Starting phenix.real_space_refine on Sat Nov 16 03:44:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pvf_17964/11_2024/8pvf_17964.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pvf_17964/11_2024/8pvf_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pvf_17964/11_2024/8pvf_17964.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pvf_17964/11_2024/8pvf_17964.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pvf_17964/11_2024/8pvf_17964.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pvf_17964/11_2024/8pvf_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-5513/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: 5.14, per 1000 atoms: 0.51 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: 2.64 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: 1.51 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: 3.31 Time building geometry restraints manager: 3.00 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.090 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: 0.080 Set scattering table: 0.090 Process input model: 24.970 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.910 ------------------------------------------------------------------------------- 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 : 1.175 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: 1.4358 time to fit residues: 469.9599 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 : 1.120 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 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 : 1.124 Fit side-chains REVERT: A 71 ASN cc_start: 0.7191 (t0) cc_final: 0.6654 (m-40) REVERT: A 119 GLU cc_start: 0.6615 (tm-30) cc_final: 0.6162 (tm-30) REVERT: A 120 GLU cc_start: 0.7680 (tt0) cc_final: 0.6987 (mp0) REVERT: A 131 LYS cc_start: 0.7720 (mmtp) cc_final: 0.7216 (mttm) REVERT: A 159 LYS cc_start: 0.7068 (mmtt) cc_final: 0.6682 (mmtt) REVERT: A 201 GLN cc_start: 0.7908 (mt0) cc_final: 0.7706 (mt0) REVERT: A 247 THR cc_start: 0.8302 (t) cc_final: 0.7983 (p) REVERT: A 252 ARG cc_start: 0.7560 (mtt180) cc_final: 0.7236 (mpp80) REVERT: A 282 GLU cc_start: 0.6786 (tt0) cc_final: 0.6454 (mt-10) REVERT: A 289 LYS cc_start: 0.7961 (ttpt) cc_final: 0.7342 (ttmm) REVERT: B 71 ASN cc_start: 0.7190 (t0) cc_final: 0.6653 (m-40) REVERT: B 119 GLU cc_start: 0.6615 (tm-30) cc_final: 0.6163 (tm-30) REVERT: B 120 GLU cc_start: 0.7680 (tt0) cc_final: 0.6986 (mp0) REVERT: B 131 LYS cc_start: 0.7721 (mmtp) cc_final: 0.7215 (mttm) REVERT: B 159 LYS cc_start: 0.7068 (mmtt) cc_final: 0.6684 (mmtt) REVERT: B 201 GLN cc_start: 0.7907 (mt0) cc_final: 0.7705 (mt0) REVERT: B 247 THR cc_start: 0.8303 (t) cc_final: 0.7982 (p) REVERT: B 252 ARG cc_start: 0.7561 (mtt180) cc_final: 0.7237 (mpp80) REVERT: B 282 GLU cc_start: 0.6785 (tt0) cc_final: 0.6454 (mt-10) REVERT: B 289 LYS cc_start: 0.7961 (ttpt) cc_final: 0.7343 (ttmm) REVERT: C 71 ASN cc_start: 0.7193 (t0) cc_final: 0.6655 (m-40) REVERT: C 119 GLU cc_start: 0.6615 (tm-30) cc_final: 0.6164 (tm-30) REVERT: C 120 GLU cc_start: 0.7680 (tt0) cc_final: 0.6987 (mp0) REVERT: C 131 LYS cc_start: 0.7719 (mmtp) cc_final: 0.7214 (mttm) REVERT: C 159 LYS cc_start: 0.7067 (mmtt) cc_final: 0.6682 (mmtt) REVERT: C 201 GLN cc_start: 0.7905 (mt0) cc_final: 0.7705 (mt0) REVERT: C 247 THR cc_start: 0.8302 (t) cc_final: 0.7982 (p) REVERT: C 252 ARG cc_start: 0.7560 (mtt180) cc_final: 0.7236 (mpp80) REVERT: C 282 GLU cc_start: 0.6787 (tt0) cc_final: 0.6456 (mt-10) REVERT: C 289 LYS cc_start: 0.7961 (ttpt) cc_final: 0.7344 (ttmm) REVERT: D 71 ASN cc_start: 0.7190 (t0) cc_final: 0.6654 (m-40) REVERT: D 119 GLU cc_start: 0.6616 (tm-30) cc_final: 0.6164 (tm-30) REVERT: D 120 GLU cc_start: 0.7679 (tt0) cc_final: 0.6986 (mp0) REVERT: D 131 LYS cc_start: 0.7720 (mmtp) cc_final: 0.7215 (mttm) REVERT: D 159 LYS cc_start: 0.7067 (mmtt) cc_final: 0.6682 (mmtt) REVERT: D 201 GLN cc_start: 0.7908 (mt0) cc_final: 0.7705 (mt0) REVERT: D 247 THR cc_start: 0.8303 (t) cc_final: 0.7982 (p) REVERT: D 252 ARG cc_start: 0.7562 (mtt180) cc_final: 0.7237 (mpp80) REVERT: D 282 GLU cc_start: 0.6785 (tt0) cc_final: 0.6455 (mt-10) REVERT: D 289 LYS cc_start: 0.7961 (ttpt) cc_final: 0.7343 (ttmm) outliers start: 20 outliers final: 8 residues processed: 240 average time/residue: 1.2552 time to fit residues: 323.3064 Evaluate side-chains 196 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 188 time to evaluate : 1.061 ------------------------------------------------------------------------------- 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 66 optimal weight: 6.9990 chunk 37 optimal weight: 0.6980 chunk 99 optimal weight: 6.9990 chunk 81 optimal weight: 4.9990 chunk 33 optimal weight: 6.9990 chunk 120 optimal weight: 4.9990 chunk 129 optimal weight: 0.9990 chunk 106 optimal weight: 2.9990 chunk 119 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 96 optimal weight: 0.0980 overall best weight: 1.5586 ------------------------------------------------------------------------------- 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 ** B 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 107 GLN B 195 HIS ** C 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 107 GLN C 195 HIS ** D 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 107 GLN D 195 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.2521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 10332 Z= 0.284 Angle : 0.560 6.534 14064 Z= 0.294 Chirality : 0.048 0.144 1640 Planarity : 0.004 0.036 1792 Dihedral : 9.040 83.961 1644 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.30 % Allowed : 2.99 % Favored : 96.72 % Rotamer: Outliers : 3.72 % Allowed : 15.61 % Favored : 80.