Starting phenix.real_space_refine on Thu Mar 5 16:56:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7jzx_22583/03_2026/7jzx_22583.cif Found real_map, /net/cci-nas-00/data/ceres_data/7jzx_22583/03_2026/7jzx_22583.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7jzx_22583/03_2026/7jzx_22583.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7jzx_22583/03_2026/7jzx_22583.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7jzx_22583/03_2026/7jzx_22583.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7jzx_22583/03_2026/7jzx_22583.map" } resolution = 3.4 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= 0.001 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 60 5.49 5 S 26 5.16 5 C 14832 2.51 5 N 4354 2.21 5 O 4676 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 119 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 23948 Number of models: 1 Model: "" Number of chains: 11 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: {'PCIS': 1, 'PTRANS': 14, '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: {'PCIS': 1, 'PTRANS': 14, '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: "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: "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: "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: "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: 2554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2554 Classifications: {'peptide': 330} Link IDs: {'PTRANS': 12, 'TRANS': 317} Chain breaks: 1 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: "A" Number of atoms: 3079 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3079 Classifications: {'peptide': 427} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 96} Link IDs: {'PTRANS': 24, 'TRANS': 402} Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 366 Unresolved non-hydrogen angles: 470 Unresolved non-hydrogen dihedrals: 306 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'ASP:plan': 11, 'GLN:plan1': 9, 'GLU:plan': 9, 'ARG:plan': 11, 'HIS:plan': 5, 'TYR:plan': 1, 'ASN:plan1': 3, 'PHE:plan': 2, 'TRP:plan': 3} Unresolved non-hydrogen planarities: 240 Chain: "M" Number of atoms: 1273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 1273 Classifications: {'DNA': 1, 'RNA': 60} Modifications used: {'5*END': 1, 'rna2p_pur': 11, 'rna2p_pyr': 17, 'rna3p_pur': 17, 'rna3p_pyr': 14} Link IDs: {'rna2p': 28, 'rna3p': 32} Unresolved chain link angles: 2 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {' C:plan': 1, ' C:plan2': 1} Unresolved non-hydrogen planarities: 11 Chain: "J" Number of atoms: 508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 508 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 2, 'TRANS': 63} Time building chain proxies: 5.45, per 1000 atoms: 0.23 Number of scatterers: 23948 At special positions: 0 Unit cell: (133.35, 157.5, 148.05, 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 26 16.00 P 60 15.00 O 4676 8.00 N 4354 7.00 C 14832 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: 2.02 Conformation dependent library (CDL) restraints added in 1.1 seconds 5854 Ramachandran restraints generated. 2927 Oldfield, 0 Emsley, 2927 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5496 Finding SS restraints... Secondary structure from input PDB file: 79 helices and 52 sheets defined 32.6% alpha, 21.8% beta 6 base pairs and 27 stacking pairs defined. Time for finding SS restraints: 2.79 Creating SS restraints... Processing helix chain 'C' and resid 16 through 36 Processing helix chain 'C' and resid 63 through 71 Processing helix chain 'C' and resid 73 through 77 removed outlier: 3.628A pdb=" N LEU C 76 " --> pdb=" O ARG C 73 " (cutoff:3.500A) Processing helix chain 'C' and resid 108 through 121 removed outlier: 3.700A 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 'C' and resid 132 through 136 removed outlier: 3.583A pdb=" N VAL C 135 " --> pdb=" O PRO C 132 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ALA C 136 " --> pdb=" O ASP C 133 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 132 through 136' Processing helix chain 'B' and resid 33 through 48 removed outlier: 4.011A pdb=" N PHE B 37 " --> pdb=" O SER B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 135 Processing helix chain 'B' and resid 165 through 178 Processing helix chain 'B' and resid 189 through 204 removed outlier: 3.866A pdb=" N LEU B 193 " --> pdb=" O ARG B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 218 Processing helix chain 'B' and resid 291 through 295 removed outlier: 3.938A pdb=" N VAL B 295 " --> pdb=" O PRO B 292 " (cutoff:3.500A) Processing helix chain 'E' and resid 51 through 55 removed outlier: 3.608A pdb=" N SER E 55 " --> pdb=" O ARG E 52 " (cutoff:3.500A) Processing helix chain 'E' and resid 82 through 92 removed outlier: 3.705A 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 209 through 223 Processing helix chain 'E' and resid 275 through 284 removed outlier: 3.568A pdb=" N ILE E 279 " --> pdb=" O HIS E 275 " (cutoff:3.500A) Processing helix chain 'E' and resid 293 through 297 removed outlier: 3.855A pdb=" N LEU E 296 " --> pdb=" O GLU E 293 " (cutoff:3.500A) Processing helix chain 'E' and resid 322 through 331 Processing helix chain 'E' and resid 338 through 352 Processing helix chain 'D' and resid 130 through 148 Processing helix chain 'D' and resid 152 through 163 Processing helix chain 'D' and resid 208 through 223 removed outlier: 3.605A pdb=" N ASP D 212 " --> pdb=" O ASP D 208 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ALA D 213 " --> pdb=" O ALA D 209 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 284 Processing helix chain 'D' and resid 322 through 331 Processing helix chain 'D' and resid 338 through 352 Processing helix chain 'F' and resid 51 through 55 Processing helix chain 'F' and resid 82 through 92 removed outlier: 3.671A pdb=" N SER F 92 " --> pdb=" O ALA F 88 " (cutoff:3.500A) Processing helix chain 'F' and resid 130 through 148 Processing helix chain 'F' and resid 151 through 163 Processing helix chain 'F' and resid 209 through 223 Processing helix chain 'F' and resid 275 through 284 Processing helix chain 'F' and resid 322 through 332 Processing helix chain 'F' and resid 338 through 352 Processing helix chain 'G' and resid 51 through 55 Processing helix chain 'G' and resid 82 through 92 removed outlier: 3.648A pdb=" N SER G 92 " --> pdb=" O ALA G 88 " (cutoff:3.500A) 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 322 through 332 removed outlier: 3.599A pdb=" N LEU G 326 " --> pdb=" O ASP G 322 " (cutoff:3.500A) Processing helix chain 'G' and resid 338 through 352 Processing helix chain 'H' and resid 82 through 92 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 322 through 331 Processing helix chain 'H' and resid 338 through 352 Processing helix chain 'I' and resid 51 through 55 removed outlier: 3.531A pdb=" N SER I 55 " --> pdb=" O ARG I 52 " (cutoff:3.500A) Processing helix chain 'I' and resid 82 through 90 Processing helix chain 'I' and resid 130 through 148 Processing helix chain 'I' and resid 152 through 163 Processing helix chain 'I' and resid 208 through 224 Processing helix chain 'I' and resid 275 through 284 Processing helix chain 'I' and resid 322 through 332 Processing helix chain 'I' and resid 338 through 352 Processing helix chain 'A' and resid 9 through 31 removed outlier: 3.650A pdb=" N LEU A 13 " --> pdb=" O THR A 9 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 47 removed outlier: 4.172A pdb=" N THR A 42 " --> pdb=" O ASP A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 60 removed outlier: 3.533A pdb=" N ALA A 54 " --> pdb=" O GLU A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 122 removed outlier: 4.010A pdb=" N PHE A 118 " --> pdb=" O ALA A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 136 removed outlier: 3.753A pdb=" N GLU A 136 " --> pdb=" O ASN A 132 " (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 196 through 212 Processing helix chain 'A' and resid 212 through 224 removed outlier: 3.909A pdb=" N ALA A 218 " --> pdb=" O ALA A 214 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N SER A 223 " --> pdb=" O ARG A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 251 removed outlier: 3.582A pdb=" N ASN A 250 " --> pdb=" O LYS A 247 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ILE