234 (ttpt) cc_final: 0.7883 (ttmm) REVERT: B 308 LYS cc_start: 0.8874 (OUTLIER) cc_final: 0.8461 (mttp) REVERT: B 319 ILE cc_start: 0.8546 (OUTLIER) cc_final: 0.8164 (tp) REVERT: C 71 ASN cc_start: 0.7707 (t0) cc_final: 0.7223 (m-40) REVERT: C 120 GLU cc_start: 0.7924 (tt0) cc_final: 0.7599 (mp0) REVERT: C 131 LYS cc_start: 0.8224 (mmtp) cc_final: 0.7744 (mttm) REVERT: C 274 GLU cc_start: 0.7880 (tp30) cc_final: 0.7600 (mm-30) REVERT: C 289 LYS cc_start: 0.8209 (ttpt) cc_final: 0.7868 (ttmm) REVERT: C 308 LYS cc_start: 0.8874 (OUTLIER) cc_final: 0.8458 (mttp) REVERT: C 319 ILE cc_start: 0.8547 (OUTLIER) cc_final: 0.8164 (tp) REVERT: D 71 ASN cc_start: 0.7722 (t0) cc_final: 0.7232 (m-40) REVERT: D 120 GLU cc_start: 0.7906 (tt0) cc_final: 0.7590 (mp0) REVERT: D 131 LYS cc_start: 0.8216 (mmtp) cc_final: 0.7733 (mttm) REVERT: D 274 GLU cc_start: 0.7874 (tp30) cc_final: 0.7590 (mm-30) REVERT: D 289 LYS cc_start: 0.8218 (ttpt) cc_final: 0.7870 (ttmm) REVERT: D 308 LYS cc_start: 0.8868 (OUTLIER) cc_final: 0.8445 (mttp) REVERT: D 319 ILE cc_start: 0.8545 (OUTLIER) cc_final: 0.8165 (tp) outliers start: 60 outliers final: 20 residues processed: 210 average time/residue: 0.5326 time to fit residues: 119.5346 Evaluate side-chains 196 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 168 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 MET Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 308 LYS Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain B residue 37 MET Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 308 LYS Chi-restraints excluded: chain B residue 319 ILE Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain C residue 37 MET Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 308 LYS Chi-restraints excluded: chain C residue 319 ILE Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain D residue 37 MET Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 308 LYS Chi-restraints excluded: chain D residue 319 ILE Chi-restraints excluded: chain D residue 342 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 60 optimal weight: 0.4980 chunk 87 optimal weight: 4.9990 chunk 62 optimal weight: 0.9990 chunk 107 optimal weight: 3.9990 chunk 102 optimal weight: 4.9990 chunk 71 optimal weight: 3.9990 chunk 31 optimal weight: 4.9990 chunk 83 optimal weight: 3.9990 chunk 116 optimal weight: 1.9990 chunk 95 optimal weight: 0.8980 chunk 115 optimal weight: 6.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 195 HIS ** A 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 195 HIS ** B 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 195 HIS ** C 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 195 HIS ** D 201 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 = 0.3143 r_free = 0.3143 target = 0.107856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.094434 restraints weight = 12664.569| |-----------------------------------------------------------------------------| r_work (start): 0.2971 rms_B_bonded: 1.38 r_work: 0.2882 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.2756 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.2824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 10332 Z= 0.190 Angle : 0.547 6.849 14064 Z= 0.286 Chirality : 0.048 0.144 1640 Planarity : 0.004 0.036 1792 Dihedral : 9.043 86.220 1644 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.30 % Allowed : 3.28 % Favored : 96.42 % Rotamer: Outliers : 4.46 % Allowed : 16.73 % Favored : 78.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.14 (0.24), residues: 1340 helix: 0.76 (0.27), residues: 396 sheet: -1.04 (0.31), residues: 280 loop : 0.40 (0.26), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 30 TYR 0.013 0.002 TYR C 146 PHE 0.014 0.002 PHE C 304 TRP 0.003 0.001 TRP C 101 HIS 0.005 0.002 HIS B 125 Details of bonding type rmsd covalent geometry : bond 0.00454 (10332) covalent geometry : angle 0.54658 (14064) hydrogen bonds : bond 0.03369 ( 400) hydrogen bonds : angle 4.72079 ( 1176) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 172 time to evaluate : 0.392 Fit side-chains REVERT: A 71 ASN cc_start: 0.7785 (t0) cc_final: 0.7390 (m-40) REVERT: A 89 LYS cc_start: 0.8235 (OUTLIER) cc_final: 0.7449 (mmtp) REVERT: A 120 GLU cc_start: 0.7994 (tt0) cc_final: 0.7592 (mp0) REVERT: A 131 LYS cc_start: 0.8182 (mmtp) cc_final: 0.7695 (mttm) REVERT: A 289 LYS cc_start: 0.8285 (ttpt) cc_final: 0.7926 (ttmm) REVERT: A 308 LYS cc_start: 0.8928 (OUTLIER) cc_final: 0.8501 (mttp) REVERT: B 71 ASN cc_start: 0.7786 (t0) cc_final: 0.7383 (m-40) REVERT: B 89 LYS cc_start: 0.8233 (OUTLIER) cc_final: 0.7449 (mmtp) REVERT: B 120 GLU cc_start: 0.8007 (tt0) cc_final: 0.7592 (mp0) REVERT: B 131 LYS cc_start: 0.8183 (mmtp) cc_final: 0.7697 (mttm) REVERT: B 289 LYS cc_start: 0.8297 (ttpt) cc_final: 0.7932 (ttmm) REVERT: B 308 LYS cc_start: 0.8893 (OUTLIER) cc_final: 0.8509 (mttp) REVERT: C 71 ASN cc_start: 0.7783 (t0) cc_final: 0.7383 (m-40) REVERT: C 89 LYS cc_start: 0.8230 (OUTLIER) cc_final: 0.7445 (mmtp) REVERT: C 120 GLU cc_start: 0.8008 (tt0) cc_final: 0.7594 (mp0) REVERT: C 131 LYS cc_start: 0.8182 (mmtp) cc_final: 0.7695 (mttm) REVERT: C 289 LYS cc_start: 0.8279 (ttpt) cc_final: 0.7917 (ttmm) REVERT: C 308 LYS cc_start: 0.8924 (OUTLIER) cc_final: 0.8496 (mttp) REVERT: D 71 ASN cc_start: 0.7796 (t0) cc_final: 0.7389 (m-40) REVERT: D 89 LYS cc_start: 0.8231 (OUTLIER) cc_final: 0.7444 (mmtp) REVERT: D 120 GLU cc_start: 0.8011 (tt0) cc_final: 0.7583 (mp0) REVERT: D 131 LYS cc_start: 0.8183 (mmtp) cc_final: 0.7694 (mttm) REVERT: D 289 LYS cc_start: 0.8283 (ttpt) cc_final: 0.7920 (ttmm) REVERT: D 308 LYS cc_start: 0.8886 (OUTLIER) cc_final: 0.8492 (mttp) outliers start: 48 outliers final: 24 residues processed: 192 average time/residue: 0.5043 time to fit residues: 104.0710 Evaluate side-chains 196 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 164 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 MET Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 89 LYS Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 308 LYS Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain B residue 37 MET Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 89 LYS Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 308 LYS Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain C residue 37 MET Chi-restraints excluded: chain C residue 42 ILE Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 89 LYS Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 308 LYS Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain D residue 37 MET Chi-restraints excluded: chain D residue 42 ILE Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 89 LYS Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 308 LYS Chi-restraints excluded: chain D residue 342 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 114 optimal weight: 2.9990 chunk 125 optimal weight: 1.9990 chunk 80 optimal weight: 0.8980 chunk 18 optimal weight: 0.1980 chunk 42 optimal weight: 4.9990 chunk 131 optimal weight: 2.9990 chunk 63 optimal weight: 0.4980 chunk 119 optimal weight: 3.9990 chunk 86 optimal weight: 2.9990 chunk 90 optimal weight: 4.9990 chunk 47 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 195 HIS ** A 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 195 HIS ** B 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 195 HIS ** C 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 195 HIS ** D 201 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 = 0.3155 r_free = 0.3155 target = 0.108719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.094967 restraints weight = 12675.017| |-----------------------------------------------------------------------------| r_work (start): 0.2985 rms_B_bonded: 1.45 r_work: 0.2893 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.2764 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.2973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10332 Z= 0.141 Angle : 0.503 6.402 14064 Z= 0.264 Chirality : 0.046 0.147 1640 Planarity : 0.004 0.037 1792 Dihedral : 8.841 87.533 1644 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.30 % Allowed : 2.99 % Favored : 96.72 % Rotamer: Outliers : 3.72 % Allowed : 16.73 % Favored : 79.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.02 (0.24), residues: 1340 helix: 0.67 (0.26), residues: 420 sheet: -1.09 (0.30), residues: 292 loop : 0.27 (0.26), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 30 TYR 0.009 0.001 TYR D 146 PHE 0.012 0.002 PHE A 304 TRP 0.003 0.001 TRP A 101 HIS 0.004 0.002 HIS B 67 Details of bonding type rmsd covalent geometry : bond 0.00334 (10332) covalent geometry : angle 0.50296 (14064) hydrogen bonds : bond 0.03167 ( 400) hydrogen bonds : angle 4.42165 ( 1176) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 184 time to evaluate : 0.331 Fit side-chains REVERT: A 71 ASN cc_start: 0.7735 (t0) cc_final: 0.7273 (m-40) REVERT: A 89 LYS cc_start: 0.8165 (OUTLIER) cc_final: 0.7302 (mmtp) REVERT: A 120 GLU cc_start: 0.7939 (tt0) cc_final: 0.7478 (mp0) REVERT: A 229 THR cc_start: 0.8408 (m) cc_final: 0.8162 (m) REVERT: A 274 GLU cc_start: 0.7783 (tp30) cc_final: 0.7510 (mm-30) REVERT: A 289 LYS cc_start: 0.8242 (ttpt) cc_final: 0.7833 (ttmm) REVERT: A 315 LYS cc_start: 0.8802 (OUTLIER) cc_final: 0.8203 (tttt) REVERT: B 71 ASN cc_start: 0.7724 (t0) cc_final: 0.7259 (m-40) REVERT: B 89 LYS cc_start: 0.8160 (OUTLIER) cc_final: 0.7301 (mmtp) REVERT: B 120 GLU cc_start: 0.7946 (tt0) cc_final: 0.7482 (mp0) REVERT: B 229 THR cc_start: 0.8414 (m) cc_final: 0.8175 (m) REVERT: B 274 GLU cc_start: 0.7804 (tp30) cc_final: 0.7530 (mm-30) REVERT: B 289 LYS cc_start: 0.8245 (ttpt) cc_final: 0.7836 (ttmm) REVERT: B 315 LYS cc_start: 0.8792 (OUTLIER) cc_final: 0.8194 (tttt) REVERT: C 71 ASN cc_start: 0.7739 (t0) cc_final: 0.7273 (m-40) REVERT: C 89 LYS cc_start: 0.8167 (OUTLIER) cc_final: 0.7307 (mmtp) REVERT: C 120 GLU cc_start: 0.7955 (tt0) cc_final: 0.7484 (mp0) REVERT: C 229 THR cc_start: 0.8412 (m) cc_final: 0.8170 (m) REVERT: C 274 GLU cc_start: 0.7807 (tp30) cc_final: 0.7534 (mm-30) REVERT: C 289 LYS cc_start: 0.8235 (ttpt) cc_final: 0.7826 (ttmm) REVERT: C 315 LYS cc_start: 0.8794 (OUTLIER) cc_final: 0.8191 (tttt) REVERT: D 71 ASN cc_start: 0.7739 (t0) cc_final: 0.7267 (m-40) REVERT: D 89 LYS cc_start: 0.8163 (OUTLIER) cc_final: 0.7302 (mmtp) REVERT: D 120 GLU cc_start: 0.7943 (tt0) cc_final: 0.7472 (mp0) REVERT: D 229 THR cc_start: 0.8400 (m) cc_final: 0.8154 (m) REVERT: D 274 GLU cc_start: 0.7807 (tp30) cc_final: 0.7532 (mm-30) REVERT: D 289 LYS cc_start: 0.8236 (ttpt) cc_final: 0.7825 (ttmm) REVERT: D 315 LYS cc_start: 0.8795 (OUTLIER) cc_final: 0.8194 (tttt) outliers start: 40 outliers final: 28 residues processed: 204 average time/residue: 0.5472 time to fit residues: 119.5031 Evaluate side-chains 196 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 160 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 MET Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 89 LYS Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 191 MET Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 315 LYS Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain B residue 37 MET Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 89 LYS Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 191 MET Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 315 LYS Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain C residue 37 MET Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 89 LYS Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 191 MET Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 315 LYS Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain D residue 37 MET Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 89 LYS Chi-restraints excluded: chain D residue 108 ILE Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 191 MET Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 315 LYS Chi-restraints excluded: chain D residue 342 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 108 optimal weight: 0.5980 chunk 9 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 33 optimal weight: 6.9990 chunk 124 optimal weight: 0.9990 chunk 39 optimal weight: 3.9990 chunk 81 optimal weight: 2.9990 chunk 14 optimal weight: 0.6980 chunk 103 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 70 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 ASN A 195 HIS ** A 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 48 ASN B 195 HIS ** B 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 48 ASN C 195 HIS ** C 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 48 ASN D 195 HIS ** D 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.110041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.096411 restraints weight = 12662.038| |-----------------------------------------------------------------------------| r_work (start): 0.3027 rms_B_bonded: 1.46 r_work: 0.2935 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2807 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.3061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10332 Z= 0.114 Angle : 0.478 6.067 14064 Z= 0.251 Chirality : 0.045 0.146 1640 Planarity : 0.004 0.036 1792 Dihedral : 8.649 88.245 1644 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.30 % Allowed : 2.39 % Favored : 97.31 % Rotamer: Outliers : 4.83 % Allowed : 16.73 % Favored : 78.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.12 (0.24), residues: 1340 helix: 0.84 (0.26), residues: 420 sheet: -1.09 (0.30), residues: 292 loop : 0.34 (0.27), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 30 TYR 0.008 0.001 TYR C 338 PHE 0.011 0.001 PHE A 304 TRP 0.003 0.001 TRP A 101 HIS 0.004 0.002 HIS A 125 Details of bonding type rmsd covalent geometry : bond 0.00272 (10332) covalent geometry : angle 0.47815 (14064) hydrogen bonds : bond 0.02952 ( 400) hydrogen bonds : angle 4.23826 ( 1176) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 180 time to evaluate : 0.270 Fit side-chains REVERT: A 71 ASN cc_start: 0.7810 (t0) cc_final: 0.7398 (m-40) REVERT: A 89 LYS cc_start: 0.8252 (OUTLIER) cc_final: 0.7449 (mmtp) REVERT: A 120 GLU cc_start: 0.7941 (tt0) cc_final: 0.7596 (mp0) REVERT: A 229 THR cc_start: 0.8382 (m) cc_final: 0.8139 (m) REVERT: A 274 GLU cc_start: 0.7824 (tp30) cc_final: 0.7580 (mm-30) REVERT: A 289 LYS cc_start: 0.8249 (ttpt) cc_final: 0.7928 (ttmm) REVERT: A 308 LYS