Starting phenix.real_space_refine on Fri Feb 14 14:12:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8pvf_17964/02_2025/8pvf_17964.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pvf_17964/02_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8pvf_17964/02_2025/8pvf_17964.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pvf_17964/02_2025/8pvf_17964.map" model { file = "/net/cci-nas-00/data/ceres_data/8pvf_17964/02_2025/8pvf_17964.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pvf_17964/02_2025/8pvf_17964.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: C, B, D Time building chain proxies: 4.88, per 1000 atoms: 0.48 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: 2.79 Conformation dependent library (CDL) restraints added in 1.3 seconds 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: 1.62 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: 3.62 Time building geometry restraints manager: 3.19 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: 0.08 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.680 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: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 25.120 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.480 ------------------------------------------------------------------------------- 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= 0.668 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.032 0.008 TRP B 101 HIS 0.008 0.004 HIS A 125 PHE 0.026 0.007 PHE D 304 TYR 0.040 0.008 TYR B 146 ARG 0.053 0.008 ARG C 252 *********************** 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 : 1.127 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: 1.4340 time to fit residues: 469.7711 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 : 1.103 ------------------------------------------------------------------------------- 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 111 optimal weight: 2.9990 chunk 100 optimal weight: 0.9980 chunk 55 optimal weight: 0.8980 chunk 34 optimal weight: 0.6980 chunk 67 optimal weight: 0.9980 chunk 53 optimal weight: 3.9990 chunk 103 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 77 optimal weight: 0.6980 chunk 119 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 A 340 ASN ** B 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 92 GLN B 107 GLN B 195 HIS B 340 ASN ** C 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 92 GLN C 107 GLN C 195 HIS C 340 ASN ** D 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 92 GLN D 107 GLN D 195 HIS D 340 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.107829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.094466 restraints weight = 12207.683| |-----------------------------------------------------------------------------| r_work (start): 0.2980 rms_B_bonded: 1.34 r_work: 0.2892 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.2766 rms_B_bonded: 3.02 restraints_weight: 0.2500 r_work (final): 0.2766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.2183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10332 Z= 0.200 Angle : 0.553 6.036 14064 Z= 0.292 Chirality : 0.047 0.157 1640 Planarity : 0.004 0.036 1792 Dihedral : 9.085 79.380 1656 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.30 % Allowed : 2.99 % Favored : 96.72 % Rotamer: Outliers : 1.86 % Allowed : 11.15 % Favored : 86.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.24), residues: 1340 helix: 0.61 (0.26), residues: 396 sheet: -1.25 (0.29), residues: 292 loop : 0.53 (0.26), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 101 HIS 0.005 0.001 HIS B 67 PHE 0.013 0.002 PHE D 304 TYR 0.011 0.001 TYR B 146 ARG 0.002 0.001 ARG B 39 *********************** 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 244 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 224 time to evaluate : 1.128 Fit side-chains REVERT: A 71 ASN cc_start: 0.7669 (t0) cc_final: 0.7185 (m-40) REVERT: A 119 GLU cc_start: 0.7205 (tm-30) cc_final: 0.6793 (tm-30) REVERT: A 120 GLU cc_start: 0.7915 (tt0) cc_final: 0.7496 (mp0) REVERT: A 131 LYS cc_start: 0.8234 (mmtp) cc_final: 0.7750 (mttm) REVERT: A 289 LYS cc_start: 0.8267 (ttpt) cc_final: 0.7806 (ttmm) REVERT: B 71 ASN cc_start: 0.7653 (t0) cc_final: 0.7172 (m-40) REVERT: B 119 GLU cc_start: 0.7208 (tm-30) cc_final: 0.6794 (tm-30) REVERT: B 120 GLU cc_start: 0.7906 (tt0) cc_final: 0.7495 (mp0) REVERT: B 131 LYS cc_start: 0.8234 (mmtp) cc_final: 0.7748 (mttm) REVERT: B 289 LYS cc_start: 0.8266 (ttpt) cc_final: 0.7810 (ttmm) REVERT: C 71 ASN cc_start: 0.7654 (t0) cc_final: 0.7172 (m-40) REVERT: C 119 GLU cc_start: 0.7202 (tm-30) cc_final: 0.6789 (tm-30) REVERT: C 120 GLU cc_start: 0.7913 (tt0) cc_final: 0.7493 (mp0) REVERT: C 131 LYS cc_start: 0.8231 (mmtp) cc_final: 0.7747 (mttm) REVERT: C 289 LYS cc_start: 0.8250 (ttpt) cc_final: 0.7802 (ttmm) REVERT: D 71 ASN cc_start: 0.7670 (t0) cc_final: 0.7186 (m-40) REVERT: D 119 GLU cc_start: 0.7193 (tm-30) cc_final: 0.6779 (tm-30) REVERT: D 120 GLU cc_start: 0.7910 (tt0) cc_final: 0.7487 (mp0) REVERT: D 131 LYS cc_start: 