Starting phenix.real_space_refine on Tue Jun 24 07:11:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tax_25789/06_2025/7tax_25789.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tax_25789/06_2025/7tax_25789.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7tax_25789/06_2025/7tax_25789.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tax_25789/06_2025/7tax_25789.map" model { file = "/net/cci-nas-00/data/ceres_data/7tax_25789/06_2025/7tax_25789.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tax_25789/06_2025/7tax_25789.cif" } resolution = 2.8 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= 0.027 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 459 atoms to isotropic. 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 98 5.49 5 S 33 5.16 5 C 17215 2.51 5 N 5054 2.21 5 O 5455 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 27855 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 3145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3145 Classifications: {'peptide': 427} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 79} Link IDs: {'PTRANS': 24, 'TRANS': 402} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 291 Unresolved non-hydrogen angles: 369 Unresolved non-hydrogen dihedrals: 235 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLN:plan1': 9, 'ASP:plan': 11, 'TYR:plan': 1, 'ASN:plan1': 3, 'TRP:plan': 1, 'HIS:plan': 3, 'PHE:plan': 1, 'GLU:plan': 9, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 196 Chain: "B" Number of atoms: 2411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2411 Classifications: {'peptide': 306} Link IDs: {'PTRANS': 24, 'TRANS': 281} Chain breaks: 1 Chain: "C" Number of atoms: 1448 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 187, 1445 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 15, 'TRANS': 171} Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 54 Conformer: "B" Number of residues, atoms: 187, 1445 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 15, 'TRANS': 171} Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 54 bond proxies already assigned to first conformer: 1480 Chain: "D" Number of atoms: 2307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2307 Classifications: {'peptide': 298} Link IDs: {'PTRANS': 10, 'TRANS': 287} Chain breaks: 2 Chain: "E" Number of atoms: 2592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2592 Classifications: {'peptide': 335} Link IDs: {'PTRANS': 12, 'TRANS': 322} Chain: "F" Number of atoms: 2592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2592 Classifications: {'peptide': 335} Link IDs: {'PTRANS': 12, 'TRANS': 322} Chain: "G" Number of atoms: 2592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2592 Classifications: {'peptide': 335} Link IDs: {'PTRANS': 12, 'TRANS': 322} Chain: "H" Number of atoms: 2592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2592 Classifications: {'peptide': 335} Link IDs: {'PTRANS': 12, 'TRANS': 322} Chain: "I" Number of atoms: 2592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2592 Classifications: {'peptide': 335} Link IDs: {'PTRANS': 12, 'TRANS': 322} Chain: "J" Number of atoms: 1766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1766 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 16, 'TRANS': 211} Chain: "K" Number of atoms: 1766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1766 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 16, 'TRANS': 211} Chain: "M" Number of atoms: 1273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 1273 Classifications: {'DNA': 1, 'RNA': 60} Modifications used: {'5*END': 1, 'rna2p_pur': 11, 'rna2p_pyr': 17, 'rna3p_pur': 17, 'rna3p_pyr': 14} Link IDs: {'rna2p': 28, 'rna3p': 32} Unresolved chain link angles: 2 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {' C:plan': 1, ' C:plan2': 1} Unresolved non-hydrogen planarities: 11 Chain: "Y" Number of atoms: 390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 390 Classifications: {'DNA': 19} Link IDs: {'rna3p': 18} Chain: "X" Number of atoms: 389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 389 Classifications: {'DNA': 19} Link IDs: {'rna3p': 18} Time building chain proxies: 16.99, per 1000 atoms: 0.61 Number of scatterers: 27855 At special positions: 0 Unit cell: (130.2, 178.5, 152.25, 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 33 16.00 P 98 15.00 O 5455 8.00 N 5054 7.00 C 17215 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: 6.70 Conformation dependent library (CDL) restraints added in 3.6 seconds 6644 Ramachandran restraints generated. 3322 Oldfield, 0 Emsley, 3322 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6226 Finding SS restraints... Secondary structure from input PDB file: 102 helices and 55 sheets defined 35.1% alpha, 21.0% beta 18 base pairs and 57 stacking pairs defined. Time for finding SS restraints: 10.30 Creating SS restraints... Processing helix chain 'A' and resid 9 through 33 removed outlier: 3.518A pdb=" N LEU A 13 " --> pdb=" O THR A 9 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 45 removed outlier: 3.508A pdb=" N THR A 42 " --> pdb=" O ASP A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 61 removed outlier: 3.743A pdb=" N LEU A 53 " --> pdb=" O ARG A 49 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLY A 61 " --> pdb=" O ALA A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 100 removed outlier: 3.667A pdb=" N GLU A 99 " --> pdb=" O GLY A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 122 Processing helix chain 'A' and resid 129 through 136 removed outlier: 3.808A pdb=" N TRP A 133 " --> pdb=" O ASN A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 161 Processing helix chain 'A' and resid 162 through 164 No H-bonds generated for 'chain 'A' and resid 162 through 164' Processing helix chain 'A' and resid 195 through 212 Processing helix chain 'A' and resid 212 through 224 Processing helix chain 'A' and resid 247 through 251 Processing helix chain 'A' and resid 253 through 258 Processing helix chain 'A' and resid 285 through 290 Processing helix chain 'A' and resid 294 through 309 removed outlier: 4.018A pdb=" N ALA A 309 " --> pdb=" O GLN A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 341 Processing helix chain 'A' and resid 346 through 350 removed outlier: 3.551A pdb=" N ALA A 349 " --> pdb=" O GLY A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 364 removed outlier: 4.021A pdb=" N LEU A 361 " --> pdb=" O ASP A 357 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N TRP A 362 " --> pdb=" O ALA A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 371 removed outlier: 4.176A pdb=" N THR A 370 " --> pdb=" O LEU A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 383 Processing helix chain 'A' and resid 385 through 398 removed outlier: 3.934A pdb=" N ASN A 389 " --> pdb=" O ALA A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 408 Processing helix chain 'A' and resid 409 through 431 removed outlier: 3.904A pdb=" N ASP A 431 " --> pdb=" O GLU A 427 " (cutoff:3.500A) Processing helix chain 'B' and resid 33 through 48 removed outlier: 3.801A pdb=" N PHE B 37 " --> pdb=" O SER B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 121 Processing helix chain 'B' and resid 122 through 135 Processing helix chain 'B' and resid 165 through 180 Processing helix chain 'B' and resid 189 through 204 Processing helix chain 'B' and resid 208 through 216 Processing helix chain 'B' and resid 291 through 295 removed outlier: 3.638A pdb=" N VAL B 295 " --> pdb=" O PRO B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 302 removed outlier: 3.586A pdb=" N LEU B 301 " --> pdb=" O LEU B 298 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU B 302 " --> pdb=" O SER B 299 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 36 removed outlier: 3.773A pdb=" N LEU C 20 " --> pdb=" O PRO C 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 63 through 73 Processing helix chain 'C' and resid 74 through 77 Processing helix chain 'C' and resid 108 through 121 removed outlier: 3.949A pdb=" N LEU C 112 " --> pdb=" O ASN C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 131 Processing helix chain 'D' and resid 51 through 55 Processing helix chain 'D' and resid 130 through 148 Processing helix chain 'D' and resid 151 through 163 Processing helix chain 'D' and resid 208 through 224 Processing helix chain 'D' and resid 275 through 284 Processing helix chain 'D' and resid 302 through 304 No H-bonds generated for 'chain 'D' and resid 302 through 304' Processing helix chain 'D' and resid 322 through 332 removed outlier: 3.547A pdb=" N LEU D 326 " --> pdb=" O ASP D 322 " (cutoff:3.500A) Processing helix chain 'D' and resid 338 through 352 Processing helix chain 'E' and resid 51 through 58 removed outlier: 5.265A pdb=" N GLN E 56 " --> pdb=" O ASP E 53 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N GLU E 57 " --> pdb=" O ALA E 54 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N TRP E 58 " --> pdb=" O SER E 55 " (cutoff:3.500A) Processing helix chain 'E' and resid 82 through 92 removed outlier: 3.549A pdb=" N SER E 92 " --> pdb=" O ALA E 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 130 through 148 Processing helix chain 'E' and resid 151 through 163 Processing helix chain 'E' and resid 208 through 223 Processing helix chain 'E' and resid 275 through 284 Processing helix chain 'E' and resid 302 through 304 No H-bonds generated for 'chain 'E' and resid 302 through 304' Processing helix chain 'E' and resid 322 through 332 Processing helix chain 'E' and resid 338 through 352 Processing helix chain 'F' and resid 51 through 58 removed outlier: 3.555A pdb=" N SER F 55 " --> pdb=" O ARG F 52 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N GLN F 56 " --> pdb=" O ASP F 53 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N GLU F 57 " --> pdb=" O ALA F 54 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 92 Processing helix chain 'F' and resid 130 through 148 Processing helix chain 'F' and resid 151 through 163 Processing helix chain 'F' and resid 208 through 223 Processing helix chain 'F' and resid 275 through 284 Processing helix chain 'F' and resid 302 through 304 No H-bonds generated for 'chain 'F' and resid 302 through 304' Processing helix chain 'F' and resid 316 through 320 Processing helix chain 'F' and resid 322 through 332 Processing helix chain 'F' and resid 338 through 352 Processing helix chain 'G' and resid 82 through 92 Processing helix chain 'G' and resid 130 through 148 Processing helix chain 'G' and resid 151 through 163 Processing helix chain 'G' and resid 208 through 223 Processing helix chain 'G' and resid 275 through 284 Processing helix chain 'G' and resid 293 through 297 removed outlier: 3.673A pdb=" N LEU G 296 " --> pdb=" O GLU G 293 " (cutoff:3.500A) Processing helix chain 'G' and resid 302 through 304 No H-bonds generated for 'chain 'G' and resid 302 through 304' Processing helix chain 'G' and resid 322 through 332 Processing helix chain 'G' and resid 338 through 352 Processing helix chain 'H' and resid 82 through 92 removed outlier: 3.629A pdb=" N SER H 92 " --> pdb=" O ALA H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 130 through 148 Processing helix chain 'H' and resid 151 through 163 Processing helix chain 'H' and resid 208 through 223 Processing helix chain 'H' and resid 275 through 284 Processing helix chain 'H' and resid 302 through 304 No H-bonds generated for 'chain 'H' and resid 302 through 304' Processing helix chain 'H' and resid 322 through 332 Processing helix chain 'H' and resid 338 through 352 Processing helix chain 'I' and resid 82 through 91 Processing helix chain 'I' and resid 130 through 148 Processing helix chain 'I' and resid 150 through 163 Processing helix chain 'I' and resid 164 through 172 removed outlier: 6.503A pdb=" N ARG I 169 " --> pdb=" O PHE I 166 " (cutoff:3.500A) Processing helix chain 'I' and resid 208 through 224 Processing helix chain 'I' and resid 275 through 284 Processing helix chain 'I' and resid 302 through 304 No H-bonds generated for 'chain 'I' and resid 302 through 304' Processing helix chain 'I' and resid 322 through 332 Processing helix chain 'I' and resid 338 through 352 Processing helix chain 'J' and resid 47 through 70 removed outlier: 3.519A pdb=" N PHE J 55 " --> pdb=" O VAL J 51 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N ASP J 57 " --> pdb=" O ASP J 53 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N ILE J 58 " --> pdb=" O GLU J 54 " (cutoff:3.500A) Processing helix chain 'J' and resid 124 through 136 Processing helix chain 'J' and resid 140 through 147 Processing helix chain 'J' and resid 163 through 168 Processing helix chain 'J' and resid 180 through 188 Processing helix chain 'J' and resid 191 through 197 Processing helix chain 'J' and resid 211 through 222 Processing helix chain 'K' and resid 47 through 70 removed outlier: 3.515A pdb=" N ASP K 53 " --> pdb=" O SER K 49 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N ASP K 57 " --> pdb=" O ASP K 53 " (cutoff:3.500A) removed outlier: 5.578A pdb=" N ILE K 58 " --> pdb=" O GLU K 54 " (cutoff:3.500A) Processing helix chain 'K' and resid 124 through 136 Processing helix chain 'K' and resid 140 through 147 Processing helix chain 'K' and resid 163 through 