cc_start: 0.8888 (OUTLIER) cc_final: 0.8500 (mttp) REVERT: B 71 ASN cc_start: 0.7819 (t0) cc_final: 0.7406 (m-40) REVERT: B 89 LYS cc_start: 0.8254 (OUTLIER) cc_final: 0.7460 (mmtp) REVERT: B 120 GLU cc_start: 0.7921 (tt0) cc_final: 0.7600 (mp0) REVERT: B 229 THR cc_start: 0.8396 (m) cc_final: 0.8159 (m) REVERT: B 274 GLU cc_start: 0.7842 (tp30) cc_final: 0.7595 (mm-30) REVERT: B 289 LYS cc_start: 0.8254 (ttpt) cc_final: 0.7928 (ttmm) REVERT: B 308 LYS cc_start: 0.8888 (OUTLIER) cc_final: 0.8499 (mttp) REVERT: C 71 ASN cc_start: 0.7814 (t0) cc_final: 0.7403 (m-40) REVERT: C 89 LYS cc_start: 0.8256 (OUTLIER) cc_final: 0.7461 (mmtp) REVERT: C 120 GLU cc_start: 0.7961 (tt0) cc_final: 0.7610 (mp0) REVERT: C 229 THR cc_start: 0.8383 (m) cc_final: 0.8145 (m) REVERT: C 274 GLU cc_start: 0.7852 (tp30) cc_final: 0.7608 (mm-30) REVERT: C 289 LYS cc_start: 0.8238 (ttpt) cc_final: 0.7923 (ttmm) REVERT: C 308 LYS cc_start: 0.8889 (OUTLIER) cc_final: 0.8492 (mttp) REVERT: D 71 ASN cc_start: 0.7832 (t0) cc_final: 0.7413 (m-40) REVERT: D 89 LYS cc_start: 0.8250 (OUTLIER) cc_final: 0.7454 (mmtp) REVERT: D 120 GLU cc_start: 0.7940 (tt0) cc_final: 0.7591 (mp0) REVERT: D 229 THR cc_start: 0.8379 (m) cc_final: 0.8138 (m) REVERT: D 274 GLU cc_start: 0.7851 (tp30) cc_final: 0.7606 (mm-30) REVERT: D 289 LYS cc_start: 0.8250 (ttpt) cc_final: 0.7929 (ttmm) REVERT: D 308 LYS cc_start: 0.8883 (OUTLIER) cc_final: 0.8487 (mttp) outliers start: 52 outliers final: 28 residues processed: 212 average time/residue: 0.4777 time to fit residues: 109.3637 Evaluate side-chains 216 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 180 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 MET Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 89 LYS Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 191 MET Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 308 LYS Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain B residue 37 MET Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 89 LYS Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 191 MET Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 308 LYS Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain C residue 37 MET Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 89 LYS Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 191 MET Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 308 LYS Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain D residue 37 MET Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 89 LYS Chi-restraints excluded: chain D residue 108 ILE Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 191 MET Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 308 LYS Chi-restraints excluded: chain D residue 342 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 59 optimal weight: 0.7980 chunk 63 optimal weight: 6.9990 chunk 8 optimal weight: 0.4980 chunk 65 optimal weight: 2.9990 chunk 121 optimal weight: 0.6980 chunk 55 optimal weight: 0.7980 chunk 47 optimal weight: 0.9990 chunk 123 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 195 HIS ** A 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 195 HIS ** B 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 195 HIS ** C 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 195 HIS ** D 201 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 = 0.3180 r_free = 0.3180 target = 0.110523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.097504 restraints weight = 12510.347| |-----------------------------------------------------------------------------| r_work (start): 0.3017 rms_B_bonded: 1.36 r_work: 0.2930 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.2807 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.3180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10332 Z= 0.111 Angle : 0.478 7.002 14064 Z= 0.249 Chirality : 0.045 0.145 1640 Planarity : 0.003 0.035 1792 Dihedral : 8.561 89.327 1644 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.30 % Allowed : 2.99 % Favored : 96.72 % Rotamer: Outliers : 3.53 % Allowed : 18.22 % Favored : 78.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.25 (0.24), residues: 1340 helix: 1.00 (0.27), residues: 420 sheet: -1.04 (0.30), residues: 292 loop : 0.40 (0.27), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 30 TYR 0.007 0.001 TYR A 338 PHE 0.010 0.001 PHE C 304 TRP 0.002 0.001 TRP D 101 HIS 0.004 0.002 HIS A 125 Details of bonding type rmsd covalent geometry : bond 0.00265 (10332) covalent geometry : angle 0.47805 (14064) hydrogen bonds : bond 0.02878 ( 400) hydrogen bonds : angle 4.19997 ( 1176) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 190 time to evaluate : 0.348 Fit side-chains REVERT: A 71 ASN cc_start: 0.7794 (t0) cc_final: 0.7439 (m-40) REVERT: A 89 LYS cc_start: 0.8168 (OUTLIER) cc_final: 