A 251 " --> pdb=" O PRO A 248 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 247 through 251' Processing helix chain 'A' and resid 253 through 258 removed outlier: 4.013A pdb=" N GLU A 257 " --> pdb=" O GLN A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 289 Processing helix chain 'A' and resid 294 through 306 removed outlier: 3.618A pdb=" N THR A 303 " --> pdb=" O ARG A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 344 removed outlier: 4.517A pdb=" N ALA A 317 " --> pdb=" O HIS A 313 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLU A 344 " --> pdb=" O LEU A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 349 Processing helix chain 'A' and resid 376 through 381 removed outlier: 3.967A pdb=" N GLY A 381 " --> pdb=" O ARG A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 399 removed outlier: 3.739A pdb=" N ARG A 390 " --> pdb=" O GLU A 386 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ASN A 393 " --> pdb=" O ASN A 389 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N TRP A 394 " --> pdb=" O ARG A 390 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU A 395 " --> pdb=" O PHE A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 407 Processing helix chain 'A' and resid 409 through 431 removed outlier: 4.040A pdb=" N ASP A 431 " --> pdb=" O GLU A 427 " (cutoff:3.500A) Processing helix chain 'J' and resid 44 through 52 Processing helix chain 'J' and resid 59 through 70 removed outlier: 4.306A pdb=" N GLU J 63 " --> pdb=" O ALA J 59 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLN J 70 " --> pdb=" O ALA J 66 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 41 through 43 Processing sheet with id=AA2, first strand: chain 'C' and resid 41 through 43 Processing sheet with id=AA3, first strand: chain 'C' and resid 97 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 100 through 102 Processing sheet with id=AA5, first strand: chain 'B' and resid 55 through 57 removed outlier: 5.335A pdb=" N LEU B 105 " --> pdb=" O GLN B 18 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N GLN B 18 " --> pdb=" O LEU B 105 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N VAL B 107 " --> pdb=" O SER B 16 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N SER B 16 " --> pdb=" O VAL B 107 " (cutoff:3.500A) removed outlier: 8.186A pdb=" N LEU B 109 " --> pdb=" O ARG B 14 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N ARG B 14 " --> pdb=" O LEU B 109 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N LEU B 111 " --> pdb=" O LEU B 12 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N LEU B 12 " --> pdb=" O LEU B 111 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N VAL B 113 " --> pdb=" O LEU B 10 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N LEU B 10 " --> pdb=" O VAL B 113 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N SER B 16 " --> pdb=" O LEU B 145 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 65 through 68 removed outlier: 5.335A pdb=" N LEU B 105 " --> pdb=" O GLN B 18 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N GLN B 18 " --> pdb=" O LEU B 105 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N VAL B 107 " --> pdb=" O SER B 16 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N SER B 16 " --> pdb=" O VAL B 107 " (cutoff:3.500A) removed outlier: 8.186A pdb=" N LEU B 109 " --> pdb=" O ARG B 14 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N ARG B 14 " --> pdb=" O LEU B 109 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N LEU B 111 " --> pdb=" O LEU B 12 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N LEU B 12 " --> pdb=" O LEU B 111 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N VAL B 113 " --> pdb=" O LEU B 10 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N LEU B 10 " --> pdb=" O VAL B 113 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ALA B 157 " --> pdb=" O LEU B 11 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 28 through 30 removed outlier: 5.953A pdb=" N TRP B 29 " --> pdb=" O SER A 267 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 70 through 71 Processing sheet with id=AA9, first strand: chain 'B' and resid 185 through 188 removed outlier: 7.545A pdb=" N PHE B 279 " --> pdb=" O ALA B 257 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N ALA B 257 " --> pdb=" O PHE B 279 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N GLU B 281 " --> pdb=" O TYR B 255 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N TYR B 255 " --> pdb=" O GLU B 281 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N LEU B 283 " --> pdb=" O ALA B 253 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N TRP B 247 " --> pdb=" O TRP B 289 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 185 through 188 Processing sheet with id=AB2, first strand: chain 'B' and resid 221 through 222 Processing sheet with id=AB3, first strand: chain 'B' and resid 304 through 306 Processing sheet with id=AB4, first strand: chain 'E' and resid 127 through 128 Processing sheet with id=AB5, first strand: chain 'E' and resid 38 through 39 removed outlier: 4.325A pdb=" N VAL E 228 " --> pdb=" O VAL E 118 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N LEU E 229 " --> pdb=" O ILE E 184 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 189 through 192 removed outlier: 6.790A pdb=" N HIS E 183 " --> pdb=" O ALA E 190 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N ALA E 192 " --> pdb=" O ILE E 181 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N ILE E 181 " --> pdb=" O ALA E 192 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N LEU E 229 " --> pdb=" O ILE E 184 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N VAL E 228 " --> pdb=" O VAL E 118 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 64 through 70 removed outlier: 3.579A pdb=" N ASN E 94 " --> pdb=" O GLY E 70 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 248 through 249 removed outlier: 4.399A pdb=" N THR E 264 " --> pdb=" O GLU E 249 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 285 through 287 Processing sheet with id=AC1, first strand: chain 'D' and resid 127 through 128 Processing sheet with id=AC2, first strand: chain 'D' and resid 38 through 39 removed outlier: 4.163A pdb=" N VAL D 228 " --> pdb=" O VAL D 118 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ARG D 191 " --> pdb=" O HIS D 183 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 38 through 39 Processing sheet with id=AC4, first strand: chain 'D' and resid 64 through 66 Processing sheet with id=AC5, first strand: chain 'D' and resid 248 through 249 removed outlier: 4.541A pdb=" N THR D 264 " --> pdb=" O GLU D 249 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 285 through 287 Processing sheet with id=AC7, first strand: chain 'D' and resid 306 through 307 Processing sheet with id=AC8, first strand: chain 'F' and resid 31 through 33 Processing sheet with id=AC9, first strand: chain 'F' and resid 38 through 39 removed outlier: 4.074A pdb=" N VAL F 228 " --> pdb=" O VAL F 118 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N LEU F 229 " --> pdb=" O ILE F 184 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 189 through 192 removed outlier: 6.808A pdb=" N HIS F 183 " --> pdb=" O ALA F 190 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N ALA F 192 " --> pdb=" O ILE F 181 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ILE F 181 " --> pdb=" O ALA F 192 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N LEU F 229 " --> pdb=" O ILE F 184 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N VAL F 228 " --> pdb=" O VAL F 118 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 64 through 70 removed outlier: 3.511A pdb=" N GLY F 70 " --> pdb=" O ASN F 94 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ASN F 94 " --> pdb=" O GLY F 70 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N ALA F 101 " --> pdb=" O VAL F 244 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 306 through 307 Processing sheet with id=AD4, first strand: chain 'G' and resid 127 through 128 removed outlier: 3.534A pdb=" N ALA G 127 " --> pdb=" O ALA G 32 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'G' and resid 38 through 39 removed outlier: 4.126A pdb=" N VAL G 228 " --> pdb=" O VAL G 118 