168 Processing helix chain 'K' and resid 180 through 189 Processing helix chain 'K' and resid 191 through 199 Processing helix chain 'K' and resid 211 through 222 Processing sheet with id=AA1, first strand: chain 'A' and resid 64 through 66 Processing sheet with id=AA2, first strand: chain 'A' and resid 94 through 95 Processing sheet with id=AA3, first strand: chain 'A' and resid 191 through 192 removed outlier: 6.423A pdb=" N ALA A 191 " --> pdb=" O VAL B 280 " (cutoff:3.500A) removed outlier: 8.458A pdb=" N ASN B 282 " --> pdb=" O ALA A 191 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N PHE B 279 " --> pdb=" O ALA B 257 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N ALA B 257 " --> pdb=" O PHE B 279 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N GLU B 281 " --> pdb=" O TYR B 255 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N TYR B 255 " --> pdb=" O GLU B 281 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N LEU B 283 " --> pdb=" O ALA B 253 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N ALA B 253 " --> pdb=" O TRP B 316 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 180 through 182 removed outlier: 4.351A pdb=" N GLY A 186 " --> pdb=" O LEU A 182 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 232 through 233 Processing sheet with id=AA6, first strand: chain 'A' and resid 239 through 240 removed outlier: 4.541A pdb=" N PHE B 81 " --> pdb=" O ILE A 240 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 265 through 267 removed outlier: 5.727A pdb=" N LEU A 265 " --> pdb=" O TRP B 29 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 54 through 61 removed outlier: 3.852A pdb=" N VAL B 59 " --> pdb=" O LEU B 110 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N LEU B 110 " --> pdb=" O VAL B 59 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N ILE B 61 " --> pdb=" O SER B 108 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N SER B 108 " --> pdb=" O ILE B 61 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N ALA B 103 " --> pdb=" O ASN B 19 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASN B 19 " --> pdb=" O ALA B 103 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N LEU B 109 " --> pdb=" O PRO B 13 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N LEU B 111 " --> pdb=" O LEU B 11 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N LEU B 11 " --> pdb=" O LEU B 111 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N VAL B 113 " --> pdb=" O LEU B 9 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N LEU B 9 " --> pdb=" O VAL B 113 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N SER B 16 " --> pdb=" O LEU B 145 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 65 through 68 removed outlier: 4.898A pdb=" N ALA B 103 " --> pdb=" O ASN B 19 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASN B 19 " --> pdb=" O ALA B 103 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N LEU B 109 " --> pdb=" O PRO B 13 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N LEU B 111 " --> pdb=" O LEU B 11 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N LEU B 11 " --> pdb=" O LEU B 111 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N VAL B 113 " --> pdb=" O LEU B 9 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N LEU B 9 " --> pdb=" O VAL B 113 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA B 157 " --> pdb=" O LEU B 11 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 41 through 43 Processing sheet with id=AB2, first strand: chain 'C' and resid 97 through 98 Processing sheet with id=AB3, first strand: chain 'C' and resid 100 through 102 Processing sheet with id=AB4, first strand: chain 'D' and resid 31 through 33 removed outlier: 3.838A pdb=" N PHE D 355 " --> pdb=" O LEU D 31 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 38 through 39 Processing sheet with id=AB6, first strand: chain 'D' and resid 38 through 39 removed outlier: 3.969A pdb=" N VAL D 228 " --> pdb=" O VAL D 118 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N LEU D 229 " --> pdb=" O ILE D 184 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N VAL D 177 " --> pdb=" O ASP D 196 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N ASP D 196 " --> pdb=" O VAL D 177 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N VAL D 179 " --> pdb=" O ARG D 194 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N ARG D 194 " --> pdb=" O VAL D 179 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N ILE D 181 " --> pdb=" O ALA D 192 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N ALA D 192 " --> pdb=" O ILE D 181 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N HIS D 183 " --> pdb=" O ALA D 190 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 42 through 43 Processing sheet with id=AB8, first strand: chain 'D' and resid 64 through 66 Processing sheet with id=AB9, first strand: chain 'D' and resid 248 through 249 removed outlier: 3.764A pdb=" N THR D 264 " --> pdb=" O GLU D 249 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 285 through 287 Processing sheet with id=AC2, first strand: chain 'D' and resid 306 through 307 Processing sheet with id=AC3, first strand: chain 'E' and resid 127 through 128 removed outlier: 3.804A pdb=" N PHE E 355 " --> pdb=" O LEU E 31 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 38 through 39 removed outlier: 4.185A pdb=" N VAL E 228 " --> pdb=" O VAL E 118 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N LEU E 229 " --> pdb=" O ILE E 184 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ALA E 176 " --> pdb=" O ARG E 237 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N VAL E 177 " --> pdb=" O ASP E 196 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N ASP E 196 " --> pdb=" O VAL E 177 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N VAL E 179 " --> pdb=" O ARG E 194 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N ARG E 194 " --> pdb=" O VAL E 179 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ILE E 181 " --> pdb=" O ALA E 192 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N ALA E 192 " --> pdb=" O ILE E 181 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N HIS E 183 " --> pdb=" O ALA E 190 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 38 through 39 Processing sheet with id=AC6, first strand: chain 'E' and resid 63 through 70 removed outlier: 3.627A pdb=" N GLY E 70 " --> pdb=" O ASN E 94 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ASN E 94 " --> pdb=" O GLY E 70 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N ALA E 101 " --> pdb=" O VAL E 244 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 285 through 287 Processing sheet with id=AC8, first strand: chain 'E' and resid 306 through 307 removed outlier: 3.723A pdb=" N LYS E 312 " --> pdb=" O VAL E 307 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 127 through 128 Processing sheet with id=AD1, first strand: chain 'F' and resid 38 through 39 removed outlier: 3.530A pdb=" N VAL F 118 " --> pdb=" O VAL F 228 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N VAL F 228 " --> pdb=" O VAL F 118 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N LEU F 229 " --> pdb=" O ILE F 184 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ALA F 176 " --> pdb=" O ARG F 237 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N VAL F 177 " --> pdb=" O ASP F 196 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N ASP F 196 " --> pdb=" O VAL F 177 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N VAL F 179 " --> pdb=" O ARG F 194 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N ARG F 194 " --> pdb=" O VAL F 179 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ILE F 181 " --> pdb=" O ALA F 192 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N ALA F 192 " --> pdb=" O ILE F 181 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N HIS F 183 " --> pdb=" O ALA F 190 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 38 through 39 Processing sheet with id=AD3, first strand: chain 'F' and resid 63 through 70 removed outlier: 3.519A pdb=" N GLN F 96 " --> pdb=" O VAL F 68 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLY F 70 " --> pdb=" O ASN F 94 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ASN F 94 " --> pdb=" O GLY F 70 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N ALA F 101 " --> pdb=" O VAL F 244 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 285 through 287 Processing sheet with id=AD5, first strand: chain 'F' and resid 306 through 307 removed outlier: 3.695A pdb=" N LYS F 312 " --> pdb=" O VAL F 307 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'G' and resid 31 through 33 Processing sheet with id=AD7, first strand: chain 'G' and resid 38 through 39 removed outlier: 4.210A pdb=" N VAL G 228 " --> pdb=" O VAL G 118 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N LEU G 229 " --> pdb=" O ILE G 184 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N VAL G 177 " --> pdb=" O ASP G 196 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N ASP G 196 " --> pdb=" O VAL G 177 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N VAL G 179 " --> pdb=" O ARG G 194 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N ARG G 194 " --> pdb=" O VAL G 179 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ILE G 181 " --> pdb=" O ALA G 192 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N ALA G 192 " --> pdb=" O ILE G 181 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N HIS G 183 " --> pdb=" O ALA G 190 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 38 through 39 Processing sheet with id=AD9, first strand: chain 'G' and resid 63 through 70 removed outlier: 3.585A pdb=" N GLY G 70 " --> pdb=" O ASN G 94 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N ALA G 101 " --> pdb=" O VAL G 244 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'G' and resid 285 through 287 Processing sheet with id=AE2, first strand: chain 'G' and resid 306 through 307 Processing sheet with id=AE3, first strand: chain 'H' and resid 127 through 128 removed outlier: 3.692A pdb=" N PHE H 355 " --> pdb=" O LEU H 31 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'H' and resid 188 through 196 removed outlier: 5.000A pdb=" N VAL H 189 " --> pdb=" O ARG H 185 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N ARG H 185 " --> pdb=" O VAL H 189 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ARG H 191 " --> pdb=" O HIS H 183 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N LEU H 229 " --> pdb=" O ILE H 184 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N VAL H 228 " --> pdb=" O VAL H 118 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'H' and resid 63 through 70 removed outlier: 3.763A pdb=" N ASN H 94 " --> pdb=" O GLY H 70 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N ALA H 101 " --> pdb=" O VAL H 244 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'H' and resid 63 through 70 removed outlier: 3.763A pdb=" N ASN H 94 " --> pdb=" O GLY H 70 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N SER H 262 " --> pdb=" O LEU H 95 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N THR H 97 " --> pdb=" O SER H 262 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N THR H 264 " --> pdb=" O THR H 97 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ASP H 99 " --> pdb=" O THR H 264 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N THR H 264 " --> pdb=" O GLU H 249 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'H' and resid 285 through 287 Processing sheet with id=AE8, first strand: chain 'H' and resid 306 through 307 removed outlier: 3.754A pdb=" N LYS H 312 " --> pdb=" O VAL H 307 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'I' and resid 127 through 128 removed outlier: 3.511A pdb=" N ALA I 127 " --> pdb=" O ALA I 32 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'I' and resid 38 through 39 removed outlier: 4.282A pdb=" N LEU I 229 " --> pdb=" O ILE I 184 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ARG I 191 " --> pdb=" O HIS I 183 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'I' and resid 38 through 39 Processing sheet with id=AF3, first strand: chain 'I' and resid 63 through 70 removed outlier: 3.964A pdb=" N ASN I 94 " --> pdb=" O GLY I 70 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'I' and resid 243 through 244 removed outlier: 4.560A pdb=" N ALA I 101 " --> pdb=" O VAL I 244 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ALA J 38 " --> pdb=" O LEU J 30 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N TYR J 32 " --> pdb=" O GLU J 36 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N GLU J 36 " --> pdb=" O TYR J 32 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'I' and resid 285 through 287 Processing sheet with id=AF6, first strand: chain 'I' and resid 306 through 307 removed outlier: 3.700A pdb=" N LYS I 312 " --> pdb=" O VAL I 307 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'J' and resid 85 through 90 removed outlier: 5.232A pdb=" N LEU J 119 " --> pdb=" O THR J 113 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N SER J 99 " --> pdb=" O GLY J 120 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'K' and resid 4 through 6 removed outlier: 6.256A pdb=" N HIS K 26 " --> pdb=" O THR K 41 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N THR K 41 " --> pdb=" O HIS K 26 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N TRP K 28 " --> pdb=" O ILE K 39 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N ILE K 39 " --> pdb=" O TRP K 28 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N LEU K 30 " --> pdb=" O MET K 37 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'K' and resid 85 through 91 Processing sheet with id=AG1, first strand: chain 'K' and resid 99 through 100 1159 hydrogen bonds defined for protein. 