0.8233 (mmtp) cc_final: 0.7744 (mttm) REVERT: D 289 LYS cc_start: 0.8263 (ttpt) cc_final: 0.7810 (ttmm) outliers start: 20 outliers final: 8 residues processed: 240 average time/residue: 1.2696 time to fit residues: 327.3742 Evaluate side-chains 188 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 180 time to evaluate : 1.173 ------------------------------------------------------------------------------- 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 105 optimal weight: 0.9990 chunk 94 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 124 optimal weight: 4.9990 chunk 80 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 36 optimal weight: 0.7980 chunk 65 optimal weight: 3.9990 chunk 5 optimal weight: 0.0470 chunk 118 optimal weight: 3.9990 chunk 55 optimal weight: 0.5980 overall best weight: 0.8882 ------------------------------------------------------------------------------- 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 107 GLN A 195 HIS ** A 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 107 GLN B 195 HIS ** B 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 107 GLN C 195 HIS ** C 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 107 GLN 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 = 0.3171 r_free = 0.3171 target = 0.109550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.095936 restraints weight = 12431.676| |-----------------------------------------------------------------------------| r_work (start): 0.2980 rms_B_bonded: 1.43 r_work: 0.2891 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.2765 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.2653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10332 Z= 0.187 Angle : 0.514 6.123 14064 Z= 0.270 Chirality : 0.047 0.145 1640 Planarity : 0.004 0.034 1792 Dihedral : 8.731 81.445 1644 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.30 % Allowed : 2.99 % Favored : 96.72 % Rotamer: Outliers : 3.35 % Allowed : 16.73 % Favored : 79.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.24), residues: 1340 helix: 0.84 (0.27), residues: 396 sheet: -1.04 (0.30), residues: 292 loop : 0.67 (0.27), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 101 HIS 0.006 0.002 HIS A 125 PHE 0.011 0.002 PHE D 304 TYR 0.010 0.001 TYR D 146 ARG 0.003 0.001 ARG A 39 *********************** 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 220 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 184 time to evaluate : 1.098 Fit side-chains REVERT: A 71 ASN cc_start: 0.7670 (t0) cc_final: 0.7176 (m-40) REVERT: A 120 GLU cc_start: 0.7893 (tt0) cc_final: 0.7514 (mp0) REVERT: A 131 LYS cc_start: 0.8198 (mmtp) cc_final: 0.7749 (mttm) REVERT: A 229 THR cc_start: 0.8181 (t) cc_final: 0.7915 (m) REVERT: A 274 GLU cc_start: 0.7841 (tp30) cc_final: 0.7555 (mm-30) REVERT: A 289 LYS cc_start: 0.8199 (ttpt) cc_final: 0.7839 (ttmm) REVERT: A 319 ILE cc_start: 0.8512 (OUTLIER) cc_final: 0.8127 (tp) REVERT: A 324 SER cc_start: 0.7992 (t) cc_final: 0.7669 (p) REVERT: B 71 ASN cc_start: 0.7663 (t0) cc_final: 0.7174 (m-40) REVERT: B 120 GLU cc_start: 0.7911 (tt0) cc_final: 0.7520 (mp0) REVERT: B 131 LYS cc_start: 0.8197 (mmtp) cc_final: 0.7746 (mttm) REVERT: B 229 THR cc_start: 0.8180 (t) cc_final: 0.7912 (m) REVERT: B 274 GLU cc_start: 0.7821 (tp30) cc_final: 0.7530 (mm-30) REVERT: B 289 LYS cc_start: 0.8204 (ttpt) cc_final: 0.7844 (ttmm) REVERT: B 319 ILE cc_start: 0.8514 (OUTLIER) cc_final: 0.8121 (tp) REVERT: B 324 SER cc_start: 0.7991 (t) cc_final: 0.7666 (p) REVERT: C 71 ASN cc_start: 0.7671 (t0) cc_final: 0.7177 (m-40) REVERT: C 120 GLU cc_start: 0.7937 (tt0) cc_final: 0.7516 (mp0) REVERT: C 131 LYS cc_start: 0.8199 (mmtp) cc_final: 0.7748 (mttm) REVERT: C 229 THR cc_start: 0.8176 (t) cc_final: 0.7910 (m) REVERT: C 274 GLU cc_start: 0.7847 (tp30) cc_final: 0.7562 (mm-30) REVERT: C 289 LYS cc_start: 0.8181 (ttpt) cc_final: 0.7834 (ttmm) REVERT: C 319 ILE cc_start: 0.8516 (OUTLIER) cc_final: 0.8128 (tp) REVERT: C 324 SER cc_start: 0.8001 (t) cc_final: 0.7678 (p) REVERT: C 342 LEU cc_start: 0.8469 (OUTLIER) cc_final: 0.8106 (mt) REVERT: D 71 ASN cc_start: 0.7688 (t0) cc_final: 0.7191 (m-40) REVERT: D 120 GLU cc_start: 0.7907 (tt0) cc_final: 0.7514 (mp0) REVERT: D 131 LYS cc_start: 0.8194 (mmtp) cc_final: 0.7746 (mttm) REVERT: D 229 THR cc_start: 0.8179 (t) cc_final: 0.7914 (m) REVERT: D 274 GLU cc_start: 0.7846 (tp30) cc_final: 0.7557 (mm-30) REVERT: D 289 LYS cc_start: 0.8188 (ttpt) cc_final: 0.7832 (ttmm) REVERT: D 319 ILE cc_start: 0.8509 (OUTLIER) cc_final: 0.8119 (tp) REVERT: D 324 SER cc_start: 0.7991 (t) cc_final: 0.7668 (p) outliers start: 36 outliers final: 15 residues processed: 204 average time/residue: 1.2757 time to fit residues: 279.3872 Evaluate side-chains 188 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 168 time to evaluate : 1.