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N LEU G 229 " --> pdb=" O ILE G 184 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N VAL G 177 " --> pdb=" O ASP G 196 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N ASP G 196 " --> pdb=" O VAL G 177 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N VAL G 179 " --> pdb=" O ARG G 194 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N ARG G 194 " --> pdb=" O VAL G 179 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ILE G 181 " --> pdb=" O ALA G 192 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N ALA G 192 " --> pdb=" O ILE G 181 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N HIS G 183 " --> pdb=" O ALA G 190 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'G' and resid 38 through 39 Processing sheet with id=AD7, first strand: chain 'G' and resid 64 through 70 removed outlier: 4.395A pdb=" N ALA G 101 " --> pdb=" O VAL G 244 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 306 through 307 Processing sheet with id=AD9, first strand: chain 'H' and resid 127 through 128 Processing sheet with id=AE1, first strand: chain 'H' and resid 38 through 39 removed outlier: 4.068A pdb=" N VAL H 228 " --> pdb=" O VAL H 118 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N LEU H 229 " --> pdb=" O ILE H 184 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'H' and resid 189 through 192 removed outlier: 6.712A pdb=" N HIS H 183 " --> pdb=" O ALA H 190 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N ALA H 192 " --> pdb=" O ILE H 181 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ILE H 181 " --> pdb=" O ALA H 192 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N LEU H 229 " --> pdb=" O ILE H 184 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N VAL H 228 " --> pdb=" O VAL H 118 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'H' and resid 64 through 70 removed outlier: 3.754A pdb=" N ASN H 94 " --> pdb=" O GLY H 70 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N ALA H 101 " --> pdb=" O VAL H 244 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'H' and resid 248 through 249 removed outlier: 4.662A pdb=" N THR H 264 " --> pdb=" O GLU H 249 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'H' and resid 306 through 307 removed outlier: 3.670A pdb=" N LYS H 312 " --> pdb=" O VAL H 307 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'I' and resid 127 through 128 Processing sheet with id=AE7, first strand: chain 'I' and resid 38 through 39 removed outlier: 4.429A pdb=" N LEU I 229 " --> pdb=" O ILE I 184 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ARG I 191 " --> pdb=" O HIS I 183 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'I' and resid 38 through 39 Processing sheet with id=AE9, first strand: chain 'I' and resid 63 through 70 removed outlier: 3.641A pdb=" N ASN I 94 " --> pdb=" O GLY I 70 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N ALA I 101 " --> pdb=" O VAL I 244 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'I' and resid 63 through 70 removed outlier: 3.641A pdb=" N ASN I 94 " --> pdb=" O GLY I 70 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N LYS I 261 " --> pdb=" O LEU I 95 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N THR I 97 " --> pdb=" O LYS I 261 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LYS I 263 " --> pdb=" O THR I 97 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'I' and resid 285 through 287 Processing sheet with id=AF3, first strand: chain 'I' and resid 306 through 307 removed outlier: 3.561A pdb=" N LYS I 312 " --> pdb=" O VAL I 307 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'A' and resid 63 through 65 Processing sheet with id=AF5, first strand: chain 'A' and resid 68 through 69 Processing sheet with id=AF6, first strand: chain 'A' and resid 180 through 181 Processing sheet with id=AF7, first strand: chain 'J' and resid 20 through 25 removed outlier: 4.206A pdb=" N PHE J 35 " --> pdb=" O VAL J 79 " (cutoff:3.500A) 1038 hydrogen bonds defined for protein. 2868 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 16 hydrogen bonds 28 hydrogen bond angles 0 basepair planarities 6 basepair parallelities 27 stacking parallelities Total time for adding SS restraints: 4.31 Time building geometry restraints manager: 2.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 5557 1.33 - 1.45: 5414 1.45 - 1.57: 13418 1.57 - 1.69: 120 1.69 - 1.81: 40 Bond restraints: 24549 Sorted by residual: bond pdb=" O3' A M 36 " pdb=" P C M 37 " ideal model delta sigma weight residual 1.607 1.672 -0.065 1.50e-02 4.44e+03 1.89e+01 bond pdb=" C LEU B 181 " pdb=" N PRO B 182 " ideal model delta sigma weight residual 1.337 1.379 -0.042 9.80e-03 1.04e+04 1.83e+01 bond pdb=" N ARG H 185 " pdb=" CA ARG H 185 " ideal model delta sigma weight residual 1.457 1.491 -0.034 1.29e-02 6.01e+03 6.92e+00 bond pdb=" N LEU B 301 " pdb=" CA LEU B 301 " ideal model delta sigma weight residual 1.462 1.500 -0.039 1.48e-02 4.57e+03 6.82e+00 bond pdb=" N ASP I 135 " pdb=" CA ASP I 135 " ideal model delta sigma weight residual 1.459 1.490 -0.031 1.23e-02 6.61e+03 6.28e+00 ... (remaining 24544 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.16: 32419 2.16 - 4.32: 1056 4.32 - 6.48: 116 6.48 - 8.64: 36 8.64 - 10.79: 3 Bond angle restraints: 33630 Sorted by residual: angle pdb=" C GLN A 124 " pdb=" N TYR A 125 " pdb=" CA TYR A 125 " ideal model delta sigma weight residual 120.79 128.74 -7.95 1.39e+00 5.18e-01 3.27e+01 angle pdb=" C LYS G 77 " pdb=" N THR G 78 " pdb=" CA THR G 78 " ideal model delta sigma weight residual 121.54 132.33 -10.79 1.91e+00 2.74e-01 3.19e+01 angle pdb=" C LYS E 77 " pdb=" N THR E 78 " pdb=" CA THR E 78 " ideal model delta sigma weight residual 121.54 130.74 -9.20 1.91e+00 2.74e-01 2.32e+01 angle pdb=" C ARG I 185 " pdb=" N GLN I 186 " pdb=" CA GLN I 186 " ideal model delta sigma weight residual 120.82 128.04 -7.22 1.50e+00 4.44e-01 2.32e+01 angle pdb=" C LYS H 77 " pdb=" N THR H 78 " pdb=" CA THR H 78 " ideal model delta sigma weight residual 121.54 129.95 -8.41 1.91e+00 2.74e-01 1.94e+01 ... (remaining 33625 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.96: 14349 35.96 - 71.92: 423 71.92 - 107.88: 43 107.88 - 143.84: 2 143.84 - 179.80: 5 Dihedral angle restraints: 14822 sinusoidal: 6316 harmonic: 8506 Sorted by residual: dihedral pdb=" O4' U M 33 " pdb=" C1' U M 33 " pdb=" N1 U M 33 " pdb=" C2 U M 33 " ideal model delta sinusoidal sigma weight residual 200.00 56.03 143.97 1 1.50e+01 4.44e-03 7.72e+01 dihedral pdb=" O4' U M 21 " pdb=" C1' U M 21 " pdb=" N1 U M 21 " pdb=" C2 U M 21 " ideal model delta sinusoidal sigma weight residual 200.00 70.81 129.19 1 1.50e+01 4.44e-03 6.96e+01 dihedral pdb=" O4' C M 20 " pdb=" C1' C M 20 " pdb=" N1 C M 20 " pdb=" C2 C M 20 " ideal model delta sinusoidal sigma weight residual -128.00 51.80 -179.80 1 1.70e+01 3.46e-03 6.64e+01 ... (remaining 14819 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 2631 0.048 - 0.096: 893 0.096 - 0.144: 228 0.144 - 0.192: 42 0.192 - 0.241: 4 Chirality restraints: 3798 Sorted by residual: chirality pdb=" C1' U M 33 " pdb=" O4' U M 33 " pdb=" C2' U M 33 " pdb=" N1 U M 33 " both_signs ideal model delta sigma weight residual False 2.47 2.23 0.24 2.00e-01 2.50e+01 1.45e+00 chirality pdb=" CA LEU B 181 " pdb=" N LEU B 181 " pdb=" C LEU B 181 " pdb=" CB LEU B 181 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.12e+00 chirality pdb=" CB ILE J 23 " pdb=" CA ILE J 23 " pdb=" CG1 ILE J 23 " pdb=" CG2 ILE J 23 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.20 2.00e-01 2.50e+01 1.04e+00 ... (remaining 3795 not shown) Planarity restraints: 4221 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A 71 " 0.048 5.00e-02 4.00e+02 7.24e-02 8.38e+00 pdb=" N PRO A 72 " -0.125 5.00e-02 4.00e+02 pdb=" CA PRO A 72 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO A 72 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER B 291 " -0.047 5.00e-02 4.00e+02 7.09e-02 8.04e+00 pdb=" N PRO B 292 " 0.123 5.00e-02 4.00e+02 pdb=" CA PRO B 292 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO B 292 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER B 25 " -0.045 5.00e-02 4.00e+02 6.70e-02 7.19e+00 pdb=" N PRO B 26 " 0.116 5.00e-02 4.00e+02 pdb=" CA PRO B 26 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO B 26 " -0.037 5.00e-02 4.00e+02 ... (remaining 4218 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 5107 2.77 - 3.30: 21176 3.30 - 3.84: 41098 3.84 - 4.37: 49237 4.37 - 4.90: 84009 Nonbonded interactions: 200627 Sorted by model distance: nonbonded pdb=" OH TYR G 324 " pdb=" O SER H 73 " model vdw 2.239 3.040 nonbonded pdb=" OG SER E 29 " pdb=" OD1 ASN E 129 " model vdw 2.260 3.040 nonbonded pdb=" OH TYR H 324 " pdb=" O SER I 73 " model vdw 2.266 3.040 nonbonded pdb=" O ARG I 69 " pdb=" O2' C M 13 " model vdw 2.278 3.040 nonbonded pdb=" OH TYR F 324 " pdb=" O SER G 73 " model vdw 2.285 3.040 ... (remaining 200622 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)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.37 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.360 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 23.370 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 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 : 0.009 0.076 24549 Z= 0.381 Angle : 0.916 10.795 33630 Z= 0.514 Chirality : 0.051 0.241 3798 Planarity : 0.006 0.072 4221 Dihedral : 17.055 179.805 9326 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.01 % Favored : 92.99 % Rotamer: Outliers : 0.40 % Allowed : 7.51 % Favored : 92.