3156 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 43 hydrogen bonds 82 hydrogen bond angles 0 basepair planarities 18 basepair parallelities 57 stacking parallelities Total time for adding SS restraints: 10.07 Time building geometry restraints manager: 7.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 4483 1.30 - 1.43: 7939 1.43 - 1.56: 15980 1.56 - 1.68: 195 1.68 - 1.81: 52 Bond restraints: 28649 Sorted by residual: bond pdb=" CA ALA G 271 " pdb=" C ALA G 271 " ideal model delta sigma weight residual 1.521 1.455 0.066 1.19e-02 7.06e+03 3.06e+01 bond pdb=" C HIS G 159 " pdb=" O HIS G 159 " ideal model delta sigma weight residual 1.237 1.175 0.061 1.19e-02 7.06e+03 2.66e+01 bond pdb=" CA HIS G 159 " pdb=" C HIS G 159 " ideal model delta sigma weight residual 1.524 1.471 0.052 1.29e-02 6.01e+03 1.63e+01 bond pdb=" CA ARG G 269 " pdb=" C ARG G 269 " ideal model delta sigma weight residual 1.530 1.474 0.055 1.44e-02 4.82e+03 1.48e+01 bond pdb=" C ALA G 158 " pdb=" O ALA G 158 " ideal model delta sigma weight residual 1.236 1.189 0.048 1.25e-02 6.40e+03 1.45e+01 ... (remaining 28644 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.34: 38820 2.34 - 4.68: 501 4.68 - 7.02: 53 7.02 - 9.36: 10 9.36 - 11.69: 2 Bond angle restraints: 39386 Sorted by residual: angle pdb=" N LEU G 161 " pdb=" CA LEU G 161 " pdb=" C LEU G 161 " ideal model delta sigma weight residual 114.04 102.35 11.69 1.24e+00 6.50e-01 8.89e+01 angle pdb=" O SER G 267 " pdb=" C SER G 267 " pdb=" N VAL G 268 " ideal model delta sigma weight residual 123.33 130.37 -7.04 1.21e+00 6.83e-01 3.39e+01 angle pdb=" C LEU G 161 " pdb=" N ALA G 162 " pdb=" CA ALA G 162 " ideal model delta sigma weight residual 120.68 111.67 9.01 1.70e+00 3.46e-01 2.81e+01 angle pdb=" N ILE D 286 " pdb=" CA ILE D 286 " pdb=" C ILE D 286 " ideal model delta sigma weight residual 113.20 108.23 4.97 9.60e-01 1.09e+00 2.68e+01 angle pdb=" CA SER G 267 " pdb=" C SER G 267 " pdb=" N VAL G 268 " ideal model delta sigma weight residual 116.01 108.52 7.49 1.51e+00 4.39e-01 2.46e+01 ... (remaining 39381 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.90: 16614 35.90 - 71.81: 474 71.81 - 107.71: 45 107.71 - 143.62: 1 143.62 - 179.52: 5 Dihedral angle restraints: 17139 sinusoidal: 7493 harmonic: 9646 Sorted by residual: dihedral pdb=" O4' U M 33 " pdb=" C1' U M 33 " pdb=" N1 U M 33 " pdb=" C2 U M 33 " ideal model delta sinusoidal sigma weight residual 200.00 55.78 144.22 1 1.50e+01 4.44e-03 7.73e+01 dihedral pdb=" O4' U M 21 " pdb=" C1' U M 21 " pdb=" N1 U M 21 " pdb=" C2 U M 21 " ideal model delta sinusoidal sigma weight residual 200.00 57.83 142.17 1 1.50e+01 4.44e-03 7.64e+01 dihedral pdb=" O4' C M 20 " pdb=" C1' C M 20 " pdb=" N1 C M 20 " pdb=" C2 C M 20 " ideal model delta sinusoidal sigma weight residual 232.00 52.48 179.52 1 1.70e+01 3.46e-03 6.64e+01 ... (remaining 17136 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 3645 0.051 - 0.103: 635 0.103 - 0.154: 140 0.154 - 0.205: 10 0.205 - 0.257: 2 Chirality restraints: 4432 Sorted by residual: chirality pdb=" CA ASP G 270 " pdb=" N ASP G 270 " pdb=" C ASP G 270 " pdb=" CB ASP G 270 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.65e+00 chirality pdb=" CB THR B 318 " pdb=" CA THR B 318 " pdb=" OG1 THR B 318 " pdb=" CG2 THR B 318 " both_signs ideal model delta sigma weight residual False 2.55 2.30 0.25 2.00e-01 2.50e+01 1.61e+00 chirality pdb=" CB THR A 301 " pdb=" CA THR A 301 " pdb=" OG1 THR A 301 " pdb=" CG2 THR A 301 " both_signs ideal model delta sigma weight residual False 2.55 2.35 0.20 2.00e-01 2.50e+01 9.74e-01 ... (remaining 4429 not shown) Planarity restraints: 4823 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A 71 " 0.051 5.00e-02 4.00e+02 7.71e-02 9.50e+00 pdb=" N PRO A 72 " -0.133 5.00e-02 4.00e+02 pdb=" CA PRO A 72 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO A 72 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA SER G 267 " 0.013 2.00e-02 2.50e+03 2.95e-02 8.72e+00 pdb=" C SER G 267 " -0.051 2.00e-02 2.50e+03 pdb=" O SER G 267 " 0.020 2.00e-02 2.50e+03 pdb=" N VAL G 268 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP A 364 " -0.048 5.00e-02 4.00e+02 7.36e-02 8.67e+00 pdb=" N PRO A 365 " 0.127 5.00e-02 4.00e+02 pdb=" CA PRO A 365 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 365 " -0.041 5.00e-02 4.00e+02 ... (remaining 4820 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 4673 2.77 - 3.30: 25724 3.30 - 3.83: 48928 3.83 - 4.37: 59225 4.37 - 4.90: 98107 Nonbonded interactions: 236657 Sorted by model distance: nonbonded pdb=" OH TYR A 179 " pdb=" OD2 ASP B 272 " model vdw 2.236 3.040 nonbonded pdb=" O VAL K 170 " pdb=" OG1 THR K 177 " model vdw 2.243 3.040 nonbonded pdb=" O GLY J 172 " pdb=" OG SER J 175 " model vdw 2.256 3.040 nonbonded pdb=" OH TYR F 324 " pdb=" O SER G 73 " model vdw 2.263 3.040 nonbonded pdb=" OH TYR H 324 " pdb=" O SER I 73 " model vdw 2.268 3.040 ... (remaining 236652 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 'D' selection = (chain 'E' and (resid 24 through 68 or resid 96 through 250 or resid 261 through \ 358)) selection = (chain 'F' and (resid 24 through 68 or resid 96 through 250 or resid 261 through \ 358)) selection = (chain 'G' and (resid 24 through 68 or resid 96 through 250 or resid 261 through \ 358)) selection = (chain 'H' and (resid 24 through 68 or resid 96 through 250 or resid 261 through \ 358)) selection = (chain 'I' and (resid 24 through 68 or resid 96 through 250 or resid 261 through \ 358)) } ncs_group { reference = chain 'J' selection = chain 'K' } 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=0.37 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: 1.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.160 Construct map_model_manager: 0.020 Extract box with map and model: 0.990 Check model and map are aligned: 0.230 Set scattering table: 0.260 Process input model: 69.370 Find NCS groups from input model: 1.060 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 87.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5452 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 28649 Z= 0.173 Angle : 0.668 11.694 39386 Z= 0.369 Chirality : 0.042 0.257 4432 Planarity : 0.005 0.077 4823 Dihedral : 16.218 179.523 10913 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % 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: -0.99 (0.13), residues: 3322 helix: -0.02 (0.14), residues: 1078 sheet: 0.76 (0.21), residues: 540 loop : -1.58 (0.14), residues: 1704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP G 49 HIS 0.009 0.001 HIS K 25 PHE 0.023 0.001 PHE A 16 TYR 0.039 0.002 TYR G 304 ARG 0.009 0.001 ARG E 191 Details of bonding type rmsd hydrogen bonds : bond 0.18486 ( 1176) hydrogen bonds : angle 7.24627 ( 3238) covalent geometry : bond 0.00311 (28649) covalent geometry : angle 0.66807 (39386) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6644 Ramachandran restraints generated. 3322 Oldfield, 0 Emsley, 3322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6644 Ramachandran restraints generated. 3322 Oldfield, 0 Emsley, 3322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 866 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 866 time to evaluate : 2.632 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 300 LEU cc_start: 0.6915 (mm) cc_final: 0.6585 (mt) REVERT: B 121 HIS cc_start: 0.5778 (m90) cc_final: 0.5506 (m-70) REVERT: D 276 SER cc_start: 0.6267 (m) cc_final: 0.6012 (t) REVERT: J 28 TRP cc_start: 0.5319 (m100) cc_final: 0.4436 (m100) outliers start: 0 outliers final: 4 residues processed: 866 average time/residue: 1.2012 time to fit residues: 1236.2970 Evaluate side-chains 514 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 510 time to evaluate : 2.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 ASP Chi-restraints excluded: chain B residue 215 ASP Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain F residue 106 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 283 optimal weight: 2.9990 chunk 254 optimal weight: 2.9990 chunk 141 optimal weight: 0.9980 chunk 86 optimal weight: 20.0000 chunk 171 optimal weight: 1.9990 chunk 136 optimal weight: 1.9990 chunk 263 optimal weight: 1.9990 chunk 101 optimal weight: 3.9990 chunk 160 optimal weight: 0.8980 chunk 196 optimal weight: 1.9990 chunk 305 optimal weight: 0.3980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 GLN A 129 ASN ** A 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 253 GLN A 255 ASN A 328 GLN A 416 GLN B 18 GLN B 21 ASN B 89 ASN B 104 HIS B 168 GLN B 282 ASN B 293 HIS C 19 GLN D 170 ASN D 281 ASN D 343 HIS F 186 GLN F 242 GLN G 160 ASN G 163 ASN G 260 GLN G 281 ASN H 96 GLN H 242 GLN I 146 ASN I 281 ASN J 26 HIS J 216 HIS ** K 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.151220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.101856 restraints weight = 48295.336| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 2.62 r_work: 0.3245 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3122 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3092 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3092 r_free = 0.3092 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3092 r_free = 0.3092 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3092 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.5586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 28649 Z= 0.237 Angle : 0.804 10.404 39386 Z= 0.418 Chirality : 0.046 0.294 4432 Planarity : 0.006 0.052 4823 Dihedral : 16.362 179.668 5032 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 4.29 % Allowed : 14.92 % Favored : 80.79 % 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: -0.67 (0.14), residues: 3322 helix: 0.39 (0.15), residues: 1051 sheet: 0.67 (0.21), residues: 550 loop : -1.38 (0.14), residues: 1721 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP H 193 HIS 0.012 0.002 HIS A 188 PHE 0.026 0.003 PHE H 150 TYR 0.029 0.003 TYR F 324 ARG 0.037 0.001 ARG H 191 Details of bonding type rmsd hydrogen bonds : bond 0.04227 ( 1176) hydrogen bonds : angle 5.23579 ( 3238) covalent geometry : bond 0.00531 (28649) covalent geometry : angle 0.80420 (39386) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6644 Ramachandran restraints generated. 3322 Oldfield, 0 Emsley, 3322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6644 Ramachandran restraints generated. 3322 Oldfield, 0 Emsley, 3322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 658 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 546 time to evaluate : 2.735 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 71 LYS cc_start: 0.6826 (tppp) cc_final: 0.6625 (tppp) REVERT: A 102 ASP cc_start: 0.7757 (p0) cc_final: 0.7548 (p0) REVERT: A 283 HIS cc_start: 0.8726 (OUTLIER) cc_final: 0.8206 (t-90) REVERT: A 296 GLU cc_start: 0.7807 (tp30) cc_final: 0.7387 (tp30) REVERT: A 299 ARG cc_start: 0.8399 (ttp80) cc_final: 0.8070 (ttp80) REVERT: A 300 LEU cc_start: 0.8355 (mm) cc_final: 0.7631 (mt) REVERT: A 321 ARG cc_start: 0.7550 (tpm170) cc_final: 0.5977 (tpm-80) REVERT: B 67 GLU cc_start: 0.7382 (tt0) cc_final: 0.7033 (tt0) REVERT: B 72 GLN cc_start: 0.8260 (pt0) cc_final: 0.7773 (tt0) REVERT: B 197 LEU cc_start: 0.8226 (tp) cc_final: 0.7953 (tm) REVERT: B 218 ARG cc_start: 0.7333 (ptt180) cc_final: 0.6887 (ptt180) REVERT: B 282 ASN cc_start: 0.8774 (OUTLIER) cc_final: 0.8340 (t0) REVERT: C 112 LEU cc_start: 0.0530 (tp) cc_final: 0.0313 (mm) REVERT: D 354 VAL cc_start: 0.8399 (t) cc_final: 0.8179 (t) REVERT: E 65 GLU cc_start: 0.8260 (mm-30) cc_final: 0.7815 (mm-30) REVERT: E 69 ARG cc_start: 0.7149 (ttp80) cc_final: 0.6691 (ttm170) REVERT: E 143 THR cc_start: 0.8676 (t) cc_final: 0.8445 (p) REVERT: E 146 ASN cc_start: 0.8157 (t0) cc_final: 0.7943 (t0) REVERT: E 206 LYS cc_start: 0.8219 (mtpp) cc_final: 0.7944 (pttp) REVERT: F 80 ASP cc_start: 0.8871 (t0) cc_final: 0.8642 (t0) REVERT: F 139 GLN cc_start: 0.8499 (tp40) cc_final: 0.8021 (tt0) REVERT: F 143 THR cc_start: 0.8968 (OUTLIER) cc_final: 0.8565 (p) REVERT: F 188 GLU cc_start: 0.7673 (mt-10) cc_final: 0.7016 (pm20) REVERT: F 301 VAL cc_start: 0.8760 (t) cc_final: 0.8465 (t) REVERT: H 38 ASP cc_start: 0.8710 (t0) cc_final: 0.8474 (t0) REVERT: H 139 GLN cc_start: 0.7857 (tp40) cc_final: 0.7614 (tp40) REVERT: H 143 THR cc_start: 0.8715 (t) cc_final: 0.8378 (p) REVERT: H 185 ARG cc_start: 0.8225 (ttp80) cc_final: 0.7603 (ttm-80) REVERT: H 186 GLN cc_start: 0.7798 (tm-30) cc_final: 0.7508 (mp10) REVERT: H 335 GLU cc_start: 0.7964 (OUTLIER) cc_final: 0.7443 (pm20) REVERT: I 136 LYS cc_start: 0.8717 (tptm) cc_final: 0.8367 (tptp) REVERT: I 320 LYS cc_start: 0.8441 (mmtm) cc_final: 0.8136 (mmmm) REVERT: I 324 TYR cc_start: 0.6992 (m-10) cc_final: 0.6665 (m-10) REVERT: J 134 GLU cc_start: 0.8029 (pp20) cc_final: 0.7786 (pp20) REVERT: J 163 THR cc_start: 0.7283 (p) cc_final: 0.7067 (p) REVERT: J 195 PHE cc_start: 0.8465 (t80) cc_final: 0.8231 (t80) REVERT: K 36 GLU cc_start: 0.7533 (tt0) cc_final: 0.7182 (tt0) REVERT: K 134 GLU cc_start: 0.7569 (tm-30) cc_final: 0.7043 (tm-30) REVERT: K 173 GLU cc_start: 0.6502 (tp30) cc_final: 0.6279 (mm-30) REVERT: K 209 LYS cc_start: 0.8075 (tppt) cc_final: 0.7692 (tppp) outliers start: 112 outliers final: 27 residues processed: 622 average time/residue: 1.2329 time to fit residues: 908.8715 Evaluate side-chains 414 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 383 time to evaluate : 3.