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.57 (0.26), residues: 396 sheet: -0.97 (0.31), residues: 280 loop : 0.49 (0.26), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 101 HIS 0.006 0.003 HIS A 125 PHE 0.013 0.002 PHE C 304 TYR 0.014 0.002 TYR D 146 ARG 0.004 0.001 ARG B 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 244 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 204 time to evaluate : 1.125 Fit side-chains REVERT: A 38 GLU cc_start: 0.6597 (mt-10) cc_final: 0.6304 (mt-10) REVERT: A 71 ASN cc_start: 0.7275 (t0) cc_final: 0.6733 (m-40) REVERT: A 119 GLU cc_start: 0.6961 (tm-30) cc_final: 0.6659 (tm-30) REVERT: A 120 GLU cc_start: 0.7687 (tt0) cc_final: 0.6892 (mp0) REVERT: A 131 LYS cc_start: 0.7702 (mmtp) cc_final: 0.7237 (mttm) REVERT: A 140 LYS cc_start: 0.6674 (mmpt) cc_final: 0.6447 (mmmm) REVERT: A 159 LYS cc_start: 0.7151 (mmtt) cc_final: 0.6760 (mmtt) REVERT: A 247 THR cc_start: 0.8209 (t) cc_final: 0.7943 (p) REVERT: A 252 ARG cc_start: 0.7610 (mtt180) cc_final: 0.7242 (mpp80) REVERT: A 274 GLU cc_start: 0.7222 (tp30) cc_final: 0.6931 (mm-30) REVERT: A 282 GLU cc_start: 0.6956 (tt0) cc_final: 0.6581 (mt-10) REVERT: A 289 LYS cc_start: 0.7942 (ttpt) cc_final: 0.7428 (ttmm) REVERT: A 319 ILE cc_start: 0.7876 (OUTLIER) cc_final: 0.7487 (tp) REVERT: A 342 LEU cc_start: 0.7506 (OUTLIER) cc_final: 0.7121 (mt) REVERT: B 38 GLU cc_start: 0.6597 (mt-10) cc_final: 0.6303 (mt-10) REVERT: B 71 ASN cc_start: 0.7274 (t0) cc_final: 0.6732 (m-40) REVERT: B 119 GLU cc_start: 0.6961 (tm-30) cc_final: 0.6660 (tm-30) REVERT: B 120 GLU cc_start: 0.7687 (tt0) cc_final: 0.6893 (mp0) REVERT: B 131 LYS cc_start: 0.7703 (mmtp) cc_final: 0.7237 (mttm) REVERT: B 140 LYS cc_start: 0.6671 (mmpt) cc_final: 0.6447 (mmmm) REVERT: B 159 LYS cc_start: 0.7151 (mmtt) cc_final: 0.6760 (mmtt) REVERT: B 247 THR cc_start: 0.8210 (t) cc_final: 0.7944 (p) REVERT: B 252 ARG cc_start: 0.7612 (mtt180) cc_final: 0.7243 (mpp80) REVERT: B 274 GLU cc_start: 0.7223 (tp30) cc_final: 0.6931 (mm-30) REVERT: B 282 GLU cc_start: 0.6955 (tt0) cc_final: 0.6582 (mt-10) REVERT: B 289 LYS cc_start: 0.7944 (ttpt) cc_final: 0.7429 (ttmm) REVERT: B 319 ILE cc_start: 0.7878 (OUTLIER) cc_final: 0.7489 (tp) REVERT: B 342 LEU cc_start: 0.7506 (OUTLIER) cc_final: 0.7121 (mt) REVERT: C 38 GLU cc_start: 0.6598 (mt-10) cc_final: 0.6305 (mt-10) REVERT: C 71 ASN cc_start: 0.7277 (t0) cc_final: 0.6735 (m-40) REVERT: C 119 GLU cc_start: 0.6962 (tm-30) cc_final: 0.6658 (tm-30) REVERT: C 120 GLU cc_start: 0.7688 (tt0) cc_final: 0.6893 (mp0) REVERT: C 131 LYS cc_start: 0.7702 (mmtp) cc_final: 0.7235 (mttm) REVERT: C 140 LYS cc_start: 0.6670 (mmpt) cc_final: 0.6446 (mmmm) REVERT: C 159 LYS cc_start: 0.7150 (mmtt) cc_final: 0.6759 (mmtt) REVERT: C 247 THR cc_start: 0.8208 (t) cc_final: 0.7942 (p) REVERT: C 252 ARG cc_start: 0.7611 (mtt180) cc_final: 0.7243 (mpp80) REVERT: C 274 GLU cc_start: 0.7224 (tp30) cc_final: 0.6933 (mm-30) REVERT: C 282 GLU cc_start: 0.6955 (tt0) cc_final: 0.6581 (mt-10) REVERT: C 289 LYS cc_start: 0.7944 (ttpt) cc_final: 0.7429 (ttmm) REVERT: C 319 ILE cc_start: 0.7877 (OUTLIER) cc_final: 0.7488 (tp) REVERT: C 342 LEU cc_start: 0.7506 (OUTLIER) cc_final: 0.7121 (mt) REVERT: D 38 GLU cc_start: 0.6599 (mt-10) cc_final: 0.6305 (mt-10) REVERT: D 71 ASN cc_start: 0.7274 (t0) cc_final: 0.6733 (m-40) REVERT: D 119 GLU cc_start: 0.6963 (tm-30) cc_final: 0.6659 (tm-30) REVERT: D 120 GLU cc_start: 0.7689 (tt0) cc_final: 0.6893 (mp0) REVERT: D 131 LYS cc_start: 0.7701 (mmtp) cc_final: 0.7236 (mttm) REVERT: D 140 LYS cc_start: 0.6670 (mmpt) cc_final: 0.6446 (mmmm) REVERT: D 159 LYS cc_start: 0.7149 (mmtt) cc_final: 0.6758 (mmtt) REVERT: D 247 THR cc_start: 0.8210 (t) cc_final: 0.7943 (p) REVERT: D 252 ARG cc_start: 0.7611 (mtt180) cc_final: 0.7242 (mpp80) REVERT: D 274 GLU cc_start: 0.7223 (tp30) cc_final: 0.6931 (mm-30) REVERT: D 282 GLU cc_start: 0.6954 (tt0) cc_final: 0.6580 (mt-10) REVERT: D 289 LYS cc_start: 0.7943 (ttpt) cc_final: 0.7427 (ttmm) REVERT: D 319 ILE cc_start: 0.7876 (OUTLIER) cc_final: 0.7489 (tp) REVERT: D 342 LEU cc_start: 0.7509 (OUTLIER) cc_final: 0.7124 (mt) outliers start: 40 outliers final: 16 residues processed: 228 average time/residue: 1.4568 time to fit residues: 354.2076 Evaluate side-chains 208 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 184 time to evaluate : 1.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 104 SER 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 104 SER 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 104 SER 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 104 SER 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 118 optimal weight: 3.9990 chunk 90 optimal weight: 5.9990 chunk 62 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 80 optimal weight: 0.6980 chunk 120 optimal weight: 5.9990 chunk 127 optimal weight: 0.7980 chunk 114 optimal weight: 3.9990 chunk 34 optimal weight: 0.6980 chunk 106 optimal weight: 3.9990 overall best weight: 1.8384 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.2734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 10332 Z= 0.319 Angle : 0.556 6.898 14064 Z= 0.291 Chirality : 0.048 0.144 1640 Planarity : 0.004 0.037 1792 Dihedral : 9.136 88.396 1644 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.30 % Allowed : 3.28 % Favored : 96.42 % Rotamer: Outliers : 5.30 % Allowed : 14.78 % 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: 0.02 (0.24), residues: 1340 helix: 0.51 (0.27), residues: 396 sheet: -0.98 (0.31), residues: 280 loop : 0.36 (0.26), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 101 HIS 0.005 0.002 HIS A 125 PHE 0.014 0.002 PHE C 304 TYR 0.014 0.002 TYR D 146 ARG 0.003 0.001 ARG A 30 *********************** 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 253 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 196 time to evaluate : 1.157 Fit side-chains REVERT: A 38 GLU cc_start: 0.6677 (mt-10) cc_final: 0.6476 (mt-10) REVERT: A 71 ASN cc_start: 0.7276 (t0) cc_final: 0.6774 (m-40) REVERT: A 89 LYS cc_start: 0.7107 (OUTLIER) cc_final: 0.6151 (mmtp) REVERT: A 119 GLU cc_start: 0.6970 (tm-30) cc_final: 0.6522 (tm-30) REVERT: A 120 GLU cc_start: 0.7684 (tt0) cc_final: 0.6881 (mt-10) REVERT: A 140 LYS cc_start: 0.6729 (mmpt) cc_final: 0.6487 (mmmm) REVERT: A 159 LYS cc_start: 0.7164 (mmtt) cc_final: 0.6807 (mmtt) REVERT: A 247 THR cc_start: 0.8230 (t) cc_final: 0.7891 (p) REVERT: A 252 ARG cc_start: 0.7638 (mtt180) cc_final: 0.7281 (mpp80) REVERT: A 282 GLU cc_start: 0.7081 (tt0) cc_final: 0.6693 (mt-10) REVERT: A 289 LYS cc_start: 0.7912 (ttpt) cc_final: 0.7366 (ttmm) REVERT: B 38 GLU cc_start: 0.6676 (mt-10) cc_final: 0.6476 (mt-10) REVERT: B 71 ASN cc_start: 0.7275 (t0) cc_final: 0.6774 (m-40) REVERT: B 89 LYS cc_start: 0.7106 (OUTLIER) cc_final: 0.6151 (mmtp) REVERT: B 119 GLU cc_start: 0.6971 (tm-30) cc_final: 0.6523 (tm-30) REVERT: B 120 GLU cc_start: 0.7685 (tt0) cc_final: 0.6881 (mt-10) REVERT: B 140 LYS cc_start: 0.6728 (mmpt) cc_final: 0.6488 (mmmm) REVERT: B 159 LYS cc_start: 0.7151 (mmtt) cc_final: 0.6800 (mmtt) REVERT: B 247 THR cc_start: 0.8230 (t) cc_final: 0.7891 (p) REVERT: B 252 ARG cc_start: 0.7639 (mtt180) cc_final: 0.7282 (mpp80) REVERT: B 282 GLU cc_start: 0.7080 (tt0) cc_final: 