Starting phenix.real_space_refine on Sun Jul 5 15:26:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7rjc_24484/07_2026/7rjc_24484_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rjc_24484/07_2026/7rjc_24484.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7rjc_24484/07_2026/7rjc_24484.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rjc_24484/07_2026/7rjc_24484.map" model { file = "/net/cci-nas-00/data/ceres_data/7rjc_24484/07_2026/7rjc_24484_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rjc_24484/07_2026/7rjc_24484_trim.cif" } resolution = 3.3 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= 0.004 sd= 0.164 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: 6 Type Number sf(0) Gaussians Fe 5 7.16 5 S 44 5.16 5 C 9471 2.51 5 N 2447 2.21 5 O 2742 1.98 5 H 13664 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Residue "D ARG 282": not complete - not flipped Time to flip 25 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 28373 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 6364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 416, 6364 Classifications: {'peptide': 416} Link IDs: {'PTRANS': 8, 'TRANS': 407} Chain: "K" Number of atoms: 6146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 6146 Classifications: {'peptide': 383} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 23, 'TRANS': 359} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "D" Number of atoms: 3736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 3736 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 21, 'TRANS': 222} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'ASP:plan': 2, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 18 Chain: "G" Number of atoms: 1978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 1978 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 7, 'TRANS': 114} Chain: "F" Number of atoms: 1399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 1399 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 4, 'TRANS': 80} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'TYR:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 10 Chain: "H" Number of atoms: 1148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 1148 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 4, 'TRANS': 67} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "I" Number of atoms: 639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 639 Classifications: {'peptide': 39} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'TRANS': 38} Chain: "B" Number of atoms: 5392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 364, 5392 Classifications: {'peptide': 364} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 345} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "M" Number of atoms: 723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 723 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 1, 'TRANS': 48} Chain: "E" Number of atoms: 664 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 664 Classifications: {'peptide': 132} Incomplete info: {'truncation_to_alanine': 103} Link IDs: {'PTRANS': 9, 'TRANS': 122} Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 386 Unresolved non-hydrogen angles: 498 Unresolved non-hydrogen dihedrals: 326 Unresolved non-hydrogen chiralities: 33 Planarities with less than four sites: {'GLU:plan': 10, 'ASN:plan1': 4, 'TRP:plan': 3, 'GLN:plan1': 3, 'PHE:plan': 4, 'ARG:plan': 6, 'HIS:plan': 4, 'ASP:plan': 10, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 209 Chain: "K" Number of atoms: 137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 137 Unusual residues: {'HEM': 2, 'U10': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 90 Unresolved non-hydrogen dihedrals: 90 Planarities with less than four sites: {'U10:plan-3': 2, 'U10:plan-4': 2, 'U10:plan-5': 2, 'U10:plan-6': 2, 'U10:plan-7': 2, 'U10:plan-8': 2, 'U10:plan-9': 2, 'U10:plan-2': 1} Unresolved non-hydrogen planarities: 75 Chain: "D" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEC': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.75, per 1000 atoms: 0.17 Number of scatterers: 28373 At special positions: 0 Unit cell: (117.42, 89.61, 159.65, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 5 26.01 S 44 16.00 O 2742 8.00 N 2447 7.00 C 9471 6.00 H 13664 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS H 89 " - pdb=" SG CYS H 111 " distance=2.03 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=7, symmetry=0 Number of additional bonds: simple=7, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.48 Conformation dependent library (CDL) restraints added in 804.2 milliseconds 3774 Ramachandran restraints generated. 1887 Oldfield, 0 Emsley, 1887 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3578 Finding SS restraints... Secondary structure from input PDB file: 92 helices and 11 sheets defined 60.0% alpha, 8.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.70 Creating SS restraints... Processing helix chain 'A' and resid 27 through 29 No H-bonds generated for 'chain 'A' and resid 27 through 29' Processing helix chain 'A' and resid 52 through 56 Processing helix chain 'A' and resid 62 through 73 Processing helix chain 'A' and resid 97 through 99 No H-bonds generated for 'chain 'A' and resid 97 through 99' Processing helix chain 'A' and resid 100 through 114 Processing helix chain 'A' and resid 114 through 121 Processing helix chain 'A' and resid 123 through 139 removed outlier: 4.500A pdb=" N HIS A 127 " --> pdb=" O ASP A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 155 Processing helix chain 'A' and resid 158 through 162 Processing helix chain 'A' and resid 167 through 172 removed outlier: 3.817A pdb=" N GLU A 172 " --> pdb=" O THR A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 187 Processing helix chain 'A' and resid 188 through 191 Processing helix chain 'A' and resid 201 through 211 Processing helix chain 'A' and resid 258 through 270 removed outlier: 4.032A pdb=" N TYR A 269 " --> pdb=" O ALA A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 281 removed outlier: 3.912A pdb=" N LYS A 280 " --> pdb=" O THR A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 291 removed outlier: 3.513A pdb=" N SER A 288 " --> pdb=" O PRO A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 322 No H-bonds generated for 'chain 'A' and resid 320 through 322' Processing helix chain 'A' and resid 323 through 339 removed outlier: 3.537A pdb=" N LEU A 338 " --> pdb=" O GLU A 334 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N SER A 339 " --> pdb=" O TRP A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 362 Processing helix chain 'A' and resid 364 through 379 Processing helix chain 'A' and resid 384 through 394 Processing helix chain 'A' and resid 396 through 408 Processing helix chain 'A' and resid 420 through 424 removed outlier: 4.451A pdb=" N ASP A 423 " --> pdb=" O LEU A 420 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 433 removed outlier: 3.865A pdb=" N ASN A 430 " --> pdb=" O ASP A 426 " (cutoff:3.500A) Processing helix chain 'K' and resid 2 through 7 Processing helix chain 'K' and resid 7 through 18 Processing helix chain 'K' and resid 28 through 30 No H-bonds generated for 'chain 'K' and resid 28 through 30' Processing helix chain 'K' and resid 31 through 52 removed outlier: 3.647A pdb=" N MET K 52 " --> pdb=" O VAL K 48 " (cutoff:3.500A) Processing helix chain 'K' and resid 60 through 71 Processing helix chain 'K' and resid 74 through 103 removed outlier: 3.605A pdb=" N ALA K 86 " --> pdb=" O HIS K 82 " (cutoff:3.500A) Processing helix chain 'K' and resid 107 through 109 No H-bonds generated for 'chain 'K' and resid 107 through 109' Processing helix chain 'K' and resid 110 through 136 removed outlier: 3.860A pdb=" N VAL K 135 " --> pdb=" O GLY K 131 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N TYR K 136 " --> pdb=" O TYR K 132 " (cutoff:3.500A) Processing helix chain 'K' and resid 137 through 152 Processing helix chain 'K' and resid 157 through 167 Proline residue: K 163 - end of helix Processing helix chain 'K' and resid 172 through 205 Proline residue: K 187 - end of helix removed outlier: 4.144A pdb=" N HIS K 204 " --> pdb=" O ALA K 200 " (cutoff:3.500A) Processing helix chain 'K' and resid 225 through 245 Processing helix chain 'K' and resid 253 through 258 Processing helix chain 'K' and resid 272 through 274 No H-bonds generated for 'chain 'K' and resid 272 through 274' Processing helix chain 'K' and resid 275 through 285 Processing helix chain 'K' and resid 287 through 309 removed outlier: 5.110A pdb=" N LEU K 302 " --> pdb=" O ALA K 298 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N LEU K 303 " --> pdb=" O ILE K 299 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N SER K 304 " --> pdb=" O LEU K 300 " (cutoff:3.500A) Proline residue: K 306 - end of helix Processing helix chain 'K' and resid 319 through 342 