Starting phenix.real_space_refine on Mon Sep 14 04:42:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7tax_25789/09_2026/7tax_25789.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tax_25789/09_2026/7tax_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/7tax_25789/09_2026/7tax_25789.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7tax_25789/09_2026/7tax_25789.cif" model { file = "/net/cci-nas-00/data/ceres_data/7tax_25789/09_2026/7tax_25789.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tax_25789/09_2026/7tax_25789.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7tax_25789/09_2026/7tax_25789.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tax_25789/09_2026/7tax_25789.map" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.027 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/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: {'ASP:plan': 11, 'GLN:plan1': 9, 'GLU:plan': 9, 'ARG:plan': 9, 'HIS:plan': 3, 'TYR:plan': 1, 'ASN:plan1': 3, 'PHE:plan': 1, 'TRP:plan': 1} 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: {'ARG:plan': 8, 'GLU:plan': 3, 'GLN:plan1': 1} 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: {'ARG:plan': 8, 'GLU:plan': 3, 'GLN:plan1': 1} 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, 'RNAv2': 60} Modifications used: {'rna2p_pur': 11, 'rna2p_pyr': 17, 'rna3p_pur': 17, 'rna3p_pyr': 14} Link IDs: {'rna2p': 28, 'rna3p': 32} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 5 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: 5.57, per 1000 atoms: 0.20 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: 2.09 Conformation dependent library (CDL) restraints added in 1.1 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: 3.21 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: 5.58 Time building geometry restraints manager: 2.83 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: 38581 2.34 - 4.68: 706 4.68 - 7.02: 84 7.02 - 9.36: 10 9.36 - 11.69: 2 Bond angle restraints: 39383 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 39378 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.03: 15224 19.03 - 38.05: 1238 38.05 - 57.08: 313 57.08 - 76.11: 134 76.11 - 95.13: 13 Dihedral angle restraints: 16922 sinusoidal: 7276 harmonic: 9646 Sorted by residual: dihedral pdb=" C4' G M 40 " pdb=" C3' G M 40 " pdb=" C2' G M 40 " pdb=" C1' G M 40 " ideal model delta sinusoidal sigma weight residual 36.34 -37.52 73.86 1 3.10e+00 1.04e-01 7.21e+02 dihedral pdb=" C4' C M 37 " pdb=" C3' C M 37 " pdb=" C2' C M 37 " pdb=" C1' C M 37 " ideal model delta sinusoidal sigma weight residual 36.35 -36.67 73.01 1 3.10e+00 1.04e-01 7.07e+02 dihedral pdb=" C4' G M 19 " pdb=" C3' G M 19 " pdb=" C2' G M 19 " pdb=" C1' G M 19 " ideal model delta sinusoidal sigma weight residual 36.34 -36.19 72.54 1 3.10e+00 1.04e-01 6.99e+02 ... (remaining 16919 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 3671 0.060 - 0.119: 584 0.119 - 0.179: 60 0.179 - 0.238: 53 0.238 - 0.298: 64 Chirality restraints: 4432 Sorted by residual: chirality pdb=" C3' G M 40 " pdb=" C4' G M 40 " pdb=" O3' G M 40 " pdb=" C2' G M 40 " both_signs ideal model delta sigma weight residual False -2.50 -2.80 0.30 2.00e-01 2.50e+01 2.21e+00 chirality pdb=" C2' C M 16 " pdb=" C3' C M 16 " pdb=" O2' C M 16 " pdb=" C1' C M 16 " both_signs ideal model delta sigma weight residual False -2.79 -2.50 -0.29 2.00e-01 2.50e+01 2.15e+00 chirality pdb=" C2' A M 8 " pdb=" C3' A M 8 " pdb=" O2' A M 8 " pdb=" C1' A M 8 " both_signs ideal model delta sigma weight residual False -2.79 -2.51 -0.28 2.00e-01 2.50e+01 2.01e+00 ... (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: 2.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.020 Extract box with map and model: 0.460 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 25.530 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.060 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:6.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5612 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= 0.214 Angle : 0.733 11.694 39383 Z= 0.409 Chirality : 0.058 0.298 4432 Planarity : 0.005 0.077 4823 Dihedral : 15.934 95.131 10696 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 6.34 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.99 (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 ARG 0.009 0.001 ARG E 191 TYR 0.039 0.002 TYR G 304 PHE 0.023 0.001 PHE A 16 TRP 0.017 0.001 TRP G 49 HIS 0.009 0.001 HIS K 25 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.21 (28649) covalent geometry : angle 0.73340 / 0.41 (39383) hydrogen bonds : bond 0.18486 / 12.88 ( 1176) hydrogen bonds : angle 7.24627 / 5.11 ( 3238) *********************** 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 : 1.004 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: A 300 LEU cc_start: 0.6915 (mm) cc_final: 0.6584 (mt) REVERT: B 121 HIS cc_start: 0.5778 (m90) cc_final: 0.5508 (m-70) REVERT: D 276 SER cc_start: 0.6268 (m) cc_final: 0.6013 (t) REVERT: J 28 TRP cc_start: 0.5319 (m100) cc_final: 0.4436 (m100) outliers start: 0 outliers final: 5 residues processed: 866 average time/residue: 0.5413 time to fit residues: 559.0148 Evaluate side-chains 506 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 501 time to evaluate : 0.994 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain I residue 170 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 0.5980 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 0.0980 chunk 207 optimal weight: 0.8980 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 4.9990 chunk 298 optimal weight: 3.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 62 GLN A 129 ASN A 253 GLN ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 328 GLN A 416 GLN B 21 ASN B 89 ASN B 104 HIS B 168 GLN B 282 ASN B 293 HIS ** C 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 170 ASN D 281 ASN E 316 GLN F 186 GLN F 242 GLN ** G 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 160 ASN G 163 ASN G 319 GLN G 343 HIS H 96 GLN H 242 GLN H 348 ASN I 94 ASN I 146 ASN I 281 ASN ** I 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 216 HIS ** K 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.151824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.103757 restraints weight = 45223.869| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 2.70 r_work: 0.3267 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3139 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3136 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3136 r_free = 0.3136 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3136 r_free = 0.3136 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.3136 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7148 moved from start: 0.3599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 28649 Z= 0.237 Angle : 1.097 24.591 39383 Z= 0.486 Chirality : 0.087 1.316 4432 Planarity : 0.006 0.062 4823 Dihedral : 14.093 140.220 4817 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 3.64 % Allowed : 15.99 % Favored : 80.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.14), residues: 3322 helix: 0.40 (0.15), residues: 1060 sheet: 0.67 (0.21), residues: 565 loop : -1.37 (0.14), residues: 1697 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.036 0.001 ARG H 191 TYR 0.037 0.003 TYR F 266 PHE 0.024 0.002 PHE I 355 TRP 0.036 0.002 TRP H 193 HIS 0.012 0.002 HIS A 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00507 / 0.24 (28649) covalent geometry : angle 1.09718 / 0.49 (39383) hydrogen bonds : bond 0.04466 / 3.11 ( 1176) hydrogen bonds : angle 5.48410 / 3.84 ( 3238) *********************** 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 661 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 566 time to evaluate : 0.973 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: A 220 GLU cc_start: 0.8128 (mt-10) cc_final: 0.7905 (tt0) REVERT: A 283 HIS cc_start: 0.8648 (OUTLIER) cc_final: 0.8348 (t-90) REVERT: A 296 GLU cc_start: 0.7516 (tp30) cc_final: 0.7185 (tp30) REVERT: A 299 ARG cc_start: 0.8247 (ttp80) cc_final: 0.7965 (ttp80) REVERT: A 300 LEU cc_start: 0.8233 (mm) cc_final: 0.7448 (mt) REVERT: A 321 ARG cc_start: 0.7404 (tpm170) cc_final: 0.6113 (tpm-80) REVERT: B 121 HIS cc_start: 0.6379 (m90) cc_final: 0.5668 (m-70) REVERT: B 159 LEU cc_start: 0.6348 (OUTLIER) cc_final: 0.5974 (tt) REVERT: B 218 ARG cc_start: 0.7035 (ptt180) cc_final: 0.6824 (ptt180) REVERT: B 284 PHE cc_start: 0.7354 (m-80) cc_final: 0.7047 (m-80) REVERT: C 112 LEU cc_start: 0.0886 (tp) cc_final: 0.0523 (mm) REVERT: D 299 ILE cc_start: 0.7728 (pp) cc_final: 0.7517 (pp) REVERT: E 266 TYR cc_start: 0.7592 (t80) cc_final: 0.7207 (t80) REVERT: F 139 GLN cc_start: 0.7647 (tp40) cc_final: 0.7421 (tt0) REVERT: G 155 ARG cc_start: 0.7244 (OUTLIER) cc_final: 0.6940 (ttp-110) REVERT: H 30 VAL cc_start: 0.7210 (t) cc_final: 0.6908 (p) REVERT: H 335 GLU cc_start: 0.6763 (OUTLIER) cc_final: 0.6525 (pm20) REVERT: I 113 ARG cc_start: 0.6433 (OUTLIER) cc_final: 0.5840 (ttm-80) REVERT: I 136 LYS cc_start: 0.8375 (tptm) cc_final: 0.8094 (tptp) REVERT: I 140 THR cc_start: 0.8727 (OUTLIER) cc_final: 0.8520 (t) REVERT: I 203 ARG cc_start: 0.5952 (ptp-110) cc_final: 0.5625 (mtp85) REVERT: I 314 TYR cc_start: 0.4602 (m-80) cc_final: 0.4171 (m-80) REVERT: I 324 TYR cc_start: 0.6133 (m-10) cc_final: 0.5794 (m-10) REVERT: I 344 TYR cc_start: 0.5620 (t80) cc_final: 0.5340 (t80) REVERT: J 81 ASP cc_start: 0.5874 (t0) cc_final: 0.5657 (t0) REVERT: K 36 GLU cc_start: 0.7463 (tt0) cc_final: 0.7216 (tt0) REVERT: K 54 GLU cc_start: 0.6498 (OUTLIER) cc_final: 0.6048 (tm-30) REVERT: K 61 GLU cc_start: 0.8188 (pt0) cc_final: 0.7820 (pp20) outliers start: 95 outliers final: 27 residues processed: 621 average time/residue: 0.5104 time to fit