Starting phenix.real_space_refine on Fri Mar 6 06:13:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7rjc_24484/03_2026/7rjc_24484_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rjc_24484/03_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_24484/03_2026/7rjc_24484.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rjc_24484/03_2026/7rjc_24484.map" model { file = "/net/cci-nas-00/data/ceres_data/7rjc_24484/03_2026/7rjc_24484_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rjc_24484/03_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-5986/lib/python3.9/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: 60 Planarities with less than four sites: {'U10:plan-5': 2, 'U10:plan-6': 2, 'U10:plan-7': 2, 'U10:plan-8': 2, 'U10:plan-9': 2, 'U10:plan-10': 2, 'U10:plan-11': 2, 'U10:plan-4': 1} Unresolved non-hydrogen planarities: 60 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: 4.96, 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: 2.70 Conformation dependent library (CDL) restraints added in 763.3 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: 0.55 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: 6.38 Time building geometry restraints manager: 3.70 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=" C ILE F 30 " pdb=" N SER F 31 " ideal model delta sigma weight residual 1.331 1.234 0.097 1.48e-02 4.57e+03 4.26e+01 ... (remaining 28734 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.54: 51403 3.54 - 7.08: 161 7.08 - 10.62: 10 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: 313 70.56 - 105.84: 35 105.84 - 141.12: 1 141.12 - 176.40: 1 Dihedral angle restraints: 13678 sinusoidal: 7048 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=" C3M U10 K 403 " pdb=" C3 U10 K 403 " pdb=" O3 U10 K 403 " pdb=" C4 U10 K 403 " ideal model delta sinusoidal sigma weight residual 244.38 105.86 138.51 1 2.00e+01 2.50e-03 4.20e+01 ... (remaining 13675 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=" CA LYS E 190 " 0.030 2.00e-02 2.50e+03 6.09e-02 3.71e+01 pdb=" C LYS E 190 " -0.105 2.00e-02 2.50e+03 pdb=" O LYS E 190 " 0.039 2.00e-02 2.50e+03 pdb=" N GLY E 191 " 0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS K 96 " 0.056 2.00e-02 2.50e+03 4.00e-02 3.60e+01 pdb=" CG HIS K 96 " -0.069 2.00e-02 2.50e+03 pdb=" ND1 HIS K 96 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 HIS K 96 " -0.053 2.00e-02 2.50e+03 pdb=" CE1 HIS K 96 " -0.006 2.00e-02 2.50e+03 pdb=" NE2 HIS K 96 " 0.060 2.00e-02 2.50e+03 pdb=" HD1 HIS K 96 " -0.001 2.00e-02 2.50e+03 pdb=" HD2 HIS K 96 " 0.009 2.00e-02 2.50e+03 pdb=" HE1 HIS K 96 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE K 184 " -0.014 2.00e-02 2.50e+03 2.57e-02 1.98e+01 pdb=" CG PHE K 184 " 0.067 2.00e-02 2.50e+03 pdb=" CD1 PHE K 184 " -0.021 2.00e-02 2.50e+03 pdb=" CD2 PHE K 184 " -0.049 2.00e-02 2.50e+03 pdb=" CE1 PHE K 184 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE K 184 " 0.018 2.00e-02 2.50e+03 pdb=" CZ PHE K 184 " -0.001 2.00e-02 2.50e+03 pdb=" HD1 PHE K 184 " -0.000 2.00e-02 2.50e+03 pdb=" HD2 PHE K 184 " 0.005 2.00e-02 2.50e+03 pdb=" HE1 PHE K 184 " -0.003 2.00e-02 2.50e+03 pdb=" HE2 PHE K 184 " -0.004 2.00e-02 2.50e+03 pdb=" HZ PHE K 184 " 0.004 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: 1.420 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: 0.400 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 26.930 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: 0.000 Load rotamer database and sin/cos tables:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6678 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 : 0.007 0.315 15083 Z= 0.389 Angle : 0.819 17.708 20546 Z= 0.534 Chirality : 0.052 0.512 2284 Planarity : 0.005 0.061 2625 Dihedral : 13.582 176.404 5270 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 covalent geometry : bond 0.00674 (15075) covalent geometry : angle 0.81854 (20544) SS BOND : bond 0.00034 ( 1) SS BOND : angle 0.75220 ( 2) hydrogen bonds : bond 0.14386 ( 838) hydrogen bonds : angle 6.67951 ( 2385) Misc. bond : bond 0.12128 ( 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 : 0.893 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: 0.3094 time to fit residues: 147.9251 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 : 0.725 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 329 HIS K 84 ASN D 59 HIS D 237 ASN ** 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.133500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.113301 restraints weight = 52082.637| |-----------------------------------------------------------------------------| r_work (start): 0.3172 rms_B_bonded: 1.92 r_work: 0.3057 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2939 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.2000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.303 15083 Z= 0.164 Angle : 0.574 12.388 20546 Z= 0.298 Chirality : 0.040 0.150 2284 Planarity : 0.004 0.054 2625 Dihedral : 8.114 177.792 2089 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 0.67 % Allowed : 6.25 % Favored : 93.08 % 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: 0.56 (0.20), residues: 1887 helix: 0.96 (0.16), residues: 983 sheet: -0.64 (0.40), residues: 164 loop : -0.02 (0.24), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG M 50 TYR 0.017 0.001 TYR K 378 PHE 0.012 0.001 PHE G 14 TRP 0.015 0.001 TRP K 142 HIS 0.009 0.001 HIS K 96 Details of bonding type rmsd covalent geometry : bond 0.00359 (15075) covalent geometry : angle 0.57379 (20544) SS BOND : bond 0.00081 ( 1) SS BOND : angle 0.48459 ( 2) hydrogen bonds : bond 0.04802 ( 838) hydrogen bonds : angle 5.01642 ( 2385) Misc. bond : bond 0.14325 ( 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 259 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 249 time to evaluate : 0.698 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: 0.8762 (t) cc_final: 0.8394 (p) REVERT: A 245 ILE cc_start: 0.9057 (pt) cc_final: 0.8835 (pt) REVERT: A 384 SER cc_start: 0.8548 (t) cc_final: 0.8284 (p) REVERT: A 391 LYS cc_start: 0.8830 (ttmm) cc_final: 0.8515 (mtpt) REVERT: K 272 GLU cc_start: 0.8280 (tt0) cc_final: 0.7918 (mm-30) REVERT: K 322 SER cc_start: 0.8704 (t) cc_final: 0.8267 (t) REVERT: D 135 TYR cc_start: 0.8441 (m-80) cc_final: 0.8009 (m-80) REVERT: G 117 LYS cc_start: 0.8246 (ttmt) cc_final: 0.7238 (mmtt) REVERT: F 21 LYS cc_start: 0.8465 (mmtp) cc_final: 0.8209 (mttm) REVERT: H 111 CYS cc_start: 0.7632 (m) cc_final: 0.7346 (m) REVERT: I 40 GLU cc_start: 0.8670 (tm-30) cc_final: 0.8457 (tp30) REVERT: B 18 LYS cc_start: 0.8182 (mtmm) cc_final: 0.7688 (mptt) REVERT: B 132 LYS cc_start: 0.8386 (ttpp) cc_final: 0.8150 (ttmm) REVERT: B 152 ARG cc_start: 0.7722 (mtt180) cc_final: 0.6920 (mmm160) REVERT: B 165 THR cc_start: 0.8789 (m) cc_final: 0.8568 (t) REVERT: B 327 LYS cc_start: 0.8537 (tppp) cc_final: 0.8018 (ttmt) REVERT: M 60 MET cc_start: 0.7827 (ttp) cc_final: 0.7531 (ttm) outliers start: 10 outliers final: 6 residues processed: 253 average time/residue: 0.2787 time to fit residues: 102.0200 Evaluate side-chains 230 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 224 time to evaluate : 0.709 ------------------------------------------------------------------------------- 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 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: 0.9990 chunk 34 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 100 optimal weight: 1.9990 chunk 186 optimal weight: 20.0000 chunk 146 optimal weight: 1.9990 chunk 182 optimal weight: 0.9990 chunk 127 optimal weight: 6.9990 chunk 156 optimal weight: 0.7980 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 101 ASN B 15 ASN B 179 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.127954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.107840 restraints weight = 52823.724| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 1.87 r_work: 0.3184 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3069 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.2703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.279 15083 Z= 0.216 Angle : 0.572 10.975 20546 Z= 0.298 Chirality : 0.041 0.216 2284 Planarity : 0.004 0.065 2625 Dihedral : 7.780 179.819 2087 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 1.34 % Allowed : 7.25 % Favored : 91.40 % 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: 0.75 (0.20), residues: 1887 helix: 1.24 (0.16), residues: 972 sheet: -0.76 (0.41), residues: 152 loop : -0.06 (0.24), residues: 763 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG M 50 TYR 0.020 0.002 TYR H 107 PHE 0.014 0.001 PHE K 278 TRP 0.011 0.001 TRP K 142 HIS 0.009 0.001 HIS H 84 Details of bonding type rmsd covalent geometry : bond 0.00490 (15075) covalent geometry : angle 0.57212 (20544) SS BOND : bond 0.00020 ( 1) SS BOND : angle 0.44478 ( 2) hydrogen bonds : bond 0.04569 ( 838) hydrogen bonds : angle 4.82683 ( 2385) Misc. bond : bond 0.12980 ( 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 258 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 238 time to evaluate : 0.736 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: 0.8789 (t) cc_final: 0.8487 (p) REVERT: A 384 SER cc_start: 0.8521 (t) cc_final: 0.8307 (p) REVERT: A 391 LYS cc_start: 0.8839 (ttmm) cc_final: 0.8540 (mtpt) REVERT: K 246 TYR cc_start: 0.8793 (m-80) cc_final: 0.8459 (m-80) REVERT: K 264 VAL cc_start: 0.9004 (t) cc_final: 0.8773 (p) REVERT: K 272 GLU cc_start: 0.8252 (tt0) cc_final: 0.7847 (mm-30) REVERT: K 322 SER cc_start: 0.8602 (t) cc_final: 0.8054 (t) REVERT: D 111 GLU cc_start: 0.7347 (OUTLIER) cc_final: 0.6985 (mp0) REVERT: D 135 TYR cc_start: 0.8627 (m-80) cc_final: 0.8231 (m-80) REVERT: G 60 ILE cc_start: 0.9238 (OUTLIER) cc_final: 0.9024 (mt) REVERT: G 117 LYS cc_start: 0.8341 (ttmt) cc_final: 0.7260 (mmtt) REVERT: F 11 MET cc_start: 0.8681 (ttp) cc_final: 0.8422 (ttp) REVERT: F 21 LYS cc_start: 0.8623 (mmtp) cc_final: 0.8417 (mttm) REVERT: H 84 HIS cc_start: 0.8244 (t70) cc_final: 0.7756 (t-90) REVERT: B 18 LYS cc_start: 0.8223 (mtmm) cc_final: 0.7634 (mmtt) REVERT: B 132 LYS cc_start: 0.8482 (ttpp) cc_final: 0.8241 (ttmm) REVERT: B 152 ARG cc_start: 0.7874 (mtt180) cc_final: 0.6985 (mmm160) REVERT: B 165 THR cc_start: 0.8807 (m) cc_final: 0.8603 (t) REVERT: B 178 GLU cc_start: 0.7046 (mm-30) cc_final: 0.6558 (tp30) REVERT: B 327 LYS cc_start: 0.8578 (tppp) cc_final: 0.8030 (ttmt) REVERT: M 60 MET cc_start: 0.8417 (ttp) cc_final: 0.8154 (ttt) outliers start: 20 outliers final: 14 residues processed: 249 average time/residue: 0.2639 time to fit residues: 96.0351 Evaluate side-chains 232 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 216 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain K residue 212 ILE Chi-restraints excluded: chain K residue 330 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 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 95 LYS Chi-restraints excluded: chain B residue 181 SER Chi-restraints excluded: chain B residue 186 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: 1.9990 chunk 178 optimal weight: 5.9990 chunk 8 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 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: 0.8980 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 129 GLN A 291 GLN K 57 ASN H 84 HIS ** I 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 15 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.126259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.106062 restraints weight = 52757.674| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 1.89 r_work: 0.3089 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2975 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.3098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.243 15083 Z= 0.240 Angle : 0.571 10.257 20546 Z= 0.299 Chirality : 0.041 0.166 2284 Planarity : 0.004 0.071 2625 Dihedral : 7.673 179.271 2087 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 1.54 % Allowed : 8.06 % Favored : 90.40 % 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: 1.25 (0.16), residues: 973 sheet: -0.89 (0.40), residues: 171 loop : -0.14 (0.24), residues: 743 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 128 TYR 0.014 0.001 TYR K 358 PHE 0.013 0.001 PHE A 327 TRP 0.011 0.001 TRP K 142 HIS 0.009 0.001 HIS H 84 Details of bonding type rmsd covalent geometry : bond 0.00550 (15075) covalent geometry : angle 0.57028 (20544) SS BOND : bond 0.01474 ( 1) SS BOND : angle 3.65502 ( 2) hydrogen bonds : bond 0.04432 ( 838) hydrogen bonds : angle 4.79693 ( 2385) Misc. bond : bond 0.12116 ( 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 248 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 225 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: symmetry clash REVERT: A 31 THR cc_start: 0.8825 (t) cc_final: 0.8526 (p) REVERT: A 384 SER cc_start: 0.8541 (t) cc_final: 0.8298 (m) REVERT: K 246 TYR cc_start: 0.8797 (m-80) cc_final: 0.8403 (m-80) REVERT: K 272 GLU cc_start: 0.8280 (tt0) cc_final: 0.7898 (mm-30) REVERT: K 322 SER cc_start: 0.8605 (t) cc_final: 0.8030 (t) REVERT: D 111 GLU cc_start: 0.7380 (OUTLIER) cc_final: 0.7036 (mp0) REVERT: D 135 TYR cc_start: 0.8670 (m-80) cc_final: 0.8311 (m-80) REVERT: G 60 ILE cc_start: 0.9227 (OUTLIER) cc_final: 0.9018 (mt) REVERT: G 97 GLU cc_start: 0.8513 (tp30) cc_final: 0.8278 (tp30) REVERT: G 117 LYS cc_start: 0.8476 (ttmt) cc_final: 0.7354 (mmpt) REVERT: F 11 MET cc_start: 0.8657 (ttp) cc_final: 0.8411 (ttp) REVERT: F 21 LYS cc_start: 0.8651 (mmtp) cc_final: 0.8394 (mttm) REVERT: F 73 ARG cc_start: 0.7829 (tmt170) cc_final: 0.7366 (mtt-85) REVERT: B 132 LYS cc_start: 0.8538 (ttpp) cc_final: 0.8307 (ttmm) REVERT: B 152 ARG cc_start: 0.7940 (mtt180) cc_final: 0.7002 (mmm160) REVERT: M 60 MET cc_start: 0.8692 (ttp) cc_final: 0.8319 (ttm) outliers start: 23 outliers final: 18 residues processed: 236 average time/residue: 0.2970 time to fit residues: 100.3833 Evaluate side-chains 232 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 212 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain K residue 212 ILE 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 D residue 265 SER Chi-restraints excluded: chain G residue 4 SER Chi-restraints excluded: chain G residue 7 SER Chi-restraints excluded: chain G residue 60 ILE Chi-restraints excluded: chain F residue 81 LEU 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 186 SER Chi-restraints excluded: chain B residue 229 GLU Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain M residue 56 MET 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: 0.9990 chunk 186 optimal weight: 0.0030 chunk 24 optimal weight: 1.9990 chunk 143 optimal weight: 0.8980 chunk 0 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 124 optimal weight: 7.9990 chunk 167 optimal weight: 2.9990 chunk 170 optimal weight: 7.9990 chunk 183 optimal weight: 20.0000 overall best weight: 1.3796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 177 GLN D 237 ASN ** 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 = 0.3320 r_free = 0.3320 target = 0.125210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.105112 restraints weight = 53307.428| |-----------------------------------------------------------------------------| r_work (start): 0.3054 rms_B_bonded: 1.90 r_work: 0.2938 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2820 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.3397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.229 15083 Z= 0.217 Angle : 0.568 11.947 20546 Z= 0.295 Chirality : 0.040 0.174 2284 Planarity : 0.004 0.089 2625 Dihedral : 7.615 179.761 