removed outlier: 3.762A pdb=" N GLN K 341 " --> pdb=" O GLY K 337 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU K 342 " --> pdb=" O ASN K 338 " (cutoff:3.500A) Processing helix chain 'K' and resid 345 through 365 removed outlier: 4.149A pdb=" N GLN K 350 " --> pdb=" O VAL K 346 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N TYR K 363 " --> pdb=" O TYR K 359 " (cutoff:3.500A) Processing helix chain 'K' and resid 365 through 383 Processing helix chain 'D' and resid 44 through 49 Processing helix chain 'D' and resid 67 through 81 Processing helix chain 'D' and resid 82 through 85 Processing helix chain 'D' and resid 92 through 97 Processing helix chain 'D' and resid 102 through 112 Processing helix chain 'D' and resid 142 through 150 Processing helix chain 'D' and resid 157 through 161 removed outlier: 4.215A pdb=" N LEU D 160 " --> pdb=" O ASP D 157 " (cutoff:3.500A) Processing helix chain 'D' and resid 168 through 177 Processing helix chain 'D' and resid 224 through 241 Processing helix chain 'D' and resid 243 through 278 Proline residue: D 275 - end of helix Processing helix chain 'G' and resid 4 through 18 removed outlier: 4.222A pdb=" N ARG G 18 " --> pdb=" O PHE G 14 " (cutoff:3.500A) Processing helix chain 'G' and resid 18 through 37 Proline residue: G 27 - end of helix removed outlier: 4.215A pdb=" N GLY G 37 " --> pdb=" O THR G 33 " (cutoff:3.500A) Processing helix chain 'G' and resid 38 through 42 Processing helix chain 'G' and resid 44 through 48 Processing helix chain 'G' and resid 53 through 62 Processing helix chain 'G' and resid 64 through 85 Processing helix chain 'G' and resid 103 through 122 Processing helix chain 'F' and resid 40 through 82 removed outlier: 3.646A pdb=" N VAL F 46 " --> pdb=" O ALA F 42 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N THR F 49 " --> pdb=" O ALA F 45 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N LEU F 58 " --> pdb=" O LYS F 54 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N TYR F 59 " --> pdb=" O ASN F 55 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N VAL F 60 " --> pdb=" O GLN F 56 " (cutoff:3.500A) Proline residue: F 63 - end of helix Processing helix chain 'F' and resid 86 through 93 Processing helix chain 'H' and resid 64 through 75 removed outlier: 3.743A pdb=" N THR H 68 " --> pdb=" O ASP H 64 " (cutoff:3.500A) Processing helix chain 'H' and resid 79 through 99 removed outlier: 3.650A pdb=" N GLU H 99 " --> pdb=" O LYS H 95 " (cutoff:3.500A) Processing helix chain 'H' and resid 101 through 105 Processing helix chain 'H' and resid 111 through 131 removed outlier: 3.890A pdb=" N CYS H 125 " --> pdb=" O CYS H 121 " (cutoff:3.500A) Proline residue: H 128 - end of helix removed outlier: 4.686A pdb=" N PHE H 131 " --> pdb=" O ALA H 127 " (cutoff:3.500A) Processing helix chain 'H' and resid 132 through 134 No H-bonds generated for 'chain 'H' and resid 132 through 134' Processing helix chain 'I' and resid 18 through 42 removed outlier: 3.712A pdb=" N PHE I 24 " --> pdb=" O PHE I 20 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA I 25 " --> pdb=" O GLY I 21 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N GLU I 39 " --> pdb=" O ASN I 35 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLU I 40 " --> pdb=" O LYS I 36 " (cutoff:3.500A) Processing helix chain 'I' and resid 46 through 55 removed outlier: 5.344A pdb=" N GLY I 52 " --> pdb=" O LYS I 48 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N LYS I 53 " --> pdb=" O ASN I 49 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N PHE I 54 " --> pdb=" O VAL I 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 55 Processing helix chain 'B' and resid 63 through 75 removed outlier: 3.741A pdb=" N ARG B 69 " --> pdb=" O LEU B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 110 removed outlier: 3.561A pdb=" N GLU B 103 " --> pdb=" O PRO B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 122 Processing helix chain 'B' and resid 123 through 136 Processing helix chain 'B' and resid 137 through 151 Processing helix chain 'B' and resid 153 through 157 removed outlier: 3.605A pdb=" N GLY B 156 " --> pdb=" O ARG B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 177 Processing helix chain 'B' and resid 181 through 183 No H-bonds generated for 'chain 'B' and resid 181 through 183' Processing helix chain 'B' and resid 193 through 204 Processing helix chain 'B' and resid 205 through 209 Processing helix chain 'B' and resid 247 through 249 No H-bonds generated for 'chain 'B' and resid 247 through 249' Processing helix chain 'B' and resid 250 through 262 Processing helix chain 'B' and resid 271 through 276 Processing helix chain 'B' and resid 299 through 315 removed outlier: 3.692A pdb=" N GLN B 305 " --> pdb=" O SER B 301 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LYS B 308 " --> pdb=" O ALA B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 325 Processing helix chain 'B' and resid 325 through 337 Processing helix chain 'B' and resid 370 through 374 Processing helix chain 'M' and resid 45 through 80 removed outlier: 4.359A pdb=" N ARG M 50 " --> pdb=" O GLY M 46 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N SER M 78 " --> pdb=" O ALA M 74 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N PHE M 79 " --> pdb=" O PHE M 75 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ALA M 80 " --> pdb=" O LEU M 76 " (cutoff:3.500A) Processing helix chain 'E' and resid 82 through 87 Processing helix chain 'E' and resid 107 through 111 removed outlier: 4.098A pdb=" N GLY E 110 " --> pdb=" O LYS E 107 " (cutoff:3.500A) Processing helix chain 'E' and resid 119 through 129 Processing helix chain 'E' and resid 139 through 144 Processing sheet with id=AA1, first strand: chain 'A' and resid 23 through 25 removed outlier: 6.521A pdb=" N THR A 31 " --> pdb=" O ILE A 194 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N ALA A 196 " --> pdb=" O THR A 31 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N ALA A 33 " --> pdb=" O ALA A 196 " (cutoff:3.500A) removed outlier: 8.722A pdb=" N GLY A 198 " --> pdb=" O ALA A 33 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N GLU A 35 " --> pdb=" O GLY A 198 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N VAL A 45 " --> pdb=" O ALA A 94 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 271 through 273 removed outlier: 6.453A pdb=" N SER A 231 " --> pdb=" O ILE A 415 " (cutoff:3.500A) removed outlier: 8.739A pdb=" N GLY A 417 " --> pdb=" O SER A 231 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N VAL A 233 " --> pdb=" O GLY A 417 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'K' and resid 22 through 23 Processing sheet with id=AA4, first strand: chain 'D' and resid 114 through 117 removed outlier: 4.681A pdb=" N ARG D 126 " --> pdb=" O ASP D 117 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 194 through 195 Processing sheet with id=AA6, first strand: chain 'B' and resid 18 through 22 removed outlier: 6.219A pdb=" N LYS B 18 " --> pdb=" O ILE B 187 " (cutoff:3.500A) removed outlier: 7.951A pdb=" N ALA B 189 " --> pdb=" O LYS B 18 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N ALA B 20 " --> pdb=" O ALA B 189 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N PHE B 93 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 18 through 22 removed outlier: 6.219A pdb=" N LYS B 18 " --> pdb=" O ILE B 187 " (cutoff:3.500A) removed outlier: 7.951A pdb=" N ALA B 189 " --> pdb=" O LYS B 18 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N ALA B 20 " --> pdb=" O ALA B 189 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 233 Processing sheet with id=AA9, first strand: chain 'E' and resid 92 through 93 removed outlier: 3.512A pdb=" N GLU E 208 " --> pdb=" O THR E 205 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ASP E 203 " --> pdb=" O LEU E 210 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 102 through 106 removed outlier: 3.502A pdb=" N LYS E 102 " --> pdb=" O HIS E 117 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE E 106 " --> pdb=" O VAL E 113 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ARG E 116 " --> pdb=" O LEU E 150 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU E 150 " --> pdb=" O ARG E 116 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 173 through 175 846 hydrogen bonds defined for protein. 2385 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.82 Time building geometry restraints manager: 3.