residues: 381.7634 Evaluate side-chains 461 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 427 time to evaluate : 0.852 ------------------------------------------------------------------------------- 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 76 ASP Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 177 GLN Chi-restraints excluded: chain A residue 283 HIS Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain E residue 29 SER Chi-restraints excluded: chain E residue 99 ASP 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 55 SER Chi-restraints excluded: chain F residue 140 THR Chi-restraints excluded: chain F residue 143 THR Chi-restraints excluded: chain G residue 72 ILE Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 118 VAL Chi-restraints excluded: chain G residue 130 ASP Chi-restraints excluded: chain G residue 155 ARG Chi-restraints excluded: chain G residue 159 HIS Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 335 GLU Chi-restraints excluded: chain I residue 113 ARG Chi-restraints excluded: chain I residue 118 VAL Chi-restraints excluded: chain I residue 140 THR Chi-restraints excluded: chain J residue 49 SER Chi-restraints excluded: chain K residue 54 GLU Chi-restraints excluded: chain K residue 75 LEU Chi-restraints excluded: chain K residue 123 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 59 optimal weight: 5.9990 chunk 222 optimal weight: 0.7980 chunk 164 optimal weight: 1.9990 chunk 136 optimal weight: 0.0050 chunk 218 optimal weight: 0.1980 chunk 304 optimal weight: 6.9990 chunk 242 optimal weight: 2.9990 chunk 210 optimal weight: 0.5980 chunk 162 optimal weight: 0.7980 chunk 12 optimal weight: 8.9990 chunk 186 optimal weight: 1.9990 overall best weight: 0.4794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 74 HIS A 253 GLN A 255 ASN ** B 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 21 ASN B 194 GLN ** B 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 19 GLN C 29 HIS D 170 ASN E 96 GLN E 146 ASN F 343 HIS G 96 GLN G 319 GLN G 348 ASN H 96 GLN I 96 GLN J 27 GLN ** J 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 216 HIS K 25 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.152442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.103131 restraints weight = 54276.671| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 2.78 r_work: 0.3236 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3266 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3266 r_free = 0.3266 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3266 r_free = 0.3266 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.3266 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7172 moved from start: 0.4311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.099 28649 Z= 0.154 Angle : 0.800 16.190 39383 Z= 0.377 Chirality : 0.063 0.928 4432 Planarity : 0.005 0.068 4823 Dihedral : 14.306 159.168 4809 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 4.18 % Allowed : 19.36 % Favored : 76.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.44 (0.14), residues: 3322 helix: 0.81 (0.15), residues: 1062 sheet: 0.68 (0.21), residues: 566 loop : -1.40 (0.14), residues: 1694 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 175 TYR 0.023 0.002 TYR D 133 PHE 0.023 0.002 PHE A 118 TRP 0.024 0.001 TRP A 155 HIS 0.011 0.001 HIS A 200 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.15 (28649) covalent geometry : angle 0.80027 / 0.38 (39383) hydrogen bonds : bond 0.03862 / 2.77 ( 1176) hydrogen bonds : angle 5.12165 / 3.60 ( 3238) *********************** 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 552 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 443 time to evaluate : 0.857 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 LEU cc_start: 0.5194 (OUTLIER) cc_final: 0.4349 (tp) REVERT: A 256 ASN cc_start: 0.6209 (t0) cc_final: 0.5661 (m-40) REVERT: A 283 HIS cc_start: 0.8543 (OUTLIER) cc_final: 0.8288 (t-90) REVERT: A 296 GLU cc_start: 0.7714 (tp30) cc_final: 0.6818 (tp30) REVERT: A 299 ARG cc_start: 0.8318 (ttp80) cc_final: 0.8003 (ttp80) REVERT: A 300 LEU cc_start: 0.8168 (OUTLIER) cc_final: 0.7193 (mt) REVERT: A 321 ARG cc_start: 0.7141 (tpm170) cc_final: 0.6577 (tpm-80) REVERT: A 329 ILE cc_start: 0.7059 (OUTLIER) cc_final: 0.6747 (mp) REVERT: B 72 GLN cc_start: 0.7923 (pt0) cc_final: 0.7537 (pm20) REVERT: B 106 GLU cc_start: 0.7159 (OUTLIER) cc_final: 0.6887 (tm-30) REVERT: B 121 HIS cc_start: 0.6295 (m90) cc_final: 0.5632 (m-70) REVERT: B 259 SER cc_start: 0.5303 (t) cc_final: 0.4942 (p) REVERT: C 102 ARG cc_start: 0.3456 (ttt180) cc_final: 0.2826 (ptp90) REVERT: C 112 LEU cc_start: 0.0848 (tp) cc_final: 0.0420 (mm) REVERT: E 310 GLN cc_start: 0.8458 (OUTLIER) cc_final: 0.7388 (mp10) REVERT: E 312 LYS cc_start: 0.8141 (ptpt) cc_final: 0.7539 (pttt) REVERT: F 34 GLU cc_start: 0.7581 (tt0) cc_final: 0.7181 (mt-10) REVERT: F 139 GLN cc_start: 0.7753 (tp40) cc_final: 0.7524 (tt0) REVERT: G 155 ARG cc_start: 0.7277 (OUTLIER) cc_final: 0.6865 (ttp-110) REVERT: G 319 GLN cc_start: 0.5346 (OUTLIER) cc_final: 0.5016 (pt0) REVERT: H 30 VAL cc_start: 0.7105 (t) cc_final: 0.6727 (p) REVERT: H 96 GLN cc_start: 0.7599 (OUTLIER) cc_final: 0.7381 (pm20) REVERT: H 143 THR cc_start: 0.8421 (OUTLIER) cc_final: 0.8178 (t) REVERT: H 185 ARG cc_start: 0.7418 (ttp80) cc_final: 0.6927 (ttm-80) REVERT: H 203 ARG cc_start: 0.6733 (mmm-85) cc_final: 0.6305 (mmm160) REVERT: H 254 LYS cc_start: 0.7733 (OUTLIER) cc_final: 0.7462 (tttm) REVERT: H 335 GLU cc_start: 0.6516 (OUTLIER) cc_final: 0.6293 (pm20) REVERT: I 113 ARG cc_start: 0.6779 (OUTLIER) cc_final: 0.6120 (ttm-80) REVERT: I 136 LYS cc_start: 0.8371 (tptm) cc_final: 0.8062 (tptp) REVERT: I 203 ARG cc_start: 0.6056 (ptp-110) cc_final: 0.5741 (mtp85) REVERT: I 320 LYS cc_start: 0.8124 (mmtm) cc_final: 0.7875 (mmmt) REVERT: I 324 TYR cc_start: 0.6300 (m-10) cc_final: 0.6045 (m-10) REVERT: I 344 TYR cc_start: 0.5926 (t80) cc_final: 0.5535 (t80) REVERT: J 37 MET cc_start: 0.8037 (OUTLIER) cc_final: 0.7717 (mtm) REVERT: K 36 GLU cc_start: 0.7458 (tt0) cc_final: 0.7194 (tt0) REVERT: K 61 GLU cc_start: 0.8202 (pt0) cc_final: 0.7869 (pp20) REVERT: K 134 GLU cc_start: 0.7607 (OUTLIER) cc_final: 0.7356 (tm-30) REVERT: K 176 PHE cc_start: 0.6865 (m-80) cc_final: 0.6562 (m-10) REVERT: K 209 LYS cc_start: 0.7889 (tppp) cc_final: 0.7507 (tppp) outliers start: 109 outliers final: 35 residues processed: 509 average time/residue: 0.5058 time to fit residues: 311.9078 Evaluate side-chains 434 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 384 time to evaluate : 0.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 THR Chi-restraints excluded: chain A residue 76 ASP Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 213 ASP Chi-restraints excluded: chain A residue 283 HIS Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 425 PHE Chi-restraints excluded: chain B residue 16 SER Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 106 GLU Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 195 GLN Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 220 ASN Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain E residue 29 SER Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 233 VAL Chi-restraints excluded: chain E residue 310 GLN Chi-restraints excluded: chain E residue 346 ILE Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 143 THR Chi-restraints excluded: chain G residue 91 GLN Chi-restraints excluded: chain G residue 155 ARG 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 96 GLN Chi-restraints excluded: chain H residue 143 THR Chi-restraints excluded: chain H residue 254 LYS Chi-restraints excluded: chain H residue 335 GLU Chi-restraints excluded: chain H residue 346 ILE Chi-restraints excluded: chain I residue 113 ARG Chi-restraints excluded: chain I residue 115 THR Chi-restraints excluded: chain I residue 118 VAL Chi-restraints excluded: chain I residue 189 VAL Chi-restraints excluded: chain J residue 37 MET Chi-restraints excluded: chain J residue 167 LEU Chi-restraints excluded: chain J residue 198 TYR Chi-restraints excluded: chain K residue 53 ASP Chi-restraints excluded: chain K residue 121 LEU Chi-restraints excluded: chain K residue 123 VAL Chi-restraints excluded: chain K residue 134 GLU Chi-restraints excluded: chain K residue 151 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 309 optimal weight: 5.9990 chunk 127 optimal weight: 0.8980 chunk 5 optimal weight: 5.9990 chunk 23 optimal weight: 0.8980 chunk 240 optimal weight: 0.9980 chunk 256 optimal weight: 0.2980 chunk 62 optimal weight: 0.2980 chunk 59 optimal weight: 5.9990 chunk 181 optimal weight: 0.6980 chunk 276 optimal weight: 0.6980 chunk 57 optimal weight: 6.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 253 GLN A 324 GLN B 19 ASN B 21 ASN D 148 GLN D 170 ASN D 343 HIS E 146 ASN G 96 GLN J 26 HIS K 216 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.152357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.103151 restraints weight = 47668.357| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 2.61 r_work: 0.3243 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3118 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3105 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3105 r_free = 0.3105 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3105 r_free = 0.3105 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.3105 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7455 moved from start: 0.5033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 28649 Z= 0.148 Angle : 0.765 14.766 39383 Z= 0.359 Chirality : 0.056 0.550 4432 Planarity : 0.004 0.056 4823 Dihedral : 14.191 159.029 4809 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 4.56 % Allowed : 19.21 % Favored : 76.