Starting phenix.real_space_refine on Tue Oct 27 06:16:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7jzx_22583/10_2026/7jzx_22583.cif Found real_map, /net/cci-nas-00/data/ceres_data/7jzx_22583/10_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/7jzx_22583/10_2026/7jzx_22583.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7jzx_22583/10_2026/7jzx_22583.cif" model { file = "/net/cci-nas-00/data/ceres_data/7jzx_22583/10_2026/7jzx_22583.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7jzx_22583/10_2026/7jzx_22583.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7jzx_22583/10_2026/7jzx_22583.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7jzx_22583/10_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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/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, 'RNAv2': 60} Modifications used: {'rna2p_pur': 11, 'rna2p_pyr': 17, 'rna3p_pur': 17, 'rna3p_pyr': 14} Link IDs: {'rna2p': 28, 'rna3p': 32} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {' C:plan': 1, ' C:plan2': 1} Unresolved non-hydrogen planarities: 11 Chain: "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: 5.87, per 1000 atoms: 0.25 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: 1.69 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: 2.30 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: 4.49 Time building geometry restraints manager: 2.32 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 1.20e-02 6.94e+03 2.96e+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: 32203 2.16 - 4.32: 1219 4.32 - 6.48: 166 6.48 - 8.64: 36 8.64 - 10.79: 3 Bond angle restraints: 33627 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 33622 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.86: 13381 22.86 - 45.73: 950 45.73 - 68.59: 223 68.59 - 91.45: 50 91.45 - 114.32: 1 Dihedral angle restraints: 14605 sinusoidal: 6099 harmonic: 8506 Sorted by residual: dihedral pdb=" C4' C M 37 " pdb=" C3' C M 37 " pdb=" C2' C M 37 " pdb=" C1' C M 37 " ideal model delta sinusoidal sigma weight residual 36.34 -38.84 75.18 1 3.10e+00 1.04e-01 7.43e+02 dihedral pdb=" C4' U M 43 " pdb=" C3' U M 43 " pdb=" C2' U M 43 " pdb=" C1' U M 43 " ideal model delta sinusoidal sigma weight residual 36.34 -37.69 74.03 1 3.10e+00 1.04e-01 7.24e+02 dihedral pdb=" C4' G M 40 " pdb=" C3' G M 40 " pdb=" C2' G M 40 " pdb=" C1' G M 40 " ideal model delta sinusoidal sigma weight residual 36.35 -36.88 73.22 1 3.10e+00 1.04e-01 7.11e+02 ... (remaining 14602 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 3075 0.067 - 0.134: 548 0.134 - 0.201: 87 0.201 - 0.268: 63 0.268 - 0.335: 25 Chirality restraints: 3798 Sorted by residual: chirality pdb=" P A M 3 " pdb=" OP1 A M 3 " pdb=" OP2 A M 3 " pdb=" O5' A M 3 " both_signs ideal model delta sigma weight residual True 2.17 -2.51 -0.33 2.00e-01 2.50e+01 2.80e+00 chirality pdb=" C3' G M 40 " pdb=" C4' G M 40 " pdb=" O3' G M 40 " pdb=" C2' G M 40 " both_signs ideal model delta sigma weight residual False -2.50 -2.81 0.31 2.00e-01 2.50e+01 2.42e+00 chirality pdb=" C2' G M 60 " pdb=" C3' G M 60 " pdb=" O2' G M 60 " pdb=" C1' G M 60 " both_signs ideal model delta sigma weight residual False -2.79 -2.48 -0.30 2.00e-01 2.50e+01 2.32e+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: 1.840 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.410 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 23.610 Find NCS groups from input model: 0.390 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:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 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= 0.382 Angle : 0.963 10.795 33627 Z= 0.522 Chirality : 0.065 0.335 3798 Planarity : 0.006 0.072 4221 Dihedral : 16.807 114.318 9109 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/Z covalent geometry : bond 0.00871 / 0.38 (24549) covalent geometry : angle 0.96267 / 0.52 (33627) hydrogen bonds : bond 0.17543 / 11.85 ( 977) hydrogen bonds : angle 7.78601 / 5.44 ( 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 : 0.706 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: 0.2211 time to fit residues: 60.1737 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 : 0.