0.6693 (mt-10) REVERT: B 289 LYS cc_start: 0.7912 (ttpt) cc_final: 0.7365 (ttmm) REVERT: C 38 GLU cc_start: 0.6678 (mt-10) cc_final: 0.6478 (mt-10) REVERT: C 71 ASN cc_start: 0.7278 (t0) cc_final: 0.6776 (m-40) REVERT: C 89 LYS cc_start: 0.7107 (OUTLIER) cc_final: 0.6152 (mmtp) REVERT: C 119 GLU cc_start: 0.6972 (tm-30) cc_final: 0.6525 (tm-30) REVERT: C 120 GLU cc_start: 0.7684 (tt0) cc_final: 0.6881 (mt-10) REVERT: C 140 LYS cc_start: 0.6727 (mmpt) cc_final: 0.6488 (mmmm) REVERT: C 159 LYS cc_start: 0.7150 (mmtt) cc_final: 0.6799 (mmtt) REVERT: C 247 THR cc_start: 0.8230 (t) cc_final: 0.7891 (p) REVERT: C 252 ARG cc_start: 0.7640 (mtt180) cc_final: 0.7279 (mpp80) REVERT: C 282 GLU cc_start: 0.7082 (tt0) cc_final: 0.6695 (mt-10) REVERT: C 289 LYS cc_start: 0.7914 (ttpt) cc_final: 0.7365 (ttmm) REVERT: D 38 GLU cc_start: 0.6677 (mt-10) cc_final: 0.6477 (mt-10) REVERT: D 71 ASN cc_start: 0.7275 (t0) cc_final: 0.6773 (m-40) REVERT: D 89 LYS cc_start: 0.7107 (OUTLIER) cc_final: 0.6153 (mmtp) REVERT: D 119 GLU cc_start: 0.6973 (tm-30) cc_final: 0.6524 (tm-30) REVERT: D 120 GLU cc_start: 0.7685 (tt0) cc_final: 0.6882 (mt-10) REVERT: D 140 LYS cc_start: 0.6725 (mmpt) cc_final: 0.6486 (mmmm) REVERT: D 159 LYS cc_start: 0.7149 (mmtt) cc_final: 0.6797 (mmtt) REVERT: D 247 THR cc_start: 0.8231 (t) cc_final: 0.7891 (p) REVERT: D 252 ARG cc_start: 0.7639 (mtt180) cc_final: 0.7282 (mpp80) REVERT: D 282 GLU cc_start: 0.7080 (tt0) cc_final: 0.6693 (mt-10) REVERT: D 289 LYS cc_start: 0.7912 (ttpt) cc_final: 0.7364 (ttmm) outliers start: 57 outliers final: 25 residues processed: 225 average time/residue: 1.3884 time to fit residues: 333.6865 Evaluate side-chains 205 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 176 time to evaluate : 1.301 ------------------------------------------------------------------------------- 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 108 ILE Chi-restraints excluded: chain A residue 143 VAL 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 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 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 193 THR 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 72 optimal weight: 5.9990 chunk 1 optimal weight: 0.6980 chunk 95 optimal weight: 0.8980 chunk 52 optimal weight: 0.6980 chunk 108 optimal weight: 0.6980 chunk 88 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 65 optimal weight: 3.9990 chunk 114 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 42 optimal weight: 4.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 195 HIS A 201 GLN ** B 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 195 HIS B 201 GLN ** C 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 195 HIS C 201 GLN ** D 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 195 HIS D 201 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.2863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10332 Z= 0.203 Angle : 0.494 6.192 14064 Z= 0.259 Chirality : 0.046 0.147 1640 Planarity : 0.004 0.037 1792 Dihedral : 8.899 89.498 1644 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.30 % Allowed : 2.99 % Favored : 96.72 % Rotamer: Outliers : 4.18 % Allowed : 16.64 % 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: -0.04 (0.24), residues: 1340 helix: 0.48 (0.26), residues: 420 sheet: -0.81 (0.32), residues: 272 loop : 0.18 (0.26), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 101 HIS 0.004 0.002 HIS A 125 PHE 0.013 0.002 PHE C 304 TYR 0.008 0.001 TYR D 146 ARG 0.002 0.000 ARG D 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 245 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 200 time to evaluate : 1.136 Fit side-chains REVERT: A 71 ASN cc_start: 0.7368 (t0) cc_final: 0.6905 (m-40) REVERT: A 119 GLU cc_start: 0.6999 (tm-30) cc_final: 0.6615 (tm-30) REVERT: A 120 GLU cc_start: 0.7654 (tt0) cc_final: 0.6897 (mt-10) REVERT: A 127 LYS cc_start: 0.6595 (mttt) cc_final: 0.5691 (mmtt) REVERT: A 140 LYS cc_start: 0.6730 (mmpt) cc_final: 0.6295 (mmpt) REVERT: A 159 LYS cc_start: 0.7119 (mmtt) cc_final: 0.6777 (mmtt) REVERT: A 229 THR cc_start: 0.7903 (t) cc_final: 0.7659 (m) REVERT: A 247 THR cc_start: 0.8133 (t) cc_final: 0.7910 (p) REVERT: A 252 ARG cc_start: 0.7694 (mtt180) cc_final: 0.7333 (mpp80) REVERT: A 282 GLU cc_start: 0.7008 (tt0) cc_final: 0.6650 (mt-10) REVERT: A 289 LYS cc_start: 0.7874 (ttpt) cc_final: 0.7331 (ttmm) REVERT: A 315 LYS cc_start: 0.7853 (OUTLIER) cc_final: 0.7528 (tttt) REVERT: A 324 SER cc_start: 0.7470 (t) cc_final: 0.7200 (p) REVERT: B 71 ASN cc_start: 0.7367 (t0) cc_final: 0.6906 (m-40) REVERT: B 119 GLU cc_start: 0.7000 (tm-30) cc_final: 0.6615 (tm-30) REVERT: B 120 GLU cc_start: 0.7656 (tt0) cc_final: 0.6898 (mt-10) REVERT: B 127 LYS cc_start: 0.6596 (mttt) cc_final: 0.5694 (mmtt) REVERT: B 140 LYS cc_start: 0.6727 (mmpt) cc_final: 0.6295 (mmpt) REVERT: B 159 LYS cc_start: 0.7119 (mmtt) cc_final: 0.6777 (mmtt) REVERT: B 229 THR cc_start: 0.7904 (t) cc_final: 0.7660 (m) REVERT: B 247 THR cc_start: 0.8134 (t) cc_final: 0.7910 (p) REVERT: B 252 ARG cc_start: 0.7694 (mtt180) cc_final: 0.7333 (mpp80) REVERT: B 282 GLU cc_start: 0.7009 (tt0) cc_final: 0.6651 (mt-10) REVERT: B 289 LYS cc_start: 0.7869 (ttpt) cc_final: 0.7320 (ttmm) REVERT: B 315 LYS cc_start: 0.7852 (OUTLIER) cc_final: 0.7526 (tttt) REVERT: B 324 SER cc_start: 0.7472 (t) cc_final: 0.7201 (p) REVERT: C 71 ASN cc_start: 0.7368 (t0) cc_final: 0.6906 (m-40) REVERT: C 119 GLU cc_start: 0.7001 (tm-30) cc_final: 0.6616 (tm-30) REVERT: C 120 GLU cc_start: 0.7654 (tt0) cc_final: 0.6898 (mt-10) REVERT: C 127 LYS cc_start: 0.6594 (mttt) cc_final: 0.5692 (mmtt) REVERT: C 140 LYS cc_start: 0.6728 (mmpt) cc_final: 0.6296 (mmpt) REVERT: C 159 LYS cc_start: 0.7119 (mmtt) cc_final: 0.6777 (mmtt) REVERT: C 229 THR cc_start: 0.7903 (t) cc_final: 0.7658 (m) REVERT: C 247 THR cc_start: 0.8133 (t) cc_final: 0.7908 (p) REVERT: C 252 ARG cc_start: 0.7694 (mtt180) cc_final: 0.7331 (mpp80) REVERT: C 282 GLU cc_start: 0.7010 (tt0) cc_final: 0.6651 (mt-10) REVERT: C 289 LYS cc_start: 0.7869 (ttpt) cc_final: 0.7320 (ttmm) REVERT: C 315 LYS cc_start: 0.7855 (OUTLIER) cc_final: 0.7530 (tttt) REVERT: C 324 SER cc_start: 0.7472 (t) cc_final: 0.7202 (p) REVERT: D 71 ASN cc_start: 0.7367 (t0) cc_final: 0.6904 (m-40) REVERT: D 119 GLU cc_start: 0.7001 (tm-30) cc_final: 0.6615 (tm-30) REVERT: D 120 GLU cc_start: 0.7655 (tt0) cc_final: 0.6899 (mt-10) REVERT: D 127 LYS cc_start: 0.6597 (mttt) cc_final: 0.5695 (mmtt) REVERT: D 140 LYS cc_start: 0.6726 (mmpt) cc_final: 0.6295 (mmpt) REVERT: D 159 LYS cc_start: 0.7117 (mmtt) cc_final: 0.6773 (mmtt) REVERT: D 229 THR cc_start: 0.7904 (t) cc_final: 0.7659 (m) REVERT: D 247 THR cc_start: 0.8134 (t) cc_final: 0.7909 (p) REVERT: D 252 ARG cc_start: 0.7694 (mtt180) cc_final: 0.7334 (mpp80) REVERT: D 282 GLU cc_start: 0.7008 (tt0) cc_final: 0.6650 (mt-10) REVERT: D 289 LYS cc_start: 0.7869 (ttpt) cc_final: 0.7319 (ttmm) REVERT: D 315 LYS cc_start: 0.7852 (OUTLIER) cc_final: 0.7528 (tttt) REVERT: D 324 SER cc_start: 0.7469 (t) cc_final: 0.7198 (p) outliers start: 45 outliers final: 24 residues processed: 221 average time/residue: 1.3624 time to fit residues: 322.0776 Evaluate side-chains 220 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 192 time to evaluate : 1.