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 THR Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 177 GLN Chi-restraints excluded: chain A residue 283 HIS Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 425 PHE Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 195 GLN Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 282 ASN Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 294 ASP Chi-restraints excluded: chain E residue 140 THR Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 233 VAL Chi-restraints excluded: chain F residue 143 THR Chi-restraints excluded: chain F residue 306 SER Chi-restraints excluded: chain G residue 67 SER Chi-restraints excluded: chain G residue 159 HIS Chi-restraints excluded: chain G residue 319 GLN Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain H residue 335 GLU Chi-restraints excluded: chain I residue 118 VAL Chi-restraints excluded: chain I residue 143 THR Chi-restraints excluded: chain J residue 48 SER Chi-restraints excluded: chain J residue 56 SER Chi-restraints excluded: chain K residue 123 VAL Chi-restraints excluded: chain K residue 151 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 77 optimal weight: 30.0000 chunk 306 optimal weight: 0.8980 chunk 231 optimal weight: 0.9980 chunk 305 optimal weight: 3.9990 chunk 238 optimal weight: 0.8980 chunk 78 optimal weight: 20.0000 chunk 174 optimal weight: 0.7980 chunk 276 optimal weight: 0.9990 chunk 131 optimal weight: 0.9980 chunk 45 optimal weight: 0.8980 chunk 257 optimal weight: 0.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 GLN A 324 GLN D 170 ASN D 183 HIS D 281 ASN E 102 ASN ** F 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 343 HIS G 96 GLN G 316 GLN G 343 HIS G 348 ASN ** H 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 96 GLN H 348 ASN I 96 GLN J 27 GLN ** J 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 5 HIS ** K 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.147966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.097991 restraints weight = 42263.911| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 2.43 r_work: 0.3180 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3056 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3057 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3057 r_free = 0.3057 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3057 r_free = 0.3057 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3057 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.6842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 28649 Z= 0.159 Angle : 0.632 10.740 39386 Z= 0.324 Chirality : 0.042 0.415 4432 Planarity : 0.005 0.052 4823 Dihedral : 15.992 178.995 5024 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 3.99 % Allowed : 19.71 % Favored : 76.30 % 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: -0.38 (0.14), residues: 3322 helix: 0.82 (0.15), residues: 1065 sheet: 0.76 (0.21), residues: 542 loop : -1.31 (0.14), residues: 1715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.001 TRP A 155 HIS 0.009 0.001 HIS B 305 PHE 0.019 0.002 PHE A 118 TYR 0.013 0.002 TYR I 133 ARG 0.017 0.001 ARG E 64 Details of bonding type rmsd hydrogen bonds : bond 0.03705 ( 1176) hydrogen bonds : angle 4.83606 ( 3238) covalent geometry : bond 0.00358 (28649) covalent geometry : angle 0.63204 (39386) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6644 Ramachandran restraints generated. 3322 Oldfield, 0 Emsley, 3322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6644 Ramachandran restraints generated. 3322 Oldfield, 0 Emsley, 3322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 502 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 398 time to evaluate : 2.966 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 PHE cc_start: 0.7342 (OUTLIER) cc_final: 0.6778 (m-80) REVERT: A 71 LYS cc_start: 0.6872 (tppp) cc_final: 0.6654 (tppp) REVERT: A 102 ASP cc_start: 0.7861 (p0) cc_final: 0.7634 (p0) REVERT: A 123 LEU cc_start: 0.5307 (mm) cc_final: 0.4174 (tp) REVERT: A 220 GLU cc_start: 0.8390 (tt0) cc_final: 0.7834 (tm-30) REVERT: A 256 ASN cc_start: 0.7086 (t0) cc_final: 0.6479 (m-40) REVERT: A 259 ARG cc_start: 0.7886 (pmm-80) cc_final: 0.7581 (mpp-170) REVERT: A 283 HIS cc_start: 0.8573 (OUTLIER) cc_final: 0.8126 (t-90) REVERT: A 296 GLU cc_start: 0.7908 (tp30) cc_final: 0.7079 (tp30) REVERT: A 299 ARG cc_start: 0.8392 (ttp80) cc_final: 0.7991 (ttp80) REVERT: A 300 LEU cc_start: 0.8192 (mm) cc_final: 0.7141 (mt) REVERT: A 321 ARG cc_start: 0.7223 (tpm170) cc_final: 0.6563 (tpm-80) REVERT: A 329 ILE cc_start: 0.7289 (OUTLIER) cc_final: 0.7043 (mp) REVERT: A 420 LYS cc_start: 0.8698 (mmmt) cc_final: 0.8490 (ptmt) REVERT: A 427 GLU cc_start: 0.7229 (tp30) cc_final: 0.7014 (tp30) REVERT: B 72 GLN cc_start: 0.8409 (pt0) cc_final: 0.8043 (tt0) REVERT: B 171 LYS cc_start: 0.8040 (mtpp) cc_final: 0.7742 (ttpp) REVERT: B 294 ARG cc_start: 0.7084 (mmp80) cc_final: 0.6622 (mpt180) REVERT: C 112 LEU cc_start: 0.0811 (tp) cc_final: 0.0480 (mm) REVERT: D 159 HIS cc_start: 0.7901 (m-70) cc_final: 0.7688 (m-70) REVERT: D 329 ASN cc_start: 0.7933 (p0) cc_final: 0.7701 (p0) REVERT: D 354 VAL cc_start: 0.8666 (t) cc_final: 0.8424 (t) REVERT: E 34 GLU cc_start: 0.8499 (tt0) cc_final: 0.8287 (tt0) REVERT: E 65 GLU cc_start: 0.7973 (mm-30) cc_final: 0.7583 (mm-30) REVERT: E 69 ARG cc_start: 0.7195 (ttp80) cc_final: 0.6767 (ttm170) REVERT: E 172 VAL cc_start: 0.8668 (OUTLIER) cc_final: 0.8356 (t) REVERT: E 203 ARG cc_start: 0.8442 (OUTLIER) cc_final: 0.8158 (mmm160) REVERT: F 34 GLU cc_start: 0.8160 (tt0) cc_final: 0.7782 (mt-10) REVERT: F 65 GLU cc_start: 0.8544 (mm-30) cc_final: 0.8288 (mm-30) REVERT: F 80 ASP cc_start: 0.8889 (t0) cc_final: 0.8579 (t70) REVERT: F 85 LYS cc_start: 0.8884 (mtmm) cc_final: 0.8656 (mtmm) REVERT: F 139 GLN cc_start: 0.8657 (tp40) cc_final: 0.8322 (tt0) REVERT: F 188 GLU cc_start: 0.8002 (mt-10) cc_final: 0.7275 (pm20) REVERT: F 301 VAL cc_start: 0.8896 (t) cc_final: 0.8626 (t) REVERT: F 304 TYR cc_start: 0.8812 (m-80) cc_final: 0.8611 (m-10) REVERT: G 65 GLU cc_start: 0.8811 (mt-10) cc_final: 0.8503 (mt-10) REVERT: G 96 GLN cc_start: 0.8789 (OUTLIER) cc_final: 0.8438 (pm20) REVERT: G 186 GLN cc_start: 0.8661 (mt0) cc_final: 0.8397 (mp10) REVERT: G 319 GLN cc_start: 0.6795 (OUTLIER) cc_final: 0.6471 (pt0) REVERT: H 139 GLN cc_start: 0.8341 (tp40) cc_final: 0.8064 (tp40) REVERT: H 143 THR cc_start: 0.8805 (OUTLIER) cc_final: 0.8556 (p) REVERT: H 185 ARG cc_start: 0.8234 (ttp80) cc_final: 0.7660 (ttm-80) REVERT: H 203 ARG cc_start: 0.7614 (mmm-85) cc_final: 0.7211 (mmm160) REVERT: I 78 THR cc_start: 0.7669 (m) cc_final: 0.7328 (p) REVERT: I 79 LYS cc_start: 0.8525 (ptmm) cc_final: 0.8172 (pmmt) REVERT: I 118 VAL cc_start: 0.8911 (OUTLIER) cc_final: 0.8685 (t) REVERT: I 206 LYS cc_start: 0.7814 (mtmm) cc_final: 0.7445 (mtmm) REVERT: I 320 LYS cc_start: 0.8659 (mmtm) cc_final: 0.8255 (mmmm) REVERT: I 324 TYR cc_start: 0.7502 (m-10) cc_final: 0.7135 (m-10) REVERT: J 54 GLU cc_start: 0.8647 (tp30) cc_final: 0.8391 (tm-30) REVERT: K 36 GLU cc_start: 0.7318 (tt0) cc_final: 0.6852 (tt0) REVERT: K 53 ASP cc_start: 0.9272 (m-30) cc_final: 0.9045 (m-30) REVERT: K 166 GLU cc_start: 0.6902 (pt0) cc_final: 0.6635 (pt0) REVERT: K 173 GLU cc_start: 0.6753 (tp30) cc_final: 0.6552 (mm-30) REVERT: K 209 LYS cc_start: 0.8221 (tppt) cc_final: 0.7842 (tppp) outliers start: 104 outliers final: 33 residues processed: 465 average time/residue: 1.3271 time to fit residues: 731.5387 Evaluate side-chains 373 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 331 time to evaluate : 3.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 PHE Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 76 ASP Chi-restraints excluded: chain A residue 119 LYS Chi-restraints excluded: chain A residue 177 GLN Chi-restraints excluded: chain A residue 283 HIS Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 431 ASP Chi-restraints excluded: chain B residue 16 SER Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain E residue 56 GLN Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 203 ARG Chi-restraints excluded: chain E residue 233 VAL Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain F residue 143 THR Chi-restraints excluded: chain G residue 96 GLN Chi-restraints excluded: chain G residue 319 GLN Chi-restraints excluded: chain H residue 31 LEU Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 74 ASN Chi-restraints excluded: chain H residue 143 THR Chi-restraints excluded: chain H residue 214 LEU Chi-restraints excluded: chain I residue 37 LEU Chi-restraints excluded: chain I residue 118 VAL Chi-restraints excluded: chain I residue 189 VAL Chi-restraints excluded: chain J residue 49 SER Chi-restraints excluded: chain J residue 152 LEU Chi-restraints excluded: chain J residue 198 TYR Chi-restraints excluded: chain K residue 102 ILE Chi-restraints excluded: chain K residue 123 VAL Chi-restraints excluded: chain K residue 151 VAL Chi-restraints excluded: chain K residue 158 GLU Chi-restraints excluded: chain K residue 170 VAL Chi-restraints excluded: chain K residue 218 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 222 optimal weight: 2.9990 chunk 193 optimal weight: 2.9990 chunk 14 optimal weight: 4.9990 chunk 257 optimal weight: 1.9990 chunk 210 optimal weight: 2.9990 chunk 131 optimal weight: 4.9990 chunk 318 optimal weight: 1.9990 chunk 17 optimal weight: 5.9990 chunk 39 optimal weight: 40.0000 chunk 86 optimal weight: 5.9990 chunk 76 optimal weight: 5.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 HIS A 324 GLN B 69 GLN B 194 GLN B 220 ASN B 282 ASN B 293 HIS D 170 ASN D 348 ASN E 102 ASN E 146 ASN E 348 ASN ** F 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 146 ASN ** H 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 96 GLN ** H 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 183 HIS I 242 GLN J 19 HIS J 216 HIS ** K 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.139230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.087454 restraints weight = 44875.812| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 2.80 r_work: 0.2923 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2800 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2813 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2813 r_free = 0.2813 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2813 r_free = 0.2813 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.2813 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.9613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.082 28649 Z= 0.305 Angle : 0.782 14.686 39386 Z= 0.402 Chirality : 0.049 0.517 4432 Planarity : 0.006 0.072 4823 Dihedral : 16.235 179.167 5024 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 5.44 % Allowed : 19.06 % Favored : 75.50 % 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: -0.70 (0.14), residues: 3322 helix: 0.44 (0.15), residues: 1071 sheet: 0.46 (0.21), residues: 525 loop : -1.36 (0.14), residues: 1726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B 247 HIS 0.010 0.001 HIS H 159 PHE 0.029 0.002 PHE A 425 TYR 0.024 0.003 TYR D 324 ARG 0.015 0.001 ARG E 64 Details of bonding type rmsd hydrogen bonds : bond 0.04301 ( 1176) hydrogen bonds : angle 5.19181 ( 3238) covalent geometry : bond 0.00702 (28649) covalent geometry : angle 0.78179 (39386) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6644 Ramachandran restraints generated. 3322 Oldfield, 0 Emsley, 3322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6644 Ramachandran restraints generated. 