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: [197, 215, 20, 132, 261, 248, 207, 155, 244, 183, 111] 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... C 19 GLN C 84 GLN C 165 GLN 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 ** both conformations clash, **PLEASE CHECK MANUALLY** I 183 HIS I 342 GLN ** A 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.070023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.054424 restraints weight = 65501.098| |-----------------------------------------------------------------------------| r_work (start): 0.2920 rms_B_bonded: 2.47 r_work: 0.2799 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2650 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2650 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2652 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2652 r_free = 0.2652 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2652 r_free = 0.2652 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.2652 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8770 moved from start: 0.1407 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= 0.149 Angle : 0.817 17.945 33627 Z= 0.363 Chirality : 0.067 0.904 3798 Planarity : 0.004 0.059 4221 Dihedral : 12.276 151.795 3945 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 1.05 % Allowed : 9.93 % Favored : 89.02 % 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: -2.43 (0.14), residues: 2927 helix: -0.72 (0.15), residues: 925 sheet: -1.09 (0.23), residues: 430 loop : -2.39 (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 C 158 TRP 0.011 0.001 TRP A 394 HIS 0.005 0.001 HIS B 305 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.15 (24549) covalent geometry : angle 0.81723 / 0.36 (33627) hydrogen bonds : bond 0.03772 / 2.58 ( 977) hydrogen bonds : angle 4.99787 / 3.49 ( 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 185 residues out of total 2385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 161 time to evaluate : 0.845 Fit side-chains REVERT: C 19 GLN cc_start: 0.8316 (tt0) cc_final: 0.7877 (tt0) REVERT: C 35 GLN cc_start: 0.8370 (tp40) cc_final: 0.7926 (tp40) REVERT: C 165 GLN cc_start: 0.7756 (tt0) cc_final: 0.7512 (tm-30) REVERT: B 137 MET cc_start: 0.9071 (mtp) cc_final: 0.8840 (mtp) REVERT: B 244 LYS cc_start: 0.8391 (mtmt) cc_final: 0.8123 (mtmm) REVERT: B 314 TYR cc_start: 0.8491 (m-80) cc_final: 0.8285 (m-80) REVERT: I 216 GLU cc_start: 0.8409 (OUTLIER) cc_final: 0.8011 (mt-10) REVERT: A 228 TRP cc_start: 0.8716 (t-100) cc_final: 0.8457 (t-100) REVERT: J 44 ASP cc_start: 0.8457 (t0) cc_final: 0.7963 (t0) outliers start: 24 outliers final: 7 residues processed: 181 average time/residue: 0.1859 time to fit residues: 50.5655 Evaluate side-chains 154 residues out of total 2385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 146 time to evaluate : 0.759 ------------------------------------------------------------------------------- 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 44 MET 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: [288, 168, 204, 238, 98, 276, 58, 0, 109, 92, 290] chunk 288 optimal weight: 10.0000 chunk 168 optimal weight: 5.9990 chunk 204 optimal weight: 0.5980 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: 0.6980 overall best weight: 2.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 19 ASN B 69 GLN ** B 293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 91 GLN D 102 ASN D 348 ASN ** F 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 348 ASN G 260 GLN H 148 GLN A 74 HIS A 335 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.068675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.052449 restraints weight = 84334.431| |-----------------------------------------------------------------------------| r_work (start): 0.2864 rms_B_bonded: 2.81 r_work: 0.2733 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2733 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2736 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2736 r_free = 0.2736 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2736 r_free = 0.2736 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (7 function evaluations) r_final: 0.2736 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8724 moved from start: 0.1673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 24549 Z= 0.197 Angle : 0.702 15.463 33627 Z= 0.328 Chirality : 0.055 0.657 3798 Planarity : 0.004 0.061 4221 Dihedral : 12.145 172.869 3945 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 1.36 % Allowed : 12.39 % Favored : 86.25 % 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: -1.68 (0.15), residues: 2927 helix: 0.32 (0.17), residues: 922 sheet: -0.92 (0.23), residues: 445 loop : -2.14 (0.14), residues: 1560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 160 TYR 0.016 0.002 TYR H 290 PHE 0.012 0.001 PHE H 114 TRP 0.016 0.001 TRP A 394 HIS 0.007 0.001 HIS B 42 Details of bonding type rmsd/Z covalent geometry : bond 0.00445 / 0.20 (24549) covalent geometry : angle 0.70211 / 0.33 (33627) hydrogen bonds : bond 0.03370 / 2.30 ( 977) hydrogen bonds : angle 4.52652 / 3.17 ( 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 185 residues out of total 