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 319 ILE Chi-restraints excluded: chain A residue 342 LEU 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 319 ILE Chi-restraints excluded: chain B residue 342 LEU 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 319 ILE Chi-restraints excluded: chain C residue 342 LEU 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 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 55 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 chunk 15 optimal weight: 3.9990 chunk 12 optimal weight: 0.0270 chunk 112 optimal weight: 2.9990 chunk 60 optimal weight: 0.6980 chunk 40 optimal weight: 3.9990 chunk 47 optimal weight: 0.8980 overall best weight: 0.9240 ------------------------------------------------------------------------------- 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 = 0.3166 r_free = 0.3166 target = 0.109456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.096253 restraints weight = 12433.716| |-----------------------------------------------------------------------------| r_work (start): 0.3005 rms_B_bonded: 1.34 r_work: 0.2919 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.2795 rms_B_bonded: 3.03 restraints_weight: 0.2500 r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.2842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10332 Z= 0.190 Angle : 0.489 5.867 14064 Z= 0.256 Chirality : 0.046 0.144 1640 Planarity : 0.004 0.034 1792 Dihedral : 8.555 82.469 1644 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.30 % Allowed : 2.69 % Favored : 97.01 % Rotamer: Outliers : 3.72 % Allowed : 17.10 % Favored : 79.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.24), residues: 1340 helix: 1.03 (0.27), residues: 396 sheet: -0.95 (0.30), residues: 292 loop : 0.67 (0.27), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP C 101 HIS 0.004 0.002 HIS C 67 PHE 0.011 0.002 PHE C 304 TYR 0.009 0.001 TYR C 146 ARG 0.003 0.001 ARG D 39 *********************** 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 216 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 176 time to evaluate : 1.199 Fit side-chains REVERT: A 71 ASN cc_start: 0.7715 (t0) cc_final: 0.7338 (m-40) REVERT: A 89 LYS cc_start: 0.8198 (OUTLIER) cc_final: 0.7452 (mmtp) REVERT: A 120 GLU cc_start: 0.7944 (tt0) cc_final: 0.7575 (mp0) REVERT: A 131 LYS cc_start: 0.8160 (mmtp) cc_final: 0.7843 (mttm) REVERT: A 229 THR cc_start: 0.8370 (t) cc_final: 0.8159 (m) REVERT: A 274 GLU cc_start: 0.7891 (tp30) cc_final: 0.7660 (mm-30) REVERT: A 289 LYS cc_start: 0.8191 (ttpt) cc_final: 0.7853 (ttmm) REVERT: A 308 LYS cc_start: 0.8780 (mttp) cc_final: 0.8577 (mttp) REVERT: A 319 ILE cc_start: 0.8546 (OUTLIER) cc_final: 0.8190 (tp) REVERT: A 324 SER cc_start: 0.7938 (t) cc_final: 0.7701 (p) REVERT: B 71 ASN cc_start: 0.7712 (t0) cc_final: 0.7334 (m-40) REVERT: B 89 LYS cc_start: 0.8194 (OUTLIER) cc_final: 0.7447 (mmtp) REVERT: B 120 GLU cc_start: 0.7963 (tt0) cc_final: 0.7577 (mp0) REVERT: B 131 LYS cc_start: 0.8161 (mmtp) cc_final: 0.7846 (mttm) REVERT: B 229 THR cc_start: 0.8366 (t) cc_final: 0.8150 (m) REVERT: B 274 GLU cc_start: 0.7892 (tp30) cc_final: 0.7662 (mm-30) REVERT: B 289 LYS cc_start: 0.8208 (ttpt) cc_final: 0.7866 (ttmm) REVERT: B 319 ILE cc_start: 0.8539 (OUTLIER) cc_final: 0.8177 (tp) REVERT: B 324 SER cc_start: 0.7932 (t) cc_final: 0.7698 (p) REVERT: C 71 ASN cc_start: 0.7708 (t0) cc_final: 0.7333 (m-40) REVERT: C 89 LYS cc_start: 0.8198 (OUTLIER) cc_final: 0.7451 (mmtp) REVERT: C 120 GLU cc_start: 0.7975 (tt0) cc_final: 0.7571 (mp0) REVERT: C 131 LYS cc_start: 0.8168 (mmtp) cc_final: 0.7854 (mttm) REVERT: C 229 THR cc_start: 0.8367 (t) cc_final: 0.8156 (m) REVERT: C 274 GLU cc_start: 0.7898 (tp30) cc_final: 0.7670 (mm-30) REVERT: C 289 LYS cc_start: 0.8188 (ttpt) cc_final: 0.7850 (ttmm) REVERT: C 319 ILE cc_start: 0.8553 (OUTLIER) cc_final: 0.8193 (tp) REVERT: C 324 SER cc_start: 0.7950 (t) cc_final: 0.7714 (p) REVERT: D 71 ASN cc_start: 0.7726 (t0) cc_final: 0.7341 (m-40) REVERT: D 89 LYS cc_start: 0.8201 (OUTLIER) cc_final: 0.7456 (mmtp) REVERT: D 120 GLU cc_start: 0.7947 (tt0) cc_final: 0.7560 (mp0) REVERT: D 131 LYS cc_start: 0.8169 (mmtp) cc_final: 0.7851 (mttm) REVERT: D 229 THR cc_start: 0.8363 (t) cc_final: 0.8153 (m) REVERT: D 274 GLU cc_start: 0.7910 (tp30) cc_final: 0.7677 (mm-30) REVERT: D 289 LYS cc_start: 0.8176 (ttpt) cc_final: 0.7848 (ttmm) REVERT: D 319 ILE cc_start: 0.8547 (OUTLIER) cc_final: 0.8187 (tp) REVERT: D 324 SER cc_start: 0.7939 (t) cc_final: 0.7696 (p) outliers start: 40 outliers final: 16 residues processed: 196 average time/residue: 1.1790 time to fit residues: 249.2491 Evaluate side-chains 197 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 173 time to evaluate : 1.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 319 ILE Chi-restraints excluded: chain A residue 342 LEU 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 319 ILE Chi-restraints excluded: chain B residue 342 LEU 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 319 ILE Chi-restraints excluded: chain C residue 342 LEU 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 319 ILE 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 18 optimal weight: 0.9990 chunk 112 optimal weight: 3.9990 chunk 33 optimal weight: 6.9990 chunk 75 optimal weight: 3.9990 chunk 20 optimal weight: 0.7980 chunk 92 optimal weight: 5.9990 chunk 19 optimal weight: 1.9990 chunk 62 optimal weight: 4.9990 chunk 26 optimal weight: 0.9990 chunk 3 optimal weight: 6.9990 chunk 39 optimal weight: 7.