2087 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 1.68 % Allowed : 8.80 % Favored : 89.52 % 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: 0.76 (0.20), residues: 1887 helix: 1.33 (0.17), residues: 973 sheet: -0.93 (0.40), residues: 171 loop : -0.13 (0.24), residues: 743 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 128 TYR 0.012 0.001 TYR K 358 PHE 0.014 0.001 PHE A 327 TRP 0.011 0.001 TRP K 142 HIS 0.006 0.001 HIS K 197 Details of bonding type rmsd covalent geometry : bond 0.00498 (15075) covalent geometry : angle 0.56561 (20544) SS BOND : bond 0.01574 ( 1) SS BOND : angle 5.62816 ( 2) hydrogen bonds : bond 0.04293 ( 838) hydrogen bonds : angle 4.69915 ( 2385) Misc. bond : bond 0.11609 ( 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 249 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 224 time to evaluate : 0.771 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: 0.8823 (t) cc_final: 0.8543 (p) REVERT: A 178 ASP cc_start: 0.7920 (OUTLIER) cc_final: 0.7690 (t0) REVERT: A 384 SER cc_start: 0.8726 (t) cc_final: 0.8461 (p) REVERT: K 246 TYR cc_start: 0.8791 (m-80) cc_final: 0.8368 (m-80) REVERT: K 272 GLU cc_start: 0.8180 (tt0) cc_final: 0.7778 (mm-30) REVERT: K 322 SER cc_start: 0.8541 (t) cc_final: 0.7942 (t) REVERT: D 111 GLU cc_start: 0.7237 (OUTLIER) cc_final: 0.6847 (mp0) REVERT: D 135 TYR cc_start: 0.8660 (m-80) cc_final: 0.8301 (m-80) REVERT: G 56 MET cc_start: 0.8456 (mmm) cc_final: 0.8230 (mmm) REVERT: G 60 ILE cc_start: 0.9185 (OUTLIER) cc_final: 0.8969 (mt) REVERT: G 97 GLU cc_start: 0.8594 (tp30) cc_final: 0.8326 (tp30) REVERT: G 117 LYS cc_start: 0.8531 (ttmt) cc_final: 0.7257 (mmpt) REVERT: F 11 MET cc_start: 0.8591 (ttp) cc_final: 0.8354 (ttp) REVERT: F 21 LYS cc_start: 0.8564 (mmtp) cc_final: 0.8305 (mttm) REVERT: F 73 ARG cc_start: 0.7683 (tmt170) cc_final: 0.7248 (mtt-85) REVERT: F 87 ARG cc_start: 0.8287 (ttp80) cc_final: 0.7993 (ttp80) REVERT: H 84 HIS cc_start: 0.8610 (t-90) cc_final: 0.8122 (t-90) REVERT: H 91 GLU cc_start: 0.7796 (tp30) cc_final: 0.7591 (tp30) REVERT: B 132 LYS cc_start: 0.8506 (ttpp) cc_final: 0.8261 (ttmm) REVERT: B 152 ARG cc_start: 0.7873 (mtt180) cc_final: 0.6921 (mmm160) REVERT: B 247 LYS cc_start: 0.8330 (mtmm) cc_final: 0.8008 (ttmm) REVERT: B 366 ASP cc_start: 0.8815 (t0) cc_final: 0.8386 (t0) REVERT: M 60 MET cc_start: 0.8744 (ttp) cc_final: 0.8433 (ttm) outliers start: 25 outliers final: 22 residues processed: 234 average time/residue: 0.2911 time to fit residues: 98.1554 Evaluate side-chains 242 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 217 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 SER Chi-restraints excluded: chain A residue 178 ASP Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain K residue 12 LEU Chi-restraints excluded: chain K residue 59 GLU Chi-restraints excluded: chain K residue 212 ILE 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 D residue 226 SER Chi-restraints excluded: chain D residue 265 SER Chi-restraints excluded: chain G residue 60 ILE Chi-restraints excluded: chain H residue 83 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 85 ASP Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 181 SER Chi-restraints excluded: chain B residue 186 SER Chi-restraints excluded: chain B residue 229 GLU Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain M residue 56 MET 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: 1.9990 chunk 135 optimal weight: 2.9990 chunk 57 optimal weight: 0.9990 chunk 183 optimal weight: 7.9990 chunk 52 optimal weight: 0.9980 chunk 84 optimal weight: 2.9990 chunk 121 optimal weight: 2.9990 chunk 165 optimal weight: 1.9990 chunk 181 optimal weight: 20.0000 chunk 70 optimal weight: 2.9990 chunk 147 optimal weight: 1.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 129 GLN D 237 ASN ** 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 = 0.3277 r_free = 0.3277 target = 0.121966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.102300 restraints weight = 53783.881| |-----------------------------------------------------------------------------| r_work (start): 0.3046 rms_B_bonded: 1.92 r_work: 0.2927 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2811 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.3664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.216 15083 Z= 0.247 Angle : 0.585 9.863 20546 Z= 0.306 Chirality : 0.041 0.165 2284 Planarity : 0.004 0.054 2625 Dihedral : 7.659 179.855 2087 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 1.68 % Allowed : 9.81 % Favored : 88.52 % 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: 0.68 (0.20), residues: 1887 helix: 1.31 (0.17), residues: 972 sheet: -1.22 (0.38), residues: 183 loop : -0.13 (0.24), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 349 TYR 0.014 0.002 TYR H 107 PHE 0.015 0.001 PHE K 89 TRP 0.010 0.001 TRP K 142 HIS 0.006 0.001 HIS K 197 Details of bonding type rmsd covalent geometry : bond 0.00569 (15075) covalent geometry : angle 0.58394 (20544) SS BOND : bond 0.01447 ( 1) SS BOND : angle 3.33931 ( 2) hydrogen bonds : bond 0.04385 ( 838) hydrogen bonds : angle 4.70589 ( 2385) Misc. bond : bond 0.11497 ( 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 