2385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 154 time to evaluate : 0.796 Fit side-chains REVERT: C 19 GLN cc_start: 0.8096 (tt0) cc_final: 0.7682 (tt0) REVERT: C 35 GLN cc_start: 0.8458 (tp40) cc_final: 0.7936 (tp40) REVERT: C 153 GLN cc_start: 0.7867 (mm-40) cc_final: 0.7648 (mp10) REVERT: B 76 LYS cc_start: 0.8903 (mttp) cc_final: 0.8606 (mttt) REVERT: B 137 MET cc_start: 0.9121 (mtp) cc_final: 0.8847 (mtp) REVERT: B 244 LYS cc_start: 0.8393 (mtmt) cc_final: 0.8187 (mtmm) REVERT: B 311 LYS cc_start: 0.8832 (ttpt) cc_final: 0.8624 (ttpp) REVERT: B 314 TYR cc_start: 0.8420 (m-80) cc_final: 0.8217 (m-80) REVERT: I 216 GLU cc_start: 0.8118 (OUTLIER) cc_final: 0.7682 (mt-10) REVERT: I 302 GLU cc_start: 0.8040 (OUTLIER) cc_final: 0.7749 (mm-30) REVERT: A 228 TRP cc_start: 0.8675 (t-100) cc_final: 0.8406 (t-100) REVERT: J 44 ASP cc_start: 0.8401 (t0) cc_final: 0.7867 (t0) outliers start: 31 outliers final: 18 residues processed: 174 average time/residue: 0.1806 time to fit residues: 47.1892 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 : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 348 ASN Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D 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 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 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 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: [116, 10, 262, 255, 30, 86, 206, 154, 20, 71, 42] chunk 116 optimal weight: 7.9990 chunk 10 optimal weight: 9.9990 chunk 262 optimal weight: 5.9990 chunk 255 optimal weight: 20.0000 chunk 30 optimal weight: 0.9980 chunk 86 optimal weight: 8.9990 chunk 206 optimal weight: 0.9990 chunk 154 optimal weight: 6.9990 chunk 20 optimal weight: 0.9980 chunk 71 optimal weight: 10.0000 chunk 42 optimal weight: 3.9990 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 51 GLN ** E 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 102 ASN H 281 ASN I 159 HIS A 74 HIS A 335 GLN J 65 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.068021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.052144 restraints weight = 76198.397| |-----------------------------------------------------------------------------| r_work (start): 0.2853 rms_B_bonded: 2.65 r_work: 0.2726 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.2726 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2729 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2729 r_free = 0.2729 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2729 r_free = 0.2729 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.2729 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8735 moved from start: 0.1835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 24549 Z= 0.233 Angle : 0.709 15.295 33627 Z= 0.331 Chirality : 0.053 0.498 3798 Planarity : 0.004 0.065 4221 Dihedral : 12.090 179.485 3945 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 1.45 % Allowed : 13.84 % Favored : 84.71 % 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: -1.37 (0.15), residues: 2927 helix: 0.74 (0.17), residues: 922 sheet: -0.80 (0.23), residues: 450 loop : -2.06 (0.15), residues: 1555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 268 TYR 0.017 0.002 TYR H 290 PHE 0.015 0.002 PHE H 114 TRP 0.016 0.001 TRP A 394 HIS 0.006 0.001 HIS B 42 Details of bonding type rmsd/Z covalent geometry : bond 0.00535 / 0.23 (24549) covalent geometry : angle 0.70901 / 0.33 (33627) hydrogen bonds : bond 0.03284 / 2.24 ( 977) hydrogen bonds : angle 4.40752 / 3.07 ( 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 184 residues out of total 2385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 151 time to evaluate : 1.043 Fit side-chains REVERT: C 19 GLN cc_start: 0.8111 (tt0) cc_final: 0.7705 (tt0) REVERT: C 35 GLN cc_start: 0.8482 (tp40) cc_final: 0.7931 (tp40) REVERT: B 311 LYS cc_start: 0.8842 (ttpt) cc_final: 0.8465 (tttm) REVERT: B 314 TYR cc_start: 0.8444 (m-80) cc_final: 0.8074 (m-80) REVERT: D 44 MET cc_start: 0.8692 (mtm) cc_final: 0.8465 (mtp) REVERT: I 216 GLU cc_start: 0.8204 (OUTLIER) cc_final: 0.7782 (mt-10) REVERT: A 228 TRP cc_start: 0.8741 (t-100) cc_final: 0.8488 (t-100) REVERT: J 44 ASP cc_start: 0.8429 (t0) cc_final: 0.7883 (t0) REVERT: J 61 VAL cc_start: 0.8365 (t) cc_final: 0.8162 (t) outliers start: 33 outliers final: 24 residues processed: 169 average time/residue: 0.1825 time to fit residues: 46.3116 Evaluate side-chains 172 residues out of total 2385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 147 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 I residue 216 GLU Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 165 VAL 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 422 LEU