0.7335 (mmtp) REVERT: A 120 GLU cc_start: 0.7925 (tt0) cc_final: 0.7558 (mp0) REVERT: A 229 THR cc_start: 0.8312 (m) cc_final: 0.8069 (m) REVERT: A 274 GLU cc_start: 0.7773 (tp30) cc_final: 0.7551 (mm-30) REVERT: A 289 LYS cc_start: 0.8215 (ttpt) cc_final: 0.7887 (ttmm) REVERT: A 308 LYS cc_start: 0.8852 (OUTLIER) cc_final: 0.8450 (mttp) REVERT: B 71 ASN cc_start: 0.7783 (t0) cc_final: 0.7429 (m-40) REVERT: B 89 LYS cc_start: 0.8173 (OUTLIER) cc_final: 0.7351 (mmtp) REVERT: B 120 GLU cc_start: 0.7932 (tt0) cc_final: 0.7563 (mp0) REVERT: B 229 THR cc_start: 0.8311 (m) cc_final: 0.8078 (m) REVERT: B 274 GLU cc_start: 0.7791 (tp30) cc_final: 0.7568 (mm-30) REVERT: B 289 LYS cc_start: 0.8220 (ttpt) cc_final: 0.7890 (ttmm) REVERT: B 308 LYS cc_start: 0.8858 (OUTLIER) cc_final: 0.8458 (mttp) REVERT: C 71 ASN cc_start: 0.7789 (t0) cc_final: 0.7439 (m-40) REVERT: C 89 LYS cc_start: 0.8178 (OUTLIER) cc_final: 0.7354 (mmtp) REVERT: C 120 GLU cc_start: 0.7956 (tt0) cc_final: 0.7564 (mp0) REVERT: C 229 THR cc_start: 0.8309 (m) cc_final: 0.8071 (m) REVERT: C 274 GLU cc_start: 0.7797 (tp30) cc_final: 0.7576 (mm-30) REVERT: C 289 LYS cc_start: 0.8207 (ttpt) cc_final: 0.7885 (ttmm) REVERT: C 308 LYS cc_start: 0.8858 (OUTLIER) cc_final: 0.8458 (mttp) REVERT: D 71 ASN cc_start: 0.7800 (t0) cc_final: 0.7439 (m-40) REVERT: D 89 LYS cc_start: 0.8175 (OUTLIER) cc_final: 0.7350 (mmtp) REVERT: D 120 GLU cc_start: 0.7928 (tt0) cc_final: 0.7554 (mp0) REVERT: D 229 THR cc_start: 0.8298 (m) cc_final: 0.8063 (m) REVERT: D 274 GLU cc_start: 0.7792 (tp30) cc_final: 0.7569 (mm-30) REVERT: D 289 LYS cc_start: 0.8217 (ttpt) cc_final: 0.7888 (ttmm) REVERT: D 308 LYS cc_start: 0.8855 (OUTLIER) cc_final: 0.8454 (mttp) outliers start: 38 outliers final: 24 residues processed: 210 average time/residue: 0.5658 time to fit residues: 126.7644 Evaluate side-chains 202 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 170 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 MET Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 89 LYS Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 191 MET Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 308 LYS Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain B residue 37 MET Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 89 LYS Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 191 MET Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 308 LYS Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain C residue 37 MET Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 89 LYS Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 191 MET Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 308 LYS Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain D residue 37 MET Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 89 LYS Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 191 MET Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 308 LYS Chi-restraints excluded: chain D residue 342 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 22 optimal weight: 2.9990 chunk 109 optimal weight: 0.8980 chunk 53 optimal weight: 2.9990 chunk 82 optimal weight: 0.9980 chunk 61 optimal weight: 0.6980 chunk 33 optimal weight: 6.9990 chunk 67 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 chunk 96 optimal weight: 3.9990 chunk 128 optimal weight: 0.8980 chunk 35 optimal weight: 0.0770 overall best weight: 0.7138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 195 HIS A 201 GLN ** B 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 195 HIS B 201 GLN ** C 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 195 HIS C 201 GLN ** D 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 195 HIS D 201 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.111440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.095313 restraints weight = 12367.939| |-----------------------------------------------------------------------------| r_work (start): 0.2989 rms_B_bonded: 1.91 r_work: 0.2878 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2734 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.3234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10332 Z= 0.109 Angle : 0.486 6.808 14064 Z= 0.252 Chirality : 0.045 0.145 1640 Planarity : 0.003 0.035 1792 Dihedral : 8.482 89.737 1644 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.30 % Allowed : 2.39 % Favored : 97.31 % Rotamer: Outliers : 3.16 % Allowed : 19.42 % Favored : 77.