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- 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 = 0.3145 r_free = 0.3145 target = 0.107975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.094525 restraints weight = 12601.601| |-----------------------------------------------------------------------------| r_work (start): 0.2971 rms_B_bonded: 1.38 r_work: 0.2884 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.2760 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.2877 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= 0.304 Angle : 0.542 6.773 14064 Z= 0.283 Chirality : 0.048 0.144 1640 Planarity : 0.004 0.036 1792 Dihedral : 8.898 86.928 1644 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.30 % Allowed : 2.99 % Favored : 96.72 % Rotamer: Outliers : 4.09 % Allowed : 17.01 % Favored : 78.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.24), residues: 1340 helix: 0.53 (0.25), residues: 420 sheet: -0.99 (0.31), residues: 280 loop : 0.27 (0.26), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP D 101 HIS 0.004 0.002 HIS A 125 PHE 0.013 0.002 PHE D 304 TYR 0.013 0.002 TYR D 146 ARG 0.003 0.001 ARG B 30 *********************** 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 221 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 177 time to evaluate : 1.179 Fit side-chains REVERT: A 71 ASN cc_start: 0.7766 (t0) cc_final: 0.7363 (m-40) REVERT: A 89 LYS cc_start: 0.8112 (OUTLIER) cc_final: 0.7289 (mmtp) REVERT: A 120 GLU cc_start: 0.7947 (tt0) cc_final: 0.7530 (mt-10) REVERT: A 289 LYS cc_start: 0.8269 (ttpt) cc_final: 0.7857 (ttmm) REVERT: A 308 LYS cc_start: 0.8795 (mttp) cc_final: 0.8578 (mttp) REVERT: A 342 LEU cc_start: 0.8612 (OUTLIER) cc_final: 0.8293 (mt) REVERT: B 71 ASN cc_start: 0.7763 (t0) cc_final: 0.7357 (m-40) REVERT: B 89 LYS cc_start: 0.8115 (OUTLIER) cc_final: 0.7293 (mmtp) REVERT: B 120 GLU cc_start: 0.7967 (tt0) cc_final: 0.7533 (mt-10) REVERT: B 289 LYS cc_start: 0.8281 (ttpt) cc_final: 0.7867 (ttmm) REVERT: B 342 LEU cc_start: 0.8606 (OUTLIER) cc_final: 0.8288 (mt) REVERT: C 71 ASN cc_start: 0.7768 (t0) cc_final: 0.7359 (m-40) REVERT: C 89 LYS cc_start: 0.8110 (OUTLIER) cc_final: 0.7285 (mmtp) REVERT: C 120 GLU cc_start: 0.7973 (tt0) cc_final: 0.7540 (mt-10) REVERT: C 289 LYS cc_start: 0.8269 (ttpt) cc_final: 0.7854 (ttmm) REVERT: C 342 LEU cc_start: 0.8614 (OUTLIER) cc_final: 0.8293 (mt) REVERT: D 71 ASN cc_start: 0.7774 (t0) cc_final: 0.7355 (m-40) REVERT: D 89 LYS cc_start: 0.8115 (OUTLIER) cc_final: 0.7290 (mmtp) REVERT: D 120 GLU cc_start: 0.7980 (tt0) cc_final: 0.7528 (mt-10) REVERT: D 289 LYS cc_start: 0.8280 (ttpt) cc_final: 0.7866 (ttmm) REVERT: D 342 LEU cc_start: 0.8612 (OUTLIER) cc_final: 0.8294 (mt) outliers start: 44 outliers final: 24 residues processed: 201 average time/residue: 1.1421 time to fit residues: 247.9859 Evaluate side-chains 186 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 154 time to evaluate : 1.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 104 SER 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 342 LEU 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 104 SER 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 342 LEU 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 104 SER 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 342 LEU 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 104 SER 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 1 optimal weight: 1.9990 chunk 93 optimal weight: 5.9990 chunk 89 optimal weight: 1.9990 chunk 121 optimal weight: 0.7980 chunk 82 optimal weight: 4.9990 chunk 116 optimal weight: 0.9980 chunk 21 optimal weight: 0.2980 chunk 18 optimal weight: 2.9990 chunk 107 optimal weight: 3.9990 chunk 69 optimal weight: 0.6980 chunk 122 optimal weight: 0.9990 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 = 0.3174 r_free = 0.3174 target = 0.110044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.096915 restraints weight = 12431.467| |-----------------------------------------------------------------------------| r_work (start): 0.3020 rms_B_bonded: 1.37 r_work: 0.2932 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.2806 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.3053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10332 Z= 0.172 Angle : 0.487 7.010 14064 Z= 0.254 Chirality : 0.045 0.147 1640 Planarity : 0.004 0.035 1792 Dihedral : 8.618 86.904 1644 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.30 % Allowed : 2.39 % Favored : 97.31 % Rotamer: Outliers : 2.51 % Allowed : 18.96 % Favored : 78.