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.12: 13655 1.12 - 1.41: 6289 1.41 - 1.70: 8708 1.70 - 1.98: 72 1.98 - 2.27: 15 Bond restraints: 28739 Sorted by residual: bond pdb=" C CYS D 82 " pdb=" O CYS D 82 " ideal model delta sigma weight residual 1.237 1.076 0.161 1.17e-02 7.31e+03 1.89e+02 bond pdb=" C2D HEC D 301 " pdb=" C3D HEC D 301 " ideal model delta sigma weight residual 1.544 1.332 0.212 2.00e-02 2.50e+03 1.13e+02 bond pdb=" CAB HEC D 301 " pdb=" CBB HEC D 301 " ideal model delta sigma weight residual 1.544 1.332 0.212 2.00e-02 2.50e+03 1.12e+02 bond pdb=" CAC HEC D 301 " pdb=" CBC HEC D 301 " ideal model delta sigma weight residual 1.544 1.336 0.208 2.00e-02 2.50e+03 1.08e+02 bond pdb=" C13 U10 K 404 " pdb=" C14 U10 K 404 " ideal model delta sigma weight residual 1.335 1.475 -0.140 2.00e-02 2.50e+03 4.87e+01 ... (remaining 28734 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.54: 51381 3.54 - 7.08: 180 7.08 - 10.62: 13 10.62 - 14.17: 8 14.17 - 17.71: 3 Bond angle restraints: 51585 Sorted by residual: angle pdb=" S1 FES E 301 " pdb="FE1 FES E 301 " pdb=" S2 FES E 301 " ideal model delta sigma weight residual 104.33 86.62 17.71 1.20e+00 6.94e-01 2.18e+02 angle pdb=" S1 FES E 301 " pdb="FE2 FES E 301 " pdb=" S2 FES E 301 " ideal model delta sigma weight residual 104.33 88.19 16.14 1.14e+00 7.69e-01 2.01e+02 angle pdb="FE1 FES E 301 " pdb=" S2 FES E 301 " pdb="FE2 FES E 301 " ideal model delta sigma weight residual 75.66 89.76 -14.10 1.14e+00 7.69e-01 1.53e+02 angle pdb="FE1 FES E 301 " pdb=" S1 FES E 301 " pdb="FE2 FES E 301 " ideal model delta sigma weight residual 75.66 90.34 -14.68 1.20e+00 6.94e-01 1.50e+02 angle pdb=" CA CYS D 82 " pdb=" C CYS D 82 " pdb=" O CYS D 82 " ideal model delta sigma weight residual 120.55 109.72 10.83 1.06e+00 8.90e-01 1.04e+02 ... (remaining 51580 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.28: 13328 35.28 - 70.56: 320 70.56 - 105.84: 33 105.84 - 141.12: 0 141.12 - 176.40: 1 Dihedral angle restraints: 13682 sinusoidal: 7052 harmonic: 6630 Sorted by residual: dihedral pdb=" CD ARG D 282 " pdb=" NE ARG D 282 " pdb=" CZ ARG D 282 " pdb=" NH1 ARG D 282 " ideal model delta sinusoidal sigma weight residual 0.00 176.40 -176.40 1 1.00e+01 1.00e-02 1.92e+02 dihedral pdb=" C HIS E 117 " pdb=" N HIS E 117 " pdb=" CA HIS E 117 " pdb=" CB HIS E 117 " ideal model delta harmonic sigma weight residual -122.60 -139.00 16.40 0 2.50e+00 1.60e-01 4.30e+01 dihedral pdb=" N PRO E 200 " pdb=" C PRO E 200 " pdb=" CA PRO E 200 " pdb=" CB PRO E 200 " ideal model delta harmonic sigma weight residual 115.10 101.80 13.30 0 2.50e+00 1.60e-01 2.83e+01 ... (remaining 13679 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.102: 2155 0.102 - 0.205: 109 0.205 - 0.307: 17 0.307 - 0.409: 2 0.409 - 0.512: 1 Chirality restraints: 2284 Sorted by residual: chirality pdb=" CA HIS E 117 " pdb=" N HIS E 117 " pdb=" C HIS E 117 " pdb=" CB HIS E 117 " both_signs ideal model delta sigma weight residual False 2.51 2.00 0.51 2.00e-01 2.50e+01 6.55e+00 chirality pdb=" CA ILE E 188 " pdb=" N ILE E 188 " pdb=" C ILE E 188 " pdb=" CB ILE E 188 " both_signs ideal model delta sigma weight residual False 2.43 2.83 -0.40 2.00e-01 2.50e+01 3.95e+00 chirality pdb=" CA TYR E 202 " pdb=" N TYR E 202 " pdb=" C TYR E 202 " pdb=" CB TYR E 202 " both_signs ideal model delta sigma weight residual False 2.51 2.82 -0.31 2.00e-01 2.50e+01 2.42e+00 ... (remaining 2281 not shown) Planarity restraints: 4301 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 U10 K 403 " -0.112 2.00e-02 2.50e+03 1.80e-01 9.70e+02 pdb=" C1M U10 K 403 " -0.252 2.00e-02 2.50e+03 pdb=" C2 U10 K 403 " 0.020 2.00e-02 2.50e+03 pdb=" C3 U10 K 403 " 0.148 2.00e-02 2.50e+03 pdb=" C4 U10 K 403 " 0.162 2.00e-02 2.50e+03 pdb=" C5 U10 K 403 " 0.028 2.00e-02 2.50e+03 pdb=" C6 U10 K 403 " -0.100 2.00e-02 2.50e+03 pdb=" C7 U10 K 403 " 0.086 2.00e-02 2.50e+03 pdb=" O2 U10 K 403 " 0.336 2.00e-02 2.50e+03 pdb=" O3 U10 K 403 " -0.217 2.00e-02 2.50e+03 pdb=" O4 U10 K 403 " -0.250 2.00e-02 2.50e+03 pdb=" O5 U10 K 403 " 0.150 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1 U10 K 404 " -0.110 2.00e-02 2.50e+03 1.68e-01 8.44e+02 pdb=" C1M U10 K 404 " -0.227 2.00e-02 2.50e+03 pdb=" C2 U10 K 404 " 0.039 2.00e-02 2.50e+03 pdb=" C3 U10 K 404 " 0.137 2.00e-02 2.50e+03 pdb=" C4 U10 K 404 " 0.132 2.00e-02 2.50e+03 pdb=" C5 U10 K 404 " -0.019 2.00e-02 2.50e+03 pdb=" C6 U10 K 404 " -0.120 2.00e-02 2.50e+03 pdb=" C7 U10 K 404 " 0.188 2.00e-02 2.50e+03 pdb=" O2 U10 K 404 " 0.313 2.00e-02 2.50e+03 pdb=" O3 U10 K 404 " -0.295 2.00e-02 2.50e+03 pdb=" O4 U10 K 404 " -0.014 2.00e-02 2.50e+03 pdb=" O5 U10 K 404 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 U10 K 404 " 0.011 2.00e-02 2.50e+03 6.69e-02 5.60e+01 pdb=" C11 U10 K 404 " -0.066 2.00e-02 2.50e+03 pdb=" C7 U10 K 404 " -0.081 2.00e-02 2.50e+03 pdb=" C8 U10 K 404 " 0.099 2.00e-02 2.50e+03 pdb=" C9 U10 K 404 " 0.037 2.00e-02 2.50e+03 ... (remaining 4298 not shown) Histogram of nonbonded interaction distances: 1.02 - 1.73: 67 1.73 - 2.45: 16815 2.45 - 3.17: 88690 3.17 - 3.88: 118189 3.88 - 4.60: 188355 Nonbonded interactions: 412116 Sorted by model distance: nonbonded pdb=" CB THR E 157 " pdb="FE1 FES E 301 " model vdw 1.018 3.180 nonbonded pdb=" H LYS F 36 " pdb=" O TYR M 40 " model vdw 1.103 2.450 nonbonded pdb=" HB2 GLN A 156 " pdb=" HG3 GLN M 34 " model vdw 1.227 2.440 nonbonded pdb=" HE2 PHE I 30 " pdb="HD12 LEU M 63 " model vdw 1.335 2.270 nonbonded pdb="HD11 LEU D 261 " pdb=" HG3 MET M 60 " model vdw 1.488 2.440 ... (remaining 412111 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.560 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: 0.180 Extract box with map and model: 0.410 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 28.050 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 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: 31.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6825 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 : 0.008 0.315 15083 Z= 0.436 Angle : 0.839 17.708 20546 Z= 0.538 Chirality : 0.052 0.512 2284 Planarity : 0.007 0.180 2625 Dihedral : 13.431 176.404 5274 Min Nonbonded Distance : 1.018 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.61 % Favored : 95.23 % Rotamer: Outliers : 0.20 % Allowed : 0.20 % Favored : 99.60 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.20), residues: 1887 helix: 0.54 (0.17), residues: 970 sheet: -0.73 (0.39), residues: 174 loop : -0.13 (0.24), residues: 743 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 282 TYR 0.023 0.002 TYR K 132 PHE 0.068 0.002 PHE K 184 TRP 0.012 0.001 TRP K 142 HIS 0.037 0.001 HIS K 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00781 / 0.43 (15075) covalent geometry : angle 0.83949 / 0.54 (20544) SS BOND : bond 0.00034 / 0.02 ( 1) SS BOND : angle 0.75220 / 0.41 ( 2) hydrogen bonds : bond 0.14386 / 10.18 ( 838) hydrogen bonds : angle 6.67951 / 4.81 ( 2385) Misc. bond : bond 0.12128 / 6.10 ( 7) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3774 Ramachandran restraints generated. 1887 Oldfield, 0 Emsley, 1887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3774 Ramachandran restraints generated. 1887 Oldfield, 0 Emsley, 1887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 112 is missing expected H atoms. Skipping. Residue LYS 124 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue TYR 43 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue SER 214 is missing expected H atoms. Skipping. Residue LYS 218 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue TYR 32 is missing expected H atoms. Skipping. Evaluate side-chains 338 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 335 time to evaluate : 0.686 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 THR cc_start: 0.8357 (t) cc_final: 0.7963 (p) REVERT: A 97 THR cc_start: 0.7310 (t) cc_final: 0.6998 (t) REVERT: A 245 ILE cc_start: 0.8469 (pt) cc_final: 0.8218 (pt) REVERT: A 256 SER cc_start: 0.8981 (m) cc_final: 0.8779 (m) REVERT: A 384 SER cc_start: 0.8481 (t) cc_final: 0.8163 (m) REVERT: A 391 LYS cc_start: 0.8546 (ttmm) cc_final: 0.8225 (mtpt) REVERT: K 246 TYR cc_start: 0.8244 (m-80) cc_final: 0.7837 (m-80) REVERT: K 272 GLU cc_start: 0.7507 (tt0) cc_final: 0.7059 (tp30) REVERT: D 135 TYR cc_start: 0.7708 (m-80) cc_final: 0.7164 (m-80) REVERT: G 61 LYS cc_start: 0.8071 (tmmt) cc_final: 0.7803 (mptt) REVERT: G 117 LYS cc_start: 0.7843 (ttmt) cc_final: 0.7009 (mmtt) REVERT: F 21 LYS cc_start: 0.8193 (mmtp) cc_final: 0.7895 (mttm) REVERT: H 111 CYS cc_start: 0.6639 (m) cc_final: 0.6198 (m) REVERT: H 121 CYS cc_start: 0.8289 (t) cc_final: 0.7642 (t) REVERT: I 40 GLU cc_start: 0.8527 (tm-30) cc_final: 0.8247 (tp30) REVERT: B 18 LYS cc_start: 0.7900 (mtmm) cc_final: 0.7360 (mptt) REVERT: B 132 LYS cc_start: 0.7891 (ttpp) cc_final: 0.7647 (ttmm) REVERT: B 152 ARG cc_start: 0.7398 (mtt180) cc_final: 0.6779 (mmm160) REVERT: B 165 THR cc_start: 0.8882 (m) cc_final: 0.8573 (t) REVERT: B 185 ILE cc_start: 0.8433 (pt) cc_final: 0.8226 (mt) REVERT: B 186 SER cc_start: 0.8335 (t) cc_final: 0.7929 (m) REVERT: B 327 LYS cc_start: 0.8230 (tppp) cc_final: 0.7630 (ttmt) outliers start: 3 outliers final: 2 residues processed: 337 average time/residue: 0.2945 time to fit residues: 143.0367 Evaluate side-chains 244 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 242 time to evaluate : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 88 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 98 optimal weight: 0.6980 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 0.2980 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 1.