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % 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: -3.94 (0.12), residues: 2927 helix: -2.81 (0.11), residues: 905 sheet: -1.73 (0.21), residues: 495 loop : -2.82 (0.13), residues: 1527 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG G 169 TYR 0.017 0.003 TYR E 304 PHE 0.022 0.003 PHE G 166 TRP 0.024 0.002 TRP I 49 HIS 0.007 0.002 HIS B 42 Details of bonding type rmsd covalent geometry : bond 0.00867 (24549) covalent geometry : angle 0.91559 (33630) hydrogen bonds : bond 0.17543 ( 977) hydrogen bonds : angle 7.78601 ( 2896) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5854 Ramachandran restraints generated. 2927 Oldfield, 0 Emsley, 2927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5854 Ramachandran restraints generated. 2927 Oldfield, 0 Emsley, 2927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 2385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 184 time to evaluate : 0.809 Fit side-chains REVERT: C 19 GLN cc_start: 0.7841 (tt0) cc_final: 0.7565 (mt0) REVERT: C 110 GLU cc_start: 0.7623 (mp0) cc_final: 0.7184 (pm20) REVERT: B 244 LYS cc_start: 0.8488 (mtmt) cc_final: 0.8231 (mtmm) REVERT: I 257 LYS cc_start: 0.7844 (mmmt) cc_final: 0.7637 (tptt) REVERT: A 228 TRP cc_start: 0.8689 (t-100) cc_final: 0.8469 (t-100) REVERT: A 299 ARG cc_start: 0.8001 (tmm160) cc_final: 0.7789 (tmm160) REVERT: J 44 ASP cc_start: 0.8331 (t0) cc_final: 0.8045 (t0) outliers start: 9 outliers final: 0 residues processed: 190 average time/residue: 0.2329 time to fit residues: 62.4692 Evaluate side-chains 136 residues out of total 2385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 136 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 0.5980 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 0.6980 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 2.9990 chunk 111 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 19 GLN C 84 GLN C 165 GLN B 293 HIS E 129 ASN E 159 HIS E 348 ASN D 102 ASN ** F 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 129 ASN G 51 GLN G 260 GLN H 148 GLN I 183 HIS I 342 GLN ** A 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 172 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.069327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.053894 restraints weight = 65696.865| |-----------------------------------------------------------------------------| r_work (start): 0.2903 rms_B_bonded: 2.45 r_work: 0.2782 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2636 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2636 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2638 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2638 r_free = 0.2638 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2638 r_free = 0.2638 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2638 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.1312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 24549 Z= 0.123 Angle : 0.545 10.876 33630 Z= 0.291 Chirality : 0.039 0.195 3798 Planarity : 0.004 0.059 4221 Dihedral : 15.378 178.922 4162 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 1.10 % Allowed : 10.19 % Favored : 88.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % 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: -2.37 (0.14), residues: 2927 helix: -0.65 (0.15), residues: 925 sheet: -1.04 (0.24), residues: 430 loop : -2.37 (0.14), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 73 TYR 0.017 0.001 TYR I 304 PHE 0.011 0.001 PHE E 166 TRP 0.012 0.001 TRP A 394 HIS 0.005 0.001 HIS B 305 Details of bonding type rmsd covalent geometry : bond 0.00262 (24549) covalent geometry : angle 0.54495 (33630) hydrogen bonds : bond 0.03534 ( 977) hydrogen bonds : angle 4.92438 ( 2896) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5854 Ramachandran restraints generated. 2927 Oldfield, 0 Emsley, 2927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5854 Ramachandran restraints generated. 2927 Oldfield, 0 Emsley, 2927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 2385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 162 time to evaluate : 0.884 Fit side-chains REVERT: C 19 GLN cc_start: 0.8392 (tt0) cc_final: 0.7995 (tt0) REVERT: C 35 GLN cc_start: 0.8372 (tp40) cc_final: 0.7931 (tp40) REVERT: C 165 GLN cc_start: 0.7825 (tt0) cc_final: 0.7569 (tm-30) REVERT: B 244 LYS cc_start: 0.8366 (mtmt) cc_final: 0.8101 (mtmm) REVERT: B 311 LYS cc_start: 0.8969 (ttpp) cc_final: 0.8272 (ttpp) REVERT: I 216 GLU cc_start: 0.8395 (OUTLIER) cc_final: 0.7994 (mt-10) REVERT: A 228 TRP cc_start: 0.8724 (t-100) cc_final: 0.8466 (t-100) REVERT: J 44 ASP cc_start: 0.8446 (t0) cc_final: 0.7967 (t0) REVERT: J 61 VAL cc_start: 0.8269 (t) cc_final: 0.8069 (t) outliers start: 25 outliers final: 7 residues processed: 182 average time/residue: 0.1883 time to fit residues: 50.8687 Evaluate side-chains 153 residues out of total 2385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 145 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain E residue 250 LEU Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain G residue 147 ASP Chi-restraints excluded: chain I residue 216 GLU Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 246 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 288 optimal weight: 10.0000 chunk 168 optimal weight: 5.9990 chunk 204 optimal weight: 0.0170 chunk 238 optimal weight: 0.9980 chunk 98 optimal weight: 8.9990 chunk 276 optimal weight: 20.0000 chunk 58 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 109 optimal weight: 3.9990 chunk 92 optimal weight: 3.9990 chunk 290 optimal weight: 5.9990 overall best weight: 3.0024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 19 ASN B 69 GLN E 91 GLN D 102 ASN D 348 ASN ** F 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 348 ASN G 260 GLN A 74 HIS A 335 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.067127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.050820 restraints weight = 84342.926| |-----------------------------------------------------------------------------| r_work (start): 0.2816 rms_B_bonded: 2.82 r_work: 0.2685 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2685 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2687 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2687 r_free = 0.2687 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2687 r_free = 0.2687 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2687 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.1454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 24549 Z= 0.258 Angle : 0.604 12.088 33630 Z= 0.314 Chirality : 0.042 0.191 3798 Planarity : 0.004 0.064 4221 Dihedral : 15.270 179.308 4162 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 1.32 % Allowed : 12.70 % Favored : 85.