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.34 (0.14), residues: 3322 helix: 1.00 (0.16), residues: 1061 sheet: 0.67 (0.21), residues: 564 loop : -1.39 (0.15), residues: 1697 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 306 TYR 0.017 0.002 TYR B 262 PHE 0.028 0.002 PHE A 291 TRP 0.017 0.001 TRP A 155 HIS 0.010 0.001 HIS B 305 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.15 (28649) covalent geometry : angle 0.76549 / 0.36 (39383) hydrogen bonds : bond 0.03399 / 2.40 ( 1176) hydrogen bonds : angle 4.94654 / 3.48 ( 3238) *********************** 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 544 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 425 time to evaluate : 0.995 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 28 LYS cc_start: 0.6407 (tppt) cc_final: 0.6205 (tppt) REVERT: A 200 HIS cc_start: 0.8523 (t-90) cc_final: 0.7764 (t-90) REVERT: A 220 GLU cc_start: 0.8353 (tt0) cc_final: 0.7716 (tm-30) REVERT: A 256 ASN cc_start: 0.6323 (t0) cc_final: 0.5744 (m-40) REVERT: A 281 MET cc_start: 0.6435 (OUTLIER) cc_final: 0.6024 (mmp) REVERT: A 283 HIS cc_start: 0.8569 (OUTLIER) cc_final: 0.8189 (t-90) REVERT: A 296 GLU cc_start: 0.7607 (tp30) cc_final: 0.6865 (tp30) REVERT: A 299 ARG cc_start: 0.8341 (ttp80) cc_final: 0.7919 (ttp80) REVERT: A 300 LEU cc_start: 0.8283 (OUTLIER) cc_final: 0.7269 (mt) REVERT: A 306 ARG cc_start: 0.7173 (ttp80) cc_final: 0.6795 (ttp80) REVERT: A 329 ILE cc_start: 0.7072 (OUTLIER) cc_final: 0.6748 (mp) REVERT: B 72 GLN cc_start: 0.8177 (pt0) cc_final: 0.7637 (pm20) REVERT: B 77 ARG cc_start: 0.6546 (tpm170) cc_final: 0.5912 (tpm170) REVERT: B 121 HIS cc_start: 0.6237 (m90) cc_final: 0.5569 (m-70) REVERT: B 197 LEU cc_start: 0.8050 (tp) cc_final: 0.7791 (tm) REVERT: B 218 ARG cc_start: 0.7037 (ptt180) cc_final: 0.6775 (ptt180) REVERT: C 102 ARG cc_start: 0.3256 (ttt180) cc_final: 0.2607 (ptp90) REVERT: C 112 LEU cc_start: 0.0945 (tp) cc_final: 0.0445 (mm) REVERT: C 117 MET cc_start: 0.1092 (ptt) cc_final: 0.0782 (mpp) REVERT: D 243 GLU cc_start: 0.6420 (OUTLIER) cc_final: 0.6194 (pp20) REVERT: D 278 LYS cc_start: 0.7659 (ttmt) cc_final: 0.7047 (tttp) REVERT: D 324 TYR cc_start: 0.6897 (m-80) cc_final: 0.6650 (m-10) REVERT: E 143 THR cc_start: 0.8553 (t) cc_final: 0.8222 (p) REVERT: E 203 ARG cc_start: 0.7820 (OUTLIER) cc_final: 0.7612 (mmm160) REVERT: E 310 GLN cc_start: 0.8523 (OUTLIER) cc_final: 0.7444 (mp10) REVERT: F 34 GLU cc_start: 0.7856 (tt0) cc_final: 0.7506 (mt-10) REVERT: F 139 GLN cc_start: 0.8205 (tp40) cc_final: 0.7866 (tt0) REVERT: F 188 GLU cc_start: 0.6911 (mt-10) cc_final: 0.6423 (pm20) REVERT: G 96 GLN cc_start: 0.8047 (OUTLIER) cc_final: 0.7619 (pm20) REVERT: G 155 ARG cc_start: 0.7633 (OUTLIER) cc_final: 0.7209 (ttp-170) REVERT: G 203 ARG cc_start: 0.6644 (OUTLIER) cc_final: 0.6026 (mtp-110) REVERT: H 30 VAL cc_start: 0.7465 (t) cc_final: 0.7119 (p) REVERT: H 79 LYS cc_start: 0.8277 (ptmm) cc_final: 0.8060 (tmmm) REVERT: H 143 THR cc_start: 0.8579 (OUTLIER) cc_final: 0.8316 (p) REVERT: H 150 PHE cc_start: 0.7877 (m-80) cc_final: 0.7427 (m-80) REVERT: H 185 ARG cc_start: 0.7791 (ttp80) cc_final: 0.7173 (ttm-80) REVERT: H 186 GLN cc_start: 0.7425 (tm-30) cc_final: 0.6671 (mp10) REVERT: H 203 ARG cc_start: 0.6959 (mmm-85) cc_final: 0.6541 (mmm160) REVERT: H 206 LYS cc_start: 0.7185 (OUTLIER) cc_final: 0.6856 (pptt) REVERT: H 254 LYS cc_start: 0.7965 (OUTLIER) cc_final: 0.7518 (tttm) REVERT: H 335 GLU cc_start: 0.6767 (OUTLIER) cc_final: 0.6505 (pm20) REVERT: I 113 ARG cc_start: 0.7167 (OUTLIER) cc_final: 0.6386 (ttm-80) REVERT: I 133 TYR cc_start: 0.7237 (t80) cc_final: 0.6933 (t80) REVERT: I 136 LYS cc_start: 0.8590 (tptm) cc_final: 0.8284 (tptp) REVERT: I 203 ARG cc_start: 0.6358 (ptp-110) cc_final: 0.5802 (mtp85) REVERT: I 320 LYS cc_start: 0.8199 (mmtm) cc_final: 0.7953 (mmmt) REVERT: I 324 TYR cc_start: 0.6598 (m-10) cc_final: 0.6272 (m-10) REVERT: J 81 ASP cc_start: 0.5878 (t0) cc_final: 0.5613 (t0) REVERT: K 53 ASP cc_start: 0.9231 (OUTLIER) cc_final: 0.8985 (m-30) REVERT: K 54 GLU cc_start: 0.6234 (OUTLIER) cc_final: 0.5719 (tm-30) REVERT: K 61 GLU cc_start: 0.8295 (pt0) cc_final: 0.7971 (pp20) REVERT: K 96 GLU cc_start: 0.7963 (pm20) cc_final: 0.7731 (mm-30) REVERT: K 127 GLU cc_start: 0.8538 (mt-10) cc_final: 0.8147 (pt0) REVERT: K 134 GLU cc_start: 0.7734 (OUTLIER) cc_final: 0.7069 (tp30) REVERT: K 155 ASP cc_start: 0.5831 (p0) cc_final: 0.4849 (p0) REVERT: K 209 LYS cc_start: 0.8074 (tppp) cc_final: 0.7827 (tppp) outliers start: 119 outliers final: 33 residues processed: 499 average time/residue: 0.4789 time to fit residues: 290.4832 Evaluate side-chains 432 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 381 time to evaluate : 0.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 THR Chi-restraints excluded: chain A residue 76 ASP Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 213 ASP Chi-restraints excluded: chain A residue 281 MET Chi-restraints excluded: chain A residue 283 HIS Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 393 ASN Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 195 GLN Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 243 GLU Chi-restraints excluded: chain D residue 308 THR Chi-restraints excluded: chain E residue 29 SER 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 E residue 310 GLN Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 143 THR Chi-restraints excluded: chain G residue 91 GLN Chi-restraints excluded: chain G residue 96 GLN Chi-restraints excluded: chain G residue 155 ARG Chi-restraints excluded: chain G residue 203 ARG Chi-restraints excluded: chain G residue 348 ASN Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain H residue 143 THR Chi-restraints excluded: chain H residue 206 LYS Chi-restraints excluded: chain H residue 254 LYS Chi-restraints excluded: chain H residue 335 GLU Chi-restraints excluded: chain H residue 346 ILE Chi-restraints excluded: chain I residue 113 ARG Chi-restraints excluded: chain I residue 115 THR Chi-restraints excluded: chain I residue 118 VAL Chi-restraints excluded: chain I residue 138 LEU Chi-restraints excluded: chain I residue 189 VAL Chi-restraints excluded: chain J residue 198 TYR Chi-restraints excluded: chain K residue 53 ASP Chi-restraints excluded: chain K residue 54 GLU Chi-restraints excluded: chain K residue 75 LEU Chi-restraints excluded: chain K residue 121 LEU Chi-restraints excluded: chain K residue 123 VAL Chi-restraints excluded: chain K residue 134 GLU Chi-restraints excluded: chain K residue 151 VAL Chi-restraints excluded: chain K residue 170 VAL 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 52 optimal weight: 2.9990 chunk 3 optimal weight: 50.0000 chunk 260 optimal weight: 0.8980 chunk 157 optimal weight: 0.8980 chunk 85 optimal weight: 4.9990 chunk 86 optimal weight: 6.9990 chunk 24 optimal weight: 4.9990 chunk 143 optimal weight: 0.1980 chunk 145 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 257 optimal weight: 0.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 111 ASN A 253 GLN B 69 GLN D 170 ASN E 96 GLN E 146 ASN E 348 ASN G 260 GLN J 194 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.149998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.101013 restraints weight = 44823.090| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 2.68 r_work: 0.3184 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3061 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3078 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3078 r_free = 0.3078 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3078 r_free = 0.3078 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3078 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.6165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.144 28649 Z= 0.191 Angle : 0.774 14.254 39383 Z= 0.375 Chirality : 0.056 0.505 4432 Planarity : 0.005 0.089 4823 Dihedral : 14.272 161.079 4809 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.22 % Favored : 95.75 % Rotamer: Outliers : 4.75 % Allowed : 20.44 % Favored : 74.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.40 (0.14), residues: 3322 helix: 0.91 (0.15), residues: 1063 sheet: 0.60 (0.21), residues: 574 loop : -1.39 (0.15), residues: 1685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG K 93 TYR 0.022 0.002 TYR G 344 PHE 0.021 0.002 PHE A 291 TRP 0.023 0.001 TRP B 247 HIS 0.022 0.001 HIS A 200 Details of bonding type rmsd/Z covalent geometry : bond 0.00423 / 0.19 (28649) covalent geometry : angle 0.77450 / 0.38 (39383) hydrogen bonds : bond 0.03501 / 2.47 ( 1176) hydrogen bonds : angle 4.93513 / 3.49 ( 3238) *********************** 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 540 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 416 time to evaluate : 1.066 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 220 GLU cc_start: 0.8319 (tt0) cc_final: 0.7657 (tm-30) REVERT: A 283 HIS cc_start: 0.8522 (OUTLIER) cc_final: 0.8135 (t-90) REVERT: A 299 ARG cc_start: 0.8435 (ttp80) cc_final: 0.8088 (ttp80) REVERT: A 321 ARG cc_start: 0.7247 (tpm170) cc_final: 0.6558 (tpm-80) REVERT: A 329 ILE cc_start: 0.7256 (OUTLIER) cc_final: 0.6975 (mp) REVERT: A 427 GLU cc_start: 0.7238 (tp30) cc_final: 0.7035 (tp30) REVERT: B 67 GLU cc_start: 0.6937 (tt0) cc_final: 0.6088 (tt0) REVERT: B 69 GLN cc_start: 0.8105 (OUTLIER) cc_final: 0.6633 (mp-120) REVERT: B 121 HIS cc_start: 0.6169 (m90) cc_final: 0.5491 (m-70) REVERT: B 218 ARG cc_start: 0.7242 (ptt180) cc_final: 0.7008 (ptt180) REVERT: B 268 ARG cc_start: 0.6044 (OUTLIER) cc_final: 0.5614 (tpt170) REVERT: C 102 ARG cc_start: 0.3252 (ttt180) cc_final: 0.2266 (ptm-80) REVERT: C 112 LEU cc_start: 0.0929 (tp) cc_final: 0.0368 (mm) REVERT: C 117 MET cc_start: 0.1403 (OUTLIER) cc_final: 0.1160 (mpp) REVERT: D 