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 329 HIS K 84 ASN ** D 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 59 ASN M 34 GLN M 47 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.134567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.114389 restraints weight = 52109.124| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 1.89 r_work: 0.3069 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2951 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.1930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.309 15083 Z= 0.167 Angle : 0.581 12.623 20546 Z= 0.301 Chirality : 0.040 0.150 2284 Planarity : 0.004 0.060 2625 Dihedral : 8.101 177.883 2093 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 0.87 % Allowed : 6.31 % Favored : 92.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.20), residues: 1887 helix: 0.96 (0.16), residues: 983 sheet: -0.63 (0.40), residues: 164 loop : -0.05 (0.24), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 128 TYR 0.017 0.001 TYR H 107 PHE 0.014 0.001 PHE I 30 TRP 0.014 0.001 TRP K 142 HIS 0.009 0.001 HIS K 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.17 (15075) covalent geometry : angle 0.58069 / 0.30 (20544) SS BOND : bond 0.00096 / 0.05 ( 1) SS BOND : angle 0.48841 / 0.26 ( 2) hydrogen bonds : bond 0.04826 / 3.30 ( 838) hydrogen bonds : angle 5.05233 / 3.60 ( 2385) Misc. bond : bond 0.14973 / 7.26 ( 7) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3774 Ramachandran restraints generated. 1887 Oldfield, 0 Emsley, 1887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3774 Ramachandran restraints generated. 1887 Oldfield, 0 Emsley, 1887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 112 is missing expected H atoms. Skipping. Residue LYS 124 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue TYR 43 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue SER 214 is missing expected H atoms. Skipping. Residue LYS 218 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue TYR 32 is missing expected H atoms. Skipping. Evaluate side-chains 257 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 244 time to evaluate : 0.730 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 THR cc_start: 0.8754 (t) cc_final: 0.8381 (p) REVERT: A 245 ILE cc_start: 0.9053 (pt) cc_final: 0.8828 (pt) REVERT: A 384 SER cc_start: 0.8547 (t) cc_final: 0.8281 (p) REVERT: A 390 GLU cc_start: 0.8493 (tp30) cc_final: 0.8159 (tp30) REVERT: A 391 LYS cc_start: 0.8831 (ttmm) cc_final: 0.8512 (mtpt) REVERT: K 272 GLU cc_start: 0.8348 (tt0) cc_final: 0.7965 (mm-30) REVERT: D 135 TYR cc_start: 0.8415 (m-80) cc_final: 0.8014 (m-80) REVERT: G 117 LYS cc_start: 0.8221 (ttmt) cc_final: 0.7245 (mmtt) REVERT: F 21 LYS cc_start: 0.8462 (mmtp) cc_final: 0.8206 (mttm) REVERT: H 111 CYS cc_start: 0.7624 (m) cc_final: 0.7341 (m) REVERT: I 40 GLU cc_start: 0.8654 (tm-30) cc_final: 0.8450 (tp30) REVERT: B 18 LYS cc_start: 0.8186 (mtmm) cc_final: 0.7696 (mptt) REVERT: B 132 LYS cc_start: 0.8388 (ttpp) cc_final: 0.8152 (ttmm) REVERT: B 152 ARG cc_start: 0.7686 (mtt180) cc_final: 0.6909 (mmm160) REVERT: B 165 THR cc_start: 0.8780 (m) cc_final: 0.8559 (t) REVERT: B 186 SER cc_start: 0.8606 (t) cc_final: 0.8403 (m) REVERT: B 327 LYS cc_start: 0.8540 (tppp) cc_final: 0.8024 (ttmt) REVERT: M 60 MET cc_start: 0.7785 (ttp) cc_final: 0.7514 (ttm) outliers start: 13 outliers final: 7 residues processed: 250 average time/residue: 0.2550 time to fit residues: 93.7638 Evaluate side-chains 224 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 217 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 116 ASP Chi-restraints excluded: chain H residue 106 HIS Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 229 GLU Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain E residue 88 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 1 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 34 optimal weight: 0.1980 chunk 37 optimal weight: 0.5980 chunk 9 optimal weight: 3.9990 chunk 100 optimal weight: 1.9990 chunk 186 optimal weight: 0.9990 chunk 146 optimal weight: 1.9990 chunk 182 optimal weight: 20.0000 chunk 127 optimal weight: 6.9990 chunk 156 optimal weight: 0.8980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 428 ASN D 59 HIS D 237 ASN G 101 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.131053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.108998 restraints weight = 52587.158| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 2.06 r_work: 0.3018 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2897 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.2607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.261 15083 Z= 0.169 Angle : 0.544 10.989 20546 Z= 0.281 Chirality : 0.040 0.185 2284 Planarity : 0.004 0.065 2625 Dihedral : 7.801 179.868 2091 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 1.07 % Allowed : 7.59 % Favored : 91.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.87 (0.20), residues: 1887 helix: 1.31 (0.16), residues: 978 sheet: -0.69 (0.41), residues: 152 loop : 0.01 (0.24), residues: 757 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 87 TYR 0.021 0.001 TYR K 378 PHE 0.011 0.001 PHE A 327 TRP 0.012 0.001 TRP K 142 HIS 0.013 0.001 HIS H 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.17 (15075) covalent geometry : angle 0.54355 / 0.28 (20544) SS BOND : bond 0.00009 / 0.00 ( 1) SS BOND : angle 0.33800 / 0.19 ( 2) hydrogen bonds : bond 0.04310 / 2.93 ( 838) hydrogen bonds : angle 4.72517 / 3.36 ( 2385) Misc. bond : bond 0.11665 / 5.37 ( 7) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3774 Ramachandran restraints generated. 1887 Oldfield, 0 Emsley, 1887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3774 Ramachandran restraints generated. 1887 Oldfield, 0 Emsley, 1887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 112 is missing expected H atoms. Skipping. Residue LYS 124 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue TYR 43 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue SER 214 is missing expected H atoms. Skipping. Residue LYS 218 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue TYR 32 is missing expected H atoms. Skipping. Evaluate side-chains 251 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 235 time to evaluate : 0.519 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 THR cc_start: 0.8771 (t) cc_final: 0.8467 (p) REVERT: A 245 ILE cc_start: 0.9079 (pt) cc_final: 0.8855 (pt) REVERT: A 384 SER cc_start: 0.8522 (t) cc_final: 0.8263 (m) REVERT: A 391 LYS cc_start: 0.8840 (ttmm) cc_final: 0.8528 (mtpt) REVERT: K 272 GLU cc_start: 0.8321 (tt0) cc_final: 0.7939 (mm-30) REVERT: D 111 GLU cc_start: 0.7258 (OUTLIER) cc_final: 0.6926 (mp0) REVERT: D 135 TYR cc_start: 0.8555 (m-80) cc_final: 0.8155 (m-80) REVERT: G 56 MET cc_start: 0.8428 (mmm) cc_final: 0.8222 (mmm) REVERT: G 60 ILE cc_start: 0.9241 (OUTLIER) cc_final: 0.9030 (mt) REVERT: G 97 GLU cc_start: 0.8508 (tp30) cc_final: 0.8147 (tp30) REVERT: G 117 LYS cc_start: 0.8285 (ttmt) cc_final: 0.7230 (mmpt) REVERT: F 21 LYS cc_start: 0.8561 (mmtp) cc_final: 0.8296 (mttm) REVERT: H 103 GLU cc_start: 0.8224 (pm20) cc_final: 0.7680 (pm20) REVERT: I 26 PHE cc_start: 0.8115 (m-10) cc_final: 0.7903 (m-80) REVERT: B 18 LYS cc_start: 0.8198 (mtmm) cc_final: 0.7703 (mptt) REVERT: B 132 LYS cc_start: 0.8439 (ttpp) cc_final: 0.8204 (ttmm) REVERT: B 152 ARG cc_start: 0.7819 (mtt180) cc_final: 0.6927 (mmm160) REVERT: B 165 THR cc_start: 0.8797 (m) cc_final: 0.8582 (t) REVERT: B 186 SER cc_start: 0.8942 (t) cc_final: 0.8484 (m) REVERT: M 60 MET cc_start: 0.8204 (ttp) cc_final: 0.7956 (ttm) outliers start: 16 outliers final: 11 residues processed: 241 average time/residue: 0.2586 time to fit residues: 92.3944 Evaluate side-chains 228 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 215 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain K residue 41 VAL Chi-restraints excluded: chain D residue 111 GLU Chi-restraints excluded: chain D residue 226 SER Chi-restraints excluded: chain G residue 60 ILE Chi-restraints excluded: chain F residue 9 THR Chi-restraints excluded: chain H residue 106 HIS Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain B residue 181 SER Chi-restraints excluded: chain B residue 229 GLU Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain E residue 88 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 109 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 178 optimal weight: 10.0000 chunk 8 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 chunk 133 optimal weight: 1.9990 chunk 105 optimal weight: 0.8980 chunk 91 optimal weight: 1.9990 chunk 162 optimal weight: 1.9990 chunk 157 optimal weight: 1.