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % 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: -1.77 (0.15), residues: 2927 helix: 0.23 (0.17), residues: 918 sheet: -1.00 (0.23), residues: 450 loop : -2.17 (0.14), residues: 1559 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 269 TYR 0.017 0.002 TYR H 290 PHE 0.016 0.002 PHE H 114 TRP 0.017 0.001 TRP A 394 HIS 0.006 0.001 HIS B 293 Details of bonding type rmsd covalent geometry : bond 0.00593 (24549) covalent geometry : angle 0.60414 (33630) hydrogen bonds : bond 0.03598 ( 977) hydrogen bonds : angle 4.66237 ( 2896) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5854 Ramachandran restraints generated. 2927 Oldfield, 0 Emsley, 2927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5854 Ramachandran restraints generated. 2927 Oldfield, 0 Emsley, 2927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 2385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 149 time to evaluate : 0.890 Fit side-chains REVERT: C 19 GLN cc_start: 0.8211 (tt0) cc_final: 0.7807 (mt0) REVERT: C 35 GLN cc_start: 0.8477 (tp40) cc_final: 0.7954 (tp40) REVERT: B 76 LYS cc_start: 0.8895 (mttp) cc_final: 0.8586 (mttt) REVERT: B 244 LYS cc_start: 0.8444 (mtmt) cc_final: 0.8240 (mtmm) REVERT: B 311 LYS cc_start: 0.8893 (ttpp) cc_final: 0.8679 (ttpp) REVERT: I 216 GLU cc_start: 0.8183 (OUTLIER) cc_final: 0.7728 (mt-10) REVERT: I 302 GLU cc_start: 0.8049 (OUTLIER) cc_final: 0.7705 (mm-30) REVERT: A 228 TRP cc_start: 0.8737 (t-100) cc_final: 0.8492 (t-100) REVERT: J 44 ASP cc_start: 0.8428 (t0) cc_final: 0.7902 (t0) REVERT: J 61 VAL cc_start: 0.8486 (t) cc_final: 0.8273 (t) outliers start: 30 outliers final: 18 residues processed: 170 average time/residue: 0.1862 time to fit residues: 47.8788 Evaluate side-chains 162 residues out of total 2385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 142 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain E residue 146 ASN Chi-restraints excluded: chain E residue 250 LEU Chi-restraints excluded: chain E residue 348 ASN Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 304 TYR Chi-restraints excluded: chain F residue 304 TYR Chi-restraints excluded: chain G residue 147 ASP Chi-restraints excluded: chain G residue 250 LEU Chi-restraints excluded: chain G residue 264 THR Chi-restraints excluded: chain G residue 307 VAL Chi-restraints excluded: chain I residue 216 GLU Chi-restraints excluded: chain I residue 302 GLU Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain J residue 23 ILE Chi-restraints excluded: chain J residue 41 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 116 optimal weight: 6.9990 chunk 10 optimal weight: 8.9990 chunk 262 optimal weight: 5.9990 chunk 255 optimal weight: 20.0000 chunk 30 optimal weight: 0.9990 chunk 86 optimal weight: 0.8980 chunk 206 optimal weight: 2.9990 chunk 154 optimal weight: 6.9990 chunk 20 optimal weight: 0.8980 chunk 71 optimal weight: 9.9990 chunk 42 optimal weight: 5.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 165 GLN E 51 GLN ** F 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 281 ASN I 159 HIS A 74 HIS ** A 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 65 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.067505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.051652 restraints weight = 75800.064| |-----------------------------------------------------------------------------| r_work (start): 0.2841 rms_B_bonded: 2.64 r_work: 0.2712 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.2712 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2715 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2715 r_free = 0.2715 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2715 r_free = 0.2715 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2715 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.1662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 24549 Z= 0.211 Angle : 0.563 11.639 33630 Z= 0.293 Chirality : 0.041 0.180 3798 Planarity : 0.004 0.066 4221 Dihedral : 15.184 179.768 4162 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 1.54 % Allowed : 13.88 % Favored : 84.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % 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: -1.44 (0.15), residues: 2927 helix: 0.67 (0.17), residues: 925 sheet: -0.77 (0.23), residues: 466 loop : -2.13 (0.15), residues: 1536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 160 TYR 0.016 0.002 TYR H 290 PHE 0.013 0.001 PHE H 114 TRP 0.014 0.001 TRP H 49 HIS 0.006 0.001 HIS B 293 Details of bonding type rmsd covalent geometry : bond 0.00484 (24549) covalent geometry : angle 0.56263 (33630) hydrogen bonds : bond 0.03265 ( 977) hydrogen bonds : angle 4.41388 ( 2896) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5854 Ramachandran restraints generated. 2927 Oldfield, 0 Emsley, 2927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5854 Ramachandran restraints generated. 2927 Oldfield, 0 Emsley, 2927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 2385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 150 time to evaluate : 0.876 Fit side-chains REVERT: C 19 GLN cc_start: 0.8176 (tt0) cc_final: 0.7752 (mt0) REVERT: C 35 GLN cc_start: 0.8477 (tp40) cc_final: 0.7939 (tp40) REVERT: B 244 LYS cc_start: 0.8413 (mtmt) cc_final: 0.8210 (mtmm) REVERT: I 216 GLU cc_start: 0.8200 (OUTLIER) cc_final: 0.7782 (mt-10) REVERT: A 228 TRP cc_start: 0.8721 (t-100) cc_final: 0.8467 (t-100) REVERT: J 44 ASP cc_start: 0.8441 (t0) cc_final: 0.7914 (t0) outliers start: 35 outliers final: 25 residues processed: 169 average time/residue: 0.1852 time to fit residues: 47.0253 Evaluate side-chains 171 residues out of total 2385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 145 time to evaluate : 0.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 165 GLN Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain E residue 146 ASN Chi-restraints excluded: chain E residue 250 LEU Chi-restraints excluded: chain E residue 251 ILE Chi-restraints excluded: chain E residue 348 ASN Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 304 TYR Chi-restraints excluded: chain F residue 304 TYR Chi-restraints excluded: chain G residue 147 ASP Chi-restraints excluded: chain G residue 250 LEU Chi-restraints excluded: chain G residue 264 THR Chi-restraints excluded: chain G residue 307 VAL Chi-restraints excluded: chain I residue 216 GLU Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 177 GLN Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain J residue 21 THR Chi-restraints excluded: chain J residue 22 SER Chi-restraints excluded: chain J residue 25 THR Chi-restraints excluded: chain J residue 41 GLN Chi-restraints excluded: chain J residue 58 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 42 optimal weight: 5.9990 chunk 126 optimal weight: 6.9990 chunk 79 optimal weight: 5.9990 chunk 267 optimal weight: 1.9990 chunk 134 optimal weight: 0.5980 chunk 279 optimal weight: 0.2980 chunk 102 optimal weight: 0.9990 chunk 34 optimal weight: 10.0000 chunk 98 optimal weight: 3.9990 chunk 193 optimal weight: 0.9980 chunk 53 optimal weight: 4.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 165 GLN E 129 ASN D 102 ASN ** F 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 65 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.068981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.052942 restraints weight = 83304.088| |-----------------------------------------------------------------------------| r_work (start): 0.2877 rms_B_bonded: 2.78 r_work: 0.2748 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.2748 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2750 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2750 r_free = 0.2750 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2750 r_free = 0.2750 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.2750 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.1874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 24549 Z= 0.119 Angle : 0.502 9.186 33630 Z= 0.263 Chirality : 0.039 0.170 3798 Planarity : 0.003 0.063 4221 Dihedral : 15.084 178.573 4162 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 1.85 % Allowed : 14.54 % Favored : 83.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % 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: -1.08 (0.15), residues: 2927 helix: 1.11 (0.17), residues: 926 sheet: -0.67 (0.23), residues: 480 loop : -1.98 (0.15), residues: 1521 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 160 TYR 0.015 0.001 TYR H 290 PHE 0.011 0.001 PHE B 152 TRP 0.010 0.001 TRP I 49 HIS 0.006 0.001 HIS B 293 Details of bonding type rmsd covalent geometry : bond 0.00265 (24549) covalent geometry : angle 0.50228 (33630) hydrogen bonds : bond 0.02890 ( 977) hydrogen bonds : angle 4.14216 ( 2896) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5854 Ramachandran restraints generated. 