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 THR 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 315 LYS Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain B residue 43 THR 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 315 LYS Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain C residue 43 THR 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 315 LYS Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain D residue 43 THR 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 315 LYS Chi-restraints excluded: chain D residue 342 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 114 optimal weight: 2.9990 chunk 25 optimal weight: 0.6980 chunk 74 optimal weight: 9.9990 chunk 31 optimal weight: 3.9990 chunk 127 optimal weight: 0.9980 chunk 106 optimal weight: 3.9990 chunk 59 optimal weight: 0.3980 chunk 10 optimal weight: 0.5980 chunk 42 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 chunk 123 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 195 HIS A 201 GLN ** B 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 195 HIS B 201 GLN ** C 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 195 HIS C 201 GLN ** D 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 195 HIS D 201 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.2964 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= 0.196 Angle : 0.485 6.952 14064 Z= 0.253 Chirality : 0.046 0.146 1640 Planarity : 0.004 0.035 1792 Dihedral : 8.725 88.742 1644 Min Nonbonded Distance : 2.636 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.30 % Allowed : 2.99 % Favored : 96.72 % Rotamer: Outliers : 3.35 % Allowed : 17.10 % Favored : 79.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.01 (0.24), residues: 1340 helix: 0.63 (0.26), residues: 420 sheet: -1.04 (0.31), residues: 292 loop : 0.28 (0.27), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 101 HIS 0.003 0.002 HIS C 67 PHE 0.011 0.001 PHE D 304 TYR 0.007 0.001 TYR D 146 ARG 0.002 0.000 ARG A 30 *********************** 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 248 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 212 time to evaluate : 0.984 Fit side-chains REVERT: A 55 GLU cc_start: 0.6980 (mp0) cc_final: 0.6548 (mp0) REVERT: A 71 ASN cc_start: 0.7364 (t0) cc_final: 0.6913 (m-40) REVERT: A 89 LYS cc_start: 0.7047 (OUTLIER) cc_final: 0.6138 (mmtp) REVERT: A 119 GLU cc_start: 0.7054 (tm-30) cc_final: 0.6735 (tm-30) REVERT: A 120 GLU cc_start: 0.7657 (tt0) cc_final: 0.6980 (mt-10) REVERT: A 123 SER cc_start: 0.7563 (p) cc_final: 0.7146 (p) REVERT: A 127 LYS cc_start: 0.6457 (mttt) cc_final: 0.5632 (mmtt) REVERT: A 140 LYS cc_start: 0.6791 (mmpt) cc_final: 0.6322 (mmpt) REVERT: A 159 LYS cc_start: 0.7151 (mmtt) cc_final: 0.6803 (mmtt) REVERT: A 229 THR cc_start: 0.7920 (t) cc_final: 0.7675 (m) REVERT: A 247 THR cc_start: 0.8006 (t) cc_final: 0.7746 (p) REVERT: A 252 ARG cc_start: 0.7706 (mtt180) cc_final: 0.7144 (mpp80) REVERT: A 282 GLU cc_start: 0.7141 (tt0) cc_final: 0.6864 (tt0) REVERT: A 289 LYS cc_start: 0.7907 (ttpt) cc_final: 0.7377 (ttmm) REVERT: A 315 LYS cc_start: 0.7876 (OUTLIER) cc_final: 0.7505 (tttt) REVERT: A 324 SER cc_start: 0.7540 (t) cc_final: 0.7255 (p) REVERT: B 55 GLU cc_start: 0.6980 (mp0) cc_final: 0.6547 (mp0) REVERT: B 71 ASN cc_start: 0.7364 (t0) cc_final: 0.6914 (m-40) REVERT: B 89 LYS cc_start: 0.7075 (OUTLIER) cc_final: 0.6181 (mmtp) REVERT: B 119 GLU cc_start: 0.7055 (tm-30) cc_final: 0.6736 (tm-30) REVERT: B 120 GLU cc_start: 0.7659 (tt0) cc_final: 0.6980 (mt-10) REVERT: B 123 SER cc_start: 0.7562 (p) cc_final: 0.7146 (p) REVERT: B 127 LYS cc_start: 0.6460 (mttt) cc_final: 0.5635 (mmtt) REVERT: B 140 LYS cc_start: 0.6789 (mmpt) cc_final: 0.6321 (mmpt) REVERT: B 159 LYS cc_start: 0.7170 (mmtt) cc_final: 0.6823 (mmtt) REVERT: B 229 THR cc_start: 0.7921 (t) cc_final: 0.7678 (m) REVERT: B 247 THR cc_start: 0.8008 (t) cc_final: 0.7743 (p) REVERT: B 252 ARG cc_start: 0.7708 (mtt180) cc_final: 0.7146 (mpp80) REVERT: B 282 GLU cc_start: 0.7142 (tt0) cc_final: 0.6866 (tt0) REVERT: B 289 LYS cc_start: 0.7907 (ttpt) cc_final: 0.7376 (ttmm) REVERT: B 324 SER cc_start: 0.7540 (t) cc_final: 0.7253 (p) REVERT: C 55 GLU cc_start: 0.6979 (mp0) cc_final: 0.6547 (mp0) REVERT: C 71 ASN cc_start: 0.7364 (t0) cc_final: 0.6914 (m-40) REVERT: C 89 LYS cc_start: 0.7076 (OUTLIER) cc_final: 0.6181 (mmtp) REVERT: C 119 GLU cc_start: 0.7054 (tm-30) cc_final: 0.6734 (tm-30) REVERT: C 120 GLU cc_start: 0.7658 (tt0) cc_final: 0.6981 (mt-10) REVERT: C 123 SER cc_start: 0.7562 (p) cc_final: 0.7147 (p) REVERT: C 127 LYS cc_start: 0.6457 (mttt) cc_final: 0.5632 (mmtt) REVERT: C 140 LYS cc_start: 0.6789 (mmpt) cc_final: 0.6323 (mmpt) REVERT: C 159 LYS cc_start: 0.7171 (mmtt) cc_final: 0.6826 (mmtt) REVERT: C 229 THR cc_start: 0.7920 (t) cc_final: 0.7676 (m) REVERT: C 247 THR cc_start: 0.8006 (t) cc_final: 0.7759 (p) REVERT: C 252 ARG cc_start: 0.7703 (mtt180) cc_final: 0.7137 (mpp80) REVERT: C 282 GLU cc_start: 0.7142 (tt0) cc_final: 0.6866 (tt0) REVERT: C 289 LYS cc_start: 0.7907 (ttpt) cc_final: 0.7376 (ttmm) REVERT: C 315 LYS cc_start: 0.7878 (OUTLIER) cc_final: 0.7510 (tttt) REVERT: C 324 SER cc_start: 0.7542 (t) cc_final: 0.7257 (p) REVERT: D 55 GLU cc_start: 0.6983 (mp0) cc_final: 0.6549 (mp0) REVERT: D 71 ASN cc_start: 0.7364 (t0) cc_final: 0.6914 (m-40) REVERT: D 89 LYS cc_start: 0.7076 (OUTLIER) cc_final: 0.6182 (mmtp) REVERT: D 119 GLU cc_start: 0.7054 (tm-30) cc_final: 0.6736 (tm-30) REVERT: D 120 GLU cc_start: 0.7658 (tt0) cc_final: 0.6981 (mt-10) REVERT: D 123 SER cc_start: 0.7565 (p) cc_final: 0.7149 (p) REVERT: D 127 LYS cc_start: 0.6461 (mttt) cc_final: 0.5635 (mmtt) REVERT: D 140 LYS cc_start: 0.6789 (mmpt) cc_final: 0.6321 (mmpt) REVERT: D 159 LYS cc_start: 0.7150 (mmtt) cc_final: 0.6800 (mmtt) REVERT: D 229 THR cc_start: 0.7921 (t) cc_final: 0.7676 (m) REVERT: D 247 THR cc_start: 0.8006 (t) cc_final: 0.7742 (p) REVERT: D 252 ARG cc_start: 0.7706 (mtt180) cc_final: 0.7145 (mpp80) REVERT: D 282 GLU cc_start: 0.7141 (tt0) cc_final: 0.6864 (tt0) REVERT: D 289 LYS cc_start: 0.7961 (ttpt) cc_final: 0.7431 (ttmm) REVERT: D 315 LYS cc_start: 0.7874 (OUTLIER) cc_final: 0.7505 (tttt) REVERT: D 324 SER cc_start: 0.7539 (t) cc_final: 0.7253 (p) outliers start: 36 outliers final: 24 residues processed: 228 average time/residue: 1.4064 time to fit residues: 341.6783 Evaluate side-chains 239 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 208 time to evaluate : 1.