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 291 GLN K 57 ASN ** I 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 179 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.126601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.106542 restraints weight = 52877.759| |-----------------------------------------------------------------------------| r_work (start): 0.3049 rms_B_bonded: 1.88 r_work: 0.2932 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2815 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.3052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.247 15083 Z= 0.268 Angle : 0.594 10.554 20546 Z= 0.311 Chirality : 0.042 0.165 2284 Planarity : 0.004 0.063 2625 Dihedral : 7.885 179.127 2091 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 1.41 % Allowed : 8.53 % Favored : 90.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.20), residues: 1887 helix: 1.27 (0.16), residues: 971 sheet: -0.87 (0.40), residues: 171 loop : -0.17 (0.24), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 349 TYR 0.015 0.002 TYR K 358 PHE 0.013 0.001 PHE K 278 TRP 0.010 0.001 TRP K 142 HIS 0.006 0.001 HIS H 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00612 / 0.27 (15075) covalent geometry : angle 0.58961 / 0.31 (20544) SS BOND : bond 0.02364 / 1.24 ( 1) SS BOND : angle 7.59916 / 4.45 ( 2) hydrogen bonds : bond 0.04481 / 3.04 ( 838) hydrogen bonds : angle 4.80578 / 3.42 ( 2385) Misc. bond : bond 0.12179 / 5.38 ( 7) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3774 Ramachandran restraints generated. 1887 Oldfield, 0 Emsley, 1887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3774 Ramachandran restraints generated. 1887 Oldfield, 0 Emsley, 1887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 112 is missing expected H atoms. Skipping. Residue LYS 124 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue TYR 43 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue SER 214 is missing expected H atoms. Skipping. Residue LYS 218 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue TYR 32 is missing expected H atoms. Skipping. Evaluate side-chains 253 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 232 time to evaluate : 0.772 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 THR cc_start: 0.8804 (t) cc_final: 0.8514 (p) REVERT: A 178 ASP cc_start: 0.7950 (OUTLIER) cc_final: 0.7704 (t0) REVERT: A 276 SER cc_start: 0.8834 (t) cc_final: 0.8621 (p) REVERT: A 384 SER cc_start: 0.8583 (t) cc_final: 0.8317 (m) REVERT: A 391 LYS cc_start: 0.8802 (ttmm) cc_final: 0.8572 (mttm) REVERT: A 436 MET cc_start: 0.6795 (mtp) cc_final: 0.6587 (mtp) REVERT: K 246 TYR cc_start: 0.8788 (m-80) cc_final: 0.8388 (m-80) REVERT: K 272 GLU cc_start: 0.8264 (tt0) cc_final: 0.7690 (mm-30) REVERT: D 111 GLU cc_start: 0.7261 (OUTLIER) cc_final: 0.6900 (mp0) REVERT: D 135 TYR cc_start: 0.8653 (m-80) cc_final: 0.8205 (m-80) REVERT: G 60 ILE cc_start: 0.9141 (OUTLIER) cc_final: 0.8920 (mt) REVERT: G 97 GLU cc_start: 0.8560 (tp30) cc_final: 0.8234 (tp30) REVERT: G 117 LYS cc_start: 0.8376 (ttmt) cc_final: 0.7207 (mmpt) REVERT: F 11 MET cc_start: 0.8600 (ttp) cc_final: 0.8305 (ttp) REVERT: F 21 LYS cc_start: 0.8591 (mmtp) cc_final: 0.8325 (mttm) REVERT: F 73 ARG cc_start: 0.7718 (tmt170) cc_final: 0.7156 (mtt-85) REVERT: H 84 HIS cc_start: 0.8158 (OUTLIER) cc_final: 0.7945 (t-90) REVERT: B 132 LYS cc_start: 0.8443 (ttpp) cc_final: 0.8193 (ttmm) REVERT: B 152 ARG cc_start: 0.7932 (mtt180) cc_final: 0.6924 (mmm160) REVERT: B 178 GLU cc_start: 0.6908 (mm-30) cc_final: 0.6344 (tp30) REVERT: B 186 SER cc_start: 0.8949 (t) cc_final: 0.8484 (m) REVERT: B 366 ASP cc_start: 0.8794 (t0) cc_final: 0.8342 (t0) REVERT: M 60 MET cc_start: 0.8534 (ttp) cc_final: 0.8160 (ttm) outliers start: 21 outliers final: 16 residues processed: 242 average time/residue: 0.2900 time to fit residues: 102.7401 Evaluate side-chains 240 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 220 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 ASP Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain K residue 212 ILE Chi-restraints excluded: chain K residue 322 SER Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain D residue 111 GLU Chi-restraints excluded: chain D residue 226 SER Chi-restraints excluded: chain D residue 265 SER Chi-restraints excluded: chain G residue 60 ILE Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain H residue 84 HIS Chi-restraints excluded: chain H residue 106 HIS Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain B residue 181 SER Chi-restraints excluded: chain B residue 229 GLU Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 88 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 80 optimal weight: 0.9980 chunk 186 optimal weight: 0.0570 chunk 24 optimal weight: 1.9990 chunk 143 optimal weight: 0.4980 chunk 0 optimal weight: 1.9990 chunk 18 optimal weight: 0.6980 chunk 42 optimal weight: 1.9990 chunk 124 optimal weight: 7.9990 chunk 167 optimal weight: 0.9980 chunk 170 optimal weight: 4.9990 chunk 183 optimal weight: 20.0000 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 177 GLN ** I 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 15 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.127019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.104844 restraints weight = 52894.403| |-----------------------------------------------------------------------------| r_work (start): 0.3083 rms_B_bonded: 2.11 r_work: 0.2991 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2869 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.3213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.221 15083 Z= 0.139 Angle : 0.525 10.152 20546 Z= 0.270 Chirality : 0.039 0.159 2284 Planarity : 0.004 0.046 2625 Dihedral : 7.683 179.753 2091 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 1.01 % Allowed : 9.74 % Favored : 89.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.20), residues: 1887 helix: 1.48 (0.17), residues: 980 sheet: -0.87 (0.40), residues: 171 loop : -0.03 (0.24), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 87 TYR 0.011 0.001 TYR K 358 PHE 0.015 0.001 PHE A 327 TRP 0.011 0.001 TRP K 142 HIS 0.005 0.001 HIS K 362 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 (15075) covalent geometry : angle 0.52249 / 0.27 (20544) SS BOND : bond 0.00839 / 0.44 ( 1) SS BOND : angle 4.87822 / 2.82 ( 2) hydrogen bonds : bond 0.04053 / 2.75 ( 838) hydrogen bonds : angle 4.57106 / 3.25 ( 2385) Misc. bond : bond 0.10942 / 4.80 ( 7) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3774 Ramachandran restraints generated. 1887 Oldfield, 0 Emsley, 1887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3774 Ramachandran restraints generated. 1887 Oldfield, 0 Emsley, 1887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 112 is missing expected H atoms. Skipping. Residue LYS 124 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue TYR 43 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue SER 214 is missing expected H atoms. Skipping. Residue LYS 218 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue TYR 32 is missing expected H atoms. Skipping. Evaluate side-chains 231 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 216 time to evaluate : 0.744 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 THR cc_start: 0.8797 (t) cc_final: 0.8508 (p) REVERT: A 178 ASP cc_start: 0.7825 (OUTLIER) cc_final: 0.7578 (t0) REVERT: A 384 SER cc_start: 0.8560 (t) cc_final: 0.8316 (m) REVERT: A 391 LYS cc_start: 0.8748 (ttmm) cc_final: 0.8529 (mttm) REVERT: A 436 MET cc_start: 0.6719 (mtp) cc_final: 0.6516 (mtp) REVERT: K 246 TYR cc_start: 0.8792 (m-80) cc_final: 0.8377 (m-80) REVERT: K 272 GLU cc_start: 0.8330 (tt0) cc_final: 0.7769 (mm-30) REVERT: D 111 GLU cc_start: 0.7203 (OUTLIER) cc_final: 0.6864 (mp0) REVERT: D 135 TYR cc_start: 0.8651 (m-80) cc_final: 0.8258 (m-80) REVERT: G 60 ILE cc_start: 0.9181 (OUTLIER) cc_final: 0.8948 (mt) REVERT: G 97 GLU cc_start: 0.8565 (tp30) cc_final: 0.8263 (tp30) REVERT: G 117 LYS cc_start: 0.8380 (ttmt) cc_final: 0.7227 (mmpt) REVERT: F 11 MET cc_start: 0.8604 (ttp) cc_final: 0.8295 (ttp) REVERT: F 21 LYS cc_start: 0.8585 (mmtp) cc_final: 0.8325 (mttm) REVERT: F 73 ARG cc_start: 0.7753 (tmt170) cc_final: 0.7204 (mtt-85) REVERT: B 132 LYS cc_start: 0.8451 (ttpp) cc_final: 0.8213 (ttmm) REVERT: B 152 ARG cc_start: 0.7870 (mtt180) cc_final: 0.6919 (mmm160) REVERT: B 186 SER cc_start: 0.8936 (t) cc_final: 0.8486 (m) REVERT: B 366 ASP cc_start: 0.8795 (t0) cc_final: 0.8350 (t0) REVERT: M 60 MET cc_start: 0.8648 (ttp) cc_final: 0.8252 (ttm) outliers start: 15 outliers final: 11 residues processed: 221 average time/residue: 0.2800 time to fit residues: 89.9490 Evaluate side-chains 222 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 208 time to evaluate : 0.