2927 Oldfield, 0 Emsley, 2927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5854 Ramachandran restraints generated. 2927 Oldfield, 0 Emsley, 2927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 2385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 151 time to evaluate : 0.901 Fit side-chains REVERT: C 19 GLN cc_start: 0.8202 (tt0) cc_final: 0.7720 (mt0) REVERT: C 35 GLN cc_start: 0.8468 (tp40) cc_final: 0.8130 (tp40) REVERT: B 76 LYS cc_start: 0.8882 (mttp) cc_final: 0.8513 (mttt) REVERT: E 318 LYS cc_start: 0.8490 (mmmt) cc_final: 0.8055 (mmtt) REVERT: E 324 TYR cc_start: 0.8246 (m-80) cc_final: 0.7460 (m-80) REVERT: J 44 ASP cc_start: 0.8454 (t0) cc_final: 0.7883 (t0) outliers start: 42 outliers final: 24 residues processed: 178 average time/residue: 0.1915 time to fit residues: 51.3742 Evaluate side-chains 166 residues out of total 2385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 142 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 165 GLN Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain E residue 250 LEU Chi-restraints excluded: chain E residue 251 ILE Chi-restraints excluded: chain E residue 304 TYR Chi-restraints excluded: chain E residue 348 ASN Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 304 TYR Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain F residue 304 TYR Chi-restraints excluded: chain G residue 250 LEU Chi-restraints excluded: chain G residue 307 VAL Chi-restraints excluded: chain H residue 44 MET Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 177 GLN Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain J residue 22 SER Chi-restraints excluded: chain J residue 41 GLN Chi-restraints excluded: chain J residue 58 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 207 optimal weight: 0.5980 chunk 59 optimal weight: 5.9990 chunk 159 optimal weight: 7.9990 chunk 202 optimal weight: 5.9990 chunk 34 optimal weight: 10.0000 chunk 143 optimal weight: 9.9990 chunk 286 optimal weight: 7.9990 chunk 33 optimal weight: 8.9990 chunk 11 optimal weight: 9.9990 chunk 147 optimal weight: 4.9990 chunk 127 optimal weight: 0.8980 overall best weight: 3.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 165 GLN D 146 ASN D 159 HIS F 159 HIS A 68 HIS A 335 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.066440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.050216 restraints weight = 84461.334| |-----------------------------------------------------------------------------| r_work (start): 0.2800 rms_B_bonded: 2.81 r_work: 0.2667 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2667 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2669 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2669 r_free = 0.2669 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2669 r_free = 0.2669 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.2669 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.1863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.059 24549 Z= 0.306 Angle : 0.623 11.774 33630 Z= 0.321 Chirality : 0.043 0.185 3798 Planarity : 0.004 0.071 4221 Dihedral : 15.149 178.068 4162 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.38 % Favored : 92.62 % Rotamer: Outliers : 2.42 % Allowed : 14.89 % Favored : 82.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % 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: -1.17 (0.15), residues: 2927 helix: 1.01 (0.17), residues: 922 sheet: -0.64 (0.24), residues: 442 loop : -2.02 (0.15), residues: 1563 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 237 TYR 0.019 0.002 TYR H 290 PHE 0.019 0.002 PHE H 114 TRP 0.018 0.002 TRP H 49 HIS 0.006 0.001 HIS B 42 Details of bonding type rmsd covalent geometry : bond 0.00707 (24549) covalent geometry : angle 0.62302 (33630) hydrogen bonds : bond 0.03455 ( 977) hydrogen bonds : angle 4.43161 ( 2896) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5854 Ramachandran restraints generated. 2927 Oldfield, 0 Emsley, 2927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5854 Ramachandran restraints generated. 2927 Oldfield, 0 Emsley, 2927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 2385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 142 time to evaluate : 0.857 Fit side-chains REVERT: C 19 GLN cc_start: 0.8193 (tt0) cc_final: 0.7775 (mt0) REVERT: C 35 GLN cc_start: 0.8539 (tp40) cc_final: 0.8200 (tp40) REVERT: B 76 LYS cc_start: 0.8972 (mttp) cc_final: 0.8570 (mttt) REVERT: H 251 ILE cc_start: 0.9111 (OUTLIER) cc_final: 0.8713 (mp) REVERT: I 216 GLU cc_start: 0.8271 (OUTLIER) cc_final: 0.7881 (mt-10) REVERT: I 290 TYR cc_start: 0.9044 (p90) cc_final: 0.8838 (p90) REVERT: I 302 GLU cc_start: 0.7823 (OUTLIER) cc_final: 0.7606 (mm-30) REVERT: J 38 GLU cc_start: 0.7984 (OUTLIER) cc_final: 0.7729 (tt0) REVERT: J 44 ASP cc_start: 0.8485 (t0) cc_final: 0.7897 (t0) outliers start: 55 outliers final: 34 residues processed: 182 average time/residue: 0.1803 time to fit residues: 50.0262 Evaluate side-chains 178 residues out of total 2385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 140 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 300 ASP Chi-restraints excluded: chain E residue 146 ASN Chi-restraints excluded: chain E residue 250 LEU Chi-restraints excluded: chain E residue 251 ILE Chi-restraints excluded: chain E residue 348 ASN Chi-restraints excluded: chain E residue 354 VAL Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain D residue 304 TYR Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain F residue 304 TYR Chi-restraints excluded: chain G residue 250 LEU Chi-restraints excluded: chain G residue 264 THR Chi-restraints excluded: chain G residue 307 VAL Chi-restraints excluded: chain G residue 340 GLU Chi-restraints excluded: chain H residue 251 ILE Chi-restraints excluded: chain I residue 44 MET Chi-restraints excluded: chain I residue 216 GLU Chi-restraints excluded: chain I residue 302 GLU Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 177 GLN Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain J residue 21 THR Chi-restraints excluded: chain J residue 22 SER Chi-restraints excluded: chain J residue 25 THR Chi-restraints excluded: chain J residue 37 VAL Chi-restraints excluded: chain J residue 38 GLU Chi-restraints excluded: chain J residue 41 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 184 optimal weight: 0.7980 chunk 167 optimal weight: 0.4980 chunk 242 optimal weight: 10.0000 chunk 126 optimal weight: 5.9990 chunk 251 optimal weight: 5.9990 chunk 81 optimal weight: 0.4980 chunk 157 optimal weight: 0.7980 chunk 287 optimal weight: 6.9990 chunk 263 optimal weight: 0.0020 chunk 65 optimal weight: 4.9990 chunk 106 optimal weight: 4.9990 overall best weight: 0.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 69 GLN ** F 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 65 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.069560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.053514 restraints weight = 87048.730| |-----------------------------------------------------------------------------| r_work (start): 0.2891 rms_B_bonded: 2.84 r_work: 0.2759 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2763 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2763 r_free = 0.2763 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2763 r_free = 0.2763 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.2763 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.2116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 24549 Z= 0.100 Angle : 0.501 10.104 33630 Z= 0.261 Chirality : 0.038 0.166 3798 Planarity : 0.003 0.062 4221 Dihedral : 14.996 178.270 4162 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 1.49 % Allowed : 15.86 % Favored : 82.