249 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 224 time to evaluate : 0.757 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: 0.8859 (t) cc_final: 0.8603 (p) REVERT: A 384 SER cc_start: 0.8705 (t) cc_final: 0.8466 (m) REVERT: K 246 TYR cc_start: 0.8837 (m-80) cc_final: 0.8411 (m-80) REVERT: K 272 GLU cc_start: 0.8250 (tt0) cc_final: 0.7863 (mm-30) REVERT: K 310 ARG cc_start: 0.8362 (mmm-85) cc_final: 0.7953 (mtp180) REVERT: K 322 SER cc_start: 0.8539 (t) cc_final: 0.7920 (t) REVERT: D 111 GLU cc_start: 0.7327 (OUTLIER) cc_final: 0.6940 (mp0) REVERT: D 135 TYR cc_start: 0.8629 (m-80) cc_final: 0.8319 (m-80) REVERT: G 56 MET cc_start: 0.8500 (mmm) cc_final: 0.8268 (mmm) REVERT: G 60 ILE cc_start: 0.9170 (OUTLIER) cc_final: 0.8957 (mt) REVERT: G 117 LYS cc_start: 0.8628 (ttmt) cc_final: 0.7344 (mmtt) REVERT: F 11 MET cc_start: 0.8656 (ttp) cc_final: 0.8437 (ttp) REVERT: F 21 LYS cc_start: 0.8593 (mmtp) cc_final: 0.8342 (mttm) REVERT: F 73 ARG cc_start: 0.7708 (tmt170) cc_final: 0.7310 (mtt-85) REVERT: F 87 ARG cc_start: 0.8327 (ttp80) cc_final: 0.8066 (ttp80) REVERT: H 84 HIS cc_start: 0.8494 (OUTLIER) cc_final: 0.8239 (t-90) REVERT: H 91 GLU cc_start: 0.7779 (tp30) cc_final: 0.7551 (tp30) REVERT: B 132 LYS cc_start: 0.8532 (ttpp) cc_final: 0.8268 (ttmm) REVERT: B 152 ARG cc_start: 0.7970 (mtt180) cc_final: 0.6882 (mmm160) REVERT: B 247 LYS cc_start: 0.8409 (mtmm) cc_final: 0.8113 (ttmm) REVERT: B 366 ASP cc_start: 0.8814 (t0) cc_final: 0.8357 (t0) REVERT: M 60 MET cc_start: 0.8752 (ttp) cc_final: 0.8485 (ttm) outliers start: 25 outliers final: 22 residues processed: 233 average time/residue: 0.3017 time to fit residues: 101.0210 Evaluate side-chains 241 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 216 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 SER Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain K residue 12 LEU Chi-restraints excluded: chain K residue 59 GLU Chi-restraints excluded: chain K residue 212 ILE 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 D residue 113 LEU Chi-restraints excluded: chain D residue 226 SER Chi-restraints excluded: chain G residue 7 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 54 PHE 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 181 SER Chi-restraints excluded: chain B residue 186 SER Chi-restraints excluded: chain B residue 229 GLU Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain M residue 56 MET 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: 30.0000 chunk 97 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 52 optimal weight: 0.9990 chunk 122 optimal weight: 2.9990 chunk 182 optimal weight: 20.0000 chunk 76 optimal weight: 1.9990 chunk 133 optimal weight: 2.9990 chunk 149 optimal weight: 1.9990 chunk 68 optimal weight: 0.9980 chunk 137 optimal weight: 1.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 14 ASN K 31 ASN ** 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 = 0.3289 r_free = 0.3289 target = 0.122904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.100476 restraints weight = 53480.591| |-----------------------------------------------------------------------------| r_work (start): 0.3041 rms_B_bonded: 2.14 r_work: 0.2954 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2835 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.3875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.211 15083 Z= 0.215 Angle : 0.569 10.550 20546 Z= 0.294 Chirality : 0.040 0.152 2284 Planarity : 0.004 0.058 2625 Dihedral : 7.559 179.001 2087 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 1.75 % Allowed : 10.21 % Favored : 88.05 % 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: 0.75 (0.20), residues: 1887 helix: 1.37 (0.17), residues: 973 sheet: -1.21 (0.38), residues: 185 loop : -0.10 (0.24), residues: 729 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 126 TYR 0.011 0.001 TYR A 269 PHE 0.016 0.001 PHE K 89 TRP 0.011 0.001 TRP K 142 HIS 0.005 0.001 HIS D 244 Details of bonding type rmsd covalent geometry : bond 0.00495 (15075) covalent geometry : angle 0.56738 (20544) SS BOND : bond 0.01585 ( 1) SS BOND : angle 4.49420 ( 2) hydrogen bonds : bond 0.04228 ( 838) hydrogen bonds : angle 4.61937 ( 2385) Misc. bond : bond 0.11232 ( 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 249 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 223 time to evaluate : 0.749 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: 0.8913 (t) cc_final: 0.8673 (p) REVERT: A 297 GLU cc_start: 0.8789 (OUTLIER) cc_final: 0.8550 (tt0) REVERT: A 384 SER cc_start: 0.8678 (t) cc_final: 0.8451 (m) REVERT: K 246 TYR cc_start: 0.8845 (m-80) cc_final: 0.8437 (m-80) REVERT: K 272 GLU cc_start: 0.8263 (tt0) cc_final: 0.7859 (mm-30) REVERT: K 310 ARG cc_start: 0.8337 (mmm-85) cc_final: 0.7947 (mtp180) REVERT: K 322 SER cc_start: 0.8546 (t) cc_final: 0.8012 (t) REVERT: D 111 GLU cc_start: 0.7364 (OUTLIER) cc_final: 0.6946 (mp0) REVERT: D 135 TYR cc_start: 0.8695 (m-80) cc_final: 0.8430 (m-80) REVERT: G 56 MET cc_start: 0.8516 (mmm) cc_final: 0.8288 (mmm) REVERT: G 60 ILE cc_start: 0.9205 (OUTLIER) cc_final: 0.8991 (mt) REVERT: G 117 LYS cc_start: 0.8734 (ttmt) cc_final: 0.7402 (mmtt) REVERT: F 21 LYS cc_start: 0.8595 (mmtp) cc_final: 0.8354 (mttm) REVERT: F 73 ARG cc_start: 0.7740 (tmt170) cc_final: 0.7354 (mtt-85) REVERT: F 87 ARG cc_start: 0.8400 (ttp80) cc_final: 0.8155 (ttp80) REVERT: H 91 GLU cc_start: 0.7828 (tp30) cc_final: 0.7580 (tp30) REVERT: B 132 LYS cc_start: 0.8583 (ttpp) cc_final: 0.8321 (ttmm) REVERT: B 144 GLU cc_start: 0.8695 (mm-30) cc_final: 0.8406 (mm-30) REVERT: B 152 ARG cc_start: 0.8003 (mtt180) cc_final: 0.6915 (mmm160) REVERT: B 247 LYS cc_start: 0.8420 (mtmm) cc_final: 0.8132 (ttmm) REVERT: B 366 ASP cc_start: 0.8810 (t0) cc_final: 0.8375 (t0) outliers start: 26 outliers final: 22 residues processed: 235 average time/residue: 0.3080 time to fit residues: 102.7311 Evaluate side-chains 241 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 216 time to evaluate : 0.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 SER Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain A residue 297 GLU Chi-restraints excluded: chain K residue 12 LEU Chi-restraints excluded: chain K residue 212 ILE 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 D residue 113 LEU Chi-restraints excluded: chain D residue 226 SER Chi-restraints excluded: chain G residue 7 SER Chi-restraints excluded: chain G residue 60 ILE 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 85 ASP Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 181 SER Chi-restraints excluded: chain B residue 186 SER Chi-restraints excluded: chain B residue 229 GLU Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain M residue 56 MET Chi-restraints excluded: chain E residue 86 LEU 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: 0.9990 chunk 18 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 153 optimal weight: 0.0570 chunk 109 optimal weight: 0.9990 chunk 60 optimal weight: 0.7980 chunk 13 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 156 optimal weight: 1.9990 chunk 75 optimal weight: 0.9980 chunk 11 optimal weight: 3.9990 overall best weight: 0.7702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 HIS A 129 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 = 0.3315 r_free = 0.3315 target = 0.124769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.105052 restraints weight = 53564.886| |-----------------------------------------------------------------------------| r_work (start): 0.3135 rms_B_bonded: 1.90 r_work: 0.3023 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2907 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.3943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.196 15083 Z= 0.148 Angle : 0.534 9.519 20546 Z= 0.274 Chirality : 0.039 0.210 2284 Planarity : 0.004 0.060 2625 Dihedral : 7.384 178.626 2087 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 1.41 % Allowed : 10.95 % Favored : 87.64 % 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: 0.98 (0.20), residues: 1887 helix: 1.55 (0.17), residues: 979 sheet: -1.16 (0.38), residues: 185 loop : 0.03 (0.25), residues: 723 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 231 TYR 0.016 0.001 TYR D 195 PHE 0.016 0.001 PHE K 89 TRP 0.012 0.001 TRP K 142 HIS 0.003 0.001 HIS K 362 Details of bonding type rmsd covalent geometry : bond 0.00343 (15075) covalent geometry : angle 0.53358 (20544) SS BOND : bond 0.01567 ( 1) SS BOND : angle 3.19978 ( 2) hydrogen bonds : bond 0.03984 ( 838) hydrogen bonds : angle 4.46368 ( 2385) Misc. bond : bond 0.10090 ( 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 238 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 217 time to evaluate : 0.665 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: 0.8865 (t) cc_final: 0.8638 (p) REVERT: A 297 GLU cc_start: 0.8758 (OUTLIER) cc_final: 0.8492 (tt0) REVERT: A 384 SER cc_start: 0.8655 (t) cc_final: 0.8431 (m) REVERT: K 272 GLU cc_start: 0.8219 (tt0) cc_final: 0.7811 (mm-30) REVERT: K 310 ARG cc_start: 0.8304 (mmm-85) cc_final: 0.7919 (mtp180) REVERT: K 322 SER cc_start: 0.8474 (t) cc_final: 0.7946 (t) REVERT: D 111 GLU cc_start: 0.7210 (OUTLIER) cc_final: 0.6812 (mp0) REVERT: D 135 TYR cc_start: 0.8669 (m-80) cc_final: 0.8408 (m-80) REVERT: D 270 ARG cc_start: 0.6597 (mmt180) cc_final: 0.4759 (mtp85) REVERT: G 56 MET cc_start: 0.8467 (mmm) cc_final: 0.8232 (mmm) REVERT: G 60 ILE cc_start: 0.9188 (OUTLIER) cc_final: 0.8959 (mt) REVERT: G 97 GLU cc_start: 0.8383 (tp30) cc_final: 0.8134 (tp30) REVERT: G 117 LYS cc_start: 0.8659 (ttmt) cc_final: 0.7179 (mmpt) REVERT: F 10 TYR cc_start: 0.8901 (m-10) cc_final: 0.8625 (m-10) REVERT: F 21 LYS cc_start: 0.8589 (mmtp) cc_final: 0.8348 (mttm) REVERT: F 73 ARG cc_start: 0.7679 (tmt170) cc_final: 0.7308 (mtt-85) REVERT: H 91 GLU cc_start: 0.7818 (tp30) cc_final: 0.7558 (tp30) REVERT: B 132 LYS cc_start: 0.8538 (ttpp) cc_final: 0.8292 (ttmm) REVERT: B 144 GLU cc_start: 0.8653 (mm-30) cc_final: 0.8315 (mm-30) REVERT: B 152 ARG cc_start: 0.7957 (mtt180) cc_final: 0.6899 (mmm160) REVERT: B 247 LYS cc_start: 0.8388 (mtmm) cc_final: 0.8090 (ttmm) REVERT: B 366 ASP cc_start: 0.8749 (t0) cc_final: 0.8340 (t0) outliers start: 21 outliers final: 16 residues processed: 227 average time/residue: 0.2810 time to fit residues: 92.3768 Evaluate side-chains 233 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 214 time to evaluate : 0.