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 178 ASP Chi-restraints excluded: chain K residue 212 ILE Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 111 GLU Chi-restraints excluded: chain G residue 60 ILE Chi-restraints excluded: chain H residue 88 GLU Chi-restraints excluded: chain H residue 106 HIS Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 229 GLU Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain E residue 88 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 94 optimal weight: 0.9990 chunk 135 optimal weight: 2.9990 chunk 57 optimal weight: 0.3980 chunk 183 optimal weight: 20.0000 chunk 52 optimal weight: 0.9990 chunk 84 optimal weight: 2.9990 chunk 121 optimal weight: 1.9990 chunk 165 optimal weight: 1.9990 chunk 181 optimal weight: 10.0000 chunk 70 optimal weight: 2.9990 chunk 147 optimal weight: 1.9990 overall best weight: 1.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 129 GLN A 291 GLN ** I 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 15 ASN B 90 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.124439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.104402 restraints weight = 53299.075| |-----------------------------------------------------------------------------| r_work (start): 0.3034 rms_B_bonded: 1.91 r_work: 0.2916 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2798 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.3473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.198 15083 Z= 0.209 Angle : 0.554 9.901 20546 Z= 0.287 Chirality : 0.040 0.149 2284 Planarity : 0.004 0.047 2625 Dihedral : 7.658 179.934 2091 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 1.41 % Allowed : 9.67 % Favored : 88.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.20), residues: 1887 helix: 1.47 (0.17), residues: 980 sheet: -0.88 (0.40), residues: 171 loop : -0.06 (0.24), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 87 TYR 0.017 0.001 TYR D 195 PHE 0.013 0.001 PHE K 89 TRP 0.010 0.001 TRP K 142 HIS 0.007 0.001 HIS H 84 Details of bonding type rmsd/Z covalent geometry : bond 0.00480 / 0.21 (15075) covalent geometry : angle 0.55289 / 0.29 (20544) SS BOND : bond 0.01428 / 0.75 ( 1) SS BOND : angle 3.87721 / 2.26 ( 2) hydrogen bonds : bond 0.04170 / 2.82 ( 838) hydrogen bonds : angle 4.59138 / 3.27 ( 2385) Misc. bond : bond 0.10570 / 4.50 ( 7) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3774 Ramachandran restraints generated. 1887 Oldfield, 0 Emsley, 1887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3774 Ramachandran restraints generated. 1887 Oldfield, 0 Emsley, 1887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 112 is missing expected H atoms. Skipping. Residue LYS 124 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue TYR 43 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue SER 214 is missing expected H atoms. Skipping. Residue LYS 218 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue TYR 32 is missing expected H atoms. Skipping. Evaluate side-chains 245 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 224 time to evaluate : 0.714 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 THR cc_start: 0.8822 (t) cc_final: 0.8554 (p) REVERT: A 297 GLU cc_start: 0.8774 (OUTLIER) cc_final: 0.8557 (tt0) REVERT: A 384 SER cc_start: 0.8570 (t) cc_final: 0.8334 (m) REVERT: A 391 LYS cc_start: 0.8749 (ttmm) cc_final: 0.8540 (mttm) REVERT: K 246 TYR cc_start: 0.8787 (m-80) cc_final: 0.8397 (m-80) REVERT: K 272 GLU cc_start: 0.8247 (tt0) cc_final: 0.7748 (mm-30) REVERT: K 310 ARG cc_start: 0.8255 (mmm-85) cc_final: 0.7813 (mtp180) REVERT: D 111 GLU cc_start: 0.7197 (OUTLIER) cc_final: 0.6806 (mp0) REVERT: D 135 TYR cc_start: 0.8657 (m-80) cc_final: 0.8268 (m-80) REVERT: G 60 ILE cc_start: 0.9166 (OUTLIER) cc_final: 0.8927 (mt) REVERT: G 97 GLU cc_start: 0.8548 (tp30) cc_final: 0.8253 (tp30) REVERT: G 117 LYS cc_start: 0.8501 (ttmt) cc_final: 0.7214 (mmpt) REVERT: F 11 MET cc_start: 0.8612 (ttp) cc_final: 0.8321 (ttp) REVERT: F 21 LYS cc_start: 0.8555 (mmtp) cc_final: 0.8318 (mttm) REVERT: F 73 ARG cc_start: 0.7641 (tmt170) cc_final: 0.7184 (mtt-85) REVERT: F 87 ARG cc_start: 0.8275 (ttp80) cc_final: 0.7998 (ttp80) REVERT: H 91 GLU cc_start: 0.7819 (tp30) cc_final: 0.7597 (tp30) REVERT: B 132 LYS cc_start: 0.8478 (ttpp) cc_final: 0.8230 (ttmm) REVERT: B 152 ARG cc_start: 0.7899 (mtt180) cc_final: 0.6837 (mmm160) REVERT: B 186 SER cc_start: 0.8932 (t) cc_final: 0.8501 (m) REVERT: B 247 LYS cc_start: 0.8297 (mtmm) cc_final: 0.7978 (ttmm) REVERT: B 366 ASP cc_start: 0.8819 (t0) cc_final: 0.8373 (t0) REVERT: M 60 MET cc_start: 0.8746 (ttp) cc_final: 0.8455 (ttm) outliers start: 21 outliers final: 17 residues processed: 231 average time/residue: 0.2859 time to fit residues: 95.7231 Evaluate side-chains 238 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 218 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain A residue 291 GLN Chi-restraints excluded: chain A residue 297 GLU Chi-restraints excluded: chain K residue 212 ILE Chi-restraints excluded: chain K residue 322 SER Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 111 GLU Chi-restraints excluded: chain D residue 226 SER Chi-restraints excluded: chain G residue 60 ILE Chi-restraints excluded: chain F residue 9 THR Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain H residue 88 GLU Chi-restraints excluded: chain H residue 106 HIS Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 229 GLU Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 358 ASN Chi-restraints excluded: chain E residue 88 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 184 optimal weight: 0.0060 chunk 97 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 chunk 52 optimal weight: 0.9980 chunk 122 optimal weight: 2.9990 chunk 182 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 133 optimal weight: 2.9990 chunk 149 optimal weight: 0.9980 chunk 68 optimal weight: 0.3980 chunk 137 optimal weight: 1.9990 overall best weight: 0.6796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 291 GLN ** I 41 HIS ** 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 = 0.3316 r_free = 0.3316 target = 0.125343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.103061 restraints weight = 52941.449| |-----------------------------------------------------------------------------| r_work (start): 0.3080 rms_B_bonded: 2.13 r_work: 0.2989 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2868 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.3561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.183 15083 Z= 0.139 Angle : 0.523 9.752 20546 Z= 0.268 Chirality : 0.039 0.149 2284 Planarity : 0.004 0.047 2625 Dihedral : 7.535 179.281 2091 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 1.21 % Allowed : 10.68 % Favored : 88.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.11 (0.20), residues: 1887 helix: 1.63 (0.17), residues: 980 sheet: -0.92 (0.40), residues: 175 loop : 0.05 (0.24), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 231 TYR 0.010 0.001 TYR A 269 PHE 0.015 0.001 PHE A 327 TRP 0.011 0.001 TRP K 142 HIS 0.004 0.001 HIS H 84 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 (15075) covalent geometry : angle 0.52167 / 0.27 (20544) SS BOND : bond 0.01280 / 0.67 ( 1) SS BOND : angle 3.81615 / 2.21 ( 2) hydrogen bonds : bond 0.03920 / 2.66 ( 838) hydrogen bonds : angle 4.45233 / 3.17 ( 2385) Misc. bond : bond 0.09745 / 4.14 ( 7) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3774 Ramachandran restraints generated. 1887 Oldfield, 0 Emsley, 1887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3774 Ramachandran restraints generated. 1887 Oldfield, 0 Emsley, 1887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 112 is missing expected H atoms. Skipping. Residue LYS 124 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue TYR 43 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue SER 214 is missing expected H atoms. Skipping. Residue LYS 218 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue TYR 32 is missing expected H atoms. Skipping. Evaluate side-chains 232 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 214 time to evaluate : 0.657 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 THR cc_start: 0.8836 (t) cc_final: 0.8577 (p) REVERT: A 297 GLU cc_start: 0.8800 (OUTLIER) cc_final: 0.8538 (tt0) REVERT: A 384 SER cc_start: 0.8629 (t) cc_final: 0.8393 (m) REVERT: A 391 LYS cc_start: 0.8773 (ttmm) cc_final: 0.8572 (mttm) REVERT: K 272 GLU cc_start: 0.8327 (tt0) cc_final: 0.7804 (mm-30) REVERT: K 310 ARG cc_start: 0.8300 (mmm-85) cc_final: 0.7875 (mtp180) REVERT: D 111 GLU cc_start: 0.7114 (OUTLIER) cc_final: 0.6735 (mp0) REVERT: D 135 TYR cc_start: 0.8659 (m-80) cc_final: 0.8286 (m-80) REVERT: D 270 ARG cc_start: 0.6739 (mmt180) cc_final: 0.4874 (mtp85) REVERT: G 60 ILE cc_start: 0.9173 (OUTLIER) cc_final: 0.8931 (mt) REVERT: G 117 LYS cc_start: 0.8478 (ttmt) cc_final: 0.7155 (mmpt) REVERT: F 11 MET cc_start: 0.8587 (ttp) cc_final: 0.8280 (ttp) REVERT: F 21 LYS cc_start: 0.8547 (mmtp) cc_final: 0.8298 (mttm) REVERT: F 73 ARG cc_start: 0.7661 (tmt170) cc_final: 0.7190 (mtt-85) REVERT: B 54 PHE cc_start: 0.8904 (OUTLIER) cc_final: 0.7885 (t80) REVERT: B 132 LYS cc_start: 0.8494 (ttpp) cc_final: 0.8250 (ttmm) REVERT: B 152 ARG cc_start: 0.7920 (mtt180) cc_final: 0.6836 (mmm160) REVERT: B 186 SER cc_start: 0.8938 (t) cc_final: 0.8535 (m) REVERT: B 247 LYS cc_start: 0.8312 (mtmm) cc_final: 0.7994 (ttmm) REVERT: B 366 ASP cc_start: 0.8822 (t0) cc_final: 0.8377 (t0) REVERT: M 60 MET cc_start: 0.8731 (ttp) cc_final: 0.8463 (ttm) outliers start: 18 outliers final: 11 residues processed: 221 average time/residue: 0.2761 time to fit residues: 88.7124 Evaluate side-chains 224 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 209 time to evaluate : 0.