278 LYS cc_start: 0.7764 (ttmt) cc_final: 0.7257 (tttp) REVERT: D 354 VAL cc_start: 0.8604 (t) cc_final: 0.8364 (t) REVERT: E 34 GLU cc_start: 0.8327 (tt0) cc_final: 0.7991 (tt0) REVERT: E 143 THR cc_start: 0.8650 (t) cc_final: 0.8400 (p) REVERT: E 310 GLN cc_start: 0.8506 (OUTLIER) cc_final: 0.7352 (mp10) REVERT: F 80 ASP cc_start: 0.8932 (t0) cc_final: 0.8637 (t0) REVERT: F 139 GLN cc_start: 0.8498 (tp40) cc_final: 0.8152 (tt0) REVERT: F 188 GLU cc_start: 0.7492 (mt-10) cc_final: 0.6775 (pm20) REVERT: F 265 LEU cc_start: 0.9026 (OUTLIER) cc_final: 0.8787 (mt) REVERT: F 270 ASP cc_start: 0.8370 (p0) cc_final: 0.7920 (m-30) REVERT: F 320 LYS cc_start: 0.8226 (mmmt) cc_final: 0.7943 (mmtt) REVERT: G 65 GLU cc_start: 0.8643 (mm-30) cc_final: 0.8420 (mm-30) REVERT: G 155 ARG cc_start: 0.8084 (OUTLIER) cc_final: 0.7564 (ttp-170) REVERT: G 269 ARG cc_start: 0.7463 (ttm110) cc_final: 0.7147 (mtm-85) REVERT: G 333 ARG cc_start: 0.7917 (ptp90) cc_final: 0.7579 (ptp90) REVERT: H 55 SER cc_start: 0.8241 (p) cc_final: 0.7997 (p) REVERT: H 74 ASN cc_start: 0.9013 (m-40) cc_final: 0.8631 (m110) REVERT: H 79 LYS cc_start: 0.8308 (ptmm) cc_final: 0.8084 (tmmm) REVERT: H 143 THR cc_start: 0.8594 (OUTLIER) cc_final: 0.8305 (p) REVERT: H 185 ARG cc_start: 0.8006 (ttp80) cc_final: 0.7368 (ttm-80) REVERT: H 186 GLN cc_start: 0.7638 (tm-30) cc_final: 0.7229 (tp40) REVERT: H 203 ARG cc_start: 0.7142 (mmm-85) cc_final: 0.6742 (mmm160) REVERT: H 206 LYS cc_start: 0.7516 (OUTLIER) cc_final: 0.7199 (pptt) REVERT: H 335 GLU cc_start: 0.7152 (OUTLIER) cc_final: 0.6849 (pm20) REVERT: I 113 ARG cc_start: 0.7873 (OUTLIER) cc_final: 0.7598 (ttt-90) REVERT: I 136 LYS cc_start: 0.8657 (tptm) cc_final: 0.8336 (tptp) REVERT: I 203 ARG cc_start: 0.6516 (ptp-110) cc_final: 0.6168 (mtp-110) REVERT: I 206 LYS cc_start: 0.7772 (mtpp) cc_final: 0.7541 (mtmm) REVERT: I 320 LYS cc_start: 0.8451 (mmtm) cc_final: 0.8134 (mmmt) REVERT: J 81 ASP cc_start: 0.6277 (t0) cc_final: 0.5987 (t0) REVERT: K 36 GLU cc_start: 0.7446 (tt0) cc_final: 0.6977 (tt0) REVERT: K 53 ASP cc_start: 0.9315 (m-30) cc_final: 0.9047 (m-30) REVERT: K 54 GLU cc_start: 0.6375 (OUTLIER) cc_final: 0.5821 (tm-30) REVERT: K 61 GLU cc_start: 0.8277 (pt0) cc_final: 0.7987 (pp20) REVERT: K 88 ARG cc_start: 0.8704 (OUTLIER) cc_final: 0.8440 (pmm-80) REVERT: K 134 GLU cc_start: 0.7647 (OUTLIER) cc_final: 0.7078 (tp30) REVERT: K 173 GLU cc_start: 0.6585 (tp30) cc_final: 0.6258 (mm-30) REVERT: K 209 LYS cc_start: 0.8059 (tppp) cc_final: 0.7746 (tppp) outliers start: 124 outliers final: 40 residues processed: 491 average time/residue: 0.5269 time to fit residues: 310.1230 Evaluate side-chains 416 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 361 time to evaluate : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 76 ASP Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 283 HIS Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain B residue 69 GLN Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 195 GLN Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 268 ARG Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 117 MET Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 294 ASP Chi-restraints excluded: chain D residue 308 THR Chi-restraints excluded: chain E residue 119 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 310 GLN Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 143 THR Chi-restraints excluded: chain F residue 265 LEU Chi-restraints excluded: chain G residue 91 GLN Chi-restraints excluded: chain G residue 155 ARG Chi-restraints excluded: chain G residue 334 ASP Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 143 THR Chi-restraints excluded: chain H residue 206 LYS Chi-restraints excluded: chain H residue 267 SER Chi-restraints excluded: chain H residue 335 GLU Chi-restraints excluded: chain I residue 37 LEU Chi-restraints excluded: chain I residue 113 ARG Chi-restraints excluded: chain I residue 115 THR Chi-restraints excluded: chain I residue 118 VAL Chi-restraints excluded: chain I residue 143 THR Chi-restraints excluded: chain I residue 189 VAL Chi-restraints excluded: chain J residue 57 ASP Chi-restraints excluded: chain J residue 124 THR Chi-restraints excluded: chain J residue 152 LEU Chi-restraints excluded: chain K residue 54 GLU Chi-restraints excluded: chain K residue 88 ARG Chi-restraints excluded: chain K residue 93 ARG Chi-restraints excluded: chain K residue 102 ILE Chi-restraints excluded: chain K residue 121 LEU Chi-restraints excluded: chain K residue 123 VAL Chi-restraints excluded: chain K residue 134 GLU Chi-restraints excluded: chain K residue 151 VAL Chi-restraints excluded: chain K residue 170 VAL Chi-restraints excluded: chain K residue 218 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 119 optimal weight: 2.9990 chunk 95 optimal weight: 4.9990 chunk 78 optimal weight: 5.9990 chunk 291 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 chunk 103 optimal weight: 0.6980 chunk 22 optimal weight: 0.5980 chunk 128 optimal weight: 3.9990 chunk 289 optimal weight: 4.9990 chunk 3 optimal weight: 40.0000 chunk 321 optimal weight: 1.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 253 GLN B 19 ASN B 282 ASN B 293 HIS D 170 ASN F 310 GLN ** G 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 348 ASN ** H 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 183 HIS J 19 HIS J 206 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.146914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.094475 restraints weight = 53648.190| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 2.75 r_work: 0.3089 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.2962 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2988 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2988 r_free = 0.2988 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2988 r_free = 0.2988 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2988 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.7665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.129 28649 Z= 0.240 Angle : 0.856 22.402 39383 Z= 0.419 Chirality : 0.058 0.483 4432 Planarity : 0.005 0.085 4823 Dihedral : 14.324 150.628 4809 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 4.60 % Allowed : 21.59 % Favored : 73.81 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.50 (0.14), residues: 3322 helix: 0.65 (0.15), residues: 1071 sheet: 0.63 (0.22), residues: 533 loop : -1.32 (0.15), residues: 1718 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 306 TYR 0.022 0.002 TYR D 324 PHE 0.020 0.002 PHE F 205 TRP 0.038 0.002 TRP B 247 HIS 0.017 0.001 HIS A 200 Details of bonding type rmsd/Z covalent geometry : bond 0.00536 / 0.24 (28649) covalent geometry : angle 0.85618 / 0.42 (39383) hydrogen bonds : bond 0.03689 / 2.58 ( 1176) hydrogen bonds : angle 4.99177 / 3.53 ( 3238) *********************** 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 498 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 378 time to evaluate : 1.090 Fit side-chains REVERT: A 28 LYS cc_start: 0.6867 (tppt) cc_final: 0.6627 (tppt) REVERT: A 102 ASP cc_start: 0.7843 (p0) cc_final: 0.7553 (p0) REVERT: A 220 GLU cc_start: 0.8427 (OUTLIER) cc_final: 0.7830 (tm-30) REVERT: A 257 GLU cc_start: 0.8064 (OUTLIER) cc_final: 0.7751 (pt0) REVERT: A 283 HIS cc_start: 0.8688 (OUTLIER) cc_final: 0.8154 (t-90) REVERT: A 300 LEU cc_start: 0.8676 (mt) cc_final: 0.8188 (mt) REVERT: A 321 ARG cc_start: 0.7336 (tpm170) cc_final: 0.6588 (tpm-80) REVERT: A 324 GLN cc_start: 0.6991 (OUTLIER) cc_final: 0.6769 (pt0) REVERT: A 343 LEU cc_start: 0.8517 (mt) cc_final: 0.8240 (mt) REVERT: A 396 ASN cc_start: 0.7508 (m110) cc_final: 0.7274 (m110) REVERT: B 67 GLU cc_start: 0.7551 (tt0) cc_final: 0.7328 (tt0) REVERT: B 121 HIS cc_start: 0.6494 (m90) cc_final: 0.6250 (m-70) REVERT: B 132 GLU cc_start: 0.8363 (OUTLIER) cc_final: 0.8061 (mp0) REVERT: B 171 LYS cc_start: 0.8154 (mtpp) cc_final: 0.7854 (ttpp) REVERT: B 268 ARG cc_start: 0.6221 (OUTLIER) cc_final: 0.5855 (tpt170) REVERT: B 282 ASN cc_start: 0.8841 (OUTLIER) cc_final: 0.8281 (t0) REVERT: B 294 ARG cc_start: 0.7130 (mmp80) cc_final: 0.6676 (mpt180) REVERT: C 112 LEU cc_start: 0.1090 (tp) cc_final: 0.0563 (mm) REVERT: D 278 LYS cc_start: 0.8020 (ttmt) cc_final: 0.7445 (tttm) REVERT: D 354 VAL cc_start: 0.8844 (OUTLIER) cc_final: 0.8577 (t) REVERT: E 34 GLU cc_start: 0.8451 (tt0) cc_final: 0.8183 (tt0) REVERT: E 65 GLU cc_start: 0.7789 (mm-30) cc_final: 0.7575 (mm-30) REVERT: E 269 ARG cc_start: 0.8288 (ptp90) cc_final: 0.8043 (mtm180) REVERT: E 310 GLN cc_start: 0.8550 (OUTLIER) cc_final: 0.7378 (mp10) REVERT: F 34 GLU cc_start: 0.8236 (tt0) cc_final: 0.7852 (mt-10) REVERT: F 65 GLU cc_start: 0.8752 (mm-30) cc_final: 0.8432 (mm-30) REVERT: F 79 LYS cc_start: 0.9274 (tmmt) cc_final: 0.8949 (ptpt) REVERT: F 117 ARG cc_start: 0.9022 (OUTLIER) cc_final: 0.7422 (mtp85) REVERT: F 139 GLN cc_start: 0.8821 (tp40) cc_final: 0.8540 (tt0) REVERT: F 188 GLU cc_start: 0.8147 (mt-10) cc_final: 0.7451 (pm20) REVERT: F 270 ASP cc_start: 0.8300 (p0) cc_final: 0.8070 (m-30) REVERT: F 301 VAL cc_start: 0.9171 (t) cc_final: 0.8925 (t) REVERT: G 155 ARG cc_start: 0.8520 (OUTLIER) cc_final: 0.8056 (ttp-110) REVERT: G 186 GLN cc_start: 0.8753 (mt0) cc_final: 0.8544 (mp10) REVERT: G 269 ARG cc_start: 0.7800 (ttm110) cc_final: 0.7581 (mtm-85) REVERT: G 335 GLU cc_start: 0.8595 (tt0) cc_final: 0.8168 (pt0) REVERT: H 34 GLU cc_start: 0.8429 (tt0) cc_final: 0.8196 (tt0) REVERT: H 69 ARG cc_start: 0.7879 (OUTLIER) cc_final: 0.7379 (ptp-170) REVERT: H 79 LYS cc_start: 0.8584 (ptmm) cc_final: 0.8316 (tmmm) REVERT: H 143 THR cc_start: 0.8895 (OUTLIER) cc_final: 0.8650 (p) REVERT: H 185 ARG cc_start: 0.8262 (ttp80) cc_final: 0.7621 (ttm-80) REVERT: H 206 LYS cc_start: 0.8006 (OUTLIER) cc_final: 