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.24 (0.24), residues: 1340 helix: 0.99 (0.26), residues: 424 sheet: -1.03 (0.30), residues: 292 loop : 0.39 (0.27), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 30 TYR 0.007 0.001 TYR C 338 PHE 0.010 0.001 PHE D 304 TRP 0.002 0.001 TRP A 101 HIS 0.004 0.002 HIS C 125 Details of bonding type rmsd covalent geometry : bond 0.00262 (10332) covalent geometry : angle 0.48617 (14064) hydrogen bonds : bond 0.02848 ( 400) hydrogen bonds : angle 4.19997 ( 1176) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 179 time to evaluate : 0.292 Fit side-chains REVERT: A 71 ASN cc_start: 0.7816 (t0) cc_final: 0.7410 (m-40) REVERT: A 89 LYS cc_start: 0.8193 (OUTLIER) cc_final: 0.7363 (mmtp) REVERT: A 120 GLU cc_start: 0.8043 (tt0) cc_final: 0.7514 (mp0) REVERT: A 229 THR cc_start: 0.8290 (m) cc_final: 0.8068 (m) REVERT: A 274 GLU cc_start: 0.7861 (tp30) cc_final: 0.7624 (mm-30) REVERT: A 289 LYS cc_start: 0.8189 (ttpt) cc_final: 0.7867 (ttmm) REVERT: A 308 LYS cc_start: 0.8895 (OUTLIER) cc_final: 0.8472 (mttp) REVERT: B 71 ASN cc_start: 0.7821 (t0) cc_final: 0.7415 (m-40) REVERT: B 89 LYS cc_start: 0.8194 (OUTLIER) cc_final: 0.7369 (mmtp) REVERT: B 120 GLU cc_start: 0.8036 (tt0) cc_final: 0.7529 (mp0) REVERT: B 229 THR cc_start: 0.8289 (m) cc_final: 0.8054 (m) REVERT: B 274 GLU cc_start: 0.7857 (tp30) cc_final: 0.7623 (mm-30) REVERT: B 289 LYS cc_start: 0.8194 (ttpt) cc_final: 0.7872 (ttmm) REVERT: B 308 LYS cc_start: 0.8895 (OUTLIER) cc_final: 0.8479 (mttp) REVERT: C 71 ASN cc_start: 0.7837 (t0) cc_final: 0.7426 (m-40) REVERT: C 89 LYS cc_start: 0.8193 (OUTLIER) cc_final: 0.7367 (mmtp) REVERT: C 120 GLU cc_start: 0.8039 (tt0) cc_final: 0.7523 (mp0) REVERT: C 229 THR cc_start: 0.8284 (m) cc_final: 0.8064 (m) REVERT: C 274 GLU cc_start: 0.7859 (tp30) cc_final: 0.7626 (mm-30) REVERT: C 289 LYS cc_start: 0.8190 (ttpt) cc_final: 0.7868 (ttmm) REVERT: C 308 LYS cc_start: 0.8893 (OUTLIER) cc_final: 0.8461 (mttp) REVERT: D 71 ASN cc_start: 0.7818 (t0) cc_final: 0.7410 (m-40) REVERT: D 89 LYS cc_start: 0.8184 (OUTLIER) cc_final: 0.7351 (mmtp) REVERT: D 120 GLU cc_start: 0.8044 (tt0) cc_final: 0.7521 (mp0) REVERT: D 229 THR cc_start: 0.8302 (m) cc_final: 0.8067 (m) REVERT: D 274 GLU cc_start: 0.7846 (tp30) cc_final: 0.7609 (mm-30) REVERT: D 289 LYS cc_start: 0.8172 (ttpt) cc_final: 0.7864 (ttmm) REVERT: D 308 LYS cc_start: 0.8897 (OUTLIER) cc_final: 0.8475 (mttp) outliers start: 34 outliers final: 20 residues processed: 199 average time/residue: 0.4930 time to fit residues: 105.5305 Evaluate side-chains 199 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 171 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 MET Chi-restraints excluded: chain A residue 89 LYS Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 191 MET Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 308 LYS Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain B residue 37 MET Chi-restraints excluded: chain B residue 89 LYS Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 191 MET Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 308 LYS Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain C residue 37 MET Chi-restraints excluded: chain C residue 89 LYS Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 191 MET Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 308 LYS Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain D residue 37 MET Chi-restraints excluded: chain D residue 89 LYS Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 191 MET Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 308 LYS Chi-restraints excluded: chain D residue 342 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 53 optimal weight: 0.9990 chunk 80 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 39 optimal weight: 6.9990 chunk 15 optimal weight: 1.9990 chunk 102 optimal weight: 5.9990 chunk 1 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 chunk 131 optimal weight: 3.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 195 HIS A 201 GLN B 48 ASN B 195 HIS B 201 GLN ** C 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 195 HIS C 201 GLN D 48 ASN D 195 HIS D 201 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.109528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.093487 restraints weight = 12497.161| |-----------------------------------------------------------------------------| r_work (start): 0.2953 rms_B_bonded: 1.89 r_work: 0.2841 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2700 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.3216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 10332 Z= 0.182 Angle : 0.547 7.528 14064 Z= 0.284 Chirality : 0.047 0.144 1640 Planarity : 0.004 0.036 1792 Dihedral : 8.699 84.807 1644 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.30 % Allowed : 3.06 % Favored : 96.64 % Rotamer: Outliers : 3.53 % Allowed : 19.80 % Favored : 76.