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.24), residues: 1340 helix: 0.78 (0.26), residues: 420 sheet: -1.13 (0.30), residues: 304 loop : 0.48 (0.27), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP D 101 HIS 0.003 0.002 HIS B 67 PHE 0.011 0.001 PHE D 304 TYR 0.008 0.001 TYR D 338 ARG 0.006 0.001 ARG D 39 *********************** 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 195 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 168 time to evaluate : 1.149 Fit side-chains REVERT: A 71 ASN cc_start: 0.7789 (t0) cc_final: 0.7442 (m-40) REVERT: A 120 GLU cc_start: 0.7945 (tt0) cc_final: 0.7571 (mp0) REVERT: A 229 THR cc_start: 0.8401 (m) cc_final: 0.8161 (m) REVERT: A 274 GLU cc_start: 0.7820 (tp30) cc_final: 0.7563 (mm-30) REVERT: A 289 LYS cc_start: 0.8230 (ttpt) cc_final: 0.7881 (ttmm) REVERT: A 308 LYS cc_start: 0.8764 (mttp) cc_final: 0.8556 (mttp) REVERT: A 315 LYS cc_start: 0.8863 (OUTLIER) cc_final: 0.8274 (tttt) REVERT: B 71 ASN cc_start: 0.7780 (t0) cc_final: 0.7432 (m-40) REVERT: B 120 GLU cc_start: 0.7962 (tt0) cc_final: 0.7582 (mp0) REVERT: B 229 THR cc_start: 0.8408 (m) cc_final: 0.8172 (m) REVERT: B 274 GLU cc_start: 0.7818 (tp30) cc_final: 0.7567 (mm-30) REVERT: B 289 LYS cc_start: 0.8228 (ttpt) cc_final: 0.7888 (ttmm) REVERT: B 308 LYS cc_start: 0.8912 (OUTLIER) cc_final: 0.8478 (mttp) REVERT: B 315 LYS cc_start: 0.8858 (OUTLIER) cc_final: 0.8269 (tttt) REVERT: C 71 ASN cc_start: 0.7790 (t0) cc_final: 0.7437 (m-40) REVERT: C 120 GLU cc_start: 0.7984 (tt0) cc_final: 0.7582 (mp0) REVERT: C 229 THR cc_start: 0.8399 (m) cc_final: 0.8162 (m) REVERT: C 274 GLU cc_start: 0.7835 (tp30) cc_final: 0.7584 (mm-30) REVERT: C 289 LYS cc_start: 0.8216 (ttpt) cc_final: 0.7880 (ttmm) REVERT: C 308 LYS cc_start: 0.8911 (OUTLIER) cc_final: 0.8473 (mttp) REVERT: C 315 LYS cc_start: 0.8857 (OUTLIER) cc_final: 0.8264 (tttt) REVERT: D 71 ASN cc_start: 0.7800 (t0) cc_final: 0.7431 (m-40) REVERT: D 120 GLU cc_start: 0.7982 (tt0) cc_final: 0.7572 (mp0) REVERT: D 229 THR cc_start: 0.8396 (m) cc_final: 0.8154 (m) REVERT: D 274 GLU cc_start: 0.7838 (tp30) cc_final: 0.7580 (mm-30) REVERT: D 289 LYS cc_start: 0.8236 (ttpt) cc_final: 0.7888 (ttmm) REVERT: D 308 LYS cc_start: 0.8902 (OUTLIER) cc_final: 0.8459 (mttp) REVERT: D 315 LYS cc_start: 0.8856 (OUTLIER) cc_final: 0.8265 (tttt) outliers start: 27 outliers final: 20 residues processed: 183 average time/residue: 1.2392 time to fit residues: 244.0054 Evaluate side-chains 183 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 156 time to evaluate : 1.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 THR 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 43 THR 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 315 LYS Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain C residue 43 THR 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 315 LYS Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain D residue 43 THR 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 315 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 105 optimal weight: 3.9990 chunk 51 optimal weight: 5.9990 chunk 69 optimal weight: 4.9990 chunk 38 optimal weight: 0.8980 chunk 70 optimal weight: 0.7980 chunk 97 optimal weight: 2.9990 chunk 118 optimal weight: 0.9990 chunk 4 optimal weight: 4.9990 chunk 68 optimal weight: 0.7980 chunk 12 optimal weight: 0.0870 chunk 74 optimal weight: 2.9990 overall best weight: 0.7160 ------------------------------------------------------------------------------- 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 107 GLN ** A 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 107 GLN B 201 GLN ** C 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 107 GLN ** C 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 201 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.110743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.097123 restraints weight = 12643.901| |-----------------------------------------------------------------------------| r_work (start): 0.3053 rms_B_bonded: 1.47 r_work: 0.2960 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2834 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.3194 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= 0.167 Angle : 0.479 6.769 14064 Z= 0.249 Chirality : 0.045 0.145 1640 Planarity : 0.003 0.034 1792 Dihedral : 8.460 87.381 1644 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.30 % Allowed : 2.69 % Favored : 97.01 % Rotamer: Outliers : 4.00 % Allowed : 18.40 % Favored : 77.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.24), residues: 1340 helix: 0.97 (0.27), residues: 420 sheet: -1.00 (0.30), residues: 292 loop : 0.41 (0.27), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP D 101 HIS 0.003 0.001 HIS C 67 PHE 0.010 0.001 PHE D 304 TYR 0.007 0.001 TYR B 338 ARG 0.001 0.000 ARG A 30 *********************** 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 209 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 166 time to evaluate : 1.190 Fit side-chains REVERT: A 39 ARG cc_start: 0.7887 (ttm170) cc_final: 0.7645 (ttm170) REVERT: A 71 ASN cc_start: 0.7829 (t0) cc_final: 0.7507 (m-40) REVERT: A 89 LYS cc_start: 0.8256 (OUTLIER) cc_final: 0.7533 (mmtp) REVERT: A 120 GLU cc_start: 0.7954 (tt0) cc_final: 0.7598 (mp0) REVERT: A 229 THR cc_start: 0.8382 (m) cc_final: 0.8134 (m) REVERT: A 274 GLU cc_start: 0.7850 (tp30) cc_final: 0.7631 (mm-30) REVERT: A 289 LYS cc_start: 0.8252 (ttpt) cc_final: 0.7882 (ttmm) REVERT: B 39 ARG cc_start: 0.7893 (ttm170) cc_final: 0.7653 (ttm170) REVERT: B 71 ASN cc_start: 0.7827 (t0) cc_final: 0.7506 (m-40) REVERT: B 89 LYS cc_start: 0.8260 (OUTLIER) cc_final: 0.7541 (mmtp) REVERT: B 120 GLU cc_start: 0.7962 (tt0) cc_final: 0.7606 (mp0) REVERT: B 229 THR cc_start: 0.8395 (m) cc_final: 0.8155 (m) REVERT: B 274 GLU cc_start: 0.7855 (tp30) cc_final: 0.7635 (mm-30) REVERT: B 289 LYS cc_start: 0.8236 (ttpt) cc_final: 0.7890 (ttmm) REVERT: B 308 LYS cc_start: 0.8866 (OUTLIER) cc_final: 0.8476 (mttp) REVERT: C 39 ARG cc_start: 0.7893 (ttm170) cc_final: 0.7654 (ttm170) REVERT: C 71 ASN cc_start: 0.7827 (t0) cc_final: 0.7505 (m-40) REVERT: C 89 LYS cc_start: 0.8262 (OUTLIER) cc_final: 0.7539 (mmtp) REVERT: C 120 GLU cc_start: 0.7987 (tt0) cc_final: 0.7606 (mp0) REVERT: C 229 THR cc_start: 0.8385 (m) cc_final: 0.8144 (m) REVERT: C 274 GLU cc_start: 0.7859 (tp30) cc_final: 0.7639 (mm-30) REVERT: C 289 LYS cc_start: 0.8221 (ttpt) cc_final: 0.7879 (ttmm) REVERT: C 308 LYS cc_start: 0.8871 (OUTLIER) cc_final: 0.8484 (mttp) REVERT: D 39 ARG cc_start: 0.7888 (ttm170) cc_final: 0.7645 (ttm170) REVERT: D 71 ASN cc_start: 0.7825 (t0) cc_final: 0.7493 (m-40) REVERT: D 89 LYS cc_start: 0.8262 (OUTLIER) cc_final: 0.7541 (mmtp) REVERT: D 120 GLU cc_start: 0.7956 (tt0) cc_final: 0.7594 (mp0) REVERT: D 229 THR cc_start: 0.8383 (m) cc_final: 0.8138 (m) REVERT: D 274 GLU cc_start: 0.7867 (tp30) cc_final: 0.7646 (mm-30) REVERT: D 289 LYS cc_start: 0.8244 (ttpt) cc_final: 0.7898 (ttmm) REVERT: D 308 LYS cc_start: 0.8875 (OUTLIER) cc_final: 0.8493 (mttp) outliers start: 43 outliers final: 24 residues processed: 193 average time/residue: 1.1841 time to fit residues: 246.8177 Evaluate side-chains 193 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 162 time to evaluate : 1.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 342 LEU 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 102 optimal weight: 5.9990 chunk 112 optimal weight: 0.1980 chunk 63 optimal weight: 0.0470 chunk 126 optimal weight: 0.9990 chunk 44 optimal weight: 3.9990 chunk 106 optimal weight: 0.9980 chunk 114 optimal weight: 2.9990 chunk 5 optimal weight: 6.9990 chunk 130 optimal weight: 3.9990 chunk 79 optimal weight: 0.9990 chunk 51 optimal weight: 5.9990 overall best weight: 0.6482 ------------------------------------------------------------------------------- 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 107 GLN A 201 GLN ** B 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 107 GLN B 201 GLN ** C 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 107 GLN C 201 GLN ** D 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 107 GLN D 201 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.111475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.097856 restraints weight = 12605.930| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 1.47 r_work: 0.3006 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2881 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.3210 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= 0.156 Angle : 0.469 6.492 14064 Z= 0.244 Chirality : 0.045 0.145 1640 Planarity : 0.003 0.035 1792 Dihedral : 8.329 87.803 1644 Min Nonbonded Distance : 2.638 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.30 % Allowed : 2.09 % Favored : 97.61 % Rotamer: Outliers : 2.51 % Allowed : 20.54 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.25), residues: 1340 helix: 1.31 (0.27), residues: 400 sheet: -1.02 (0.30), residues: 292 loop : 0.63 (0.27), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 101 HIS 0.003 0.001 HIS A 67 PHE 0.010 0.001 PHE A 304 TYR 0.007 0.001 TYR B 338 ARG 0.001 0.000 ARG B 30 *********************** 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 202 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 175 time to evaluate : 1.105 Fit side-chains REVERT: A 39 ARG cc_start: 0.7854 (ttm170) cc_final: 0.7611 (ttm170) REVERT: A 71 ASN cc_start: 0.7809 (t0) cc_final: 0.7476 (m-40) REVERT: A 89 LYS cc_start: 0.8226 (OUTLIER) cc_final: 0.7462 (mmtp) REVERT: A 120 GLU cc_start: 0.7993 (tt0) cc_final: 0.7636 (mp0) REVERT: A 229 THR cc_start: 0.8292 (m) cc_final: 0.8053 (m) REVERT: A 289 LYS cc_start: 0.8136 (ttpt) cc_final: 0.7789 (ttmm) REVERT: B 39 ARG cc_start: 0.7847 (ttm170) cc_final: 0.7607 (ttm170) REVERT: B 71 ASN cc_start: 0.7800 (t0) cc_final: 0.7471 (m-40) REVERT: B 89 LYS cc_start: 0.8231 (OUTLIER) cc_final: 0.7473 (mmtp) REVERT: B 120 GLU cc_start: 0.8002 (tt0) cc_final: 0.7644 (mp0) REVERT: B 229 THR cc_start: 0.8305 (m) cc_final: 0.8073 (m) REVERT: B 289 LYS cc_start: 0.8175 (ttpt) cc_final: 0.7824 (ttmm) REVERT: C 39 ARG cc_start: 0.7838 (ttm170) cc_final: 0.7599 (ttm170) REVERT: C 71 ASN cc_start: 0.7804 (t0) cc_final: 0.7476 (m-40) REVERT: C 89 LYS cc_start: 0.8234 (OUTLIER) cc_final: 0.7472 (mmtp) REVERT: C 120 GLU cc_start: 0.8025 (tt0) cc_final: 0.7641 (mp0) REVERT: C 229 THR cc_start: 0.8303 (m) cc_final: 0.8070 (m) REVERT: C 289 LYS cc_start: 0.8146 (ttpt) cc_final: 0.7813 (ttmm) REVERT: D 39 ARG cc_start: 0.7834 (ttm170) cc_final: 0.7594 (ttm170) REVERT: D 71 ASN cc_start: 0.7805 (t0) cc_final: 0.7470 (m-40) REVERT: D 89 LYS cc_start: 0.8230 (OUTLIER) cc_final: 0.7467 (mmtp) REVERT: D 120 GLU cc_start: 0.7983 (tt0) cc_final: 0.7630 (mp0) REVERT: D 229 THR cc_start: 0.8295 (m) cc_final: 0.8060 (m) REVERT: D 289 LYS cc_start: 0.8137 (ttpt) cc_final: 0.7795 (ttmm) outliers start: 27 outliers final: 16 residues processed: 194 average time/residue: 1.1133 time to fit residues: 233.7749 Evaluate side-chains 183 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 163 time to evaluate : 1.