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 52 MET Chi-restraints excluded: chain A residue 89 LYS Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 191 MET Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 315 LYS Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 52 MET Chi-restraints excluded: chain B residue 89 LYS Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 191 MET Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 52 MET Chi-restraints excluded: chain C residue 89 LYS Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 191 MET Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 315 LYS Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 52 MET Chi-restraints excluded: chain D residue 89 LYS Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 191 MET Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 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 14 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 93 optimal weight: 0.0470 chunk 107 optimal weight: 4.9990 chunk 71 optimal weight: 2.9990 chunk 127 optimal weight: 0.3980 chunk 79 optimal weight: 1.9990 chunk 77 optimal weight: 6.9990 chunk 58 optimal weight: 0.0570 chunk 78 optimal weight: 0.6980 chunk 50 optimal weight: 0.7980 overall best weight: 0.3996 ------------------------------------------------------------------------------- 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 B 48 ASN B 195 HIS B 201 GLN C 48 ASN C 195 HIS C 201 GLN D 48 ASN D 195 HIS D 201 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.3156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 10332 Z= 0.128 Angle : 0.450 6.068 14064 Z= 0.235 Chirality : 0.044 0.149 1640 Planarity : 0.003 0.035 1792 Dihedral : 8.360 88.687 1644 Min Nonbonded Distance : 2.640 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.30 % Allowed : 2.39 % Favored : 97.31 % Rotamer: Outliers : 2.23 % Allowed : 19.42 % Favored : 78.35 % 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: 0.91 (0.27), residues: 424 sheet: -1.01 (0.30), residues: 292 loop : 0.38 (0.28), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 101 HIS 0.004 0.002 HIS D 125 PHE 0.010 0.001 PHE B 304 TYR 0.008 0.001 TYR C 338 ARG 0.002 0.000 ARG A 341 *********************** 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 235 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 211 time to evaluate : 1.151 Fit side-chains REVERT: A 55 GLU cc_start: 0.6975 (mp0) cc_final: 0.6505 (mp0) REVERT: A 71 ASN cc_start: 0.7352 (t0) cc_final: 0.6915 (m-40) REVERT: A 89 LYS cc_start: 0.7019 (OUTLIER) cc_final: 0.6071 (mmtp) REVERT: A 119 GLU cc_start: 0.7115 (tm-30) cc_final: 0.6726 (tm-30) REVERT: A 120 GLU cc_start: 0.7670 (tt0) cc_final: 0.6951 (mt-10) REVERT: A 127 LYS cc_start: 0.6486 (mttt) cc_final: 0.5687 (mmtt) REVERT: A 140 LYS cc_start: 0.6751 (mmpt) cc_final: 0.6512 (mmmm) REVERT: A 159 LYS cc_start: 0.7070 (mmtt) cc_final: 0.6714 (mmtt) REVERT: A 229 THR cc_start: 0.7904 (t) cc_final: 0.7657 (m) REVERT: A 252 ARG cc_start: 0.7659 (mtt180) cc_final: 0.7121 (mpp80) REVERT: A 274 GLU cc_start: 0.7094 (tp30) cc_final: 0.6544 (mp0) REVERT: A 282 GLU cc_start: 0.7185 (tt0) cc_final: 0.6768 (mt-10) REVERT: A 289 LYS cc_start: 0.7840 (ttpt) cc_final: 0.7358 (ttmm) REVERT: A 324 SER cc_start: 0.7559 (t) cc_final: 0.7229 (p) REVERT: B 71 ASN cc_start: 0.7351 (t0) cc_final: 0.6915 (m-40) REVERT: B 89 LYS cc_start: 0.7018 (OUTLIER) cc_final: 0.6073 (mmtp) REVERT: B 119 GLU cc_start: 0.7118 (tm-30) cc_final: 0.6707 (tm-30) REVERT: B 120 GLU cc_start: 0.7671 (tt0) cc_final: 0.6955 (mt-10) REVERT: B 127 LYS cc_start: 0.6488 (mttt) cc_final: 0.5691 (mmtt) REVERT: B 140 LYS cc_start: 0.6751 (mmpt) cc_final: 0.6511 (mmmm) REVERT: B 159 LYS cc_start: 0.7072 (mmtt) cc_final: 0.6716 (mmtt) REVERT: B 229 THR cc_start: 0.7866 (t) cc_final: 0.7615 (m) REVERT: B 252 ARG cc_start: 0.7662 (mtt180) cc_final: 0.7123 (mpp80) REVERT: B 274 GLU cc_start: 0.7151 (tp30) cc_final: 0.6907 (mm-30) REVERT: B 282 GLU cc_start: 0.7202 (tt0) cc_final: 0.6784 (mt-10) REVERT: B 289 LYS cc_start: 0.7840 (ttpt) cc_final: 0.7359 (ttmm) REVERT: B 324 SER cc_start: 0.7558 (t) cc_final: 0.7226 (p) REVERT: C 55 GLU cc_start: 0.6976 (mp0) cc_final: 0.6505 (mp0) REVERT: C 71 ASN cc_start: 0.7351 (t0) cc_final: 0.6915 (m-40) REVERT: C 89 LYS cc_start: 0.7016 (OUTLIER) cc_final: 0.6070 (mmtp) REVERT: C 119 GLU cc_start: 0.7116 (tm-30) cc_final: 0.6726 (tm-30) REVERT: C 120 GLU cc_start: 0.7670 (tt0) cc_final: 0.6952 (mt-10) REVERT: C 127 LYS cc_start: 0.6487 (mttt) cc_final: 0.5689 (mmtt) REVERT: C 140 LYS cc_start: 0.6750 (mmpt) cc_final: 0.6512 (mmmm) REVERT: C 159 LYS cc_start: 0.7072 (mmtt) cc_final: 0.6716 (mmtt) REVERT: C 229 THR cc_start: 0.7921 (t) cc_final: 0.7668 (m) REVERT: C 252 ARG cc_start: 0.7661 (mtt180) cc_final: 0.7123 (mpp80) REVERT: C 274 GLU cc_start: 0.7092 (tp30) cc_final: 0.6541 (mp0) REVERT: C 282 GLU cc_start: 0.7188 (tt0) cc_final: 0.6771 (mt-10) REVERT: C 289 LYS cc_start: 0.7840 (ttpt) cc_final: 0.7358 (ttmm) REVERT: C 324 SER cc_start: 0.7561 (t) cc_final: 0.7230 (p) REVERT: D 55 GLU cc_start: 0.6977 (mp0) cc_final: 0.6506 (mp0) REVERT: D 71 ASN cc_start: 0.7351 (t0) cc_final: 0.6914 (m-40) REVERT: D 89 LYS cc_start: 0.7019 (OUTLIER) cc_final: 0.6072 (mmtp) REVERT: D 119 GLU cc_start: 0.7117 (tm-30) cc_final: 0.6727 (tm-30) REVERT: D 120 GLU cc_start: 0.7671 (tt0) cc_final: 0.6952 (mt-10) REVERT: D 127 LYS cc_start: 0.6487 (mttt) cc_final: 0.5689 (mmtt) REVERT: D 140 LYS cc_start: 0.6751 (mmpt) cc_final: 0.6512 (mmmm) REVERT: D 159 LYS cc_start: 0.7071 (mmtt) cc_final: 0.6714 (mmtt) REVERT: D 229 THR cc_start: 0.7865 (t) cc_final: 