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 297 GLU Chi-restraints excluded: chain K residue 212 ILE Chi-restraints excluded: chain K residue 322 SER Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 111 GLU Chi-restraints excluded: chain G residue 7 SER Chi-restraints excluded: chain G residue 60 ILE Chi-restraints excluded: chain H residue 88 GLU Chi-restraints excluded: chain H residue 106 HIS Chi-restraints excluded: chain B residue 54 PHE Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 229 GLU Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain E residue 88 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 81 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 chunk 153 optimal weight: 0.9980 chunk 109 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 156 optimal weight: 0.9980 chunk 75 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 129 GLN ** I 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 15 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.123346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.103439 restraints weight = 53792.218| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 1.94 r_work: 0.2932 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2815 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.3729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.195 15083 Z= 0.195 Angle : 0.548 9.924 20546 Z= 0.282 Chirality : 0.039 0.150 2284 Planarity : 0.004 0.045 2625 Dihedral : 7.560 177.338 2091 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 1.21 % Allowed : 11.28 % Favored : 87.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.05 (0.20), residues: 1887 helix: 1.61 (0.17), residues: 980 sheet: -1.13 (0.39), residues: 185 loop : 0.06 (0.25), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 231 TYR 0.014 0.001 TYR A 314 PHE 0.017 0.001 PHE K 89 TRP 0.009 0.001 TRP K 142 HIS 0.005 0.001 HIS K 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00452 / 0.19 (15075) covalent geometry : angle 0.54690 / 0.28 (20544) SS BOND : bond 0.01316 / 0.69 ( 1) SS BOND : angle 3.70073 / 2.14 ( 2) hydrogen bonds : bond 0.04056 / 2.75 ( 838) hydrogen bonds : angle 4.48997 / 3.20 ( 2385) Misc. bond : bond 0.09981 / 4.16 ( 7) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3774 Ramachandran restraints generated. 1887 Oldfield, 0 Emsley, 1887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3774 Ramachandran restraints generated. 1887 Oldfield, 0 Emsley, 1887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 112 is missing expected H atoms. Skipping. Residue LYS 124 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue TYR 43 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue SER 214 is missing expected H atoms. Skipping. Residue LYS 218 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue TYR 32 is missing expected H atoms. Skipping. Evaluate side-chains 240 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 222 time to evaluate : 0.621 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 THR cc_start: 0.8822 (t) cc_final: 0.8594 (p) REVERT: A 297 GLU cc_start: 0.8798 (OUTLIER) cc_final: 0.8534 (tt0) REVERT: A 384 SER cc_start: 0.8635 (t) cc_final: 0.8412 (m) REVERT: A 391 LYS cc_start: 0.8802 (ttmm) cc_final: 0.8595 (mttm) REVERT: K 246 TYR cc_start: 0.8793 (m-80) cc_final: 0.8377 (m-80) REVERT: K 272 GLU cc_start: 0.8257 (tt0) cc_final: 0.7786 (mm-30) REVERT: K 307 TYR cc_start: 0.8993 (m-80) cc_final: 0.8775 (m-10) REVERT: K 310 ARG cc_start: 0.8289 (mmm-85) cc_final: 0.7895 (mtp180) REVERT: D 111 GLU cc_start: 0.7153 (OUTLIER) cc_final: 0.6779 (mp0) REVERT: D 135 TYR cc_start: 0.8646 (m-80) cc_final: 0.8300 (m-80) REVERT: G 60 ILE cc_start: 0.9194 (OUTLIER) cc_final: 0.8954 (mt) REVERT: G 117 LYS cc_start: 0.8587 (ttmt) cc_final: 0.7317 (mmtt) REVERT: F 11 MET cc_start: 0.8619 (ttp) cc_final: 0.8328 (ttp) REVERT: F 21 LYS cc_start: 0.8560 (mmtp) cc_final: 0.8318 (mttm) REVERT: F 73 ARG cc_start: 0.7636 (tmt170) cc_final: 0.7229 (mtt-85) REVERT: B 54 PHE cc_start: 0.8969 (OUTLIER) cc_final: 0.7909 (t80) REVERT: B 132 LYS cc_start: 0.8510 (ttpp) cc_final: 0.8249 (ttmm) REVERT: B 152 ARG cc_start: 0.7955 (mtt180) cc_final: 0.6833 (mmm160) REVERT: B 186 SER cc_start: 0.8901 (t) cc_final: 0.8534 (m) REVERT: B 247 LYS cc_start: 0.8384 (mtmm) cc_final: 0.8081 (ttmm) REVERT: B 366 ASP cc_start: 0.8789 (t0) cc_final: 0.8355 (t0) REVERT: M 60 MET cc_start: 0.8734 (ttp) cc_final: 0.8495 (ttm) outliers start: 18 outliers final: 14 residues processed: 230 average time/residue: 0.2823 time to fit residues: 94.4781 Evaluate side-chains 240 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 222 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 297 GLU Chi-restraints excluded: chain K residue 212 ILE Chi-restraints excluded: chain K residue 322 SER Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 111 GLU Chi-restraints excluded: chain G residue 7 SER Chi-restraints excluded: chain G residue 60 ILE Chi-restraints excluded: chain F residue 9 THR Chi-restraints excluded: chain H residue 88 GLU Chi-restraints excluded: chain H residue 106 HIS Chi-restraints excluded: chain B residue 54 PHE Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 229 GLU Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 358 ASN Chi-restraints excluded: chain E residue 88 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 133 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 chunk 61 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 84 optimal weight: 0.8980 chunk 106 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 291 GLN K 31 ASN K 375 ASN ** I 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.122750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.100503 restraints weight = 53440.211| |-----------------------------------------------------------------------------| r_work (start): 0.3099 rms_B_bonded: 2.13 r_work: 0.3010 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2890 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.3873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.205 15083 Z= 0.199 Angle : 0.550 9.577 20546 Z= 0.284 Chirality : 0.040 0.152 2284 Planarity : 0.004 0.047 2625 Dihedral : 7.581 174.594 2091 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 1.28 % Allowed : 11.42 % Favored : 87.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.04 (0.20), residues: 1887 helix: 1.61 (0.17), residues: 981 sheet: -1.16 (0.38), residues: 185 loop : 0.05 (0.25), residues: 721 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 231 TYR 0.012 0.001 TYR A 269 PHE 0.019 0.001 PHE K 89 TRP 0.009 0.001 TRP K 142 HIS 0.005 0.001 HIS D 244 Details of bonding type rmsd/Z covalent geometry : bond 0.00460 / 0.20 (15075) covalent geometry : angle 0.54879 / 0.28 (20544) SS BOND : bond 0.01275 / 0.67 ( 1) SS BOND : angle 3.79450 / 2.19 ( 2) hydrogen bonds : bond 0.04064 / 2.76 ( 838) hydrogen bonds : angle 4.45830 / 3.18 ( 2385) Misc. bond : bond 0.10251 / 4.23 ( 7) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3774 Ramachandran restraints generated. 1887 Oldfield, 0 Emsley, 1887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3774 Ramachandran restraints generated. 