0.7779 (pptt) REVERT: I 43 LEU cc_start: 0.9055 (OUTLIER) cc_final: 0.8826 (mm) REVERT: I 78 THR cc_start: 0.8024 (m) cc_final: 0.7774 (p) REVERT: I 155 ARG cc_start: 0.8435 (OUTLIER) cc_final: 0.8179 (ttp80) REVERT: I 203 ARG cc_start: 0.7114 (ptp-110) cc_final: 0.6724 (mtp-110) REVERT: I 320 LYS cc_start: 0.8714 (mmtm) cc_final: 0.8305 (mmmm) REVERT: I 324 TYR cc_start: 0.7961 (m-10) cc_final: 0.7575 (m-10) REVERT: J 81 ASP cc_start: 0.7011 (t0) cc_final: 0.6135 (t0) REVERT: J 83 ASP cc_start: 0.7474 (p0) cc_final: 0.7189 (p0) REVERT: J 124 THR cc_start: 0.8574 (OUTLIER) cc_final: 0.8201 (p) REVERT: J 208 GLN cc_start: 0.7491 (mt0) cc_final: 0.7210 (mt0) REVERT: J 220 ASP cc_start: 0.8719 (t0) cc_final: 0.8412 (t70) REVERT: K 4 ILE cc_start: 0.6844 (OUTLIER) cc_final: 0.6348 (tt) REVERT: K 36 GLU cc_start: 0.7138 (tt0) cc_final: 0.6863 (tt0) REVERT: K 54 GLU cc_start: 0.6519 (OUTLIER) cc_final: 0.5922 (tm-30) REVERT: K 61 GLU cc_start: 0.8378 (pt0) cc_final: 0.8085 (pp20) REVERT: K 73 ASP cc_start: 0.7621 (OUTLIER) cc_final: 0.7221 (m-30) REVERT: K 88 ARG cc_start: 0.8928 (OUTLIER) cc_final: 0.8432 (ptp90) REVERT: K 127 GLU cc_start: 0.8760 (mt-10) cc_final: 0.8549 (pt0) REVERT: K 134 GLU cc_start: 0.7920 (tm-30) cc_final: 0.7443 (tp30) REVERT: K 166 GLU cc_start: 0.7259 (pt0) cc_final: 0.7001 (pt0) REVERT: K 173 GLU cc_start: 0.6903 (tp30) cc_final: 0.6445 (mm-30) REVERT: K 188 LEU cc_start: 0.8255 (OUTLIER) cc_final: 0.8043 (mt) REVERT: K 209 LYS cc_start: 0.8243 (tppp) cc_final: 0.7895 (tppp) outliers start: 120 outliers final: 37 residues processed: 461 average time/residue: 0.5913 time to fit residues: 321.6005 Evaluate side-chains 378 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 319 time to evaluate : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 74 HIS Chi-restraints excluded: chain A residue 76 ASP Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 220 GLU Chi-restraints excluded: chain A residue 257 GLU 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 B residue 132 GLU Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 268 ARG Chi-restraints excluded: chain B residue 282 ASN Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 308 THR Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain E residue 95 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 310 GLN Chi-restraints excluded: chain E residue 333 ARG Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 117 ARG Chi-restraints excluded: chain F residue 143 THR Chi-restraints excluded: chain F residue 288 THR Chi-restraints excluded: chain G residue 155 ARG Chi-restraints excluded: chain G residue 306 SER 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 69 ARG Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain H residue 143 THR Chi-restraints excluded: chain H residue 206 LYS Chi-restraints excluded: chain H residue 214 LEU Chi-restraints excluded: chain H residue 267 SER Chi-restraints excluded: chain I residue 43 LEU Chi-restraints excluded: chain I residue 118 VAL Chi-restraints excluded: chain I residue 143 THR Chi-restraints excluded: chain I residue 155 ARG Chi-restraints excluded: chain I residue 189 VAL Chi-restraints excluded: chain I residue 222 LEU Chi-restraints excluded: chain J residue 50 GLU Chi-restraints excluded: chain J residue 124 THR Chi-restraints excluded: chain J residue 152 LEU Chi-restraints excluded: chain J residue 202 ASP Chi-restraints excluded: chain K residue 4 ILE Chi-restraints excluded: chain K residue 54 GLU Chi-restraints excluded: chain K residue 73 ASP Chi-restraints excluded: chain K residue 88 ARG Chi-restraints excluded: chain K residue 123 VAL Chi-restraints excluded: chain K residue 151 VAL Chi-restraints excluded: chain K residue 170 VAL Chi-restraints excluded: chain K residue 188 LEU Chi-restraints excluded: chain K residue 218 LEU Chi-restraints excluded: chain K residue 219 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 196 optimal weight: 0.6980 chunk 230 optimal weight: 1.9990 chunk 71 optimal weight: 4.9990 chunk 10 optimal weight: 9.9990 chunk 274 optimal weight: 4.9990 chunk 124 optimal weight: 0.4980 chunk 157 optimal weight: 1.9990 chunk 146 optimal weight: 0.9990 chunk 131 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 83 HIS B 69 GLN B 220 ASN B 305 HIS D 170 ASN D 227 HIS E 102 ASN E 129 ASN G 91 GLN G 96 GLN G 310 GLN J 194 ASN ** J 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 216 HIS K 5 HIS K 216 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.146434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.093837 restraints weight = 53869.865| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 2.75 r_work: 0.3103 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2978 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2975 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2975 r_free = 0.2975 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2975 r_free = 0.2975 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2975 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.8250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 28649 Z= 0.185 Angle : 0.750 14.377 39383 Z= 0.364 Chirality : 0.054 0.471 4432 Planarity : 0.004 0.043 4823 Dihedral : 14.283 148.815 4809 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 3.68 % Allowed : 23.54 % Favored : 72.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.14), residues: 3322 helix: 0.83 (0.15), residues: 1068 sheet: 0.62 (0.22), residues: 535 loop : -1.32 (0.14), residues: 1719 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 306 TYR 0.018 0.002 TYR B 262 PHE 0.018 0.002 PHE A 20 TRP 0.034 0.001 TRP B 247 HIS 0.006 0.001 HIS H 159 Details of bonding type rmsd/Z covalent geometry : bond 0.00414 / 0.18 (28649) covalent geometry : angle 0.75013 / 0.36 (39383) hydrogen bonds : bond 0.03493 / 2.47 ( 1176) hydrogen bonds : angle 4.87521 / 3.44 ( 3238) *********************** 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 439 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 343 time to evaluate : 0.857 Fit side-chains revert: symmetry clash REVERT: A 28 LYS cc_start: 0.6489 (tppt) cc_final: 0.6218 (tppt) REVERT: A 102 ASP cc_start: 0.7899 (p0) cc_final: 0.7578 (p0) REVERT: A 107 ASP cc_start: 0.7423 (m-30) cc_final: 0.7068 (m-30) REVERT: A 220 GLU cc_start: 0.8527 (OUTLIER) cc_final: 0.7793 (tm-30) REVERT: A 254 LEU cc_start: 0.7317 (mt) cc_final: 0.7064 (mp) REVERT: A 257 GLU cc_start: 0.8002 (pp20) cc_final: 0.7712 (pt0) REVERT: A 283 HIS cc_start: 0.8711 (OUTLIER) cc_final: 0.8261 (t-90) REVERT: A 321 ARG cc_start: 0.7382 (tpm170) cc_final: 0.6430 (tpm-80) REVERT: A 324 GLN cc_start: 0.7019 (OUTLIER) cc_final: 0.6495 (pm20) REVERT: A 420 LYS cc_start: 0.8880 (mtpp) cc_final: 0.8535 (ptmt) REVERT: B 106 GLU cc_start: 0.8329 (OUTLIER) cc_final: 0.6476 (tm-30) REVERT: B 121 HIS cc_start: 0.6646 (m90) cc_final: 0.6044 (m-70) REVERT: B 171 LYS cc_start: 0.8180 (mtpp) cc_final: 0.7854 (ttpp) REVERT: B 175 ARG cc_start: 0.6924 (OUTLIER) cc_final: 0.6636 (ttp80) REVERT: B 268 ARG cc_start: 0.6434 (OUTLIER) cc_final: 0.6096 (tpt-90) REVERT: B 294 ARG cc_start: 0.7196 (mmp80) cc_final: 0.6712 (mpt180) REVERT: C 112 LEU cc_start: 0.0877 (tp) cc_final: 0.0348 (mm) REVERT: D 278 LYS cc_start: 0.7972 (ttmt) cc_final: 0.7584 (tttp) REVERT: D 354 VAL cc_start: 0.8895 (OUTLIER) cc_final: 0.8626 (t) REVERT: E 34 GLU cc_start: 0.8402 (tt0) cc_final: 0.8172 (tt0) REVERT: E 37 LEU cc_start: 0.8672 (OUTLIER) cc_final: 0.8371 (mp) REVERT: E 56 GLN cc_start: 0.8801 (OUTLIER) cc_final: 0.8529 (pm20) REVERT: E 172 VAL cc_start: 0.8799 (OUTLIER) cc_final: 0.8538 (t) REVERT: E 269 ARG cc_start: 0.8294 (ptp90) cc_final: 0.8053 (mtm180) REVERT: E 310 GLN cc_start: 0.8428 (OUTLIER) cc_final: 0.7272 (mp10) REVERT: E 335 GLU cc_start: 0.8441 (tt0) cc_final: 0.8170 (mt-10) REVERT: F 34 GLU cc_start: 0.8226 (tt0) cc_final: 0.7871 (mt-10) REVERT: F 65 GLU cc_start: 0.8839 (mm-30) cc_final: 0.8503 (mm-30) REVERT: F 80 ASP cc_start: 0.8980 (m-30) cc_final: 0.8752 (m-30) REVERT: F 139 GLN cc_start: 0.8722 (tp40) cc_final: 0.8330 (tt0) REVERT: F 143 THR cc_start: 0.9163 (OUTLIER) cc_final: 0.8844 (p) REVERT: F 188 GLU cc_start: 0.8276 (mt-10) cc_final: 0.7662 (pm20) REVERT: G 206 LYS cc_start: 0.8283 (ptpp) cc_final: 0.8005 (mtpp) REVERT: G 269 ARG cc_start: 0.7812 (ttm110) cc_final: 0.7604 (mtm-85) REVERT: G 335 GLU cc_start: 0.8564 (tt0) cc_final: 0.8220 (pt0) REVERT: H 34 GLU cc_start: 0.8487 (tt0) cc_final: 0.8257 (tt0) REVERT: H 69 ARG cc_start: 0.7835 (OUTLIER) cc_final: 0.7368 (ptp-170) REVERT: H 79 LYS cc_start: 0.8513 (ptmm) cc_final: 0.8289 (tmmm) REVERT: H 143 THR cc_start: 0.9039 (OUTLIER) cc_final: 0.8823 (p) REVERT: H 185 ARG cc_start: 0.8327 (ttp80) cc_final: 0.7680 (ttm-80) REVERT: H 186 GLN cc_start: 0.8195 (OUTLIER) cc_final: 0.7757 (mp10) REVERT: H 214 LEU cc_start: 0.9020 (OUTLIER) cc_final: 0.8768 (tt) REVERT: H 249 GLU cc_start: 0.9256 (mm-30) cc_final: 0.8998 (mm-30) REVERT: I 43 LEU cc_start: 0.9163 (OUTLIER) cc_final: 0.8951 (mm) REVERT: I 133 TYR cc_start: 0.8141 (t80) cc_final: 0.7915 (t80) REVERT: I 155 ARG cc_start: 0.8482 (OUTLIER) cc_final: 0.8266 (ttp80) REVERT: I 203 ARG cc_start: 0.7303 (ptp-110) cc_final: 0.6848 (mtp-110) REVERT: I 320 LYS cc_start: 0.8729 (mmtm) cc_final: 0.8327 (mmmm) REVERT: I 324 TYR cc_start: 0.8276 (m-10) cc_final: 0.7993 (m-10) REVERT: J 124 THR cc_start: 0.8543 (OUTLIER) cc_final: 0.8242 (p) REVERT: J 220 ASP cc_start: 0.8887 (t0) cc_final: 0.8567 (t70) REVERT: K 36 GLU cc_start: 0.7127 (tt0) cc_final: 0.6897 (tt0) REVERT: K 54 GLU cc_start: 0.6597 (OUTLIER) cc_final: 0.6086 (tm-30) REVERT: K 61 GLU cc_start: 0.8463 (pt0) cc_final: 0.8152 (pp20) REVERT: K 127 GLU cc_start: 0.8730 (mt-10) cc_final: 0.8343 (pt0) REVERT: K 134 