3322 Oldfield, 0 Emsley, 3322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 486 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 344 time to evaluate : 2.729 Fit side-chains revert: symmetry clash REVERT: A 71 LYS cc_start: 0.7768 (tppp) cc_final: 0.7217 (tppt) REVERT: A 102 ASP cc_start: 0.8250 (p0) cc_final: 0.7939 (p0) REVERT: A 220 GLU cc_start: 0.8628 (OUTLIER) cc_final: 0.7895 (tm-30) REVERT: A 246 THR cc_start: 0.8328 (p) cc_final: 0.8101 (p) REVERT: A 256 ASN cc_start: 0.8120 (t0) cc_final: 0.7845 (t0) REVERT: A 283 HIS cc_start: 0.8728 (OUTLIER) cc_final: 0.8154 (t-90) REVERT: A 296 GLU cc_start: 0.7928 (tp30) cc_final: 0.7169 (tp30) REVERT: A 299 ARG cc_start: 0.8496 (ttp80) cc_final: 0.8227 (ttp80) REVERT: A 300 LEU cc_start: 0.8407 (mm) cc_final: 0.7714 (mt) REVERT: A 307 PHE cc_start: 0.7924 (m-80) cc_final: 0.7697 (m-80) REVERT: A 329 ILE cc_start: 0.7890 (OUTLIER) cc_final: 0.7603 (mp) REVERT: A 331 ASP cc_start: 0.7362 (m-30) cc_final: 0.7143 (m-30) REVERT: A 343 LEU cc_start: 0.8244 (OUTLIER) cc_final: 0.8035 (pt) REVERT: A 347 TRP cc_start: 0.8296 (p-90) cc_final: 0.7794 (p-90) REVERT: A 427 GLU cc_start: 0.7769 (tp30) cc_final: 0.7351 (tm-30) REVERT: B 132 GLU cc_start: 0.8373 (OUTLIER) cc_final: 0.8004 (mp0) REVERT: B 171 LYS cc_start: 0.8457 (mtpp) cc_final: 0.8194 (ttpp) REVERT: B 294 ARG cc_start: 0.7608 (mmp80) cc_final: 0.7219 (mpt180) REVERT: C 112 LEU cc_start: 0.0695 (tp) cc_final: 0.0394 (mm) REVERT: D 169 ARG cc_start: 0.8607 (ttt90) cc_final: 0.7972 (ttm-80) REVERT: E 65 GLU cc_start: 0.8326 (mm-30) cc_final: 0.7957 (mm-30) REVERT: E 69 ARG cc_start: 0.7526 (ttp80) cc_final: 0.6870 (ttm170) REVERT: E 153 LEU cc_start: 0.8561 (OUTLIER) cc_final: 0.8348 (mt) REVERT: E 335 GLU cc_start: 0.8339 (tt0) cc_final: 0.8118 (mt-10) REVERT: F 34 GLU cc_start: 0.8510 (tt0) cc_final: 0.8138 (mt-10) REVERT: F 37 LEU cc_start: 0.8845 (OUTLIER) cc_final: 0.8534 (mp) REVERT: F 79 LYS cc_start: 0.9272 (tmmt) cc_final: 0.9026 (ptpt) REVERT: F 81 ARG cc_start: 0.8920 (OUTLIER) cc_final: 0.8611 (mmm-85) REVERT: F 188 GLU cc_start: 0.8547 (mt-10) cc_final: 0.7827 (pm20) REVERT: F 269 ARG cc_start: 0.8724 (ptp-110) cc_final: 0.8503 (ptp90) REVERT: F 335 GLU cc_start: 0.8712 (tt0) cc_final: 0.8426 (mt-10) REVERT: G 65 GLU cc_start: 0.9149 (mt-10) cc_final: 0.8841 (mt-10) REVERT: G 92 SER cc_start: 0.8736 (m) cc_final: 0.8432 (p) REVERT: G 186 GLN cc_start: 0.9047 (OUTLIER) cc_final: 0.8827 (mp10) REVERT: G 206 LYS cc_start: 0.8694 (ptpp) cc_final: 0.8387 (mtpp) REVERT: G 269 ARG cc_start: 0.8436 (OUTLIER) cc_final: 0.8065 (mtp180) REVERT: G 324 TYR cc_start: 0.9171 (m-80) cc_final: 0.8774 (m-80) REVERT: G 335 GLU cc_start: 0.8674 (tt0) cc_final: 0.8301 (pt0) REVERT: H 74 ASN cc_start: 0.8708 (OUTLIER) cc_final: 0.8251 (p0) REVERT: H 143 THR cc_start: 0.9115 (OUTLIER) cc_final: 0.8811 (p) REVERT: H 148 GLN cc_start: 0.7357 (mp10) cc_final: 0.7004 (pm20) REVERT: H 214 LEU cc_start: 0.9108 (OUTLIER) cc_final: 0.8908 (tt) REVERT: I 34 GLU cc_start: 0.8602 (tm-30) cc_final: 0.8219 (tm-30) REVERT: I 79 LYS cc_start: 0.8956 (ptmm) cc_final: 0.8586 (ptpt) REVERT: I 90 ILE cc_start: 0.8484 (OUTLIER) cc_final: 0.8267 (mt) REVERT: I 126 SER cc_start: 0.9084 (OUTLIER) cc_final: 0.8861 (t) REVERT: I 138 LEU cc_start: 0.9057 (OUTLIER) cc_final: 0.8786 (mm) REVERT: I 203 ARG cc_start: 0.7759 (mtp-110) cc_final: 0.7488 (mtm180) REVERT: I 269 ARG cc_start: 0.8485 (ptp-110) cc_final: 0.8262 (mtm-85) REVERT: I 320 LYS cc_start: 0.8975 (mmtm) cc_final: 0.8618 (mmmm) REVERT: J 48 SER cc_start: 0.9107 (OUTLIER) cc_final: 0.8870 (t) REVERT: J 54 GLU cc_start: 0.8971 (tp30) cc_final: 0.8762 (tp30) REVERT: K 53 ASP cc_start: 0.9122 (OUTLIER) cc_final: 0.8792 (m-30) REVERT: K 54 GLU cc_start: 0.6505 (OUTLIER) cc_final: 0.6010 (tm-30) REVERT: K 134 GLU cc_start: 0.8075 (OUTLIER) cc_final: 0.7460 (tp30) REVERT: K 150 GLU cc_start: 0.8569 (OUTLIER) cc_final: 0.7825 (pt0) outliers start: 142 outliers final: 37 residues processed: 448 average time/residue: 1.3298 time to fit residues: 696.3226 Evaluate side-chains 316 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 258 time to evaluate : 2.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 177 GLN Chi-restraints excluded: chain A residue 220 GLU Chi-restraints excluded: chain A residue 283 HIS Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 132 GLU Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 308 THR Chi-restraints excluded: chain E residue 29 SER Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 233 VAL Chi-restraints excluded: chain E residue 264 THR Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 81 ARG Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain G residue 186 GLN Chi-restraints excluded: chain G residue 269 ARG Chi-restraints excluded: chain G residue 319 GLN Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 31 LEU Chi-restraints excluded: chain H residue 43 LEU Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 74 ASN Chi-restraints excluded: chain H residue 96 GLN Chi-restraints excluded: chain H residue 143 THR Chi-restraints excluded: chain H residue 214 LEU Chi-restraints excluded: chain H residue 318 LYS Chi-restraints excluded: chain I residue 89 SER Chi-restraints excluded: chain I residue 90 ILE Chi-restraints excluded: chain I residue 99 ASP Chi-restraints excluded: chain I residue 126 SER Chi-restraints excluded: chain I residue 138 LEU Chi-restraints excluded: chain I residue 143 THR Chi-restraints excluded: chain I residue 189 VAL Chi-restraints excluded: chain I residue 326 LEU Chi-restraints excluded: chain J residue 6 ILE Chi-restraints excluded: chain J residue 48 SER Chi-restraints excluded: chain J residue 50 GLU Chi-restraints excluded: chain J residue 134 GLU Chi-restraints excluded: chain J residue 152 LEU Chi-restraints excluded: chain J residue 202 ASP Chi-restraints excluded: chain K residue 11 ILE Chi-restraints excluded: chain K residue 53 ASP Chi-restraints excluded: chain K residue 54 GLU Chi-restraints excluded: chain K residue 57 ASP Chi-restraints excluded: chain K residue 123 VAL Chi-restraints excluded: chain K residue 134 GLU Chi-restraints excluded: chain K residue 150 GLU Chi-restraints excluded: chain K residue 151 VAL Chi-restraints excluded: chain K residue 158 GLU Chi-restraints excluded: chain K residue 218 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 39 optimal weight: 7.9990 chunk 69 optimal weight: 5.9990 chunk 198 optimal weight: 0.5980 chunk 288 optimal weight: 0.6980 chunk 276 optimal weight: 0.7980 chunk 249 optimal weight: 6.9990 chunk 314 optimal weight: 0.0670 chunk 77 optimal weight: 50.0000 chunk 188 optimal weight: 3.9990 chunk 44 optimal weight: 0.1980 chunk 154 optimal weight: 0.9990 overall best weight: 0.4718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 HIS A 83 HIS A 177 GLN B 282 ASN B 305 HIS D 170 ASN E 129 ASN G 94 ASN ** I 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 27 GLN ** J 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.144003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.092001 restraints weight = 46707.890| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 2.52 r_work: 0.3035 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2912 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2932 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2932 r_free = 0.2932 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2932 r_free = 0.2932 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.2932 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.9695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 28649 Z= 0.122 Angle : 0.593 11.324 39386 Z= 0.304 Chirality : 0.041 0.329 4432 Planarity : 0.004 0.056 4823 Dihedral : 15.928 178.602 5024 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.91 % Favored : 96.06 % Rotamer: Outliers : 3.64 % Allowed : 21.89 % Favored : 74.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.14), residues: 3322 helix: 1.07 (0.15), residues: 1069 sheet: 0.70 (0.21), residues: 533 loop : -1.27 (0.14), residues: 1720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 414 HIS 0.008 0.001 HIS H 159 PHE 0.011 0.001 PHE B 284 TYR 0.022 0.001 TYR D 133 ARG 0.015 0.001 ARG E 64 Details of bonding type rmsd hydrogen bonds : bond 0.03279 ( 1176) hydrogen bonds : angle 4.74344 ( 3238) covalent geometry : bond 0.00272 (28649) covalent geometry : angle 0.59312 (39386) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6644 Ramachandran restraints generated. 3322 Oldfield, 0 Emsley, 3322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6644 Ramachandran restraints generated. 3322 Oldfield, 0 Emsley, 3322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 323 time to evaluate : 3.124 Fit side-chains revert: symmetry clash REVERT: A 71 LYS cc_start: 0.7509 (tppp) cc_final: 0.7000 (tppt) REVERT: A 220 GLU cc_start: 0.8614 (tt0) cc_final: 0.7984 (tm-30) REVERT: A 223 SER cc_start: 0.7682 (OUTLIER) cc_final: 0.7313 (p) REVERT: A 246 THR cc_start: 0.8293 (p) cc_final: 0.8088 (p) REVERT: A 283 HIS cc_start: 0.8582 (OUTLIER) cc_final: 0.8102 (t-90) REVERT: A 290 ASP cc_start: 0.8402 (p0) cc_final: 0.7531 (p0) REVERT: A 296 GLU cc_start: 0.7954 (tp30) cc_final: 0.7029 (tp30) REVERT: A 299 ARG cc_start: 0.8476 (ttp80) cc_final: 0.8194 (ttp80) REVERT: A 300 LEU cc_start: 0.8315 (mm) cc_final: 0.7736 (mt) REVERT: A 307 PHE cc_start: 0.7934 (m-80) cc_final: 0.7662 (m-80) REVERT: A 332 GLU cc_start: 0.6918 (OUTLIER) cc_final: 0.6705 (tp30) REVERT: A 343 LEU cc_start: 0.8150 (pt) cc_final: 0.7860 (pt) REVERT: A 347 TRP cc_start: 0.8248 (p-90) cc_final: 0.7718 (p-90) REVERT: A 427 GLU cc_start: 0.7912 (tp30) cc_final: 0.7480 (tm-30) REVERT: B 132 GLU cc_start: 0.8199 (OUTLIER) cc_final: 0.7901 (mp0) REVERT: B 171 LYS cc_start: 0.8460 (mtpp) cc_final: 0.8239 (ttpp) REVERT: B 294 ARG cc_start: 0.7542 (mmp80) cc_final: 0.7039 (mmp-170) REVERT: C 112 LEU cc_start: 0.0998 (tp) cc_final: 0.0648 (mm) REVERT: D 182 ASN cc_start: 0.7997 (m-40) cc_final: 0.7701 (m-40) REVERT: E 65 GLU cc_start: 0.8352 (mm-30) cc_final: 0.7888 (mm-30) REVERT: E 208 ASP cc_start: 0.7873 (t0) cc_final: 0.7672 (t0) REVERT: F 34 GLU cc_start: 0.8146 (tt0) cc_final: 0.7913 (mt-10) REVERT: F 38 ASP cc_start: 0.8869 (m-30) cc_final: 0.8647 (m-30) REVERT: F 65 GLU cc_start: 0.9113 (OUTLIER) cc_final: 0.8832 (mm-30) REVERT: F 79 LYS cc_start: 0.9128 (tmmt) cc_final: 0.8770 (tmmt) REVERT: F 80 ASP cc_start: 0.8956 (m-30) cc_final: 0.8645 (m-30) REVERT: F 85 LYS cc_start: 0.9060 (mtpp) cc_final: 0.8688 (mtmm) REVERT: F 188 GLU cc_start: 0.8569 (mt-10) cc_final: 0.7864 (pm20) REVERT: G 57 GLU cc_start: 0.8563 (mp0) cc_final: 0.8226 (pm20) REVERT: G 65 GLU cc_start: 0.9041 (mt-10) cc_final: 0.8789 (mm-30) REVERT: G 92 SER cc_start: 0.8097 (m) cc_final: 0.7771 (p) REVERT: G 96 GLN cc_start: 0.9163 (OUTLIER) cc_final: 0.8962 (pm20) REVERT: G 206 LYS cc_start: 0.8614 (ptpp) cc_final: 0.8377 (mtpp) REVERT: G 216 GLU cc_start: 0.8794 (OUTLIER) cc_final: 0.8449 (mt-10) REVERT: G 242 GLN cc_start: 0.9226 (mm-40) cc_final: 0.8882 (mm110) REVERT: G 319 GLN cc_start: 0.7835 (OUTLIER) cc_final: 0.7537 (pt0) REVERT: G 324 TYR cc_start: 0.9116 (m-80) cc_final: 0.8740 (m-80) REVERT: H 74 ASN cc_start: 0.8717 (OUTLIER) cc_final: 0.8265 (p0) REVERT: H 148 GLN cc_start: 0.7213 (mp10) cc_final: 0.6962 (pm20) REVERT: H 185 ARG cc_start: 0.8429 (ttp80) cc_final: 0.7850 (ttm-80) REVERT: H 186 GLN cc_start: 0.8735 (OUTLIER) cc_final: 0.8505 (mp10) REVERT: H 249 GLU cc_start: 0.9213 (mm-30) cc_final: 0.8976 (mm-30) REVERT: I 79 LYS cc_start: 0.8865 (ptmm) cc_final: 0.8563 (ptpt) REVERT: I 135 ASP cc_start: 0.9029 (m-30) cc_final: 0.8677 (m-30) REVERT: I 138 LEU cc_start: 0.8991 (tm) cc_final: 0.8752 (mm) REVERT: I 203 ARG cc_start: 0.7791 (mtp-110) cc_final: 0.7493 (mtm180) REVERT: I 326 LEU cc_start: 0.8342 (OUTLIER) cc_final: 0.8123 (mp) REVERT: J 54 GLU cc_start: 0.8917 (tp30) cc_final: 0.8715 (tp30) REVERT: J 167 LEU cc_start: 0.8996 (OUTLIER) cc_final: 0.8536 (mt) REVERT: J 206 ASN cc_start: 0.8825 (m-40) cc_final: 0.8345 (m110) REVERT: K 53 ASP cc_start: 0.9164 (OUTLIER) cc_final: 0.8858 (m-30) REVERT: K 54 GLU cc_start: 0.6750 (OUTLIER) cc_final: 0.6300 (tm-30) REVERT: K 73 ASP cc_start: 0.7841 (OUTLIER) cc_final: 0.7128 (m-30) REVERT: K 76 GLU cc_start: 0.6829 (mp0) cc_final: 0.6453 (mp0) REVERT: K 113 THR cc_start: 0.8244 (t) cc_final: 0.7984 (p) REVERT: K 134 GLU cc_start: 0.8073 (tm-30) cc_final: 0.7564 (tp30) REVERT: K 155 ASP cc_start: 0.6965 (p0) cc_final: 0.5524 (p0) REVERT: K 157 GLU cc_start: 0.7764 (pm20) cc_final: 0.7471 (pm20) REVERT: K 173 GLU cc_start: 0.7398 (tp30) cc_final: 0.7081 (mm-30) outliers start: 95 outliers final: 24 residues processed: 392 average time/residue: 1.8011 time to fit residues: 848.8974 Evaluate side-chains 307 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 268 time to evaluate : 6.