1887 Oldfield, 0 Emsley, 1887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 112 is missing expected H atoms. Skipping. Residue LYS 124 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue TYR 43 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue SER 214 is missing expected H atoms. Skipping. Residue LYS 218 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue TYR 32 is missing expected H atoms. Skipping. Evaluate side-chains 237 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 218 time to evaluate : 0.729 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 THR cc_start: 0.8878 (t) cc_final: 0.8665 (p) REVERT: A 297 GLU cc_start: 0.8804 (OUTLIER) cc_final: 0.8517 (tt0) REVERT: A 384 SER cc_start: 0.8628 (t) cc_final: 0.8410 (m) REVERT: A 391 LYS cc_start: 0.8779 (ttmm) cc_final: 0.8573 (mttm) REVERT: K 246 TYR cc_start: 0.8825 (m-80) cc_final: 0.8354 (m-80) REVERT: K 272 GLU cc_start: 0.8280 (tt0) cc_final: 0.7892 (mm-30) REVERT: K 307 TYR cc_start: 0.9003 (m-80) cc_final: 0.8791 (m-10) REVERT: K 310 ARG cc_start: 0.8284 (mmm-85) cc_final: 0.7856 (mtp180) REVERT: D 111 GLU cc_start: 0.7162 (OUTLIER) cc_final: 0.6763 (mp0) REVERT: G 60 ILE cc_start: 0.9174 (OUTLIER) cc_final: 0.8930 (mt) REVERT: G 117 LYS cc_start: 0.8604 (ttmt) cc_final: 0.7239 (mmtt) REVERT: F 11 MET cc_start: 0.8598 (ttp) cc_final: 0.8304 (ttp) REVERT: F 21 LYS cc_start: 0.8583 (mmtp) cc_final: 0.8350 (mttm) REVERT: F 73 ARG cc_start: 0.7654 (tmt170) cc_final: 0.7218 (mtt-85) REVERT: H 91 GLU cc_start: 0.7963 (tp30) cc_final: 0.7665 (tp30) REVERT: B 54 PHE cc_start: 0.8980 (OUTLIER) cc_final: 0.7919 (t80) REVERT: B 132 LYS cc_start: 0.8509 (ttpp) cc_final: 0.8252 (ttmm) REVERT: B 144 GLU cc_start: 0.8629 (mm-30) cc_final: 0.8273 (mm-30) REVERT: B 152 ARG cc_start: 0.7986 (mtt180) cc_final: 0.6860 (mmm160) REVERT: B 178 GLU cc_start: 0.6810 (mm-30) cc_final: 0.6187 (tp30) REVERT: B 186 SER cc_start: 0.8908 (t) cc_final: 0.8538 (m) REVERT: B 247 LYS cc_start: 0.8382 (mtmm) cc_final: 0.8074 (ttmm) REVERT: B 366 ASP cc_start: 0.8778 (t0) cc_final: 0.8353 (t0) outliers start: 19 outliers final: 15 residues processed: 228 average time/residue: 0.2979 time to fit residues: 97.2903 Evaluate side-chains 235 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 216 time to evaluate : 0.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain A residue 291 GLN Chi-restraints excluded: chain A residue 297 GLU Chi-restraints excluded: chain K residue 212 ILE Chi-restraints excluded: chain K residue 322 SER Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 111 GLU Chi-restraints excluded: chain G residue 7 SER Chi-restraints excluded: chain G residue 60 ILE Chi-restraints excluded: chain H residue 83 ASP Chi-restraints excluded: chain H residue 88 GLU Chi-restraints excluded: chain B residue 54 PHE Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 229 GLU Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 358 ASN Chi-restraints excluded: chain E residue 88 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 101 optimal weight: 0.9990 chunk 170 optimal weight: 5.9990 chunk 12 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 174 optimal weight: 6.9990 chunk 122 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 169 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 138 optimal weight: 1.9990 overall best weight: 1.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 129 GLN A 291 GLN K 84 ASN ** I 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.123393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.101046 restraints weight = 53244.766| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 2.14 r_work: 0.2999 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2878 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.3949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.206 15083 Z= 0.194 Angle : 0.552 9.709 20546 Z= 0.284 Chirality : 0.039 0.151 2284 Planarity : 0.004 0.045 2625 Dihedral : 7.593 176.482 2091 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 1.34 % Allowed : 11.48 % Favored : 87.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.04 (0.20), residues: 1887 helix: 1.60 (0.17), residues: 981 sheet: -1.14 (0.39), residues: 185 loop : 0.07 (0.25), residues: 721 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 87 TYR 0.015 0.001 TYR H 107 PHE 0.018 0.001 PHE K 89 TRP 0.009 0.001 TRP K 142 HIS 0.006 0.001 HIS H 84 Details of bonding type rmsd/Z covalent geometry : bond 0.00451 / 0.19 (15075) covalent geometry : angle 0.55038 / 0.28 (20544) SS BOND : bond 0.01353 / 0.71 ( 1) SS BOND : angle 3.71300 / 2.15 ( 2) hydrogen bonds : bond 0.04053 / 2.75 ( 838) hydrogen bonds : angle 4.45638 / 3.18 ( 2385) Misc. bond : bond 0.10306 / 4.26 ( 7) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3774 Ramachandran restraints generated. 1887 Oldfield, 0 Emsley, 1887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3774 Ramachandran restraints generated. 1887 Oldfield, 0 Emsley, 1887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 112 is missing expected H atoms. Skipping. Residue LYS 124 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue TYR 43 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue SER 214 is missing expected H atoms. Skipping. Residue LYS 218 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue TYR 32 is missing expected H atoms. Skipping. Evaluate side-chains 235 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 215 time to evaluate : 0.819 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 THR cc_start: 0.8879 (t) cc_final: 0.8667 (p) REVERT: A 297 GLU cc_start: 0.8777 (OUTLIER) cc_final: 0.8503 (tt0) REVERT: A 384 SER cc_start: 0.8640 (t) cc_final: 0.8434 (m) REVERT: K 246 TYR cc_start: 0.8836 (m-80) cc_final: 0.8383 (m-80) REVERT: K 272 GLU cc_start: 0.8322 (tt0) cc_final: 0.7976 (mm-30) REVERT: K 307 TYR cc_start: 0.9022 (m-80) cc_final: 0.8821 (m-10) REVERT: K 310 ARG cc_start: 0.8314 (mmm-85) cc_final: 0.7901 (mtp180) REVERT: D 111 GLU cc_start: 0.7242 (OUTLIER) cc_final: 0.6861 (mp0) REVERT: G 60 ILE cc_start: 0.9214 (OUTLIER) cc_final: 0.8972 (mt) REVERT: G 97 GLU cc_start: 0.8358 (tp30) cc_final: 0.8114 (tp30) REVERT: G 117 LYS cc_start: 0.8659 (ttmt) cc_final: 0.7296 (mmtt) REVERT: F 11 MET cc_start: 0.8641 (ttp) cc_final: 0.8360 (ttp) REVERT: F 21 LYS cc_start: 0.8606 (mmtp) cc_final: 0.8376 (mttm) REVERT: F 73 ARG cc_start: 0.7719 (tmt170) cc_final: 0.7321 (mtt-85) REVERT: H 91 GLU cc_start: 0.7915 (tp30) cc_final: 0.7612 (tp30) REVERT: B 54 PHE cc_start: 0.9013 (OUTLIER) cc_final: 0.7974 (t80) REVERT: B 132 LYS cc_start: 0.8563 (ttpp) cc_final: 0.8308 (ttmm) REVERT: B 144 GLU cc_start: 0.8629 (mm-30) cc_final: 0.8262 (mm-30) REVERT: B 152 ARG cc_start: 0.7984 (mtt180) cc_final: 0.6907 (mmm160) REVERT: B 178 GLU cc_start: 0.6783 (mm-30) cc_final: 0.6210 (tp30) REVERT: B 186 SER cc_start: 0.8890 (t) cc_final: 0.8558 (m) REVERT: B 247 LYS cc_start: 0.8433 (mtmm) cc_final: 0.8135 (ttmm) REVERT: B 366 ASP cc_start: 0.8776 (t0) cc_final: 0.8361 (t0) outliers start: 20 outliers final: 15 residues processed: 226 average time/residue: 0.2988 time to fit residues: 96.6546 Evaluate side-chains 232 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 213 time to evaluate : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain A residue 297 GLU Chi-restraints excluded: chain K residue 147 ILE Chi-restraints excluded: chain K residue 212 ILE Chi-restraints excluded: chain K residue 322 SER Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 111 GLU Chi-restraints excluded: chain G residue 7 SER Chi-restraints excluded: chain G residue 60 ILE Chi-restraints excluded: chain H residue 83 ASP Chi-restraints excluded: chain H residue 88 GLU Chi-restraints excluded: chain B residue 54 PHE Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 229 GLU Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 358 ASN Chi-restraints excluded: chain E residue 88 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 168 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 181 optimal weight: 10.0000 chunk 183 optimal weight: 20.0000 chunk 77 optimal weight: 0.0270 chunk 150 optimal weight: 2.9990 chunk 155 optimal weight: 0.5980 chunk 175 optimal weight: 10.0000 chunk 161 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 overall best weight: 1.1042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 57 HIS A 291 GLN ** I 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.123212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.101151 restraints weight = 53414.504| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 2.12 r_work: 0.3075 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2956 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.4022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.202 15083 Z= 0.181 Angle : 0.545 9.694 20546 Z= 0.280 Chirality : 0.039 0.151 2284 Planarity : 0.004 0.044 2625 Dihedral : 7.579 176.927 2091 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 1.48 % Allowed : 11.42 % Favored : 87.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.08 (0.20), residues: 1887 helix: 1.66 (0.17), residues: 980 sheet: -1.16 (0.38), residues: 186 loop : 0.05 (0.25), residues: 721 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 87 TYR 0.013 0.001 TYR D 195 PHE 0.019 0.001 PHE K 89 TRP 0.009 0.001 TRP K 142 HIS 0.009 0.001 HIS H 84 Details of bonding type rmsd/Z covalent geometry : bond 0.00419 / 0.18 (15075) covalent geometry : angle 0.54388 / 0.28 (20544) SS BOND : bond 0.01356 / 0.71 ( 1) SS BOND : angle 3.59596 / 2.08 ( 2) hydrogen bonds : bond 0.03982 / 2.71 ( 838) hydrogen bonds : angle 4.41379 / 3.15 ( 2385) Misc. bond : bond 0.10088 / 4.17 ( 7) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6274.14 seconds wall clock time: 107 minutes 20.23 seconds (6440.23 seconds total)