Chi-restraints excluded: chain J residue 22 SER Chi-restraints excluded: chain J residue 23 ILE Chi-restraints excluded: chain J residue 25 THR Chi-restraints excluded: chain J residue 41 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: [42, 126, 79, 267, 134, 279, 102, 34, 98, 193, 53] chunk 42 optimal weight: 5.9990 chunk 126 optimal weight: 6.9990 chunk 79 optimal weight: 0.8980 chunk 267 optimal weight: 0.0270 chunk 134 optimal weight: 0.4980 chunk 279 optimal weight: 6.9990 chunk 102 optimal weight: 0.9990 chunk 34 optimal weight: 10.0000 chunk 98 optimal weight: 7.9990 chunk 193 optimal weight: 0.9980 chunk 53 optimal weight: 9.9990 overall best weight: 0.6840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 69 GLN ** B 293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 129 ASN ** F 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 65 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.070465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.054480 restraints weight = 83637.507| |-----------------------------------------------------------------------------| r_work (start): 0.2921 rms_B_bonded: 2.80 r_work: 0.2791 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2794 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2794 r_free = 0.2794 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2794 r_free = 0.2794 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2794 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8672 moved from start: 0.2160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 24549 Z= 0.110 Angle : 0.612 12.600 33627 Z= 0.286 Chirality : 0.047 0.358 3798 Planarity : 0.003 0.062 4221 Dihedral : 11.802 178.651 3945 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 1.49 % Allowed : 14.46 % Favored : 84.05 % 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: -0.98 (0.15), residues: 2927 helix: 1.20 (0.17), residues: 926 sheet: -0.68 (0.23), residues: 469 loop : -1.88 (0.15), residues: 1532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 268 TYR 0.014 0.001 TYR H 290 PHE 0.012 0.001 PHE B 152 TRP 0.009 0.001 TRP I 49 HIS 0.004 0.001 HIS B 305 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.11 (24549) covalent geometry : angle 0.61225 / 0.29 (33627) hydrogen bonds : bond 0.02796 / 1.92 ( 977) hydrogen bonds : angle 4.04916 / 2.83 ( 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 191 residues out of total 2385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 157 time to evaluate : 0.762 Fit side-chains REVERT: C 1 MET cc_start: 0.6046 (mtp) cc_final: 0.5271 (mpp) REVERT: C 35 GLN cc_start: 0.8487 (tp40) cc_final: 0.8137 (tp40) REVERT: B 76 LYS cc_start: 0.8815 (mttp) cc_final: 0.8445 (mttt) REVERT: B 244 LYS cc_start: 0.8544 (mtmm) cc_final: 0.8324 (mtmm) REVERT: E 318 LYS cc_start: 0.8447 (mmmt) cc_final: 0.8032 (mmtt) REVERT: E 324 TYR cc_start: 0.8169 (m-80) cc_final: 0.7314 (m-80) REVERT: E 354 VAL cc_start: 0.8999 (OUTLIER) cc_final: 0.8676 (p) REVERT: I 251 ILE cc_start: 0.9211 (mt) cc_final: 0.8943 (mt) REVERT: J 44 ASP cc_start: 0.8441 (t0) cc_final: 0.7916 (t0) outliers start: 34 outliers final: 23 residues processed: 180 average time/residue: 0.1781 time to fit residues: 48.7343 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 : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 100 VAL 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 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 H residue 44 MET Chi-restraints excluded: chain I residue 68 VAL Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 165 VAL 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 422 LEU Chi-restraints excluded: chain J residue 22 SER Chi-restraints excluded: chain J residue 41 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: [207, 59, 159, 202, 34, 143, 286, 33, 11, 147, 127] chunk 207 optimal weight: 0.8980 chunk 59 optimal weight: 5.9990 chunk 159 optimal weight: 7.9990 chunk 202 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 143 optimal weight: 7.9990 chunk 286 optimal weight: 5.9990 chunk 33 optimal weight: 0.7980 chunk 11 optimal weight: 0.8980 chunk 147 optimal weight: 5.9990 chunk 127 optimal weight: 0.9980 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 102 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.069779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.053733 restraints weight = 84095.033| |-----------------------------------------------------------------------------| r_work (start): 0.2900 rms_B_bonded: 2.80 r_work: 0.2770 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2772 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2772 r_free = 0.2772 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2772 