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain A residue 283 HIS Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 332 GLU Chi-restraints excluded: chain B residue 132 GLU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 308 THR Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain E residue 29 SER Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 233 VAL Chi-restraints excluded: chain F residue 65 GLU Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain G residue 96 GLN Chi-restraints excluded: chain G residue 216 GLU Chi-restraints excluded: chain G residue 299 ILE Chi-restraints excluded: chain G residue 319 GLN Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 31 LEU Chi-restraints excluded: chain H residue 43 LEU Chi-restraints excluded: chain H residue 74 ASN Chi-restraints excluded: chain H residue 186 GLN Chi-restraints excluded: chain I residue 189 VAL Chi-restraints excluded: chain I residue 326 LEU Chi-restraints excluded: chain J residue 6 ILE Chi-restraints excluded: chain J residue 49 SER Chi-restraints excluded: chain J residue 64 ILE Chi-restraints excluded: chain J residue 94 LEU Chi-restraints excluded: chain J residue 152 LEU Chi-restraints excluded: chain J residue 167 LEU Chi-restraints excluded: chain K residue 11 ILE Chi-restraints excluded: chain K residue 53 ASP Chi-restraints excluded: chain K residue 54 GLU Chi-restraints excluded: chain K residue 73 ASP Chi-restraints excluded: chain K residue 123 VAL Chi-restraints excluded: chain K residue 135 LEU Chi-restraints excluded: chain K residue 151 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 120 optimal weight: 1.9990 chunk 72 optimal weight: 9.9990 chunk 71 optimal weight: 0.0270 chunk 11 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 chunk 192 optimal weight: 2.9990 chunk 126 optimal weight: 6.9990 chunk 41 optimal weight: 3.9990 chunk 299 optimal weight: 1.9990 chunk 12 optimal weight: 5.9990 chunk 326 optimal weight: 9.9990 overall best weight: 1.8046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 256 ASN ** A 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 324 GLN B 64 HIS B 82 ASN B 121 HIS B 220 ASN B 282 ASN D 170 ASN D 348 ASN E 102 ASN E 348 ASN F 310 GLN G 248 GLN I 102 ASN J 27 GLN ** J 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 154 HIS ** K 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.139279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.086073 restraints weight = 51389.445| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 2.97 r_work: 0.2921 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.2794 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2811 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2811 r_free = 0.2811 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2811 r_free = 0.2811 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.2811 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 1.0029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 28649 Z= 0.216 Angle : 0.643 9.610 39386 Z= 0.330 Chirality : 0.043 0.318 4432 Planarity : 0.005 0.092 4823 Dihedral : 16.024 179.211 5024 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 3.53 % Allowed : 22.12 % Favored : 74.35 % 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: -0.23 (0.14), residues: 3322 helix: 1.03 (0.16), residues: 1078 sheet: 0.61 (0.21), residues: 545 loop : -1.23 (0.15), residues: 1699 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 414 HIS 0.008 0.001 HIS H 159 PHE 0.026 0.002 PHE A 425 TYR 0.023 0.002 TYR D 133 ARG 0.018 0.001 ARG E 64 Details of bonding type rmsd hydrogen bonds : bond 0.03641 ( 1176) hydrogen bonds : angle 4.79119 ( 3238) covalent geometry : bond 0.00496 (28649) covalent geometry : angle 0.64252 (39386) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6644 Ramachandran restraints generated. 3322 Oldfield, 0 Emsley, 3322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6644 Ramachandran restraints generated. 3322 Oldfield, 0 Emsley, 3322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 289 time to evaluate : 2.861 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 LYS cc_start: 0.7993 (tppp) cc_final: 0.7482 (tppt) REVERT: A 220 GLU cc_start: 0.8648 (tt0) cc_final: 0.7987 (tm-30) REVERT: A 223 SER cc_start: 0.7903 (OUTLIER) cc_final: 0.7526 (p) REVERT: A 235 TYR cc_start: 0.8815 (m-80) cc_final: 0.8586 (m-80) REVERT: A 246 THR cc_start: 0.8412 (p) cc_final: 0.8173 (p) REVERT: A 296 GLU cc_start: 0.7866 (tp30) cc_final: 0.6993 (tp30) REVERT: A 299 ARG cc_start: 0.8515 (ttp80) cc_final: 0.8200 (ttp80) REVERT: A 300 LEU cc_start: 0.8346 (mm) cc_final: 0.7890 (mt) REVERT: A 331 ASP cc_start: 0.7544 (m-30) cc_final: 0.7199 (m-30) REVERT: A 343 LEU cc_start: 0.8173 (pt) cc_final: 0.7929 (pt) REVERT: A 347 TRP cc_start: 0.8354 (p-90) cc_final: 0.7776 (p-90) REVERT: A 427 GLU cc_start: 0.8109 (tp30) cc_final: 0.7595 (tm-30) REVERT: B 132 GLU cc_start: 0.8313 (OUTLIER) cc_final: 0.8048 (mp0) REVERT: B 171 LYS cc_start: 0.8474 (mtpp) cc_final: 0.8243 (ttpp) REVERT: B 288 GLU cc_start: 0.8908 (OUTLIER) cc_final: 0.8110 (tm-30) REVERT: B 294 ARG cc_start: 0.7602 (mmp80) cc_final: 0.7346 (mmp-170) REVERT: C 12 ASP cc_start: 0.5811 (t0) cc_final: 0.5461 (t70) REVERT: C 112 LEU cc_start: 0.0984 (tp) cc_final: 0.0603 (mm) REVERT: D 25 LEU cc_start: 0.8412 (OUTLIER) cc_final: 0.8118 (tt) REVERT: D 182 ASN cc_start: 0.8115 (m-40) cc_final: 0.7814 (m-40) REVERT: E 65 GLU cc_start: 0.8433 (mm-30) cc_final: 0.7951 (mm-30) REVERT: E 153 LEU cc_start: 0.8593 (OUTLIER) cc_final: 0.8380 (mt) REVERT: E 208 ASP cc_start: 0.7992 (t0) cc_final: 0.7771 (t0) REVERT: F 64 ARG cc_start: 0.8660 (ptt-90) cc_final: 0.8354 (ptt90) REVERT: F 188 GLU cc_start: 0.8622 (mt-10) cc_final: 0.8016 (pm20) REVERT: G 65 GLU cc_start: 0.9081 (mt-10) cc_final: 0.8739 (mt-10) REVERT: G 92 SER cc_start: 0.8617 (m) cc_final: 0.8311 (p) REVERT: G 206 LYS cc_start: 0.8725 (ptpp) cc_final: 0.8498 (mtpp) REVERT: G 318 LYS cc_start: 0.8750 (ttpp) cc_final: 0.8259 (tptm) REVERT: G 319 GLN cc_start: 0.8149 (OUTLIER) cc_final: 0.7466 (pt0) REVERT: G 324 TYR cc_start: 0.9189 (m-80) cc_final: 0.8830 (m-80) REVERT: G 335 GLU cc_start: 0.8365 (tt0) cc_final: 0.8123 (pt0) REVERT: G 351 ARG cc_start: 0.9279 (OUTLIER) cc_final: 0.7982 (ttt90) REVERT: H 74 ASN cc_start: 0.8688 (OUTLIER) cc_final: 0.8379 (p0) REVERT: H 185 ARG cc_start: 0.8500 (ttp80) cc_final: 0.7876 (ttm-80) REVERT: H 186 GLN cc_start: 0.8794 (OUTLIER) cc_final: 0.8435 (mp10) REVERT: I 79 LYS cc_start: 0.8968 (ptmm) cc_final: 0.8556 (ptpp) REVERT: I 135 ASP cc_start: 0.9119 (m-30) cc_final: 0.8780 (m-30) REVERT: I 138 LEU cc_start: 0.9077 (OUTLIER) cc_final: 0.8842 (mm) REVERT: I 203 ARG cc_start: 0.7956 (mtp-110) cc_final: 0.7648 (mtm180) REVERT: J 206 ASN cc_start: 0.8888 (m-40) cc_final: 0.8277 (m110) REVERT: K 37 MET cc_start: 0.7735 (ptm) cc_final: 0.6520 (ppp) REVERT: K 53 ASP cc_start: 0.9196 (m-30) cc_final: 0.8830 (m-30) REVERT: K 54 GLU cc_start: 0.6957 (OUTLIER) cc_final: 0.6494 (tm-30) REVERT: K 76 GLU cc_start: 0.7167 (mp0) cc_final: 0.6921 (mp0) REVERT: K 134 GLU cc_start: 0.8221 (tm-30) cc_final: 0.7738 (tp30) REVERT: K 155 ASP cc_start: 0.7248 (p0) cc_final: 0.6448 (p0) REVERT: K 157 GLU cc_start: 0.7715 (pm20) cc_final: 0.7071 (pm20) REVERT: K 158 GLU cc_start: 0.8191 (pt0) cc_final: 0.7620 (pm20) REVERT: K 173 GLU cc_start: 0.7511 (tp30) cc_final: 0.7001 (tp30) outliers start: 92 outliers final: 39 residues processed: 359 average time/residue: 1.3962 time to fit residues: 584.2900 Evaluate side-chains 324 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 274 time to evaluate : 2.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 THR Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain A residue 283 HIS Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 132 GLU Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain C residue 81 ASP Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain D residue 159 HIS Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 308 THR Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 29 SER Chi-restraints excluded: chain E residue 56 GLN Chi-restraints excluded: chain E residue 148 GLN Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 233 VAL Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain F residue 211 LEU Chi-restraints excluded: chain G residue 35 ARG Chi-restraints excluded: chain G residue 97 THR Chi-restraints excluded: chain G residue 299 ILE Chi-restraints excluded: chain G residue 319 GLN Chi-restraints excluded: chain G residue 351 ARG Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 31 LEU Chi-restraints excluded: chain H residue 43 LEU Chi-restraints excluded: chain H residue 74 ASN Chi-restraints excluded: chain H residue 186 GLN Chi-restraints excluded: chain H residue 302 GLU Chi-restraints excluded: chain I residue 138 LEU Chi-restraints excluded: chain I residue 189 VAL Chi-restraints excluded: chain J residue 6 ILE Chi-restraints excluded: chain J residue 64 ILE Chi-restraints excluded: chain J residue 94 LEU Chi-restraints excluded: chain J residue 125 LEU Chi-restraints excluded: chain J residue 152 LEU Chi-restraints excluded: chain K residue 11 ILE Chi-restraints excluded: chain K residue 54 GLU Chi-restraints excluded: chain K residue 57 ASP Chi-restraints excluded: chain K residue 123 VAL Chi-restraints excluded: chain K residue 151 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 279 optimal weight: 4.9990 chunk 49 optimal weight: 0.6980 chunk 81 optimal weight: 1.9990 chunk 161 optimal weight: 0.7980 chunk 302 optimal weight: 0.9980 chunk 269 optimal weight: 1.9990 chunk 160 optimal weight: 0.9980 chunk 97 optimal weight: 5.9990 chunk 197 optimal weight: 0.5980 chunk 113 optimal weight: 0.9980 chunk 4 optimal weight: 6.9990 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 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 324 GLN B 220 ASN B 282 ASN D 170 ASN ** F 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 310 GLN I 102 ASN ** I 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 27 GLN ** J 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.141917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.088178 restraints weight = 59433.596| |-----------------------------------------------------------------------------| r_work (start): 0.3122 rms_B_bonded: 2.86 r_work: 0.2999 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2997 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2997 r_free = 0.2997 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2997 r_free = 0.2997 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2997 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 1.0179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 28649 Z= 0.135 Angle : 0.595 10.611 39386 Z= 0.303 Chirality : 0.041 0.267 4432 Planarity : 0.004 0.073 4823 Dihedral : 15.892 178.338 5024 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 3.07 % Allowed : 23.27 % Favored : 73.66 % 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: -0.09 (0.14), residues: 3322 helix: 1.25 (0.16), residues: 1075 sheet: 0.70 (0.21), residues: 537 loop : -1.20 (0.15), residues: 1710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 414 HIS 0.005 0.001 HIS H 159 PHE 0.012 0.001 PHE A 20 TYR 0.025 0.001 TYR D 133 ARG 0.017 0.000 ARG E 64 Details of bonding type rmsd hydrogen bonds : bond 0.03184 ( 1176) hydrogen bonds : angle 4.65678 ( 3238) covalent geometry : bond 0.00306 (28649) covalent geometry : angle 0.59542 (39386) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6644 Ramachandran restraints generated. 3322 Oldfield, 0 Emsley, 3322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6644 Ramachandran restraints generated. 3322 Oldfield, 0 Emsley, 3322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 296 time to evaluate : 3.059 Fit side-chains revert: symmetry clash REVERT: A 71 LYS cc_start: 0.7819 (tppp) cc_final: 0.7305 (tppt) REVERT: A 220 GLU cc_start: 0.8624 (tt0) cc_final: 0.8069 (pp20) REVERT: A 223 SER cc_start: 0.7960 (OUTLIER) cc_final: 0.7560 (p) REVERT: A 283 HIS cc_start: 0.8699 (OUTLIER) cc_final: 0.8258 (t-90) REVERT: A 296 GLU cc_start: 0.7871 (tp30) cc_final: 0.6790 (tp30) REVERT: A 299 ARG cc_start: 0.8497 (ttp80) cc_final: 0.8215 (ttp80) REVERT: A 300 LEU cc_start: 0.8403 (mm) cc_final: 0.7457 (mt) REVERT: A 331 ASP cc_start: 0.7699 (m-30) cc_final: 0.7260 (m-30) REVERT: A 347 TRP cc_start: 0.8472 (p-90) cc_final: 0.7885 (p-90) REVERT: B 132 GLU cc_start: 0.8099 (OUTLIER) cc_final: 0.7734 (mp0) REVERT: B 171 LYS cc_start: 0.8447 (mtpp) cc_final: 0.8196 (ttpp) REVERT: B 268 ARG cc_start: 0.6568 (tpt-90) cc_final: 0.6213 (tpt-90) REVERT: B 288 GLU cc_start: 0.8643 (OUTLIER) cc_final: 0.7715 (tm-30) REVERT: B 294 ARG cc_start: 0.7730 (mmp80) cc_final: 0.7490 (mmp-170) REVERT: C 80 ARG cc_start: 0.7668 (mpt-90) cc_final: 0.7174 (ptp90) REVERT: C 112 LEU cc_start: 0.1095 (tp) cc_final: 0.0688 (mm) REVERT: D 25 LEU cc_start: 0.8399 (OUTLIER) cc_final: 0.8195 (tt) REVERT: D 182 ASN cc_start: 0.7909 (m-40) cc_final: 0.7617 (m-40) REVERT: D 249 GLU cc_start: 0.7095 (OUTLIER) cc_final: 0.6752 (mm-30) REVERT: E 65 GLU cc_start: 0.8256 (mm-30) cc_final: 0.7664 (mm-30) REVERT: E 69 ARG cc_start: 0.7527 (ttp80) cc_final: 0.6873 (tmm-80) REVERT: F 78 THR cc_start: 0.8756 (m) cc_final: 0.8377 (p) REVERT: F 85 LYS cc_start: 0.9167 (mtpp) cc_final: 0.8806 (mtmm) REVERT: F 188 GLU cc_start: 0.8513 (mt-10) cc_final: 0.7945 (pm20) REVERT: G 65 GLU cc_start: 0.8859 (mt-10) cc_final: 0.8624 (mt-10) REVERT: G 92 SER cc_start: 0.8242 (m) cc_final: 0.7898 (p) REVERT: G 302 GLU cc_start: 0.8790 (mm-30) cc_final: 0.8530 (mm-30) REVERT: G 318 LYS cc_start: 0.8624 (ttpp) cc_final: 0.8197 (tptt) REVERT: G 319 GLN cc_start: 0.8044 (OUTLIER) cc_final: 0.7396 (pt0) REVERT: G 324 TYR cc_start: 0.9066 (m-80) cc_final: 0.8772 (m-80) REVERT: G 335 GLU cc_start: 0.8069 (tt0) cc_final: 0.7817 (pt0) REVERT: G 351 ARG cc_start: 0.9176 (OUTLIER) cc_final: 0.7739 (ttt90) REVERT: H 74 ASN cc_start: 0.8553 (m110) cc_final: 0.8294 (p0) REVERT: H 102 ASN cc_start: 0.8673 (p0) cc_final: 0.8457 (p0) REVERT: H 185 ARG cc_start: 0.8411 (ttp80) cc_final: 0.7885 (ttm-80) REVERT: I 79 LYS cc_start: 0.8935 (ptmm) cc_final: 0.8552 (ptpp) REVERT: I 135 ASP cc_start: 0.9003 (m-30) cc_final: 0.8636 (m-30) REVERT: I 138 LEU cc_start: 0.9002 (tm) cc_final: 0.8765 (mm) REVERT: I 203 ARG cc_start: 0.7779 (mtp-110) cc_final: 0.7444 (mtm180) REVERT: J 157 GLU cc_start: 0.8419 (mp0) cc_final: 0.7975 (mm-30) REVERT: J 167 LEU cc_start: 0.8872 (OUTLIER) cc_final: 0.8583 (mm) REVERT: J 206 ASN cc_start: 0.8796 (m-40) cc_final: 0.8491 (m-40) REVERT: K 37 MET cc_start: 0.7623 (ptm) cc_final: 0.6592 (ppp) REVERT: K 53 ASP cc_start: 0.9149 (m-30) cc_final: 0.8890 (m-30) REVERT: K 54 GLU cc_start: 0.6978 (OUTLIER) cc_final: 0.6506 (tm-30) REVERT: K 134 GLU cc_start: 0.8152 (OUTLIER) cc_final: 0.7690 (tp30) REVERT: K 155 ASP cc_start: 0.7084 (p0) cc_final: 0.6830 (p0) REVERT: K 209 LYS cc_start: 0.8535 (ttmm) cc_final: 0.8203 (mtpt) outliers start: 80 outliers final: 30 residues processed: 356 average time/residue: 1.5708 time to fit residues: 665.6541 Evaluate side-chains 302 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 261 time to evaluate : 3.