0.7614 (m) REVERT: D 252 ARG cc_start: 0.7661 (mtt180) cc_final: 0.7122 (mpp80) REVERT: D 274 GLU cc_start: 0.7093 (tp30) cc_final: 0.6543 (mp0) REVERT: D 282 GLU cc_start: 0.7184 (tt0) cc_final: 0.6769 (mt-10) REVERT: D 289 LYS cc_start: 0.7840 (ttpt) cc_final: 0.7357 (ttmm) REVERT: D 324 SER cc_start: 0.7552 (t) cc_final: 0.7223 (p) outliers start: 24 outliers final: 12 residues processed: 230 average time/residue: 1.3805 time to fit residues: 338.9854 Evaluate side-chains 219 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 203 time to evaluate : 1.130 ------------------------------------------------------------------------------- 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 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 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 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 193 THR 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 75 optimal weight: 0.2980 chunk 38 optimal weight: 3.9990 chunk 24 optimal weight: 4.9990 chunk 80 optimal weight: 4.9990 chunk 86 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 11 optimal weight: 5.9990 chunk 100 optimal weight: 1.9990 chunk 115 optimal weight: 0.7980 chunk 121 optimal weight: 2.9990 chunk 111 optimal weight: 0.8980 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 195 HIS A 201 GLN ** B 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 195 HIS B 201 GLN ** C 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 195 HIS C 201 GLN ** D 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 195 HIS D 201 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 moved from start: 0.3058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 10332 Z= 0.254 Angle : 0.507 6.926 14064 Z= 0.264 Chirality : 0.047 0.143 1640 Planarity : 0.004 0.035 1792 Dihedral : 8.575 84.745 1644 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.30 % Allowed : 2.69 % Favored : 97.01 % Rotamer: Outliers : 2.97 % Allowed : 18.96 % Favored : 78.07 % 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: 0.67 (0.26), residues: 420 sheet: -0.79 (0.32), residues: 272 loop : 0.28 (0.26), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 331 HIS 0.004 0.002 HIS D 125 PHE 0.011 0.002 PHE B 304 TYR 0.011 0.001 TYR A 146 ARG 0.003 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 236 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 204 time to evaluate : 1.041 Fit side-chains REVERT: A 55 GLU cc_start: 0.6915 (mp0) cc_final: 0.6528 (mp0) REVERT: A 71 ASN cc_start: 0.7394 (t0) cc_final: 0.6907 (m-40) REVERT: A 89 LYS cc_start: 0.7069 (OUTLIER) cc_final: 0.6116 (mmtp) REVERT: A 119 GLU cc_start: 0.7022 (tm-30) cc_final: 0.6655 (tm-30) REVERT: A 120 GLU cc_start: 0.7730 (tt0) cc_final: 0.6965 (mt-10) REVERT: A 123 SER cc_start: 0.7540 (p) cc_final: 0.7123 (p) REVERT: A 127 LYS cc_start: 0.6376 (mttt) cc_final: 0.5489 (mmtt) REVERT: A 140 LYS cc_start: 0.6781 (OUTLIER) cc_final: 0.6517 (mmmm) REVERT: A 159 LYS cc_start: 0.7059 (mmtt) cc_final: 0.6797 (mmtt) REVERT: A 252 ARG cc_start: 0.7736 (mtt180) cc_final: 0.7184 (mpp80) REVERT: A 282 GLU cc_start: 0.7063 (tt0) cc_final: 0.6694 (mt-10) REVERT: A 289 LYS cc_start: 0.7897 (ttpt) cc_final: 0.7390 (ttmm) REVERT: A 324 SER cc_start: 0.7580 (t) cc_final: 0.7301 (p) REVERT: B 55 GLU cc_start: 0.6915 (mp0) cc_final: 0.6528 (mp0) REVERT: B 71 ASN cc_start: 0.7393 (t0) cc_final: 0.6907 (m-40) REVERT: B 89 LYS cc_start: 0.7097 (OUTLIER) cc_final: 0.6150 (mmtp) REVERT: B 119 GLU cc_start: 0.7023 (tm-30) cc_final: 0.6654 (tm-30) REVERT: B 120 GLU cc_start: 0.7732 (tt0) cc_final: 0.6971 (mt-10) REVERT: B 123 SER cc_start: 0.7539 (p) cc_final: 0.7122 (p) REVERT: B 127 LYS cc_start: 0.6381 (mttt) cc_final: 0.5494 (mmtt) REVERT: B 140 LYS cc_start: 0.6816 (OUTLIER) cc_final: 0.6558 (mmmm) REVERT: B 159 LYS cc_start: 0.7060 (mmtt) cc_final: 0.6798 (mmtt) REVERT: B 252 ARG cc_start: 0.7739 (mtt180) cc_final: 0.7186 (mpp80) REVERT: B 282 GLU cc_start: 0.7065 (tt0) cc_final: 0.6695 (mt-10) REVERT: B 289 LYS cc_start: 0.7900 (ttpt) cc_final: 0.7392 (ttmm) REVERT: B 324 SER cc_start: 0.7578 (t) cc_final: 0.7297 (p) REVERT: C 55 GLU cc_start: 0.6915 (mp0) cc_final: 0.6527 (mp0) REVERT: C 71 ASN cc_start: 0.7393 (t0) cc_final: 0.6907 (m-40) REVERT: C 89 LYS cc_start: 0.7096 (OUTLIER) cc_final: 0.6150 (mmtp) REVERT: C 119 GLU cc_start: 0.7022 (tm-30) cc_final: 0.6652 (tm-30) REVERT: C 120 GLU cc_start: 0.7731 (tt0) cc_final: 0.6972 (mt-10) REVERT: C 123 SER cc_start: 0.7538 (p) cc_final: 0.7121 (p) REVERT: C 127 LYS cc_start: 0.6379 (mttt) cc_final: 0.5491 (mmtt) REVERT: C 140 LYS cc_start: 0.6777 (OUTLIER) cc_final: 0.6516 (mmmm) REVERT: C 159 LYS cc_start: 0.7074 (mmtt) cc_final: 0.6815 (mmtt) REVERT: C 252 ARG cc_start: 0.7736 (mtt180) cc_final: 0.7183 (mpp80) REVERT: C 282 GLU cc_start: 0.7065 (tt0) cc_final: 0.6696 (mt-10) REVERT: C 289 LYS cc_start: 0.7898 (ttpt) cc_final: 0.7390 (ttmm) REVERT: C 324 SER cc_start: 0.7579 (t) cc_final: 0.7301 (p) REVERT: D 55 GLU cc_start: 0.6916 (mp0) cc_final: 0.6529 (mp0) REVERT: D 71 ASN cc_start: 0.7394 (t0) cc_final: 0.6907 (m-40) REVERT: D 89 LYS cc_start: 0.7097 (OUTLIER) cc_final: 0.6151 (mmtp) REVERT: D 119 GLU cc_start: 0.7022 (tm-30) cc_final: 0.6652 (tm-30) REVERT: D 120 GLU cc_start: 0.7731 (tt0) cc_final: 0.6973 (mt-10) REVERT: D 123 SER cc_start: 0.7542 (p) cc_final: 0.7125 (p) REVERT: D 127 LYS cc_start: 0.6379 (mttt) cc_final: 0.5492 (mmtt) REVERT: D 140 LYS cc_start: 0.6816 (OUTLIER) cc_final: 0.6559 (mmmm) REVERT: D 159 LYS cc_start: 0.7059 (mmtt) cc_final: 0.6796 (mmtt) REVERT: D 252 ARG cc_start: 0.7736 (mtt180) cc_final: 0.7184 (mpp80) REVERT: D 282 GLU cc_start: 0.7064 (tt0) cc_final: 0.6694 (mt-10) REVERT: D 289 LYS cc_start: 0.7891 (ttpt) cc_final: 0.7379 (ttmm) REVERT: D 319 ILE cc_start: 0.7832 (OUTLIER) cc_final: 0.7476 (tp) REVERT: D 324 SER cc_start: 0.7574 (t) cc_final: 0.7296 (p) outliers start: 32 outliers final: 18 residues processed: 224 average time/residue: 1.4085 time to fit residues: 340.2046 Evaluate side-chains 226 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 199 time to evaluate : 1.