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 342 LEU 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 342 LEU 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 342 LEU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 32 optimal weight: 4.9990 chunk 79 optimal weight: 1.9990 chunk 84 optimal weight: 7.9990 chunk 104 optimal weight: 1.9990 chunk 25 optimal weight: 0.0670 chunk 86 optimal weight: 1.9990 chunk 88 optimal weight: 0.4980 chunk 48 optimal weight: 3.9990 chunk 26 optimal weight: 4.9990 chunk 81 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 overall best weight: 1.3124 ------------------------------------------------------------------------------- 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 107 GLN A 201 GLN ** B 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 107 GLN B 201 GLN ** C 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 107 GLN C 201 GLN ** D 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 107 GLN D 201 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.109129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.095893 restraints weight = 12765.531| |-----------------------------------------------------------------------------| r_work (start): 0.3010 rms_B_bonded: 1.39 r_work: 0.2920 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.2794 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.3204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 10332 Z= 0.250 Angle : 0.528 7.888 14064 Z= 0.274 Chirality : 0.047 0.142 1640 Planarity : 0.004 0.035 1792 Dihedral : 8.618 88.561 1644 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.30 % Allowed : 2.99 % Favored : 96.72 % Rotamer: Outliers : 2.60 % Allowed : 21.56 % Favored : 75.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.24), residues: 1340 helix: 0.80 (0.26), residues: 420 sheet: -0.90 (0.32), residues: 272 loop : 0.35 (0.26), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 331 HIS 0.003 0.001 HIS B 67 PHE 0.011 0.002 PHE A 304 TYR 0.010 0.001 TYR A 146 ARG 0.003 0.000 ARG A 30 *********************** 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 191 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 163 time to evaluate : 1.086 Fit side-chains REVERT: A 71 ASN cc_start: 0.7841 (t0) cc_final: 0.7428 (m-40) REVERT: A 89 LYS cc_start: 0.8218 (OUTLIER) cc_final: 0.7480 (mmtp) REVERT: A 119 GLU cc_start: 0.7562 (tm-30) cc_final: 0.7289 (tp30) REVERT: A 120 GLU cc_start: 0.7927 (tt0) cc_final: 0.7620 (mp0) REVERT: A 229 THR cc_start: 0.8346 (m) cc_final: 0.8080 (m) REVERT: A 289 LYS cc_start: 0.8266 (ttpt) cc_final: 0.7951 (ttmm) REVERT: B 71 ASN cc_start: 0.7826 (t0) cc_final: 0.7414 (m-40) REVERT: B 89 LYS cc_start: 0.8220 (OUTLIER) cc_final: 0.7489 (mmtp) REVERT: B 119 GLU cc_start: 0.7564 (tm-30) cc_final: 0.7294 (tp30) REVERT: B 120 GLU cc_start: 0.7945 (tt0) cc_final: 0.7620 (mp0) REVERT: B 229 THR cc_start: 0.8351 (m) cc_final: 0.8090 (m) REVERT: B 289 LYS cc_start: 0.8254 (ttpt) cc_final: 0.7928 (ttmm) REVERT: C 71 ASN cc_start: 0.7840 (t0) cc_final: 0.7430 (m-40) REVERT: C 89 LYS cc_start: 0.8217 (OUTLIER) cc_final: 0.7478 (mmtp) REVERT: C 120 GLU cc_start: 0.7969 (tt0) cc_final: 0.7620 (mp0) REVERT: C 229 THR cc_start: 0.8343 (m) cc_final: 0.8095 (m) REVERT: C 289 LYS cc_start: 0.8256 (ttpt) cc_final: 0.7945 (ttmm) REVERT: D 71 ASN cc_start: 0.7839 (t0) cc_final: 0.7421 (m-40) REVERT: D 89 LYS cc_start: 0.8216 (OUTLIER) cc_final: 0.7479 (mmtp) REVERT: D 119 GLU cc_start: 0.7554 (tm-30) cc_final: 0.7287 (tp30) REVERT: D 120 GLU cc_start: 0.7954 (tt0) cc_final: 0.7616 (mp0) REVERT: D 229 THR cc_start: 0.8330 (m) cc_final: 0.8064 (m) REVERT: D 289 LYS cc_start: 0.8261 (ttpt) cc_final: 0.7956 (ttmm) outliers start: 28 outliers final: 20 residues processed: 175 average time/residue: 1.2070 time to fit residues: 227.4605 Evaluate side-chains 187 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 163 time to evaluate : 1.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 342 LEU 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 342 LEU 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 342 LEU 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 76 optimal weight: 0.8980 chunk 88 optimal weight: 0.9990 chunk 46 optimal weight: 0.7980 chunk 72 optimal weight: 5.9990 chunk 110 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 chunk 43 optimal weight: 0.8980 chunk 87 optimal weight: 0.7980 chunk 113 optimal weight: 0.9990 chunk 9 optimal weight: 0.0000 overall best weight: 0.