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.10 (0.24), residues: 1340 helix: 0.73 (0.26), residues: 420 sheet: -1.02 (0.31), residues: 272 loop : 0.32 (0.26), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 30 TYR 0.012 0.002 TYR B 146 PHE 0.012 0.002 PHE D 304 TRP 0.003 0.001 TRP B 331 HIS 0.003 0.002 HIS B 125 Details of bonding type rmsd covalent geometry : bond 0.00439 (10332) covalent geometry : angle 0.54746 (14064) hydrogen bonds : bond 0.03279 ( 400) hydrogen bonds : angle 4.59584 ( 1176) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 160 time to evaluate : 0.251 Fit side-chains REVERT: A 71 ASN cc_start: 0.7865 (t0) cc_final: 0.7422 (m-40) REVERT: A 89 LYS cc_start: 0.8265 (OUTLIER) cc_final: 0.7460 (mmtp) REVERT: A 120 GLU cc_start: 0.8016 (tt0) cc_final: 0.7525 (mp0) REVERT: A 229 THR cc_start: 0.8368 (m) cc_final: 0.8112 (m) REVERT: A 289 LYS cc_start: 0.8283 (ttpt) cc_final: 0.7920 (ttmm) REVERT: B 71 ASN cc_start: 0.7875 (t0) cc_final: 0.7423 (m-40) REVERT: B 89 LYS cc_start: 0.8247 (OUTLIER) cc_final: 0.7441 (mmtp) REVERT: B 120 GLU cc_start: 0.8026 (tt0) cc_final: 0.7541 (mp0) REVERT: B 229 THR cc_start: 0.8358 (m) cc_final: 0.8103 (m) REVERT: B 289 LYS cc_start: 0.8288 (ttpt) cc_final: 0.7927 (ttmm) REVERT: C 71 ASN cc_start: 0.7898 (t0) cc_final: 0.7447 (m-40) REVERT: C 89 LYS cc_start: 0.8259 (OUTLIER) cc_final: 0.7454 (mmtp) REVERT: C 120 GLU cc_start: 0.8021 (tt0) cc_final: 0.7526 (mp0) REVERT: C 229 THR cc_start: 0.8360 (m) cc_final: 0.8103 (m) REVERT: C 289 LYS cc_start: 0.8283 (ttpt) cc_final: 0.7923 (ttmm) REVERT: D 71 ASN cc_start: 0.7882 (t0) cc_final: 0.7429 (m-40) REVERT: D 89 LYS cc_start: 0.8245 (OUTLIER) cc_final: 0.7433 (mmtp) REVERT: D 120 GLU cc_start: 0.8012 (tt0) cc_final: 0.7519 (mp0) REVERT: D 229 THR cc_start: 0.8357 (m) cc_final: 0.8100 (m) REVERT: D 289 LYS cc_start: 0.8270 (ttpt) cc_final: 0.7917 (ttmm) outliers start: 38 outliers final: 21 residues processed: 182 average time/residue: 0.4943 time to fit residues: 96.8114 Evaluate side-chains 183 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 158 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 MET Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 89 LYS Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 191 MET Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain B residue 37 MET Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 89 LYS Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 191 MET Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain C residue 37 MET Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 89 LYS Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 191 MET Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain D residue 37 MET Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 89 LYS Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 191 MET Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 342 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 89 optimal weight: 0.9980 chunk 59 optimal weight: 4.9990 chunk 61 optimal weight: 1.9990 chunk 46 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 chunk 78 optimal weight: 0.4980 chunk 17 optimal weight: 2.9990 chunk 58 optimal weight: 0.2980 chunk 104 optimal weight: 0.0000 chunk 102 optimal weight: 0.6980 chunk 115 optimal weight: 0.8980 overall best weight: 0.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 201 GLN ** B 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 201 GLN ** C 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 201 GLN ** D 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 201 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.111955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.096264 restraints weight = 12262.984| |-----------------------------------------------------------------------------| r_work (start): 0.3005 rms_B_bonded: 1.83 r_work: 0.2898 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2757 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.3328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 10332 Z= 0.097 Angle : 0.497 6.726 14064 Z= 0.257 Chirality : 0.045 0.145 1640 Planarity : 0.003 0.035 1792 Dihedral : 8.320 83.840 1644 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.30 % Allowed : 2.16 % Favored : 97.54 % Rotamer: Outliers : 2.70 % Allowed : 20.72 % Favored : 76.