r_free = 0.2772 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (6 function evaluations) r_final: 0.2772 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8690 moved from start: 0.2219 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= 0.142 Angle : 0.623 12.719 33627 Z= 0.291 Chirality : 0.048 0.390 3798 Planarity : 0.003 0.063 4221 Dihedral : 11.717 179.111 3945 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 1.63 % Allowed : 15.20 % Favored : 83.17 % 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: -0.85 (0.15), residues: 2927 helix: 1.35 (0.17), residues: 926 sheet: -0.61 (0.23), residues: 469 loop : -1.83 (0.15), residues: 1532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 237 TYR 0.014 0.001 TYR H 290 PHE 0.010 0.001 PHE H 114 TRP 0.013 0.001 TRP H 49 HIS 0.005 0.001 HIS B 42 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 (24549) covalent geometry : angle 0.62344 / 0.29 (33627) hydrogen bonds : bond 0.02826 / 1.94 ( 977) hydrogen bonds : angle 4.04710 / 2.83 ( 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 188 residues out of total 2385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 151 time to evaluate : 0.823 Fit side-chains REVERT: C 1 MET cc_start: 0.6027 (mtp) cc_final: 0.5242 (mpp) REVERT: C 35 GLN cc_start: 0.8496 (tp40) cc_final: 0.8226 (tt0) REVERT: B 76 LYS cc_start: 0.8838 (mttp) cc_final: 0.8484 (mttt) REVERT: B 158 GLU cc_start: 0.7664 (OUTLIER) cc_final: 0.7326 (tt0) REVERT: B 244 LYS cc_start: 0.8582 (mtmm) cc_final: 0.8367 (mtmm) REVERT: E 324 TYR cc_start: 0.8240 (m-80) cc_final: 0.7422 (m-80) REVERT: I 251 ILE cc_start: 0.9217 (mt) cc_final: 0.8894 (mt) REVERT: J 44 ASP cc_start: 0.8444 (t0) cc_final: 0.7910 (t0) outliers start: 37 outliers final: 30 residues processed: 176 average time/residue: 0.1791 time to fit residues: 48.1600 Evaluate side-chains 175 residues out of total 2385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 144 time to evaluate : 0.649 ------------------------------------------------------------------------------- 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 158 GLU Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 209 THR 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 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 340 GLU Chi-restraints excluded: chain H residue 44 MET Chi-restraints excluded: chain I residue 44 MET Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 165 VAL 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 A residue 422 LEU Chi-restraints excluded: chain J residue 22 SER 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: [184, 167, 242, 126, 251, 81, 157, 287, 263, 65, 106] chunk 184 optimal weight: 4.9990 chunk 167 optimal weight: 0.7980 chunk 242 optimal weight: 9.9990 chunk 126 optimal weight: 7.9990 chunk 251 optimal weight: 4.9990 chunk 81 optimal weight: 8.9990 chunk 157 optimal weight: 2.9990 chunk 287 optimal weight: 5.9990 chunk 263 optimal weight: 0.0670 chunk 65 optimal weight: 5.9990 chunk 106 optimal weight: 0.9980 overall best weight: 1.9722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 19 GLN ** B 293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 159 HIS J 65 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.068940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.052796 restraints weight = 87790.105| |-----------------------------------------------------------------------------| r_work (start): 0.2870 rms_B_bonded: 2.85 r_work: 0.2740 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2743 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2743 r_free = 0.2743 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2743 r_free = 0.2743 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2743 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8716 moved from start: 0.2208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 24549 Z= 0.184 Angle : 0.650 12.788 33627 Z= 0.304 Chirality : 0.049 0.399 3798 Planarity : 0.004 0.065 4221 Dihedral : 11.758 177.439 3945 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 2.11 % Allowed : 15.33 % Favored : 82.56 % 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: -0.82 (0.16), residues: 2927 helix: 1.36 (0.17), residues: 927 sheet: -0.53 (0.23), residues: 457 loop : -1.83 (0.15), residues: 1543 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG H 269 TYR 0.016 0.002 TYR H 290 PHE 0.013 0.001 PHE H 114 TRP 0.012 0.001 TRP H 49 HIS 0.005 0.001 HIS B 42 Details of bonding type rmsd/Z covalent geometry : bond 0.00424 / 0.18 (24549) covalent geometry : angle 0.64973 / 0.30 (33627) hydrogen bonds : bond 0.02949 / 2.02 ( 977) hydrogen bonds : angle 4.12390 / 2.88 ( 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 