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 297 GLU 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 D residue 226 SER 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 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 181 SER Chi-restraints excluded: chain B residue 186 SER Chi-restraints excluded: chain B residue 229 GLU Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain M residue 56 MET Chi-restraints excluded: chain E residue 86 LEU 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: 0.3980 chunk 36 optimal weight: 3.9990 chunk 4 optimal weight: 0.9980 chunk 61 optimal weight: 0.9990 chunk 51 optimal weight: 0.5980 chunk 32 optimal weight: 2.9990 chunk 84 optimal weight: 0.9980 chunk 106 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 100 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 84 ASN ** 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 = 0.3321 r_free = 0.3321 target = 0.125218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.103181 restraints weight = 53095.550| |-----------------------------------------------------------------------------| r_work (start): 0.3032 rms_B_bonded: 2.11 r_work: 0.2939 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2817 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.3997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.187 15083 Z= 0.149 Angle : 0.538 12.082 20546 Z= 0.276 Chirality : 0.039 0.230 2284 Planarity : 0.004 0.045 2625 Dihedral : 7.331 178.874 2087 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 1.21 % Allowed : 11.35 % Favored : 87.44 % 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: 1.06 (0.20), residues: 1887 helix: 1.64 (0.17), residues: 979 sheet: -1.16 (0.38), residues: 185 loop : 0.04 (0.25), residues: 723 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 231 TYR 0.010 0.001 TYR A 269 PHE 0.016 0.001 PHE K 89 TRP 0.012 0.001 TRP K 142 HIS 0.005 0.001 HIS H 87 Details of bonding type rmsd covalent geometry : bond 0.00348 (15075) covalent geometry : angle 0.53106 (20544) SS BOND : bond 0.00375 ( 1) SS BOND : angle 8.72707 ( 2) hydrogen bonds : bond 0.03935 ( 838) hydrogen bonds : angle 4.42458 ( 2385) Misc. bond : bond 0.09461 ( 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 232 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 214 time to evaluate : 0.732 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: 0.8853 (t) cc_final: 0.8630 (p) REVERT: A 297 GLU cc_start: 0.8810 (OUTLIER) cc_final: 0.8538 (tt0) REVERT: A 384 SER cc_start: 0.8675 (t) cc_final: 0.8442 (m) REVERT: K 246 TYR cc_start: 0.8819 (m-80) cc_final: 0.8398 (m-80) REVERT: K 272 GLU cc_start: 0.8185 (tt0) cc_final: 0.7722 (mm-30) REVERT: K 310 ARG cc_start: 0.8169 (mmm-85) cc_final: 0.7807 (mtp180) REVERT: K 322 SER cc_start: 0.8475 (t) cc_final: 0.7929 (t) REVERT: D 111 GLU cc_start: 0.7084 (OUTLIER) cc_final: 0.6681 (mp0) REVERT: D 135 TYR cc_start: 0.8670 (m-80) cc_final: 0.8401 (m-80) REVERT: D 270 ARG cc_start: 0.6766 (mmt180) cc_final: 0.4824 (mtp85) REVERT: G 56 MET cc_start: 0.8464 (mmm) cc_final: 0.8213 (mmm) REVERT: G 60 ILE cc_start: 0.9155 (OUTLIER) cc_final: 0.8927 (mt) REVERT: G 97 GLU cc_start: 0.8372 (tp30) cc_final: 0.8134 (tp30) REVERT: G 117 LYS cc_start: 0.8603 (ttmt) cc_final: 0.7080 (mmpt) REVERT: F 21 LYS cc_start: 0.8558 (mmtp) cc_final: 0.8328 (mttm) REVERT: F 73 ARG cc_start: 0.7643 (tmt170) cc_final: 0.7204 (mtt-85) REVERT: B 54 PHE cc_start: 0.8965 (OUTLIER) cc_final: 0.7912 (t80) REVERT: B 132 LYS cc_start: 0.8508 (ttpp) cc_final: 0.8251 (ttmm) REVERT: B 144 GLU cc_start: 0.8658 (mm-30) cc_final: 0.8305 (mm-30) REVERT: B 152 ARG cc_start: 0.7983 (mtt180) cc_final: 0.6822 (mmm160) REVERT: B 247 LYS cc_start: 0.8382 (mtmm) cc_final: 0.8074 (ttmm) REVERT: B 366 ASP cc_start: 0.8765 (t0) cc_final: 0.8350 (t0) REVERT: M 60 MET cc_start: 0.8656 (ttp) cc_final: 0.8173 (ttm) outliers start: 18 outliers final: 13 residues processed: 223 average time/residue: 0.3027 time to fit residues: 96.6896 Evaluate side-chains 231 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 214 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 297 GLU Chi-restraints excluded: chain A residue 341 SER 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 7 SER Chi-restraints excluded: chain G residue 60 ILE 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 181 SER Chi-restraints excluded: chain B residue 186 SER Chi-restraints excluded: chain B residue 229 GLU Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain M residue 56 MET 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: 1.9990 chunk 170 optimal weight: 5.9990 chunk 12 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 chunk 174 optimal weight: 6.9990 chunk 122 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 169 optimal weight: 0.8980 chunk 49 optimal weight: 0.8980 chunk 29 optimal weight: 0.5980 chunk 138 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 129 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 = 0.3299 r_free = 0.3299 target = 0.123742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.101386 restraints weight = 53073.832| |-----------------------------------------------------------------------------| r_work (start): 0.3087 rms_B_bonded: 2.14 r_work: 0.2998 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2877 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.4095 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= 0.184 Angle : 0.555 12.871 20546 Z= 0.286 Chirality : 0.040 0.254 2284 Planarity : 0.004 0.045 2625 Dihedral : 7.340 178.797 2087 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 1.07 % Allowed : 11.55 % Favored : 87.