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 THR Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain A residue 283 HIS Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 132 GLU Chi-restraints excluded: chain B residue 220 ASN Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain C residue 81 ASP Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 249 GLU Chi-restraints excluded: chain D residue 294 ASP Chi-restraints excluded: chain D residue 308 THR Chi-restraints excluded: chain E residue 29 SER Chi-restraints excluded: chain E residue 56 GLN Chi-restraints excluded: chain E residue 148 GLN Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 233 VAL Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain F residue 211 LEU Chi-restraints excluded: chain G residue 97 THR Chi-restraints excluded: chain G residue 299 ILE Chi-restraints excluded: chain G residue 319 GLN Chi-restraints excluded: chain G residue 351 ARG Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 31 LEU Chi-restraints excluded: chain H residue 43 LEU Chi-restraints excluded: chain I residue 189 VAL Chi-restraints excluded: chain J residue 6 ILE Chi-restraints excluded: chain J residue 48 SER Chi-restraints excluded: chain J residue 125 LEU Chi-restraints excluded: chain J residue 152 LEU Chi-restraints excluded: chain J residue 167 LEU Chi-restraints excluded: chain K residue 11 ILE Chi-restraints excluded: chain K residue 54 GLU Chi-restraints excluded: chain K residue 123 VAL Chi-restraints excluded: chain K residue 134 GLU Chi-restraints excluded: chain K residue 151 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 306 optimal weight: 5.9990 chunk 79 optimal weight: 10.0000 chunk 12 optimal weight: 6.9990 chunk 261 optimal weight: 5.9990 chunk 253 optimal weight: 2.9990 chunk 275 optimal weight: 0.9980 chunk 170 optimal weight: 5.9990 chunk 263 optimal weight: 1.9990 chunk 179 optimal weight: 0.1980 chunk 224 optimal weight: 0.5980 chunk 201 optimal weight: 0.2980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 282 ASN D 170 ASN F 310 GLN ** I 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.141798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.088042 restraints weight = 53717.269| |-----------------------------------------------------------------------------| r_work (start): 0.3130 rms_B_bonded: 2.75 r_work: 0.3008 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2878 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2886 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2886 r_free = 0.2886 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2886 r_free = 0.2886 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2886 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 1.0282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 28649 Z= 0.137 Angle : 0.603 11.403 39386 Z= 0.307 Chirality : 0.041 0.256 4432 Planarity : 0.004 0.049 4823 Dihedral : 15.864 178.007 5024 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 2.95 % Allowed : 23.58 % Favored : 73.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.14), residues: 3322 helix: 1.30 (0.16), residues: 1076 sheet: 0.68 (0.21), residues: 547 loop : -1.16 (0.15), residues: 1699 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP A 414 HIS 0.005 0.001 HIS H 159 PHE 0.027 0.001 PHE A 425 TYR 0.025 0.001 TYR D 133 ARG 0.013 0.000 ARG A 306 Details of bonding type rmsd hydrogen bonds : bond 0.03201 ( 1176) hydrogen bonds : angle 4.60463 ( 3238) covalent geometry : bond 0.00311 (28649) covalent geometry : angle 0.60323 (39386) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6644 Ramachandran restraints generated. 3322 Oldfield, 0 Emsley, 3322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6644 Ramachandran restraints generated. 3322 Oldfield, 0 Emsley, 3322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 271 time to evaluate : 2.867 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 71 LYS cc_start: 0.7963 (tppp) cc_final: 0.7456 (tppt) REVERT: A 107 ASP cc_start: 0.8102 (m-30) cc_final: 0.7855 (m-30) REVERT: A 210 ARG cc_start: 0.8205 (OUTLIER) cc_final: 0.7800 (mtm180) REVERT: A 220 GLU cc_start: 0.8637 (tt0) cc_final: 0.8059 (pp20) REVERT: A 223 SER cc_start: 0.7964 (OUTLIER) cc_final: 0.7590 (p) REVERT: A 283 HIS cc_start: 0.8740 (OUTLIER) cc_final: 0.8309 (t-90) REVERT: A 296 GLU cc_start: 0.7900 (tp30) cc_final: 0.6775 (tp30) REVERT: A 299 ARG cc_start: 0.8483 (ttp80) cc_final: 0.8195 (ttp80) REVERT: A 300 LEU cc_start: 0.8402 (mm) cc_final: 0.7517 (mt) REVERT: A 331 ASP cc_start: 0.7568 (m-30) cc_final: 0.7151 (m-30) REVERT: A 332 GLU cc_start: 0.7807 (mm-30) cc_final: 0.7592 (mm-30) REVERT: A 347 TRP cc_start: 0.8511 (p-90) cc_final: 0.7850 (p-90) REVERT: A 424 MET cc_start: 0.8483 (mtp) cc_final: 0.8111 (mtp) REVERT: B 132 GLU cc_start: 0.8314 (OUTLIER) cc_final: 0.7946 (mp0) REVERT: B 201 ARG cc_start: 0.8856 (mtt180) cc_final: 0.8604 (mtt-85) REVERT: B 268 ARG cc_start: 0.6961 (tpt-90) cc_final: 0.6596 (tpt-90) REVERT: B 288 GLU cc_start: 0.8926 (OUTLIER) cc_final: 0.8095 (tm-30) REVERT: B 294 ARG cc_start: 0.7854 (mmp80) cc_final: 0.7652 (mmp-170) REVERT: C 80 ARG cc_start: 0.7609 (mpt-90) cc_final: 0.7124 (ptp90) REVERT: C 112 LEU cc_start: 0.1092 (tp) cc_final: 0.0668 (mm) REVERT: D 182 ASN cc_start: 0.8219 (m-40) cc_final: 0.7896 (m-40) REVERT: D 249 GLU cc_start: 0.7236 (OUTLIER) cc_final: 0.6888 (mm-30) REVERT: D 354 VAL cc_start: 0.9247 (OUTLIER) cc_final: 0.9032 (t) REVERT: E 65 GLU cc_start: 0.8439 (mm-30) cc_final: 0.7930 (mm-30) REVERT: E 69 ARG cc_start: 0.7805 (ttp80) cc_final: 0.7106 (tmm-80) REVERT: F 188 GLU cc_start: 0.8661 (mt-10) cc_final: 0.8151 (pm20) REVERT: G 96 GLN cc_start: 0.9172 (OUTLIER) cc_final: 0.8952 (pm20) REVERT: G 302 GLU cc_start: 0.8905 (mm-30) cc_final: 0.8701 (mm-30) REVERT: G 318 LYS cc_start: 0.8662 (ttpp) cc_final: 0.8259 (tptt) REVERT: G 319 GLN cc_start: 0.8118 (OUTLIER) cc_final: 0.7475 (pt0) REVERT: G 324 TYR cc_start: 0.9153 (m-80) cc_final: 0.8889 (m-80) REVERT: G 351 ARG cc_start: 0.9324 (OUTLIER) cc_final: 0.7960 (ttt90) REVERT: H 102 ASN cc_start: 0.8866 (p0) cc_final: 0.8654 (p0) REVERT: H 185 ARG cc_start: 0.8545 (ttp80) cc_final: 0.8053 (ttm-80) REVERT: I 65 GLU cc_start: 0.8809 (mt-10) cc_final: 0.8508 (tp30) REVERT: I 72 ILE cc_start: 0.9167 (OUTLIER) cc_final: 0.8956 (pp) REVERT: I 79 LYS cc_start: 0.8907 (ptmm) cc_final: 0.8571 (ptpp) REVERT: I 135 ASP cc_start: 0.9047 (m-30) cc_final: 0.8731 (m-30) REVERT: I 138 LEU cc_start: 0.9156 (OUTLIER) cc_final: 0.8952 (mm) REVERT: I 203 ARG cc_start: 0.7902 (mtp-110) cc_final: 0.7601 (mtm180) REVERT: J 206 ASN cc_start: 0.8783 (m-40) cc_final: 0.8505 (m-40) REVERT: K 37 MET cc_start: 0.7602 (ptm) cc_final: 0.6703 (ppp) REVERT: K 53 ASP cc_start: 0.9120 (m-30) cc_final: 0.8758 (m-30) REVERT: K 54 GLU cc_start: 0.7197 (OUTLIER) cc_final: 0.6739 (tm-30) REVERT: K 134 GLU cc_start: 0.8303 (tm-30) cc_final: 0.7833 (tp30) REVERT: K 157 GLU cc_start: 0.7465 (pm20) cc_final: 0.6614 (pm20) REVERT: K 158 GLU cc_start: 0.8058 (pt0) cc_final: 0.7387 (pm20) REVERT: K 209 LYS cc_start: 0.8572 (ttmm) cc_final: 0.8240 (mtpt) outliers start: 77 outliers final: 34 residues processed: 332 average time/residue: 1.6246 time to fit residues: 637.0221 Evaluate side-chains 308 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 261 time to evaluate : 4.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 THR Chi-restraints excluded: chain A residue 210 ARG Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain A residue 283 HIS Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 132 GLU Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain C residue 81 ASP Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 249 GLU Chi-restraints excluded: chain D residue 308 THR Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain E residue 29 SER Chi-restraints excluded: chain E residue 56 GLN Chi-restraints excluded: chain E residue 96 GLN Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 233 VAL Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain F residue 211 LEU Chi-restraints excluded: chain G residue 96 GLN Chi-restraints excluded: chain G residue 97 THR Chi-restraints excluded: chain G residue 299 ILE Chi-restraints excluded: chain G residue 308 THR Chi-restraints excluded: chain G residue 319 GLN Chi-restraints excluded: chain G residue 351 ARG Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 31 LEU Chi-restraints excluded: chain H residue 43 LEU Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain I residue 72 ILE Chi-restraints excluded: chain I residue 138 LEU Chi-restraints excluded: chain I residue 189 VAL Chi-restraints excluded: chain J residue 6 ILE Chi-restraints excluded: chain J residue 48 SER Chi-restraints excluded: chain J residue 125 LEU Chi-restraints excluded: chain J residue 152 LEU Chi-restraints excluded: chain K residue 11 ILE Chi-restraints excluded: chain K residue 54 GLU Chi-restraints excluded: chain K residue 57 ASP Chi-restraints excluded: chain K residue 123 VAL Chi-restraints excluded: chain K residue 190 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 167 optimal weight: 0.6980 chunk 116 optimal weight: 4.9990 chunk 225 optimal weight: 4.9990 chunk 211 optimal weight: 0.6980 chunk 36 optimal weight: 3.9990 chunk 154 optimal weight: 3.9990 chunk 158 optimal weight: 1.9990 chunk 164 optimal weight: 0.5980 chunk 285 optimal weight: 5.9990 chunk 246 optimal weight: 0.0970 chunk 160 optimal weight: 0.6980 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 256 ASN ** A 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 282 ASN D 170 ASN E 342 GLN ** F 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 310 GLN I 129 ASN ** I 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 194 ASN K 208 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.143366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.090075 restraints weight = 53623.541| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 2.74 r_work: 0.3045 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2914 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2917 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2917 r_free = 0.2917 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2917 r_free = 0.2917 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2917 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 1.0412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 28649 Z= 0.119 Angle : 0.594 10.187 39386 Z= 0.301 Chirality : 0.040 0.217 4432 Planarity : 0.004 0.052 4823 Dihedral : 15.772 177.262 5024 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 2.42 % Allowed : 23.85 % Favored : 73.73 % 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 (0.14), residues: 3322 helix: 1.38 (0.16), residues: 1077 sheet: 0.67 (0.21), residues: 562 loop : -1.23 (0.15), residues: 1683 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP A 414 HIS 0.004 0.001 HIS H 159 PHE 0.044 0.001 PHE A 425 TYR 0.024 0.001 TYR D 133 ARG 0.015 0.000 ARG A 306 Details of bonding type rmsd hydrogen bonds : bond 0.03044 ( 1176) hydrogen bonds : angle 4.51897 ( 3238) covalent geometry : bond 0.00269 (28649) covalent geometry : angle 0.59372 (39386) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6644 Ramachandran restraints generated. 3322 Oldfield, 0 Emsley, 3322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6644 Ramachandran restraints generated. 