GLU cc_start: 0.8067 (tm-30) cc_final: 0.7726 (tp30) REVERT: K 173 GLU cc_start: 0.6881 (tp30) cc_final: 0.6455 (mm-30) REVERT: K 209 LYS cc_start: 0.8258 (tppp) cc_final: 0.7903 (tppp) outliers start: 96 outliers final: 35 residues processed: 403 average time/residue: 0.5663 time to fit residues: 270.0643 Evaluate side-chains 364 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 309 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 HIS Chi-restraints excluded: chain A residue 76 ASP Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 220 GLU Chi-restraints excluded: chain A residue 283 HIS Chi-restraints excluded: chain A residue 324 GLN Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 106 GLU Chi-restraints excluded: chain B residue 175 ARG Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 268 ARG Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 218 ILE 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 37 LEU Chi-restraints excluded: chain E residue 56 GLN Chi-restraints excluded: chain E residue 148 GLN 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 310 GLN Chi-restraints excluded: chain E residue 333 ARG 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 306 SER Chi-restraints excluded: chain H residue 25 LEU Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 31 LEU Chi-restraints excluded: chain H residue 69 ARG Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 143 THR Chi-restraints excluded: chain H residue 186 GLN Chi-restraints excluded: chain H residue 214 LEU Chi-restraints excluded: chain H residue 267 SER Chi-restraints excluded: chain I residue 37 LEU Chi-restraints excluded: chain I residue 43 LEU Chi-restraints excluded: chain I residue 99 ASP Chi-restraints excluded: chain I residue 118 VAL Chi-restraints excluded: chain I residue 126 SER Chi-restraints excluded: chain I residue 155 ARG Chi-restraints excluded: chain I residue 189 VAL Chi-restraints excluded: chain I residue 222 LEU Chi-restraints excluded: chain J residue 6 ILE Chi-restraints excluded: chain J residue 50 GLU Chi-restraints excluded: chain J residue 124 THR 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 151 VAL Chi-restraints excluded: chain K residue 218 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 58 optimal weight: 0.9980 chunk 309 optimal weight: 1.9990 chunk 258 optimal weight: 0.9980 chunk 194 optimal weight: 1.9990 chunk 174 optimal weight: 0.3980 chunk 135 optimal weight: 0.0270 chunk 15 optimal weight: 3.9990 chunk 75 optimal weight: 3.9990 chunk 14 optimal weight: 9.9990 chunk 111 optimal weight: 0.9990 chunk 306 optimal weight: 8.9990 overall best weight: 0.6840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 ASN D 170 ASN E 146 ASN H 310 GLN ** I 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 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 = 0.3940 r_free = 0.3940 target = 0.147407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.095476 restraints weight = 44184.037| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 2.52 r_work: 0.3134 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3011 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3012 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3012 r_free = 0.3012 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3012 r_free = 0.3012 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3012 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.8468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.103 28649 Z= 0.144 Angle : 0.743 14.217 39383 Z= 0.355 Chirality : 0.054 0.634 4432 Planarity : 0.004 0.117 4823 Dihedral : 14.208 150.004 4809 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 3.11 % Allowed : 24.77 % Favored : 72.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.14), residues: 3322 helix: 0.94 (0.15), residues: 1071 sheet: 0.63 (0.22), residues: 535 loop : -1.28 (0.15), residues: 1716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG E 64 TYR 0.023 0.002 TYR D 133 PHE 0.030 0.001 PHE A 425 TRP 0.035 0.001 TRP B 247 HIS 0.006 0.001 HIS K 169 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.14 (28649) covalent geometry : angle 0.74311 / 0.35 (39383) hydrogen bonds : bond 0.03341 / 2.34 ( 1176) hydrogen bonds : angle 4.76366 / 3.35 ( 3238) *********************** 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 403 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 322 time to evaluate : 0.995 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 LYS cc_start: 0.6672 (tppt) cc_final: 0.6434 (tppt) REVERT: A 102 ASP cc_start: 0.7883 (p0) cc_final: 0.7548 (p0) REVERT: A 107 ASP cc_start: 0.7438 (m-30) cc_final: 0.7149 (m-30) REVERT: A 220 GLU cc_start: 0.8520 (OUTLIER) cc_final: 0.8004 (pp20) REVERT: A 223 SER cc_start: 0.7648 (t) cc_final: 0.7234 (p) REVERT: A 242 LYS cc_start: 0.8717 (mppt) cc_final: 0.8433 (mmmt) REVERT: A 254 LEU cc_start: 0.7408 (mt) cc_final: 0.7158 (mp) REVERT: A 257 GLU cc_start: 0.8041 (pp20) cc_final: 0.7828 (pt0) REVERT: A 321 ARG cc_start: 0.7410 (tpm170) cc_final: 0.6744 (tpm-80) REVERT: A 324 GLN cc_start: 0.7029 (OUTLIER) cc_final: 0.6453 (pt0) REVERT: A 331 ASP cc_start: 0.7263 (m-30) cc_final: 0.6750 (m-30) REVERT: A 420 LYS cc_start: 0.8899 (mtpp) cc_final: 0.8562 (ptmt) REVERT: B 106 GLU cc_start: 0.8360 (OUTLIER) cc_final: 0.6527 (tm-30) REVERT: B 121 HIS cc_start: 0.6219 (m90) cc_final: 0.5845 (m-70) REVERT: B 132 GLU cc_start: 0.8241 (OUTLIER) cc_final: 0.7968 (mp0) REVERT: B 171 LYS cc_start: 0.8157 (mtpp) cc_final: 0.7860 (ttpp) REVERT: B 175 ARG cc_start: 0.7317 (OUTLIER) cc_final: 0.7011 (ttp80) REVERT: B 268 ARG cc_start: 0.6391 (OUTLIER) cc_final: 0.6031 (tpt-90) REVERT: B 294 ARG cc_start: 0.7124 (mmp80) cc_final: 0.6722 (mpt180) REVERT: C 112 LEU cc_start: 0.0859 (tp) cc_final: 0.0360 (mm) REVERT: D 278 LYS cc_start: 0.7900 (ttmt) cc_final: 0.7571 (tttp) REVERT: D 354 VAL cc_start: 0.8949 (OUTLIER) cc_final: 0.8683 (t) REVERT: E 34 GLU cc_start: 0.8347 (tt0) cc_final: 0.8128 (tt0) REVERT: E 56 GLN cc_start: 0.8798 (OUTLIER) cc_final: 0.8517 (pm20) REVERT: E 172 VAL cc_start: 0.8806 (OUTLIER) cc_final: 0.8550 (t) REVERT: E 269 ARG cc_start: 0.8232 (ptp90) cc_final: 0.7922 (mtm-85) REVERT: E 335 GLU cc_start: 0.8364 (tt0) cc_final: 0.8138 (mt-10) REVERT: F 34 GLU cc_start: 0.8126 (tt0) cc_final: 0.7797 (mt-10) REVERT: F 65 GLU cc_start: 0.8862 (mm-30) cc_final: 0.8541 (mm-30) REVERT: F 80 ASP cc_start: 0.8917 (m-30) cc_final: 0.8648 (m-30) REVERT: F 117 ARG cc_start: 0.9031 (OUTLIER) cc_final: 0.7477 (mtp85) REVERT: F 139 GLN cc_start: 0.8748 (tp40) cc_final: 0.8341 (tt0) REVERT: F 143 THR cc_start: 0.9125 (OUTLIER) cc_final: 0.8821 (p) REVERT: F 188 GLU cc_start: 0.8260 (mt-10) cc_final: 0.7680 (pm20) REVERT: F 206 LYS cc_start: 0.7855 (pptt) cc_final: 0.7588 (mmpt) REVERT: F 335 GLU cc_start: 0.8450 (tt0) cc_final: 0.8167 (mt-10) REVERT: G 206 LYS cc_start: 0.8293 (ptpp) cc_final: 0.8020 (mtpp) REVERT: G 335 GLU cc_start: 0.8487 (tt0) cc_final: 0.8149 (pt0) REVERT: H 34 GLU cc_start: 0.8526 (tt0) cc_final: 0.8310 (tt0) REVERT: H 69 ARG cc_start: 0.7865 (OUTLIER) cc_final: 0.7454 (ptp-170) REVERT: H 79 LYS cc_start: 0.8501 (ptmm) cc_final: 0.8292 (tmmm) REVERT: H 139 GLN cc_start: 0.8633 (tp40) cc_final: 0.8411 (tt0) REVERT: H 185 ARG cc_start: 0.8298 (ttp80) cc_final: 0.7683 (ttm-80) REVERT: H 186 GLN cc_start: 0.8318 (OUTLIER) cc_final: 0.7908 (mp10) REVERT: H 249 GLU cc_start: 0.9224 (mm-30) cc_final: 0.8999 (mm-30) REVERT: H 320 LYS cc_start: 0.8424 (mmmm) cc_final: 0.8127 (mmtp) REVERT: I 34 GLU cc_start: 0.8525 (tm-30) cc_final: 0.8288 (tm-30) REVERT: I 79 LYS cc_start: 0.8680 (ptmt) cc_final: 0.8168 (ptpp) REVERT: I 133 TYR cc_start: 0.8133 (t80) cc_final: 0.7877 (t80) REVERT: I 320 LYS cc_start: 0.8742 (mmtm) cc_final: 0.8336 (mmmm) REVERT: I 324 TYR cc_start: 0.8358 (m-10) cc_final: 0.8099 (m-10) REVERT: J 44 ASP cc_start: 0.9013 (m-30) cc_final: 0.8684 (m-30) REVERT: J 73 ASP cc_start: 0.7946 (p0) cc_final: 0.7493 (p0) REVERT: J 124 THR cc_start: 0.8562 (OUTLIER) cc_final: 0.8241 (p) REVERT: J 173 GLU cc_start: 0.8399 (pm20) cc_final: 0.8038 (mp0) REVERT: J 194 ASN cc_start: 0.8630 (t160) cc_final: 0.8425 (t0) REVERT: J 220 ASP cc_start: 0.8942 (t0) cc_final: 0.8734 (t70) REVERT: K 37 MET cc_start: 0.6996 (ptm) cc_final: 0.5775 (ppp) REVERT: K 54 GLU cc_start: 0.6712 (OUTLIER) cc_final: 0.6212 (tm-30) REVERT: K 61 GLU cc_start: 0.8522 (pt0) cc_final: 0.8210 (pp20) REVERT: K 75 LEU cc_start: 0.8451 (mp) cc_final: 0.8220 (mp) REVERT: K 76 GLU cc_start: 0.7003 (mp0) cc_final: 0.6690 (mp0) REVERT: K 127 GLU cc_start: 0.8668 (mt-10) cc_final: 0.8274 (pt0) REVERT: K 134 GLU cc_start: 0.8073 (tm-30) cc_final: 0.7733 (tp30) REVERT: K 166 GLU cc_start: 0.7424 (pt0) cc_final: 0.7159 (pt0) REVERT: K 173 GLU cc_start: 0.6958 (tp30) cc_final: 0.6432 (mm-30) REVERT: K 209 LYS cc_start: 0.8257 (tppp) cc_final: 0.7961 (tppp) outliers start: 81 outliers final: 33 residues processed: 376 average time/residue: 0.5948 time to fit residues: 262.0461 Evaluate side-chains 346 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 298 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 HIS Chi-restraints excluded: chain A residue 220 GLU Chi-restraints excluded: chain A residue 283 HIS Chi-restraints excluded: chain A residue 324 GLN Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 106 GLU Chi-restraints excluded: chain B residue 132 GLU Chi-restraints excluded: chain B residue 175 ARG Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 268 ARG Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 354 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 233 VAL Chi-restraints excluded: chain E residue 333 ARG Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain F residue 117 ARG Chi-restraints excluded: chain F residue 143 THR Chi-restraints excluded: chain H residue 25 LEU Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 31 LEU Chi-restraints excluded: chain H residue 69 ARG Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 186 GLN Chi-restraints excluded: chain H residue 251 ILE Chi-restraints excluded: chain H residue 267 SER Chi-restraints excluded: chain H residue 296 LEU Chi-restraints excluded: chain I residue 37 LEU Chi-restraints excluded: chain I residue 91 GLN Chi-restraints excluded: chain I residue 99 ASP Chi-restraints excluded: chain I residue 118 VAL Chi-restraints excluded: chain I residue 126 SER Chi-restraints excluded: chain I residue 189 VAL Chi-restraints excluded: chain I residue 222 LEU Chi-restraints excluded: chain J residue 6 ILE Chi-restraints excluded: chain J residue 50 GLU Chi-restraints excluded: chain J residue 124 THR Chi-restraints excluded: chain J residue 152 LEU Chi-restraints excluded: chain J residue 202 ASP Chi-restraints excluded: chain K residue 4 ILE 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 151 VAL Chi-restraints excluded: chain K residue 218 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 45 optimal weight: 2.9990 chunk 207 optimal weight: 0.1980 chunk 46 optimal weight: 4.9990 chunk 228 optimal weight: 0.9990 chunk 288 optimal weight: 0.6980 chunk 185 optimal weight: 2.9990 chunk 125 optimal weight: 0.9980 chunk 49 optimal weight: 0.9990 chunk 181 optimal weight: 0.6980 chunk 84 optimal weight: 20.0000 chunk 270 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 328 GLN B 220 ASN D 170 ASN E 146 ASN G 102 ASN ** I 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 242 GLN I 341 GLN ** J 194 ASN ** 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 = 0.3945 r_free = 0.3945 target = 0.147648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.095397 restraints weight = 51607.809| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 2.71 r_work: 0.3138 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3008 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3008 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3008 r_free = 0.3008 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3008 r_free = 0.3008 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3008 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.8752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 28649 Z= 0.140 Angle : 0.718 13.798 39383 Z= 0.347 Chirality : 0.052 0.454 4432 Planarity : 0.004 0.068 4823 Dihedral : 14.112 148.841 4807 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 2.88 % Allowed : 25.15 % Favored : 71.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.30 (0.14), residues: 3322 helix: 1.02 (0.15), residues: 1083 sheet: 0.54 (0.21), residues: 567 loop : -1.32 (0.15), residues: 1672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG C 114 TYR 0.017 0.001 TYR D 324 PHE 0.048 0.001 PHE A 425 TRP 0.034 0.001 TRP A 414 HIS 0.005 0.001 HIS H 159 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 (28649) covalent geometry : angle 0.71838 / 0.35 (39383) hydrogen bonds : bond 0.03266 / 2.27 ( 1176) hydrogen bonds : angle 4.72837 / 3.33 ( 3238) *********************** 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 389 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 314 time to evaluate : 0.994 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 28 LYS cc_start: 0.6694 (tppt) cc_final: 0.6492 (tppt) REVERT: A 102 ASP cc_start: 0.7947 (p0) cc_final: 0.7621 (p0) REVERT: A 220 GLU cc_start: 0.8573 (OUTLIER) cc_final: 0.8049 (pp20) REVERT: A 223 SER cc_start: 0.7605 (OUTLIER) cc_final: 0.7229 (p) REVERT: A 242 LYS cc_start: 0.8725 (mppt) cc_final: 0.8459 (mmmt) REVERT: A 254 LEU cc_start: 0.7532 (mt) cc_final: 0.7325 (mp) REVERT: A 283 HIS cc_start: 0.8741 (OUTLIER) cc_final: 0.8282 (t-90) REVERT: A 306 ARG cc_start: 0.7654 (ttp80) cc_final: 0.7270 (ttp80) REVERT: A 321 ARG cc_start: 0.7453 (tpm170) cc_final: 0.7215 (tpm-80) REVERT: A 331 ASP cc_start: 0.7432 (m-30) cc_final: 0.6866 (m-30) REVERT: A 332 GLU cc_start: 0.6652 (OUTLIER) cc_final: 0.6382 (tp30) REVERT: A 420 LYS cc_start: 0.8817 (mtpp) cc_final: 0.8537 (ptpp) REVERT: A 427 GLU cc_start: 0.7497 (tp30) cc_final: 0.6943 (tm-30) REVERT: B 106 GLU cc_start: 0.8655 (OUTLIER) cc_final: 0.6973 (tm-30) REVERT: B 121 HIS cc_start: 0.6275 (m90) cc_final: 0.5841 (m-70) REVERT: B 132 GLU cc_start: 0.8281 (OUTLIER) cc_final: 0.8021 (mp0) REVERT: B 171 LYS cc_start: 0.8301 (mtpp) cc_final: 0.8033 (ttpp) REVERT: B 175 ARG cc_start: 0.7512 (OUTLIER) cc_final: 0.7226 (ttp80) REVERT: B 294 ARG cc_start: 0.7169 (mmp80) cc_final: 0.6861 (mpt180) REVERT: C 112 LEU cc_start: 0.0797 (tp) cc_final: 0.0272 (mm) REVERT: D 278 LYS cc_start: 0.8075 (ttmt) cc_final: 0.7803 (tttp) REVERT: D 354 VAL cc_start: 0.8997 (OUTLIER) cc_final: 0.8723 (t) REVERT: E 56 GLN cc_start: 0.8832 (OUTLIER) cc_final: 0.8572 (pm20) REVERT: E 172 VAL cc_start: 0.8844 (OUTLIER) cc_final: 0.8577 (t) REVERT: E 269 ARG cc_start: 0.8213 (ptp90) cc_final: 0.7934 (mtm-85) REVERT: E 333 ARG cc_start: 0.8773 (OUTLIER) cc_final: 0.8230 (ptp90) REVERT: F 34 GLU cc_start: 0.8062 (tt0) cc_final: 0.7814 (mt-10) REVERT: F 65 GLU cc_start: 0.8829 (mm-30) cc_final: 0.8541 (mm-30) REVERT: F 69 ARG cc_start: 0.8591 (ttt180) cc_final: 0.8371 (ttp80) REVERT: F 80 ASP cc_start: 0.8999 (m-30) cc_final: 0.8765 (m-30) REVERT: F 117 ARG cc_start: 0.9080 (OUTLIER) cc_final: 0.7663 (mtp85) REVERT: F 139 GLN cc_start: 0.8925 (tp40) cc_final: 0.8540 (tt0) REVERT: F 143 THR cc_start: 0.9194 (OUTLIER) cc_final: 0.8916 (p) REVERT: F 188 GLU cc_start: 0.8346 (mt-10) cc_final: 0.7894 (pm20) REVERT: G 92 SER cc_start: 0.8273 (m) cc_final: 0.7974 (p) REVERT: G 203 ARG cc_start: 0.7666 (mmm-85) cc_final: 0.7424 (mmm-85) REVERT: G 206 LYS cc_start: 0.8322 (ptpp) cc_final: 0.8044 (mtpp) REVERT: G 335 GLU cc_start: 0.8477 (tt0) cc_final: 0.8247 (pt0) REVERT: H 69 ARG cc_start: 0.7894 (OUTLIER) cc_final: 0.7478 (ptp-170) REVERT: H 79 LYS cc_start: 0.8521 (ptmm) cc_final: 0.8300 (tmmm) REVERT: H 185 ARG cc_start: 0.8405 (ttp80) cc_final: 0.7945 (ttm-80) REVERT: H 320 LYS cc_start: 0.8457 (mmmm) cc_final: 0.8218 (mmtp) REVERT: I 34 GLU cc_start: 0.8600 (tm-30) cc_final: 0.8380 (tm-30) REVERT: I 79 LYS cc_start: 0.8704 (ptmt) cc_final: 0.8244 (ptpp) REVERT: I 203 ARG cc_start: 0.7256 (ptp-110) cc_final: 0.6856 (mtp-110) REVERT: I 324 TYR cc_start: 0.8482 (m-10) cc_final: 0.8195 (m-10) REVERT: J 44 ASP cc_start: 0.9033 (m-30) cc_final: 0.8724 (m-30) REVERT: J 83 ASP cc_start: 0.8202 (p0) cc_final: 0.7642 (p0) REVERT: J 124 THR cc_start: 0.8774 (OUTLIER) cc_final: 0.8516 (p) REVERT: J 194 ASN cc_start: 0.8783 (t160) cc_final: 0.8568 (t0) REVERT: J 220 ASP cc_start: 0.8883 (t0) cc_final: 0.8584 (t70) REVERT: K 36 GLU cc_start: 0.7377 (tt0) cc_final: 0.7099 (tt0) REVERT: K 37 MET cc_start: 0.6838 (ptm) cc_final: 0.5773 (ppp) REVERT: K 52 ARG cc_start: 0.8711 (ppt170) cc_final: 0.8506 (ptm-80) REVERT: K 53 ASP cc_start: 0.9107 (m-30) cc_final: 0.8806 (m-30) REVERT: K 54 GLU cc_start: 0.6609 (OUTLIER) cc_final: 0.6221 (tm-30) REVERT: K 61 GLU cc_start: 0.8533 (pt0) cc_final: 0.8196 (pp20) REVERT: K 75 LEU cc_start: 0.8611 (mp) cc_final: 0.8355 (mp) REVERT: K 76 GLU cc_start: 0.7275 (mp0) cc_final: 0.7059 (mp0) REVERT: K 127 GLU cc_start: 0.8708 (mt-10) cc_final: 0.8293 (pt0) REVERT: K 134 GLU cc_start: 0.8170 (tm-30) cc_final: 0.7848 (tp30) REVERT: K 166 GLU cc_start: 0.7733 (pt0) cc_final: 0.7500 (pt0) REVERT: K 173 GLU cc_start: 0.7038 (tp30) cc_final: 0.6641 (mm-30) REVERT: K 190 MET cc_start: 0.7731 (ptm) cc_final: 0.7529 (ptp) outliers start: 75 outliers final: 33 residues processed: 364 average time/residue: 0.5995 time to fit residues: 256.7291 Evaluate side-chains 344 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 295 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 220 GLU Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain A residue 283 HIS Chi-restraints excluded: chain A residue 332 GLU Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 72 GLN Chi-restraints excluded: chain B residue 106 GLU Chi-restraints excluded: chain B residue 132 GLU Chi-restraints excluded: chain B residue 175 ARG Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 354 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 233 VAL Chi-restraints excluded: chain E residue 333 ARG Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain F residue 117 ARG Chi-restraints excluded: chain F residue 143 THR Chi-restraints excluded: chain G residue 299 ILE Chi-restraints excluded: chain H residue 25 LEU Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 31 LEU Chi-restraints excluded: chain H residue 69 ARG Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 251 ILE Chi-restraints excluded: chain H residue 267 SER Chi-restraints excluded: chain H residue 296 LEU Chi-restraints excluded: chain I residue 37 LEU Chi-restraints excluded: chain I residue 99 ASP Chi-restraints excluded: chain I residue 118 VAL Chi-restraints excluded: chain I residue 189 VAL Chi-restraints excluded: chain I residue 222 LEU Chi-restraints excluded: chain J residue 124 THR Chi-restraints excluded: chain J residue 125 LEU 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 54 GLU Chi-restraints excluded: chain K residue 123 VAL Chi-restraints excluded: chain K residue 131 LEU Chi-restraints excluded: chain K residue 151 VAL Chi-restraints excluded: chain K residue 218 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 17 optimal weight: 4.9990 chunk 130 optimal weight: 2.9990 chunk 178 optimal weight: 1.9990 chunk 136 optimal weight: 0.6980 chunk 154 optimal weight: 0.7980 chunk 71 optimal weight: 0.8980 chunk 157 optimal weight: 0.9990 chunk 139 optimal weight: 4.9990 chunk 231 optimal weight: 0.7980 chunk 155 optimal weight: 2.9990 chunk 100 optimal weight: 3.