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.01 (0.20), residues: 1887 helix: 1.63 (0.17), residues: 980 sheet: -1.22 (0.38), residues: 185 loop : -0.03 (0.24), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 231 TYR 0.015 0.001 TYR A 314 PHE 0.019 0.001 PHE K 89 TRP 0.009 0.001 TRP K 142 HIS 0.004 0.001 HIS K 362 Details of bonding type rmsd covalent geometry : bond 0.00431 (15075) covalent geometry : angle 0.54755 (20544) SS BOND : bond 0.00127 ( 1) SS BOND : angle 9.10422 ( 2) hydrogen bonds : bond 0.04021 ( 838) hydrogen bonds : angle 4.44947 ( 2385) Misc. bond : bond 0.09923 ( 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: 16 poor density : 219 time to evaluate : 0.786 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: A 31 THR cc_start: 0.8894 (t) cc_final: 0.8671 (p) REVERT: A 297 GLU cc_start: 0.8767 (OUTLIER) cc_final: 0.8500 (tt0) REVERT: A 384 SER cc_start: 0.8677 (t) cc_final: 0.8467 (m) REVERT: K 246 TYR cc_start: 0.8843 (m-80) cc_final: 0.8383 (m-80) REVERT: K 272 GLU cc_start: 0.8254 (tt0) cc_final: 0.7850 (mm-30) REVERT: K 310 ARG cc_start: 0.8188 (mmm-85) cc_final: 0.7845 (mtp180) REVERT: D 43 MET cc_start: 0.7660 (ptt) cc_final: 0.7093 (ptp) REVERT: D 111 GLU cc_start: 0.7205 (OUTLIER) cc_final: 0.6816 (mp0) REVERT: D 135 TYR cc_start: 0.8687 (m-80) cc_final: 0.8451 (m-80) REVERT: G 56 MET cc_start: 0.8504 (mmm) cc_final: 0.8259 (mmm) REVERT: G 60 ILE cc_start: 0.9203 (OUTLIER) cc_final: 0.8976 (mt) REVERT: G 97 GLU cc_start: 0.8372 (tp30) cc_final: 0.8133 (tp30) REVERT: G 117 LYS cc_start: 0.8684 (ttmt) cc_final: 0.7285 (mmtt) REVERT: F 10 TYR cc_start: 0.8859 (m-10) cc_final: 0.8494 (m-10) REVERT: F 21 LYS cc_start: 0.8595 (mmtp) cc_final: 0.8365 (mttm) REVERT: F 73 ARG cc_start: 0.7700 (tmt170) cc_final: 0.7365 (mtt-85) REVERT: H 91 GLU cc_start: 0.7852 (tp30) cc_final: 0.7503 (tp30) REVERT: B 54 PHE cc_start: 0.9006 (OUTLIER) cc_final: 0.7998 (t80) REVERT: B 132 LYS cc_start: 0.8587 (ttpp) cc_final: 0.8323 (ttmm) REVERT: B 144 GLU cc_start: 0.8679 (mm-30) cc_final: 0.8316 (mm-30) REVERT: B 152 ARG cc_start: 0.7956 (mtt180) cc_final: 0.6878 (mmm160) REVERT: B 247 LYS cc_start: 0.8446 (mtmm) cc_final: 0.8164 (ttmm) REVERT: B 366 ASP cc_start: 0.8764 (t0) cc_final: 0.8359 (t0) outliers start: 16 outliers final: 12 residues processed: 227 average time/residue: 0.3202 time to fit residues: 103.2738 Evaluate side-chains 234 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 218 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 297 GLU Chi-restraints excluded: chain A residue 341 SER 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 7 SER Chi-restraints excluded: chain G residue 60 ILE 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 181 SER Chi-restraints excluded: chain B residue 186 SER Chi-restraints excluded: chain B residue 229 GLU Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain M residue 56 MET 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: 0.0670 chunk 21 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 181 optimal weight: 20.0000 chunk 183 optimal weight: 20.0000 chunk 77 optimal weight: 0.2980 chunk 150 optimal weight: 0.9990 chunk 155 optimal weight: 0.6980 chunk 175 optimal weight: 10.0000 chunk 161 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 overall best weight: 0.8122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.124473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.104689 restraints weight = 53191.135| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 1.91 r_work: 0.2954 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2835 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.4133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.184 15083 Z= 0.148 Angle : 0.534 10.948 20546 Z= 0.272 Chirality : 0.039 0.243 2284 Planarity : 0.004 0.055 2625 Dihedral : 7.188 173.600 2087 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 1.21 % Allowed : 11.75 % Favored : 87.04 % 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: 1.14 (0.20), residues: 1887 helix: 1.75 (0.17), residues: 978 sheet: -1.16 (0.38), residues: 185 loop : 0.02 (0.25), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 231 TYR 0.010 0.001 TYR F 82 PHE 0.017 0.001 PHE K 89 TRP 0.011 0.001 TRP K 142 HIS 0.004 0.001 HIS D 244 Details of bonding type rmsd covalent geometry : bond 0.00345 (15075) covalent geometry : angle 0.52801 (20544) SS BOND : bond 0.00031 ( 1) SS BOND : angle 7.80902 ( 2) hydrogen bonds : bond 0.03871 ( 838) hydrogen bonds : angle 4.36163 ( 2385) Misc. bond : bond 0.09042 ( 7) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6263.22 seconds wall clock time: 107 minutes 7.30 seconds (6427.30 seconds total)