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % 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: -0.83 (0.15), residues: 2927 helix: 1.41 (0.17), residues: 926 sheet: -0.62 (0.23), residues: 469 loop : -1.85 (0.15), residues: 1532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 268 TYR 0.014 0.001 TYR H 290 PHE 0.012 0.001 PHE B 152 TRP 0.010 0.001 TRP I 49 HIS 0.006 0.001 HIS B 293 Details of bonding type rmsd covalent geometry : bond 0.00217 (24549) covalent geometry : angle 0.50102 (33630) hydrogen bonds : bond 0.02764 ( 977) hydrogen bonds : angle 4.03483 ( 2896) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5854 Ramachandran restraints generated. 2927 Oldfield, 0 Emsley, 2927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5854 Ramachandran restraints generated. 2927 Oldfield, 0 Emsley, 2927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 2385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 156 time to evaluate : 0.892 Fit side-chains revert: symmetry clash REVERT: C 1 MET cc_start: 0.5807 (mtp) cc_final: 0.5173 (mpp) REVERT: C 4 TYR cc_start: 0.8447 (p90) cc_final: 0.8203 (p90) REVERT: C 19 GLN cc_start: 0.8200 (tt0) cc_final: 0.7703 (mt0) REVERT: C 35 GLN cc_start: 0.8408 (tp40) cc_final: 0.8154 (tt0) REVERT: B 76 LYS cc_start: 0.8874 (mttp) cc_final: 0.8505 (mttt) REVERT: B 161 MET cc_start: 0.7672 (mmm) cc_final: 0.7139 (mmm) REVERT: E 324 TYR cc_start: 0.8204 (m-80) cc_final: 0.7321 (m-80) REVERT: I 251 ILE cc_start: 0.9177 (mt) cc_final: 0.8931 (mt) REVERT: J 44 ASP cc_start: 0.8480 (t0) cc_final: 0.7877 (t0) outliers start: 34 outliers final: 24 residues processed: 179 average time/residue: 0.1935 time to fit residues: 51.5616 Evaluate side-chains 167 residues out of total 2385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 143 time to evaluate : 0.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain E residue 250 LEU Chi-restraints excluded: chain E residue 304 TYR Chi-restraints excluded: chain E residue 348 ASN Chi-restraints excluded: chain E residue 354 VAL Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 304 TYR Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain F residue 304 TYR Chi-restraints excluded: chain G residue 264 THR Chi-restraints excluded: chain G residue 307 VAL Chi-restraints excluded: chain G residue 340 GLU Chi-restraints excluded: chain H residue 44 MET Chi-restraints excluded: chain A residue 177 GLN Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain J residue 22 SER Chi-restraints excluded: chain J residue 25 THR Chi-restraints excluded: chain J residue 37 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 144 optimal weight: 3.9990 chunk 51 optimal weight: 0.0000 chunk 54 optimal weight: 0.5980 chunk 184 optimal weight: 4.9990 chunk 136 optimal weight: 5.9990 chunk 21 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 chunk 215 optimal weight: 0.8980 chunk 188 optimal weight: 5.9990 chunk 191 optimal weight: 1.9990 chunk 286 optimal weight: 7.9990 overall best weight: 1.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 102 ASN ** I 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 65 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.068799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.053059 restraints weight = 74459.019| |-----------------------------------------------------------------------------| r_work (start): 0.2881 rms_B_bonded: 2.62 r_work: 0.2756 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2758 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2758 r_free = 0.2758 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2758 r_free = 0.2758 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.2758 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.2154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 24549 Z= 0.136 Angle : 0.508 9.020 33630 Z= 0.264 Chirality : 0.039 0.161 3798 Planarity : 0.004 0.063 4221 Dihedral : 14.929 179.185 4162 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 1.45 % Allowed : 16.26 % Favored : 82.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % 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: -0.75 (0.16), residues: 2927 helix: 1.49 (0.17), residues: 926 sheet: -0.53 (0.23), residues: 469 loop : -1.83 (0.15), residues: 1532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG H 269 TYR 0.015 0.001 TYR H 290 PHE 0.010 0.001 PHE H 114 TRP 0.010 0.001 TRP H 49 HIS 0.005 0.001 HIS B 293 Details of bonding type rmsd covalent geometry : bond 0.00309 (24549) covalent geometry : angle 0.50799 (33630) hydrogen bonds : bond 0.02830 ( 977) hydrogen bonds : angle 4.03881 ( 2896) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5854 Ramachandran restraints generated. 2927 Oldfield, 0 Emsley, 2927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5854 Ramachandran restraints generated. 2927 Oldfield, 0 Emsley, 2927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 2385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 146 time to evaluate : 0.657 Fit side-chains REVERT: C 1 MET cc_start: 0.5728 (mtp) cc_final: 0.5106 (mpp) REVERT: C 19 GLN cc_start: 0.8186 (tt0) cc_final: 0.7688 (mt0) REVERT: C 35 GLN cc_start: 0.8390 (tp40) cc_final: 0.8133 (tt0) REVERT: B 76 LYS cc_start: 0.8898 (mttp) cc_final: 0.8522 (mttt) REVERT: B 161 MET cc_start: 0.7677 (mmm) cc_final: 0.7164 (mmm) REVERT: E 318 LYS cc_start: 0.8447 (mmmt) cc_final: 0.7978 (mmtt) REVERT: E 324 TYR cc_start: 0.8258 (m-80) cc_final: 0.7389 (m-80) REVERT: I 251 ILE cc_start: 0.9154 (mt) cc_final: 0.8837 (mt) REVERT: J 44 ASP cc_start: 0.8483 (t0) cc_final: 0.7888 (t0) outliers start: 33 outliers final: 28 residues processed: 169 average time/residue: 0.1891 time to fit residues: 48.2576 Evaluate side-chains 172 residues out of total 2385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 144 time to evaluate : 0.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain E residue 250 LEU Chi-restraints excluded: chain E residue 348 ASN Chi-restraints excluded: chain E residue 354 VAL Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 304 TYR Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain F residue 304 TYR Chi-restraints excluded: chain G residue 264 THR Chi-restraints excluded: chain G residue 307 VAL Chi-restraints excluded: chain G residue 340 GLU Chi-restraints excluded: chain H residue 44 MET Chi-restraints excluded: chain H residue 90 ILE Chi-restraints excluded: chain I residue 228 VAL Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 177 GLN Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain J residue 22 SER Chi-restraints excluded: chain J residue 25 THR Chi-restraints excluded: chain J residue 37 VAL Chi-restraints excluded: chain J residue 41 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 257 optimal weight: 0.9990 chunk 47 optimal weight: 0.2980 chunk 146 optimal weight: 5.9990 chunk 190 optimal weight: 3.9990 chunk 147 optimal weight: 5.9990 chunk 136 optimal weight: 0.9990 chunk 285 optimal weight: 6.9990 chunk 196 optimal weight: 2.9990 chunk 173 optimal weight: 5.9990 chunk 86 optimal weight: 1.9990 chunk 166 optimal weight: 9.9990 overall best weight: 1.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 65 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.068685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.052903 restraints weight = 75727.464| |-----------------------------------------------------------------------------| r_work (start): 0.2876 rms_B_bonded: 2.64 r_work: 0.2749 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2751 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2751 r_free = 0.2751 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2751 r_free = 0.2751 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.2751 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.2175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 24549 Z= 0.146 Angle : 0.516 14.132 33630 Z= 0.267 Chirality : 0.039 0.165 3798 Planarity : 0.003 0.063 4221 Dihedral : 14.913 179.680 4162 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 1.54 % Allowed : 16.08 % Favored : 82.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % 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: -0.69 (0.16), residues: 2927 helix: 1.53 (0.17), residues: 926 sheet: -0.38 (0.24), residues: 451 loop : -1.82 (0.15), residues: 1550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 269 TYR 0.015 0.001 TYR H 290 PHE 0.011 0.001 PHE B 152 TRP 0.010 0.001 TRP H 49 HIS 0.005 0.001 HIS B 305 Details of bonding type rmsd covalent geometry : bond 0.00333 (24549) covalent geometry : angle 0.51622 (33630) hydrogen bonds : bond 0.02840 ( 977) hydrogen bonds : angle 4.04307 ( 2896) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5854 Ramachandran restraints generated. 