3322 Oldfield, 0 Emsley, 3322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 288 time to evaluate : 3.219 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 71 LYS cc_start: 0.7782 (tppp) cc_final: 0.7397 (tppt) REVERT: A 220 GLU cc_start: 0.8617 (tt0) cc_final: 0.8029 (pp20) REVERT: A 223 SER cc_start: 0.8028 (OUTLIER) cc_final: 0.7637 (p) REVERT: A 283 HIS cc_start: 0.8722 (OUTLIER) cc_final: 0.8330 (t-90) REVERT: A 296 GLU cc_start: 0.7962 (tp30) cc_final: 0.7027 (tp30) REVERT: A 299 ARG cc_start: 0.8523 (ttp80) cc_final: 0.8251 (ttp80) REVERT: A 300 LEU cc_start: 0.8437 (mm) cc_final: 0.7626 (mt) REVERT: A 331 ASP cc_start: 0.7541 (m-30) cc_final: 0.7082 (m-30) REVERT: A 347 TRP cc_start: 0.8468 (p-90) cc_final: 0.7805 (p-90) REVERT: A 424 MET cc_start: 0.8446 (mtp) cc_final: 0.8077 (mtp) REVERT: B 132 GLU cc_start: 0.8311 (OUTLIER) cc_final: 0.8058 (mp0) REVERT: C 79 LEU cc_start: 0.7562 (mp) cc_final: 0.7322 (mm) REVERT: C 80 ARG cc_start: 0.7592 (mpt-90) cc_final: 0.7128 (ptp90) REVERT: C 112 LEU cc_start: 0.0993 (tp) cc_final: 0.0573 (mm) REVERT: D 159 HIS cc_start: 0.7994 (OUTLIER) cc_final: 0.7733 (m-70) REVERT: D 169 ARG cc_start: 0.8364 (ttt90) cc_final: 0.8031 (ttm-80) REVERT: D 182 ASN cc_start: 0.8291 (m-40) cc_final: 0.8002 (m-40) REVERT: D 249 GLU cc_start: 0.7216 (OUTLIER) cc_final: 0.6868 (mm-30) REVERT: D 278 LYS cc_start: 0.8122 (ttmt) cc_final: 0.7846 (tttp) REVERT: E 65 GLU cc_start: 0.8406 (mm-30) cc_final: 0.7990 (mm-30) REVERT: E 69 ARG cc_start: 0.7673 (ttp80) cc_final: 0.7024 (tmm-80) REVERT: F 78 THR cc_start: 0.8773 (m) cc_final: 0.8434 (p) REVERT: F 85 LYS cc_start: 0.9216 (mtpp) cc_final: 0.8834 (mtmm) REVERT: F 188 GLU cc_start: 0.8634 (mt-10) cc_final: 0.8135 (pm20) REVERT: G 94 ASN cc_start: 0.8761 (m110) cc_final: 0.8378 (m-40) REVERT: G 96 GLN cc_start: 0.9067 (OUTLIER) cc_final: 0.8865 (pm20) REVERT: G 319 GLN cc_start: 0.8047 (OUTLIER) cc_final: 0.7673 (pt0) REVERT: G 351 ARG cc_start: 0.9334 (OUTLIER) cc_final: 0.8002 (ttt90) REVERT: H 185 ARG cc_start: 0.8531 (ttp80) cc_final: 0.8070 (ttm-80) REVERT: H 188 GLU cc_start: 0.9001 (mt-10) cc_final: 0.8788 (mm-30) REVERT: I 65 GLU cc_start: 0.8729 (mt-10) cc_final: 0.8480 (tp30) REVERT: I 72 ILE cc_start: 0.9184 (OUTLIER) cc_final: 0.8978 (pp) REVERT: I 79 LYS cc_start: 0.8898 (ptmm) cc_final: 0.8537 (ptpp) REVERT: I 135 ASP cc_start: 0.9063 (m-30) cc_final: 0.8779 (m-30) REVERT: I 138 LEU cc_start: 0.9153 (OUTLIER) cc_final: 0.8944 (mm) REVERT: I 203 ARG cc_start: 0.8012 (mtp-110) cc_final: 0.7642 (mtp85) REVERT: I 296 LEU cc_start: 0.8614 (mp) cc_final: 0.7745 (mp) REVERT: J 206 ASN cc_start: 0.8807 (m-40) cc_final: 0.8537 (m-40) REVERT: K 37 MET cc_start: 0.7275 (ptm) cc_final: 0.6513 (ppp) REVERT: K 54 GLU cc_start: 0.7188 (OUTLIER) cc_final: 0.6870 (tm-30) REVERT: K 134 GLU cc_start: 0.8344 (tm-30) cc_final: 0.7881 (tp30) REVERT: K 209 LYS cc_start: 0.8519 (ttmm) cc_final: 0.8148 (ttpt) outliers start: 63 outliers final: 30 residues processed: 330 average time/residue: 1.4671 time to fit residues: 578.3151 Evaluate side-chains 312 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 271 time to evaluate : 2.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 THR Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain A residue 283 HIS Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 132 GLU Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain C residue 81 ASP Chi-restraints excluded: chain D residue 159 HIS Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 249 GLU Chi-restraints excluded: chain D residue 308 THR Chi-restraints excluded: chain E residue 29 SER Chi-restraints excluded: chain E residue 56 GLN Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 233 VAL Chi-restraints excluded: chain F residue 96 GLN Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain F residue 211 LEU Chi-restraints excluded: chain G residue 96 GLN Chi-restraints excluded: chain G residue 97 THR Chi-restraints excluded: chain G residue 299 ILE Chi-restraints excluded: chain G residue 319 GLN Chi-restraints excluded: chain G residue 351 ARG Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 31 LEU Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain I residue 72 ILE Chi-restraints excluded: chain I residue 138 LEU Chi-restraints excluded: chain I residue 189 VAL Chi-restraints excluded: chain J residue 6 ILE Chi-restraints excluded: chain J residue 48 SER Chi-restraints excluded: chain J residue 125 LEU Chi-restraints excluded: chain J residue 152 LEU Chi-restraints excluded: chain K residue 54 GLU Chi-restraints excluded: chain K residue 123 VAL Chi-restraints excluded: chain K residue 135 LEU Chi-restraints excluded: chain K residue 195 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 275 optimal weight: 0.6980 chunk 197 optimal weight: 0.7980 chunk 32 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 213 optimal weight: 0.7980 chunk 220 optimal weight: 2.9990 chunk 44 optimal weight: 0.2980 chunk 227 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 153 optimal weight: 0.9980 chunk 70 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 256 ASN ** A 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 324 GLN B 220 ASN B 282 ASN D 170 ASN ** F 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 310 GLN ** H 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.142619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.090814 restraints weight = 46283.161| |-----------------------------------------------------------------------------| r_work (start): 0.3129 rms_B_bonded: 2.86 r_work: 0.2994 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2865 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2892 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2892 r_free = 0.2892 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2892 r_free = 0.2892 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2892 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 1.0509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 28649 Z= 0.129 Angle : 0.606 11.828 39386 Z= 0.307 Chirality : 0.041 0.246 4432 Planarity : 0.004 0.049 4823 Dihedral : 15.769 177.240 5024 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 2.22 % Allowed : 24.16 % Favored : 73.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 (0.14), residues: 3322 helix: 1.40 (0.16), residues: 1077 sheet: 0.80 (0.21), residues: 533 loop : -1.16 (0.15), residues: 1712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP A 414 HIS 0.005 0.001 HIS D 159 PHE 0.027 0.001 PHE A 425 TYR 0.024 0.001 TYR D 133 ARG 0.016 0.000 ARG A 306 Details of bonding type rmsd hydrogen bonds : bond 0.03070 ( 1176) hydrogen bonds : angle 4.50726 ( 3238) covalent geometry : bond 0.00296 (28649) covalent geometry : angle 0.60639 (39386) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6644 Ramachandran restraints generated. 3322 Oldfield, 0 Emsley, 3322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6644 Ramachandran restraints generated. 3322 Oldfield, 0 Emsley, 3322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 281 time to evaluate : 3.203 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 71 LYS cc_start: 0.7745 (tppp) cc_final: 0.7254 (tppt) REVERT: A 220 GLU cc_start: 0.8612 (tt0) cc_final: 0.8014 (pp20) REVERT: A 223 SER cc_start: 0.8144 (OUTLIER) cc_final: 0.7761 (p) REVERT: A 281 MET cc_start: 0.6833 (mmt) cc_final: 0.6413 (mmp) REVERT: A 283 HIS cc_start: 0.8728 (OUTLIER) cc_final: 0.8269 (t-90) REVERT: A 296 GLU cc_start: 0.8076 (tp30) cc_final: 0.6988 (tp30) REVERT: A 299 ARG cc_start: 0.8480 (ttp80) cc_final: 0.8202 (ttp80) REVERT: A 300 LEU cc_start: 0.8410 (mm) cc_final: 0.7562 (mt) REVERT: A 324 GLN cc_start: 0.7309 (OUTLIER) cc_final: 0.6829 (pm20) REVERT: A 347 TRP cc_start: 0.8409 (p-90) cc_final: 0.7826 (p-90) REVERT: A 420 LYS cc_start: 0.8562 (ptmt) cc_final: 0.8347 (ptmm) REVERT: A 424 MET cc_start: 0.8484 (mtp) cc_final: 0.8115 (mtp) REVERT: B 132 GLU cc_start: 0.8272 (OUTLIER) cc_final: 0.8002 (mp0) REVERT: B 294 ARG cc_start: 0.7789 (mmp-170) cc_final: 0.7567 (mmp-170) REVERT: C 79 LEU cc_start: 0.7564 (mp) cc_final: 0.7339 (mm) REVERT: C 80 ARG cc_start: 0.7545 (mpt-90) cc_final: 0.7077 (ptp90) REVERT: C 112 LEU cc_start: 0.1024 (tp) cc_final: 0.0599 (mm) REVERT: D 169 ARG cc_start: 0.8291 (ttt90) cc_final: 0.8047 (ttm-80) REVERT: D 170 ASN cc_start: 0.8206 (m-40) cc_final: 0.7913 (m110) REVERT: D 182 ASN cc_start: 0.8133 (m-40) cc_final: 0.7875 (m-40) REVERT: D 249 GLU cc_start: 0.7151 (OUTLIER) cc_final: 0.6773 (mm-30) REVERT: D 278 LYS cc_start: 0.8027 (ttmt) cc_final: 0.7758 (tttp) REVERT: E 65 GLU cc_start: 0.8299 (mm-30) cc_final: 0.7835 (mm-30) REVERT: E 69 ARG cc_start: 0.7616 (ttp80) cc_final: 0.6927 (tmm-80) REVERT: F 188 GLU cc_start: 0.8615 (mt-10) cc_final: 0.7992 (pm20) REVERT: G 65 GLU cc_start: 0.8827 (mm-30) cc_final: 0.8578 (mm-30) REVERT: G 94 ASN cc_start: 0.8815 (m110) cc_final: 0.8399 (m-40) REVERT: G 96 GLN cc_start: 0.9013 (OUTLIER) cc_final: 0.8669 (pm20) REVERT: G 302 GLU cc_start: 0.8944 (mm-30) cc_final: 0.8717 (mm-30) REVERT: G 318 LYS cc_start: 0.8607 (ttpp) cc_final: 0.8157 (tptm) REVERT: G 319 GLN cc_start: 0.8075 (OUTLIER) cc_final: 0.7368 (pt0) REVERT: G 324 TYR cc_start: 0.9106 (m-10) cc_final: 0.8746 (m-80) REVERT: G 351 ARG cc_start: 0.9268 (OUTLIER) cc_final: 0.7933 (ttt90) REVERT: H 185 ARG cc_start: 0.8464 (ttp80) cc_final: 0.7944 (ttm-80) REVERT: H 188 GLU cc_start: 0.8946 (mt-10) cc_final: 0.8705 (mm-30) REVERT: H 208 ASP cc_start: 0.8465 (t0) cc_final: 0.8229 (t0) REVERT: I 65 GLU cc_start: 0.8816 (mt-10) cc_final: 0.8512 (tp30) REVERT: I 72 ILE cc_start: 0.9231 (OUTLIER) cc_final: 0.9030 (pp) REVERT: I 79 LYS cc_start: 0.8990 (ptmm) cc_final: 0.8557 (ptpp) REVERT: I 135 ASP cc_start: 0.9135 (m-30) cc_final: 0.8801 (m-30) REVERT: I 138 LEU cc_start: 0.9107 (OUTLIER) cc_final: 0.8882 (mm) REVERT: I 203 ARG cc_start: 0.8058 (mtp-110) cc_final: 0.7591 (mtp85) REVERT: I 296 LEU cc_start: 0.8523 (mp) cc_final: 0.7671 (mp) REVERT: J 206 ASN cc_start: 0.8730 (m-40) cc_final: 0.8428 (m-40) REVERT: K 37 MET cc_start: 0.7322 (ptm) cc_final: 0.6738 (ppp) REVERT: K 54 GLU cc_start: 0.7430 (OUTLIER) cc_final: 0.7027 (tm-30) REVERT: K 134 GLU cc_start: 0.8306 (OUTLIER) cc_final: 0.7861 (tp30) REVERT: K 157 GLU cc_start: 0.7276 (pm20) cc_final: 0.7012 (pm20) outliers start: 58 outliers final: 32 residues processed: 318 average time/residue: 1.4905 time to fit residues: 554.6898 Evaluate side-chains 308 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 264 time to evaluate : 2.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 THR Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain A residue 283 HIS Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 324 GLN Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 132 GLU Chi-restraints excluded: chain B residue 220 ASN Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 249 GLU Chi-restraints excluded: chain D residue 308 THR Chi-restraints excluded: chain D residue 329 ASN Chi-restraints excluded: chain E residue 29 SER Chi-restraints excluded: chain E residue 56 GLN Chi-restraints excluded: chain E residue 96 GLN Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 233 VAL Chi-restraints excluded: chain F residue 96 GLN Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain F residue 211 LEU Chi-restraints excluded: chain G residue 96 GLN Chi-restraints excluded: chain G residue 97 THR Chi-restraints excluded: chain G residue 299 ILE Chi-restraints excluded: chain G residue 319 GLN Chi-restraints excluded: chain G residue 351 ARG Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 31 LEU Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 318 LYS Chi-restraints excluded: chain I residue 72 ILE Chi-restraints excluded: chain I residue 138 LEU Chi-restraints excluded: chain I residue 189 VAL Chi-restraints excluded: chain J residue 6 ILE Chi-restraints excluded: chain J residue 48 SER Chi-restraints excluded: chain J residue 125 LEU Chi-restraints excluded: chain J residue 152 LEU Chi-restraints excluded: chain K residue 54 GLU Chi-restraints excluded: chain K residue 123 VAL Chi-restraints excluded: chain K residue 134 GLU Chi-restraints excluded: chain K residue 195 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 154 optimal weight: 4.9990 chunk 266 optimal weight: 2.9990 chunk 131 optimal weight: 0.3980 chunk 81 optimal weight: 9.9990 chunk 315 optimal weight: 6.9990 chunk 253 optimal weight: 0.5980 chunk 283 optimal weight: 2.9990 chunk 223 optimal weight: 3.9990 chunk 71 optimal weight: 5.9990 chunk 19 optimal weight: 5.9990 chunk 146 optimal weight: 1.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 256 ASN A 273 GLN ** A 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 282 ASN F 310 GLN ** I 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.142506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.091044 restraints weight = 41667.086| |-----------------------------------------------------------------------------| r_work (start): 0.3162 rms_B_bonded: 2.55 r_work: 0.3037 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2915 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2914 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2914 r_free = 0.2914 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2914 r_free = 0.2914 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2914 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 1.0508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.316 28649 Z= 0.233 Angle : 0.790 59.183 39386 Z= 0.447 Chirality : 0.043 0.684 4432 Planarity : 0.005 0.194 4823 Dihedral : 15.775 177.249 5024 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 2.07 % Allowed : 24.46 % Favored : 73.47 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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 (0.14), residues: 3322 helix: 1.41 (0.16), residues: 1077 sheet: 0.80 (0.21), residues: 533 loop : -1.17 (0.15), residues: 1712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP A 414 HIS 0.005 0.001 HIS D 159 PHE 0.022 0.001 PHE A 425 TYR 0.022 0.001 TYR D 133 ARG 0.014 0.000 ARG A 306 Details of bonding type rmsd hydrogen bonds : bond 0.03082 ( 1176) hydrogen bonds : angle 4.50678 ( 3238) covalent geometry : bond 0.00482 (28649) covalent geometry : angle 0.78961 (39386) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 29995.10 seconds wall clock time: 521 minutes 46.23 seconds (31306.23 seconds total)