194 residues out of total 2385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 146 time to evaluate : 0.602 Fit side-chains revert: symmetry clash REVERT: C 1 MET cc_start: 0.5875 (mtp) cc_final: 0.5191 (mpp) REVERT: C 35 GLN cc_start: 0.8501 (tp40) cc_final: 0.8247 (tt0) REVERT: B 76 LYS cc_start: 0.8925 (mttp) cc_final: 0.8537 (mttt) REVERT: B 244 LYS cc_start: 0.8632 (mtmm) cc_final: 0.8431 (mtmm) REVERT: E 324 TYR cc_start: 0.8341 (m-80) cc_final: 0.7537 (m-80) REVERT: H 251 ILE cc_start: 0.9077 (OUTLIER) cc_final: 0.8754 (mp) REVERT: J 44 ASP cc_start: 0.8455 (t0) cc_final: 0.7912 (t0) outliers start: 48 outliers final: 31 residues processed: 179 average time/residue: 0.1718 time to fit residues: 46.3551 Evaluate side-chains 175 residues out of total 2385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 143 time to evaluate : 0.841 ------------------------------------------------------------------------------- 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 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 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 340 GLU Chi-restraints excluded: chain H residue 44 MET Chi-restraints excluded: chain H residue 90 ILE Chi-restraints excluded: chain H residue 251 ILE Chi-restraints excluded: chain I residue 44 MET Chi-restraints excluded: chain A residue 105 VAL 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 A residue 422 LEU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: [144, 51, 54, 184, 136, 21, 106, 215, 188, 191, 286] chunk 144 optimal weight: 3.9990 chunk 51 optimal weight: 8.9990 chunk 54 optimal weight: 0.9980 chunk 184 optimal weight: 3.9990 chunk 136 optimal weight: 0.9990 chunk 21 optimal weight: 0.6980 chunk 106 optimal weight: 0.9990 chunk 215 optimal weight: 7.9990 chunk 188 optimal weight: 3.9990 chunk 191 optimal weight: 0.9990 chunk 286 optimal weight: 5.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 165 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 = 0.3316 r_free = 0.3316 target = 0.070301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.054586 restraints weight = 74489.092| |-----------------------------------------------------------------------------| r_work (start): 0.2922 rms_B_bonded: 2.61 r_work: 0.2799 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2800 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2800 r_free = 0.2800 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2800 r_free = 0.2800 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.2800 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8665 moved from start: 0.2385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 24549 Z= 0.119 Angle : 0.611 11.868 33627 Z= 0.285 Chirality : 0.046 0.359 3798 Planarity : 0.003 0.062 4221 Dihedral : 11.627 179.597 3945 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 1.63 % Allowed : 15.25 % Favored : 83.13 % 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: -0.68 (0.16), residues: 2927 helix: 1.53 (0.17), residues: 926 sheet: -0.41 (0.24), residues: 459 loop : -1.79 (0.15), residues: 1542 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 0.008 0.001 PHE E 166 TRP 0.010 0.001 TRP H 49 HIS 0.006 0.001 HIS B 305 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 (24549) covalent geometry : angle 0.61078 / 0.29 (33627) hydrogen bonds : bond 0.02708 / 1.86 ( 977) hydrogen bonds : angle 3.99366 / 2.79 ( 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 187 residues out of total 2385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 150 time to evaluate : 0.700 Fit side-chains revert: symmetry clash REVERT: C 1 MET cc_start: 0.5799 (mtp) cc_final: 0.5241 (mpp) REVERT: C 35 GLN cc_start: 0.8420 (tp40) cc_final: 0.8198 (tt0) REVERT: B 76 LYS cc_start: 0.8881 (mttp) cc_final: 0.8519 (mttt) REVERT: E 79 LYS cc_start: 0.8424 (ptpt) cc_final: 0.7991 (ptpp) REVERT: E 324 TYR cc_start: 0.8246 (m-80) cc_final: 0.7360 (m-80) REVERT: I 251 ILE cc_start: 0.9187 (mt) cc_final: 0.8889 (mt) REVERT: A 228 TRP cc_start: 0.8675 (t-100) cc_final: 0.8149 (t-100) REVERT: J 44 ASP cc_start: 0.8422 (t0) cc_final: 0.7879 (t0) outliers start: 37 outliers final: 32 residues processed: 176 average time/residue: 0.1814 time to fit residues: 48.3541 Evaluate side-chains 174 residues out of total 2385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 142 time to evaluate : 0.880 ------------------------------------------------------------------------------- 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 159 LEU 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 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 340 GLU Chi-restraints excluded: chain H residue 44 