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 324 GLN B 220 ASN D 170 ASN E 102 ASN E 146 ASN ** F 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 102 ASN I 102 ASN ** I 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 208 GLN ** 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 = 0.3936 r_free = 0.3936 target = 0.146950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.094427 restraints weight = 53517.650| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 2.74 r_work: 0.3123 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2994 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2950 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2950 r_free = 0.2950 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2950 r_free = 0.2950 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.2950 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.8996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 28649 Z= 0.149 Angle : 0.723 13.454 39383 Z= 0.350 Chirality : 0.051 0.415 4432 Planarity : 0.004 0.043 4823 Dihedral : 14.115 148.265 4807 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 2.07 % Allowed : 26.07 % Favored : 71.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.24 (0.14), residues: 3322 helix: 1.04 (0.16), residues: 1077 sheet: 0.62 (0.21), residues: 544 loop : -1.25 (0.15), residues: 1701 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 269 TYR 0.024 0.002 TYR D 133 PHE 0.024 0.001 PHE A 425 TRP 0.040 0.001 TRP A 414 HIS 0.006 0.001 HIS J 5 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.15 (28649) covalent geometry : angle 0.72318 / 0.35 (39383) hydrogen bonds : bond 0.03306 / 2.32 ( 1176) hydrogen bonds : angle 4.71761 / 3.34 ( 3238) ********************** 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 354 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 300 time to evaluate : 0.943 Fit side-chains revert: symmetry clash REVERT: A 102 ASP cc_start: 0.8059 (p0) cc_final: 0.7701 (p0) REVERT: A 116 ASP cc_start: 0.7289 (OUTLIER) cc_final: 0.6938 (m-30) REVERT: A 220 GLU cc_start: 0.8646 (OUTLIER) cc_final: 0.8091 (pp20) REVERT: A 223 SER cc_start: 0.7670 (OUTLIER) cc_final: 0.7283 (p) REVERT: A 283 HIS cc_start: 0.8735 (OUTLIER) cc_final: 0.8265 (t-90) REVERT: A 306 ARG cc_start: 0.7625 (ttp80) cc_final: 0.6999 (ttp80) REVERT: A 321 ARG cc_start: 0.7433 (tpm170) cc_final: 0.7090 (tpm-80) REVERT: A 324 GLN cc_start: 0.7497 (pt0) cc_final: 0.7200 (pm20) REVERT: A 331 ASP cc_start: 0.7374 (m-30) cc_final: 0.6800 (m-30) REVERT: A 332 GLU cc_start: 0.6695 (OUTLIER) cc_final: 0.6416 (tp30) REVERT: A 420 LYS cc_start: 0.8818 (mtpp) cc_final: 0.8493 (ptpp) REVERT: A 427 GLU cc_start: 0.7682 (tp30) cc_final: 0.7323 (tm-30) REVERT: B 121 HIS cc_start: 0.6376 (m90) cc_final: 0.6025 (m-70) REVERT: B 132 GLU cc_start: 0.8253 (OUTLIER) cc_final: 0.7958 (mp0) REVERT: B 171 LYS cc_start: 0.8434 (mtpp) cc_final: 0.8168 (ttpp) REVERT: B 175 ARG cc_start: 0.7589 (OUTLIER) cc_final: 0.7261 (ttp80) REVERT: B 294 ARG cc_start: 0.7210 (mmp80) cc_final: 0.6933 (mpt180) REVERT: C 112 LEU cc_start: 0.0705 (tp) cc_final: 0.0190 (mm) REVERT: D 278 LYS cc_start: 0.8115 (ttmt) cc_final: 0.7812 (tttp) REVERT: D 322 ASP cc_start: 0.7513 (p0) cc_final: 0.7036 (p0) REVERT: D 354 VAL cc_start: 0.9084 (OUTLIER) cc_final: 0.8785 (t) REVERT: E 56 GLN cc_start: 0.8847 (OUTLIER) cc_final: 0.8585 (pm20) REVERT: E 172 VAL cc_start: 0.8883 (OUTLIER) cc_final: 0.8607 (t) REVERT: E 269 ARG cc_start: 0.8289 (ptp90) cc_final: 0.8012 (mtm-85) REVERT: F 65 GLU cc_start: 0.8859 (mm-30) cc_final: 0.8572 (mm-30) REVERT: F 69 ARG cc_start: 0.8611 (ttt180) cc_final: 0.8389 (ttp80) REVERT: F 117 ARG cc_start: 0.9102 (OUTLIER) cc_final: 0.7667 (mtp85) REVERT: F 139 GLN cc_start: 0.8927 (tp40) cc_final: 0.8593 (tt0) REVERT: F 143 THR cc_start: 0.9187 (OUTLIER) cc_final: 0.8906 (p) REVERT: F 188 GLU cc_start: 0.8367 (mt-10) cc_final: 0.7930 (pm20) REVERT: G 65 GLU cc_start: 0.8757 (mm-30) cc_final: 0.8519 (mm-30) REVERT: G 92 SER cc_start: 0.8365 (m) cc_final: 0.8055 (p) REVERT: G 206 LYS cc_start: 0.8460 (ptpp) cc_final: 0.8207 (mtpp) REVERT: G 335 GLU cc_start: 0.8502 (tt0) cc_final: 0.8288 (pt0) REVERT: H 69 ARG cc_start: 0.7965 (OUTLIER) cc_final: 0.7607 (ptp-170) REVERT: H 79 LYS cc_start: 0.8497 (ptmm) cc_final: 0.8287 (tmmm) REVERT: H 185 ARG cc_start: 0.8424 (ttp80) cc_final: 0.7932 (ttm-80) REVERT: H 186 GLN cc_start: 0.8646 (OUTLIER) cc_final: 0.8307 (mp10) REVERT: H 320 LYS cc_start: 0.8487 (mmmm) cc_final: 0.8250 (mmtp) REVERT: I 34 GLU cc_start: 0.8622 (tm-30) cc_final: 0.8394 (tm-30) REVERT: I 79 LYS cc_start: 0.8776 (ptmt) cc_final: 0.8309 (ptpp) REVERT: I 203 ARG cc_start: 0.7459 (ptp-110) cc_final: 0.6538 (mtp85) REVERT: I 324 TYR cc_start: 0.8623 (m-10) cc_final: 0.8320 (m-10) REVERT: J 81 ASP cc_start: 0.7426 (t70) cc_final: 0.7074 (t0) REVERT: J 124 THR cc_start: 0.8870 (OUTLIER) cc_final: 0.8624 (p) REVERT: J 220 ASP cc_start: 0.8994 (t0) cc_final: 0.8675 (t70) REVERT: K 37 MET cc_start: 0.6594 (ptm) cc_final: 0.6333 (ppp) REVERT: K 53 ASP cc_start: 0.9165 (m-30) cc_final: 0.8912 (m-30) REVERT: K 54 GLU cc_start: 0.6697 (OUTLIER) cc_final: 0.6228 (tm-30) REVERT: K 61 GLU cc_start: 0.8540 (pt0) cc_final: 0.8199 (pp20) REVERT: K 75 LEU cc_start: 0.8547 (mp) cc_final: 0.8289 (mp) REVERT: K 76 GLU cc_start: 0.7295 (mp0) cc_final: 0.7058 (mp0) REVERT: K 127 GLU cc_start: 0.8700 (mt-10) cc_final: 0.8260 (pt0) REVERT: K 134 GLU cc_start: 0.8225 (tm-30) cc_final: 0.7937 (tp30) REVERT: K 166 GLU cc_start: 0.7809 (pt0) cc_final: 0.7546 (pt0) REVERT: K 173 GLU cc_start: 0.7136 (tp30) cc_final: 0.6715 (mm-30) outliers start: 54 outliers final: 31 residues processed: 334 average time/residue: 0.6037 time to fit residues: 237.4031 Evaluate side-chains 334 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 287 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 220 GLU Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain A residue 283 HIS Chi-restraints excluded: chain A residue 332 GLU Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 72 GLN Chi-restraints excluded: chain B residue 132 GLU Chi-restraints excluded: chain B residue 175 ARG Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 354 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 233 VAL Chi-restraints excluded: chain E residue 333 ARG Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain F residue 117 ARG Chi-restraints excluded: chain F residue 143 THR Chi-restraints excluded: chain G residue 299 ILE Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 31 LEU Chi-restraints excluded: chain H residue 69 ARG Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 186 GLN Chi-restraints excluded: chain H residue 251 ILE Chi-restraints excluded: chain H residue 252 LEU Chi-restraints excluded: chain H residue 296 LEU Chi-restraints excluded: chain I residue 37 LEU Chi-restraints excluded: chain I residue 78 THR Chi-restraints excluded: chain I residue 99 ASP Chi-restraints excluded: chain I residue 118 VAL Chi-restraints excluded: chain I residue 189 VAL Chi-restraints excluded: chain I residue 222 LEU Chi-restraints excluded: chain J residue 124 THR Chi-restraints excluded: chain J residue 125 LEU Chi-restraints excluded: chain J residue 152 LEU Chi-restraints excluded: chain J residue 202 ASP Chi-restraints excluded: chain K residue 54 GLU Chi-restraints excluded: chain K residue 123 VAL Chi-restraints excluded: chain K residue 131 LEU Chi-restraints excluded: chain K residue 218 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 310 optimal weight: 5.9990 chunk 124 optimal weight: 0.9990 chunk 45 optimal weight: 0.8980 chunk 206 optimal weight: 2.9990 chunk 15 optimal weight: 8.9990 chunk 67 optimal weight: 3.9990 chunk 281 optimal weight: 0.8980 chunk 163 optimal weight: 1.9990 chunk 228 optimal weight: 0.9980 chunk 204 optimal weight: 0.6980 chunk 168 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 256 ASN B 64 HIS B 220 ASN D 170 ASN E 102 ASN E 146 ASN F 129 ASN ** H 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 102 ASN ** I 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.146818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.094624 restraints weight = 47176.163| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 2.58 r_work: 0.3126 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2998 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2992 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2992 r_free = 0.2992 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2992 r_free = 0.2992 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2992 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.9215 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= 0.147 Angle : 0.721 13.340 39383 Z= 0.348 Chirality : 0.051 0.406 4432 Planarity : 0.004 0.042 4823 Dihedral : 14.117 148.334 4807 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.40 % Favored : 95.57 % Rotamer: Outliers : 2.03 % Allowed : 26.27 % Favored : 71.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.14), residues: 3322 helix: 1.04 (0.15), residues: 1084 sheet: 0.57 (0.22), residues: 516 loop : -1.28 (0.14), residues: 1722 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG D 269 TYR 0.023 0.002 TYR D 133 PHE 0.032 0.001 PHE A 425 TRP 0.039 0.002 TRP B 247 HIS 0.005 0.001 HIS H 159 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.15 (28649) covalent geometry : angle 0.72083 / 0.35 (39383) hydrogen bonds : bond 0.03273 / 2.29 ( 1176) hydrogen bonds : angle 4.69903 / 3.31 ( 3238) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12676.62 seconds wall clock time: 215 minutes 32.58 seconds (12932.58 seconds total)