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.21 (0.24), residues: 1340 helix: 1.03 (0.26), residues: 424 sheet: -1.11 (0.30), residues: 292 loop : 0.36 (0.27), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 341 TYR 0.007 0.001 TYR D 338 PHE 0.010 0.001 PHE B 325 TRP 0.003 0.001 TRP D 101 HIS 0.004 0.002 HIS B 125 Details of bonding type rmsd covalent geometry : bond 0.00237 (10332) covalent geometry : angle 0.49710 (14064) hydrogen bonds : bond 0.02765 ( 400) hydrogen bonds : angle 4.17109 ( 1176) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 176 time to evaluate : 0.363 Fit side-chains REVERT: A 71 ASN cc_start: 0.7820 (t0) cc_final: 0.7419 (m-40) REVERT: A 89 LYS cc_start: 0.8260 (OUTLIER) cc_final: 0.7448 (mmtp) REVERT: A 119 GLU cc_start: 0.7700 (tm-30) cc_final: 0.7423 (tp30) REVERT: A 120 GLU cc_start: 0.8068 (tt0) cc_final: 0.7572 (mp0) REVERT: A 229 THR cc_start: 0.8270 (m) cc_final: 0.8030 (m) REVERT: A 274 GLU cc_start: 0.7870 (tp30) cc_final: 0.7624 (mm-30) REVERT: A 289 LYS cc_start: 0.8136 (ttpt) cc_final: 0.7820 (ttmm) REVERT: A 342 LEU cc_start: 0.8618 (tt) cc_final: 0.8383 (mt) REVERT: B 71 ASN cc_start: 0.7839 (t0) cc_final: 0.7430 (m-40) REVERT: B 89 LYS cc_start: 0.8244 (OUTLIER) cc_final: 0.7434 (mmtp) REVERT: B 119 GLU cc_start: 0.7724 (tm-30) cc_final: 0.7448 (tp30) REVERT: B 120 GLU cc_start: 0.8054 (tt0) cc_final: 0.7587 (mp0) REVERT: B 229 THR cc_start: 0.8269 (m) cc_final: 0.8033 (m) REVERT: B 274 GLU cc_start: 0.7853 (tp30) cc_final: 0.7610 (mm-30) REVERT: B 289 LYS cc_start: 0.8139 (ttpt) cc_final: 0.7826 (ttmm) REVERT: B 342 LEU cc_start: 0.8612 (tt) cc_final: 0.8375 (mt) REVERT: C 71 ASN cc_start: 0.7837 (t0) cc_final: 0.7432 (m-40) REVERT: C 89 LYS cc_start: 0.8252 (OUTLIER) cc_final: 0.7442 (mmtp) REVERT: C 119 GLU cc_start: 0.7714 (tm-30) cc_final: 0.7438 (tp30) REVERT: C 120 GLU cc_start: 0.8035 (tt0) cc_final: 0.7577 (mp0) REVERT: C 229 THR cc_start: 0.8267 (m) cc_final: 0.8030 (m) REVERT: C 274 GLU cc_start: 0.7864 (tp30) cc_final: 0.7622 (mm-30) REVERT: C 289 LYS cc_start: 0.8131 (ttpt) cc_final: 0.7819 (ttmm) REVERT: C 342 LEU cc_start: 0.8612 (tt) cc_final: 0.8375 (mt) REVERT: D 71 ASN cc_start: 0.7824 (t0) cc_final: 0.7415 (m-40) REVERT: D 89 LYS cc_start: 0.8243 (OUTLIER) cc_final: 0.7432 (mmtp) REVERT: D 119 GLU cc_start: 0.7599 (tm-30) cc_final: 0.7354 (tp30) REVERT: D 120 GLU cc_start: 0.8056 (tt0) cc_final: 0.7566 (mp0) REVERT: D 229 THR cc_start: 0.8284 (m) cc_final: 0.8049 (m) REVERT: D 274 GLU cc_start: 0.7844 (tp30) cc_final: 0.7600 (mm-30) REVERT: D 289 LYS cc_start: 0.8125 (ttpt) cc_final: 0.7822 (ttmm) outliers start: 29 outliers final: 17 residues processed: 188 average time/residue: 0.4862 time to fit residues: 98.5273 Evaluate side-chains 186 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 165 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 MET Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 89 LYS Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain B residue 37 MET Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 89 LYS Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain C residue 37 MET Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 89 LYS Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain D residue 37 MET Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 89 LYS Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 342 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 32 optimal weight: 4.9990 chunk 75 optimal weight: 4.9990 chunk 81 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 12 optimal weight: 0.7980 chunk 0 optimal weight: 7.9990 chunk 80 optimal weight: 2.9990 chunk 28 optimal weight: 0.0040 chunk 72 optimal weight: 2.9990 chunk 115 optimal weight: 0.6980 chunk 65 optimal weight: 0.5980 overall best weight: 0.6194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 201 GLN ** B 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 201 GLN ** C 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 201 GLN ** D 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 201 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.112218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.096553 restraints weight = 12321.005| |-----------------------------------------------------------------------------| r_work (start): 0.3008 rms_B_bonded: 1.82 r_work: 0.2902 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2760 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.3416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 10332 Z= 0.103 Angle : 0.483 6.705 14064 Z= 0.251 Chirality : 0.045 0.143 1640 Planarity : 0.003 0.035 1792 Dihedral : 8.138 81.623 1644 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.30 % Allowed : 3.13 % Favored : 96.57 % Rotamer: Outliers : 2.60 % Allowed : 20.45 % Favored : 76.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.29 (0.24), residues: 1340 helix: 1.06 (0.27), residues: 424 sheet: -1.06 (0.30), residues: 292 loop : 0.42 (0.27), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 341 TYR 0.007 0.001 TYR D 332 PHE 0.010 0.001 PHE A 325 TRP 0.003 0.001 TRP D 101 HIS 0.003 0.001 HIS B 67 Details of bonding type rmsd covalent geometry : bond 0.00249 (10332) covalent geometry : angle 0.48330 (14064) hydrogen bonds : bond 0.02792 ( 400) hydrogen bonds : angle 4.15611 ( 1176) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3044.40 seconds wall clock time: 52 minutes 50.35 seconds (3170.35 seconds total)