MET Chi-restraints excluded: chain H residue 90 ILE Chi-restraints excluded: chain I residue 68 VAL Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 105 VAL 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 A residue 422 LEU Chi-restraints excluded: chain J residue 21 THR 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: [257, 47, 146, 190, 147, 136, 285, 196, 173, 86, 166] chunk 257 optimal weight: 0.6980 chunk 47 optimal weight: 0.7980 chunk 146 optimal weight: 0.9990 chunk 190 optimal weight: 0.7980 chunk 147 optimal weight: 2.9990 chunk 136 optimal weight: 3.9990 chunk 285 optimal weight: 5.9990 chunk 196 optimal weight: 3.9990 chunk 173 optimal weight: 4.9990 chunk 86 optimal weight: 7.9990 chunk 166 optimal weight: 9.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 102 ASN ** I 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 68 HIS J 65 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.070048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.054222 restraints weight = 75718.133| |-----------------------------------------------------------------------------| r_work (start): 0.2912 rms_B_bonded: 2.64 r_work: 0.2788 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2790 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2790 r_free = 0.2790 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2790 r_free = 0.2790 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (6 function evaluations) r_final: 0.2790 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 moved from start: 0.2424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 24549 Z= 0.137 Angle : 0.618 13.902 33627 Z= 0.288 Chirality : 0.047 0.367 3798 Planarity : 0.003 0.062 4221 Dihedral : 11.574 179.942 3945 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 1.71 % Allowed : 15.33 % Favored : 82.95 % 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: -0.65 (0.16), residues: 2927 helix: 1.55 (0.17), residues: 926 sheet: -0.38 (0.24), residues: 459 loop : -1.78 (0.15), residues: 1542 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 0.011 0.001 TRP A 155 HIS 0.005 0.001 HIS B 42 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.14 (24549) covalent geometry : angle 0.61756 / 0.29 (33627) hydrogen bonds : bond 0.02747 / 1.88 ( 977) hydrogen bonds : angle 3.99438 / 2.79 ( 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 183 residues out of total 2385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 144 time to evaluate : 0.911 Fit side-chains revert: symmetry clash REVERT: C 1 MET cc_start: 0.5773 (mtp) cc_final: 0.5243 (mpp) REVERT: C 35 GLN cc_start: 0.8466 (tp40) cc_final: 0.8256 (tt0) REVERT: C 108 ASN cc_start: 0.5734 (t0) cc_final: 0.5502 (t0) REVERT: B 76 LYS cc_start: 0.8896 (mttp) cc_final: 0.8534 (mttt) REVERT: E 79 LYS cc_start: 0.8432 (ptpt) cc_final: 0.8036 (ptpp) REVERT: E 324 TYR cc_start: 0.8266 (m-80) cc_final: 0.7416 (m-80) REVERT: I 251 ILE cc_start: 0.9188 (mt) cc_final: 0.8845 (mt) REVERT: J 44 ASP cc_start: 0.8435 (t0) cc_final: 0.7893 (t0) outliers start: 39 outliers final: 35 residues processed: 172 average time/residue: 0.1770 time to fit residues: 46.6630 Evaluate side-chains 178 residues out of total 2385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 143 time to evaluate : 0.843 ------------------------------------------------------------------------------- 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 159 LEU 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 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 147 ASP Chi-restraints excluded: chain G residue 264 THR 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 68 VAL Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 105 VAL 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 A residue 422 LEU Chi-restraints excluded: chain J residue 21 THR 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: [50, 60, 64, 16, 219, 70, 246, 113, 117, 191, 277] chunk 50 optimal weight: 7.9990 chunk 60 optimal weight: 2.9990 chunk 64 optimal weight: 7.9990 chunk 16 optimal weight: 7.9990 chunk 219 optimal weight: 3.9990 chunk 70 optimal weight: 0.9980 chunk 246 optimal weight: 10.0000 chunk 113 optimal weight: 5.9990 chunk 117 optimal weight: 1.9990 chunk 191 optimal weight: 1.9990 chunk 277 optimal weight: 10.0000 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 146 ASN ** I 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.068614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.052562 restraints weight = 84427.958| |-----------------------------------------------------------------------------| r_work (start): 0.2863 rms_B_bonded: 2.78 r_work: 0.2734 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.2734 