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 ASN A 201 GLN ** B 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 201 GLN C 48 ASN C 201 GLN ** D 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 201 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.112831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.097386 restraints weight = 12313.358| |-----------------------------------------------------------------------------| r_work (start): 0.2998 rms_B_bonded: 1.79 r_work: 0.2893 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2755 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.3325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10332 Z= 0.174 Angle : 0.498 7.077 14064 Z= 0.258 Chirality : 0.045 0.146 1640 Planarity : 0.003 0.034 1792 Dihedral : 8.401 87.812 1644 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.30 % Allowed : 2.09 % Favored : 97.61 % Rotamer: Outliers : 3.16 % Allowed : 21.19 % Favored : 75.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.24), residues: 1340 helix: 1.00 (0.26), residues: 424 sheet: -1.09 (0.30), residues: 292 loop : 0.39 (0.27), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP D 101 HIS 0.003 0.001 HIS A 67 PHE 0.010 0.001 PHE B 304 TYR 0.007 0.001 TYR C 338 ARG 0.002 0.000 ARG A 341 ********************** 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 210 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 176 time to evaluate : 1.174 Fit side-chains REVERT: A 71 ASN cc_start: 0.7836 (t0) cc_final: 0.7438 (m-40) REVERT: A 89 LYS cc_start: 0.8227 (OUTLIER) cc_final: 0.7462 (mmtp) REVERT: A 119 GLU cc_start: 0.7598 (tm-30) cc_final: 0.7319 (tp30) REVERT: A 120 GLU cc_start: 0.8091 (tt0) cc_final: 0.7600 (mp0) REVERT: A 229 THR cc_start: 0.8284 (m) cc_final: 0.8047 (m) REVERT: A 289 LYS cc_start: 0.8151 (ttpt) cc_final: 0.7841 (ttmm) REVERT: B 71 ASN cc_start: 0.7830 (t0) cc_final: 0.7429 (m-40) REVERT: B 89 LYS cc_start: 0.8215 (OUTLIER) cc_final: 0.7455 (mmtp) REVERT: B 119 GLU cc_start: 0.7616 (tm-30) cc_final: 0.7339 (tp30) REVERT: B 120 GLU cc_start: 0.8084 (tt0) cc_final: 0.7609 (mp0) REVERT: B 229 THR cc_start: 0.8278 (m) cc_final: 0.8041 (m) REVERT: B 289 LYS cc_start: 0.8196 (ttpt) cc_final: 0.7884 (ttmm) REVERT: C 71 ASN cc_start: 0.7841 (t0) cc_final: 0.7436 (m-40) REVERT: C 89 LYS cc_start: 0.8222 (OUTLIER) cc_final: 0.7467 (mmtp) REVERT: C 120 GLU cc_start: 0.8070 (tt0) cc_final: 0.7591 (mp0) REVERT: C 229 THR cc_start: 0.8284 (m) cc_final: 0.8052 (m) REVERT: C 289 LYS cc_start: 0.8139 (ttpt) cc_final: 0.7837 (ttmm) REVERT: D 71 ASN cc_start: 0.7829 (t0) cc_final: 0.7425 (m-40) REVERT: D 89 LYS cc_start: 0.8219 (OUTLIER) cc_final: 0.7456 (mmtp) REVERT: D 119 GLU cc_start: 0.7595 (tm-30) cc_final: 0.7317 (tp30) REVERT: D 120 GLU cc_start: 0.8074 (tt0) cc_final: 0.7595 (mp0) REVERT: D 229 THR cc_start: 0.8293 (m) cc_final: 0.8056 (m) REVERT: D 289 LYS cc_start: 0.8188 (ttpt) cc_final: 0.7887 (ttmm) outliers start: 34 outliers final: 20 residues processed: 190 average time/residue: 1.1521 time to fit residues: 237.1761 Evaluate side-chains 198 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 174 time to evaluate : 1.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 342 LEU 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 342 LEU 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 342 LEU 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 117 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 126 optimal weight: 0.4980 chunk 76 optimal weight: 0.8980 chunk 115 optimal weight: 0.9990 chunk 86 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 chunk 53 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 48 ASN ** B 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 48 ASN ** D 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.112359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.096458 restraints weight = 12069.130| |-----------------------------------------------------------------------------| r_work (start): 0.3028 rms_B_bonded: 1.85 r_work: 0.2923 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2783 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.3393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10332 Z= 0.185 Angle : 0.506 6.901 14064 Z= 0.262 Chirality : 0.045 0.145 1640 Planarity : 0.003 0.034 1792 Dihedral : 8.331 86.627 1644 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.30 % Allowed : 2.99 % Favored : 96.72 % Rotamer: Outliers : 2.42 % Allowed : 20.82 % Favored : 76.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.24), residues: 1340 helix: 0.97 (0.26), residues: 424 sheet: -1.01 (0.31), residues: 292 loop : 0.41 (0.27), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP C 101 HIS 0.003 0.001 HIS B 67 PHE 0.010 0.002 PHE C 325 TYR 0.007 0.001 TYR C 338 ARG 0.001 0.000 ARG D 30 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6673.71 seconds wall clock time: 119 minutes 5.91 seconds (7145.91 seconds total)