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 LYS Chi-restraints excluded: chain A residue 140 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 140 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 140 LYS Chi-restraints excluded: chain C residue 143 VAL 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 140 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 319 ILE 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 118 optimal weight: 0.0980 chunk 121 optimal weight: 0.6980 chunk 71 optimal weight: 0.5980 chunk 51 optimal weight: 2.9990 chunk 93 optimal weight: 0.0170 chunk 36 optimal weight: 0.6980 chunk 107 optimal weight: 5.9990 chunk 112 optimal weight: 4.9990 chunk 77 optimal weight: 5.9990 chunk 125 optimal weight: 0.9980 chunk 76 optimal weight: 0.9980 overall best weight: 0.4218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 195 HIS A 201 GLN ** B 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 195 HIS B 201 GLN ** C 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 195 HIS C 201 GLN ** D 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 195 HIS D 201 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.3206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 10332 Z= 0.128 Angle : 0.455 7.186 14064 Z= 0.235 Chirality : 0.045 0.145 1640 Planarity : 0.003 0.035 1792 Dihedral : 8.213 83.780 1644 Min Nonbonded Distance : 2.636 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.30 % Allowed : 2.09 % Favored : 97.61 % Rotamer: Outliers : 2.79 % Allowed : 19.14 % Favored : 78.07 % 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: 0.26 (0.24), residues: 1340 helix: 0.96 (0.27), residues: 424 sheet: -0.97 (0.30), residues: 292 loop : 0.40 (0.28), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 101 HIS 0.003 0.001 HIS A 125 PHE 0.010 0.001 PHE B 325 TYR 0.007 0.001 TYR B 338 ARG 0.002 0.000 ARG B 341 *********************** 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 242 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 212 time to evaluate : 1.157 Fit side-chains REVERT: A 71 ASN cc_start: 0.7367 (t0) cc_final: 0.6929 (m-40) REVERT: A 89 LYS cc_start: 0.7056 (OUTLIER) cc_final: 0.6126 (mmtp) REVERT: A 119 GLU cc_start: 0.7118 (tm-30) cc_final: 0.6720 (tm-30) REVERT: A 120 GLU cc_start: 0.7692 (tt0) cc_final: 0.6969 (mt-10) REVERT: A 127 LYS cc_start: 0.6483 (mttt) cc_final: 0.5614 (mmtt) REVERT: A 140 LYS cc_start: 0.6776 (OUTLIER) cc_final: 0.6521 (mmmm) REVERT: A 159 LYS cc_start: 0.6970 (mmtt) cc_final: 0.6694 (mmtt) REVERT: A 229 THR cc_start: 0.7866 (m) cc_final: 0.7643 (m) REVERT: A 252 ARG cc_start: 0.7698 (mtt180) cc_final: 0.7165 (mpp80) REVERT: A 274 GLU cc_start: 0.7091 (tp30) cc_final: 0.6877 (mm-30) REVERT: A 282 GLU cc_start: 0.7185 (tt0) cc_final: 0.6781 (mt-10) REVERT: A 289 LYS cc_start: 0.7830 (ttpt) cc_final: 0.7342 (ttmm) REVERT: A 324 SER cc_start: 0.7612 (t) cc_final: 0.7273 (p) REVERT: B 71 ASN cc_start: 0.7367 (t0) cc_final: 0.6929 (m-40) REVERT: B 89 LYS cc_start: 0.7055 (OUTLIER) cc_final: 0.6128 (mmtp) REVERT: B 119 GLU cc_start: 0.7121 (tm-30) cc_final: 0.6723 (tm-30) REVERT: B 120 GLU cc_start: 0.7694 (tt0) cc_final: 0.6969 (mt-10) REVERT: B 127 LYS cc_start: 0.6486 (mttt) cc_final: 0.5617 (mmtt) REVERT: B 140 LYS cc_start: 0.6752 (OUTLIER) cc_final: 0.6512 (mmmm) REVERT: B 159 LYS cc_start: 0.6972 (mmtt) cc_final: 0.6695 (mmtt) REVERT: B 229 THR cc_start: 0.7863 (m) cc_final: 0.7641 (m) REVERT: B 252 ARG cc_start: 0.7699 (mtt180) cc_final: 0.7165 (mpp80) REVERT: B 274 GLU cc_start: 0.7133 (tp30) cc_final: 0.6886 (mm-30) REVERT: B 282 GLU cc_start: 0.7188 (tt0) cc_final: 0.6782 (mt-10) REVERT: B 289 LYS cc_start: 0.7830 (ttpt) cc_final: 0.7341 (ttmm) REVERT: B 324 SER cc_start: 0.7609 (t) cc_final: 0.7269 (p) REVERT: C 71 ASN cc_start: 0.7367 (t0) cc_final: 0.6928 (m-40) REVERT: C 89 LYS cc_start: 0.7056 (OUTLIER) cc_final: 0.6128 (mmtp) REVERT: C 119 GLU cc_start: 0.7119 (tm-30) cc_final: 0.6722 (tm-30) REVERT: C 120 GLU cc_start: 0.7692 (tt0) cc_final: 0.6970 (mt-10) REVERT: C 127 LYS cc_start: 0.6485 (mttt) cc_final: 0.5617 (mmtt) REVERT: C 140 LYS cc_start: 0.6775 (OUTLIER) cc_final: 0.6521 (mmmm) REVERT: C 159 LYS cc_start: 0.6971 (mmtt) cc_final: 0.6696 (mmtt) REVERT: C 229 THR cc_start: 0.7867 (m) cc_final: 0.7642 (m) REVERT: C 252 ARG cc_start: 0.7697 (mtt180) cc_final: 0.7163 (mpp80) REVERT: C 274 GLU cc_start: 0.7093 (tp30) cc_final: 0.6879 (mm-30) REVERT: C 282 GLU cc_start: 0.7186 (tt0) cc_final: 0.6781 (mt-10) REVERT: C 289 LYS cc_start: 0.7829 (ttpt) cc_final: 0.7340 (ttmm) REVERT: C 324 SER cc_start: 0.7610 (t) cc_final: 0.7271 (p) REVERT: D 71 ASN cc_start: 0.7367 (t0) cc_final: 0.6928 (m-40) REVERT: D 89 LYS cc_start: 0.7057 (OUTLIER) cc_final: 0.6129 (mmtp) REVERT: D 119 GLU cc_start: 0.7120 (tm-30) cc_final: 0.6723 (tm-30) REVERT: D 120 GLU cc_start: 0.7694 (tt0) cc_final: 0.6971 (mt-10) REVERT: D 127 LYS cc_start: 0.6485 (mttt) cc_final: 0.5616 (mmtt) REVERT: D 140 LYS cc_start: 0.6750 (OUTLIER) cc_final: 0.6514 (mmmm) REVERT: D 159 LYS cc_start: 0.6971 (mmtt) cc_final: 0.6694 (mmtt) REVERT: D 229 THR cc_start: 0.7864 (m) cc_final: 0.7641 (m) REVERT: D 252 ARG cc_start: 0.7699 (mtt180) cc_final: 0.7165 (mpp80) REVERT: D 274 GLU cc_start: 0.7089 (tp30) cc_final: 0.6878 (mm-30) REVERT: D 282 GLU cc_start: 0.7186 (tt0) cc_final: 0.6781 (mt-10) REVERT: D 289 LYS cc_start: 0.7830 (ttpt) cc_final: 0.7341 (ttmm) REVERT: D 324 SER cc_start: 0.7605 (t) cc_final: 0.7265 (p) outliers start: 30 outliers final: 12 residues processed: 228 average time/residue: 1.3153 time to fit residues: 320.9140 Evaluate side-chains 230 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 210 time to evaluate : 1.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 LYS Chi-restraints excluded: chain A residue 140 LYS Chi-restraints excluded: chain A residue 143 VAL 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 140 LYS Chi-restraints excluded: chain B residue 143 VAL 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 140 LYS Chi-restraints excluded: chain C residue 143 VAL 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 140 LYS Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 342 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 59 optimal weight: 5.9990 chunk 87 optimal weight: 3.9990 chunk 131 optimal weight: 4.9990 chunk 121 optimal weight: 0.7980 chunk 104 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 80 optimal weight: 0.8980 chunk 64 optimal weight: 0.6980 chunk 83 optimal weight: 5.9990 chunk 111 optimal weight: 0.0970 chunk 32 optimal weight: 4.9990 overall best weight: 1.0980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 195 HIS A 201 GLN ** B 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 195 HIS B 201 GLN ** C 