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2735 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2735 r_free = 0.2735 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 = 0.2735 r_free = 0.2735 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2735 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8722 moved from start: 0.2349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 24549 Z= 0.216 Angle : 0.675 14.149 33627 Z= 0.315 Chirality : 0.050 0.399 3798 Planarity : 0.004 0.064 4221 Dihedral : 11.689 177.662 3945 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.53 % Favored : 93.47 % Rotamer: Outliers : 1.58 % Allowed : 15.47 % Favored : 82.95 % 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: -0.77 (0.16), residues: 2927 helix: 1.44 (0.17), residues: 922 sheet: -0.59 (0.23), residues: 477 loop : -1.80 (0.15), residues: 1528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 269 TYR 0.016 0.002 TYR H 290 PHE 0.014 0.001 PHE H 114 TRP 0.013 0.001 TRP A 155 HIS 0.005 0.001 HIS B 42 Details of bonding type rmsd/Z covalent geometry : bond 0.00501 / 0.22 (24549) covalent geometry : angle 0.67467 / 0.31 (33627) hydrogen bonds : bond 0.03021 / 2.06 ( 977) hydrogen bonds : angle 4.16524 / 2.91 ( 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 177 residues out of total 2385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 141 time to evaluate : 0.896 Fit side-chains REVERT: C 4 TYR cc_start: 0.8419 (p90) cc_final: 0.8173 (p90) REVERT: C 35 GLN cc_start: 0.8498 (tp40) cc_final: 0.8274 (tt0) REVERT: C 108 ASN cc_start: 0.5671 (t0) cc_final: 0.5471 (t0) REVERT: B 76 LYS cc_start: 0.8945 (mttp) cc_final: 0.8557 (mttt) REVERT: E 79 LYS cc_start: 0.8472 (ptpt) cc_final: 0.8080 (ptpp) REVERT: E 324 TYR cc_start: 0.8379 (m-80) cc_final: 0.7533 (m-80) REVERT: J 44 ASP cc_start: 0.8452 (t0) cc_final: 0.7906 (t0) outliers start: 36 outliers final: 35 residues processed: 164 average time/residue: 0.1720 time to fit residues: 43.2874 Evaluate side-chains 176 residues out of total 2385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 141 time to evaluate : 0.751 ------------------------------------------------------------------------------- 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 159 LEU Chi-restraints excluded: chain B residue 181 LEU 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 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 147 ASP Chi-restraints excluded: chain G residue 264 THR 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 105 VAL 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 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: [72, 165, 104, 17, 14, 240, 169, 285, 179, 261, 92] chunk 72 optimal weight: 0.9980 chunk 165 optimal weight: 0.0980 chunk 104 optimal weight: 0.2980 chunk 17 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 chunk 240 optimal weight: 0.9980 chunk 169 optimal weight: 5.9990 chunk 285 optimal weight: 5.9990 chunk 179 optimal weight: 1.9990 chunk 261 optimal weight: 0.7980 chunk 92 optimal weight: 0.3980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 29 HIS ** C 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.071151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.055642 restraints weight = 70850.302| |-----------------------------------------------------------------------------| r_work (start): 0.2949 rms_B_bonded: 2.54 r_work: 0.2828 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2830 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2830 r_free = 0.2830 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2830 r_free = 0.2830 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2830 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 moved from start: 0.2599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 24549 Z= 0.101 Angle : 0.603 14.246 33627 Z= 0.282 Chirality : 0.045 0.342 3798 Planarity : 0.003 0.060 4221 Dihedral : 11.484 177.262 3945 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 1.45 % Allowed : 15.82 % Favored : 82.73 % 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: -0.57 (0.16), residues: 2927 helix: 1.64 (0.17), residues: 926 sheet: -0.48 (0.23), residues: 480 loop : -1.71 (0.15), residues: 1521 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 0.010 0.001 PHE B 152 TRP 0.010 0.001 TRP A 155 HIS 0.004 0.001 HIS B 305 Details of bonding type rmsd/Z covalent geometry : bond 0.00220 / 0.10 (24549) covalent geometry : angle 0.60292 / 0.28 (33627) hydrogen bonds : bond 0.02624 / 1.82 ( 977) hydrogen bonds : angle 3.92134 / 2.74 ( 2896) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4918.05 seconds wall clock time: 85 minutes 9.47 seconds (5109.47 seconds total)