2927 Oldfield, 0 Emsley, 2927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5854 Ramachandran restraints generated. 2927 Oldfield, 0 Emsley, 2927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 2385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 146 time to evaluate : 0.802 Fit side-chains revert: symmetry clash REVERT: C 1 MET cc_start: 0.5750 (mtp) cc_final: 0.5114 (mpp) REVERT: C 19 GLN cc_start: 0.8194 (tt0) cc_final: 0.7702 (mt0) REVERT: C 35 GLN cc_start: 0.8410 (tp40) cc_final: 0.8174 (tt0) REVERT: B 76 LYS cc_start: 0.8910 (mttp) cc_final: 0.8528 (mttt) REVERT: E 324 TYR cc_start: 0.8284 (m-80) cc_final: 0.7450 (m-80) REVERT: I 251 ILE cc_start: 0.9157 (mt) cc_final: 0.8844 (mt) REVERT: J 44 ASP cc_start: 0.8489 (t0) cc_final: 0.7897 (t0) outliers start: 35 outliers final: 33 residues processed: 168 average time/residue: 0.1792 time to fit residues: 45.9004 Evaluate side-chains 178 residues out of total 2385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 145 time to evaluate : 0.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain E residue 250 LEU Chi-restraints excluded: chain E residue 251 ILE Chi-restraints excluded: chain E residue 348 ASN Chi-restraints excluded: chain E residue 354 VAL Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 304 TYR Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain F residue 304 TYR Chi-restraints excluded: chain G residue 250 LEU Chi-restraints excluded: chain G residue 264 THR Chi-restraints excluded: chain G residue 307 VAL Chi-restraints excluded: chain G residue 340 GLU Chi-restraints excluded: chain H residue 44 MET Chi-restraints excluded: chain H residue 90 ILE Chi-restraints excluded: chain I residue 228 VAL Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 177 GLN Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain J residue 22 SER Chi-restraints excluded: chain J residue 25 THR Chi-restraints excluded: chain J residue 37 VAL Chi-restraints excluded: chain J residue 41 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 50 optimal weight: 8.9990 chunk 60 optimal weight: 0.8980 chunk 64 optimal weight: 8.9990 chunk 16 optimal weight: 0.0670 chunk 219 optimal weight: 0.9990 chunk 70 optimal weight: 0.9990 chunk 246 optimal weight: 10.0000 chunk 113 optimal weight: 5.9990 chunk 117 optimal weight: 0.8980 chunk 191 optimal weight: 3.9990 chunk 277 optimal weight: 20.0000 overall best weight: 0.7722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.069897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.053994 restraints weight = 83749.181| |-----------------------------------------------------------------------------| r_work (start): 0.2905 rms_B_bonded: 2.80 r_work: 0.2773 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2776 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2776 r_free = 0.2776 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2776 r_free = 0.2776 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.2776 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.2357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 24549 Z= 0.105 Angle : 0.489 14.446 33630 Z= 0.253 Chirality : 0.038 0.164 3798 Planarity : 0.003 0.061 4221 Dihedral : 14.840 179.013 4162 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 1.49 % Allowed : 16.21 % Favored : 82.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % 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: -0.56 (0.16), residues: 2927 helix: 1.65 (0.17), residues: 926 sheet: -0.30 (0.24), residues: 459 loop : -1.76 (0.15), residues: 1542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 269 TYR 0.015 0.001 TYR H 290 PHE 0.008 0.001 PHE I 114 TRP 0.009 0.001 TRP A 155 HIS 0.006 0.001 HIS C 3 Details of bonding type rmsd covalent geometry : bond 0.00232 (24549) covalent geometry : angle 0.48895 (33630) hydrogen bonds : bond 0.02651 ( 977) hydrogen bonds : angle 3.92010 ( 2896) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5854 Ramachandran restraints generated. 2927 Oldfield, 0 Emsley, 2927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5854 Ramachandran restraints generated. 2927 Oldfield, 0 Emsley, 2927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 2385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 150 time to evaluate : 0.954 Fit side-chains revert: symmetry clash REVERT: C 19 GLN cc_start: 0.8220 (tt0) cc_final: 0.7690 (mt0) REVERT: C 35 GLN cc_start: 0.8392 (tp40) cc_final: 0.8179 (tt0) REVERT: C 108 ASN cc_start: 0.5710 (t0) cc_final: 0.5498 (t0) REVERT: B 76 LYS cc_start: 0.8878 (mttp) cc_final: 0.8504 (mttt) REVERT: E 79 LYS cc_start: 0.8496 (ptpt) cc_final: 0.8098 (ptpp) REVERT: E 324 TYR cc_start: 0.8143 (m-80) cc_final: 0.7316 (m-80) REVERT: I 251 ILE cc_start: 0.9083 (mt) cc_final: 0.8825 (mt) REVERT: J 44 ASP cc_start: 0.8491 (t0) cc_final: 0.7918 (t0) outliers start: 34 outliers final: 32 residues processed: 172 average time/residue: 0.1881 time to fit residues: 49.5542 Evaluate side-chains 178 residues out of total 2385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 146 time to evaluate : 0.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain E residue 250 LEU Chi-restraints excluded: chain E residue 251 ILE Chi-restraints excluded: chain E residue 348 ASN Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 304 TYR Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain F residue 304 TYR Chi-restraints excluded: chain G residue 264 THR Chi-restraints excluded: chain G residue 307 VAL Chi-restraints excluded: chain G residue 340 GLU Chi-restraints excluded: chain H residue 44 MET Chi-restraints excluded: chain H residue 90 ILE Chi-restraints excluded: chain I residue 228 VAL Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 177 GLN Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain J residue 21 THR Chi-restraints excluded: chain J residue 22 SER Chi-restraints excluded: chain J residue 25 THR Chi-restraints excluded: chain J residue 37 VAL Chi-restraints excluded: chain J residue 41 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 72 optimal weight: 0.1980 chunk 165 optimal weight: 3.9990 chunk 104 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 chunk 14 optimal weight: 6.9990 chunk 240 optimal weight: 0.9990 chunk 169 optimal weight: 7.9990 chunk 285 optimal weight: 6.9990 chunk 179 optimal weight: 1.9990 chunk 261 optimal weight: 6.9990 chunk 92 optimal weight: 0.9990 overall best weight: 1.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 65 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.069055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.053482 restraints weight = 71043.728| |-----------------------------------------------------------------------------| r_work (start): 0.2888 rms_B_bonded: 2.56 r_work: 0.2764 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2767 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2767 r_free = 0.2767 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2767 r_free = 0.2767 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.2767 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.2311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 24549 Z= 0.144 Angle : 0.512 13.716 33630 Z= 0.264 Chirality : 0.039 0.182 3798 Planarity : 0.003 0.063 4221 Dihedral : 14.862 179.638 4162 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 1.58 % Allowed : 16.39 % Favored : 82.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % 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: -0.61 (0.16), residues: 2927 helix: 1.62 (0.17), residues: 926 sheet: -0.44 (0.24), residues: 466 loop : -1.75 (0.15), residues: 1535 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 269 TYR 0.015 0.001 TYR H 290 PHE 0.011 0.001 PHE B 152 TRP 0.012 0.001 TRP A 155 HIS 0.005 0.001 HIS B 42 Details of bonding type rmsd covalent geometry : bond 0.00327 (24549) covalent geometry : angle 0.51160 (33630) hydrogen bonds : bond 0.02799 ( 977) hydrogen bonds : angle 3.98407 ( 2896) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4951.96 seconds wall clock time: 85 minutes 39.33 seconds (5139.33 seconds total)