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 195 HIS C 201 GLN ** D 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 195 HIS D 201 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.3166 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= 0.215 Angle : 0.487 7.300 14064 Z= 0.252 Chirality : 0.046 0.143 1640 Planarity : 0.004 0.035 1792 Dihedral : 8.323 80.240 1644 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.30 % Allowed : 2.99 % Favored : 96.72 % Rotamer: Outliers : 2.60 % Allowed : 18.87 % 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: 0.24 (0.24), residues: 1340 helix: 0.80 (0.26), residues: 420 sheet: -0.83 (0.32), residues: 272 loop : 0.38 (0.27), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 331 HIS 0.003 0.002 HIS D 125 PHE 0.010 0.002 PHE B 304 TYR 0.008 0.001 TYR D 146 ARG 0.003 0.000 ARG D 39 ********************** 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 222 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 194 time to evaluate : 1.316 Fit side-chains REVERT: A 71 ASN cc_start: 0.7345 (t0) cc_final: 0.6888 (m-40) REVERT: A 89 LYS cc_start: 0.7069 (OUTLIER) cc_final: 0.6151 (mmtp) REVERT: A 119 GLU cc_start: 0.7107 (tm-30) cc_final: 0.6730 (tm-30) REVERT: A 120 GLU cc_start: 0.7729 (tt0) cc_final: 0.6940 (mt-10) REVERT: A 140 LYS cc_start: 0.6798 (OUTLIER) cc_final: 0.6542 (mmmm) REVERT: A 159 LYS cc_start: 0.7043 (mmtt) cc_final: 0.6784 (mmtt) REVERT: A 229 THR cc_start: 0.7720 (m) cc_final: 0.7469 (m) REVERT: A 252 ARG cc_start: 0.7729 (mtt180) cc_final: 0.7153 (mpp80) REVERT: A 282 GLU cc_start: 0.7237 (tt0) cc_final: 0.6844 (mt-10) REVERT: A 289 LYS cc_start: 0.7929 (ttpt) cc_final: 0.7409 (ttmm) REVERT: A 324 SER cc_start: 0.7587 (t) cc_final: 0.7296 (p) REVERT: B 71 ASN cc_start: 0.7343 (t0) cc_final: 0.6888 (m-40) REVERT: B 89 LYS cc_start: 0.7070 (OUTLIER) cc_final: 0.6153 (mmtp) REVERT: B 119 GLU cc_start: 0.7109 (tm-30) cc_final: 0.6733 (tm-30) REVERT: B 120 GLU cc_start: 0.7731 (tt0) cc_final: 0.6940 (mt-10) REVERT: B 140 LYS cc_start: 0.6797 (OUTLIER) cc_final: 0.6541 (mmmm) REVERT: B 159 LYS cc_start: 0.7044 (mmtt) cc_final: 0.6786 (mmtt) REVERT: B 229 THR cc_start: 0.7720 (m) cc_final: 0.7469 (m) REVERT: B 252 ARG cc_start: 0.7732 (mtt180) cc_final: 0.7155 (mpp80) REVERT: B 282 GLU cc_start: 0.7238 (tt0) cc_final: 0.6843 (mt-10) REVERT: B 289 LYS cc_start: 0.7930 (ttpt) cc_final: 0.7411 (ttmm) REVERT: B 324 SER cc_start: 0.7589 (t) cc_final: 0.7298 (p) REVERT: C 71 ASN cc_start: 0.7345 (t0) cc_final: 0.6889 (m-40) REVERT: C 89 LYS cc_start: 0.7073 (OUTLIER) cc_final: 0.6154 (mmtp) REVERT: C 119 GLU cc_start: 0.7108 (tm-30) cc_final: 0.6731 (tm-30) REVERT: C 120 GLU cc_start: 0.7730 (tt0) cc_final: 0.6940 (mt-10) REVERT: C 140 LYS cc_start: 0.6796 (OUTLIER) cc_final: 0.6542 (mmmm) REVERT: C 159 LYS cc_start: 0.7042 (mmtt) cc_final: 0.6784 (mmtt) REVERT: C 229 THR cc_start: 0.7702 (m) cc_final: 0.7454 (m) REVERT: C 252 ARG cc_start: 0.7727 (mtt180) cc_final: 0.7149 (mpp80) REVERT: C 282 GLU cc_start: 0.7237 (tt0) cc_final: 0.6844 (mt-10) REVERT: C 289 LYS cc_start: 0.7930 (ttpt) cc_final: 0.7409 (ttmm) REVERT: C 324 SER cc_start: 0.7587 (t) cc_final: 0.7298 (p) REVERT: D 71 ASN cc_start: 0.7344 (t0) cc_final: 0.6887 (m-40) REVERT: D 89 LYS cc_start: 0.7072 (OUTLIER) cc_final: 0.6155 (mmtp) REVERT: D 119 GLU cc_start: 0.7108 (tm-30) cc_final: 0.6731 (tm-30) REVERT: D 120 GLU cc_start: 0.7731 (tt0) cc_final: 0.6941 (mt-10) REVERT: D 140 LYS cc_start: 0.6793 (OUTLIER) cc_final: 0.6540 (mmmm) REVERT: D 159 LYS cc_start: 0.7043 (mmtt) cc_final: 0.6785 (mmtt) REVERT: D 229 THR cc_start: 0.7720 (m) cc_final: 0.7470 (m) REVERT: D 252 ARG cc_start: 0.7730 (mtt180) cc_final: 0.7153 (mpp80) REVERT: D 282 GLU cc_start: 0.7237 (tt0) cc_final: 0.6845 (mt-10) REVERT: D 289 LYS cc_start: 0.7931 (ttpt) cc_final: 0.7409 (ttmm) REVERT: D 324 SER cc_start: 0.7590 (t) cc_final: 0.7295 (p) outliers start: 28 outliers final: 13 residues processed: 206 average time/residue: 1.4606 time to fit residues: 320.4485 Evaluate side-chains 210 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 189 time to evaluate : 1.165 ------------------------------------------------------------------------------- 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 140 LYS Chi-restraints excluded: chain A residue 143 VAL 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 140 LYS Chi-restraints excluded: chain B residue 143 VAL 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 140 LYS Chi-restraints excluded: chain C residue 143 VAL 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 140 LYS Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 342 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 96 optimal weight: 0.8980 chunk 15 optimal weight: 2.9990 chunk 29 optimal weight: 0.6980 chunk 104 optimal weight: 3.9990 chunk 43 optimal weight: 0.7980 chunk 107 optimal weight: 0.8980 chunk 13 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 92 optimal weight: 5.9990 chunk 5 optimal weight: 5.9990 chunk 75 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 201 GLN ** B 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 201 GLN ** C 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 201 GLN ** D 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 201 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.112021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.095894 restraints weight = 11940.883| |-----------------------------------------------------------------------------| r_work (start): 0.3025 rms_B_bonded: 1.83 r_work: 0.2920 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2781 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.3243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10332 Z= 0.176 Angle : 0.473 7.571 14064 Z= 0.244 Chirality : 0.045 0.146 1640 Planarity : 0.003 0.035 1792 Dihedral : 8.218 78.012 1644 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.30 % Allowed : 2.39 % Favored : 97.31 % Rotamer: Outliers : 2.32 % Allowed : 19.24 % Favored : 78.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.85 (0.26), residues: 424 sheet: -0.84 (0.32), residues: 272 loop : 0.35 (0.27), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP D 101 HIS 0.003 0.001 HIS B 125 PHE 0.011 0.001 PHE B 325 TYR 0.007 0.001 TYR C 146 ARG 0.003 0.000 ARG C 39 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5024.48 seconds wall clock time: 91 minutes 3.74 seconds (5463.74 seconds total)