Starting phenix.real_space_refine on Sun Jul 5 15:36:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7rjd_24485/07_2026/7rjd_24485_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rjd_24485/07_2026/7rjd_24485.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7rjd_24485/07_2026/7rjd_24485.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rjd_24485/07_2026/7rjd_24485.map" model { file = "/net/cci-nas-00/data/ceres_data/7rjd_24485/07_2026/7rjd_24485_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rjd_24485/07_2026/7rjd_24485_trim.cif" } resolution = 3.2 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= 0.184 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 9501 2.51 5 N 2452 2.21 5 O 2749 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 26 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 28415 Number of models: 1 Model: "" Number of chains: 13 Chain: "E" Number of atoms: 706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 706 Classifications: {'peptide': 137} Incomplete info: {'truncation_to_alanine': 103} Link IDs: {'PTRANS': 9, 'TRANS': 127} 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: "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} 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: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 137 Unusual residues: {'HEM': 2, 'U10': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 90 Unresolved non-hydrogen dihedrals: 90 Planarities with less than four sites: {'U10:plan-3': 2, 'U10:plan-4': 2, 'U10:plan-5': 2, 'U10:plan-6': 2, 'U10:plan-7': 2, 'U10:plan-8': 2, 'U10:plan-9': 2, 'U10:plan-2': 1} Unresolved non-hydrogen planarities: 75 Chain: "D" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEC': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.70, per 1000 atoms: 0.13 Number of scatterers: 28415 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 2749 8.00 N 2452 7.00 C 9501 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: 1.96 Conformation dependent library (CDL) restraints added in 751.7 milliseconds 3784 Ramachandran restraints generated. 1892 Oldfield, 0 Emsley, 1892 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3588 Finding SS restraints... Secondary structure from input PDB file: 91 helices and 11 sheets defined 59.5% alpha, 8.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.75 Creating SS restraints... Processing helix chain 'E' and resid 76 through 80 Processing helix chain 'E' and resid 119 through 129 Processing helix chain 'E' and resid 139 through 144 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 sheet with id=AA1, first strand: chain 'E' and resid 93 through 94 Processing sheet with id=AA2, first strand: chain 'E' and resid 107 through 108 Processing sheet with id=AA3, first strand: chain 'E' and resid 173 through 175 Processing sheet with id=AA4, 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=AA5, 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=AA6, first strand: chain 'K' and resid 22 through 23 Processing sheet with id=AA7, 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=AA8, first strand: chain 'D' and resid 194 through 195 Processing sheet with id=AA9, 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=AB1, 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=AB2, first strand: chain 'B' and resid 229 through 233 841 hydrogen bonds defined for protein. 2364 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: 6.21 Time building geometry restraints manager: 2.89 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: 6311 1.41 - 1.70: 8730 1.70 - 1.98: 72 1.98 - 2.27: 15 Bond restraints: 28783 Sorted by residual: bond pdb=" C CYS D 82 " pdb=" O CYS D 82 " ideal model delta sigma weight residual 1.237 1.076 0.161 1.17e-02 7.31e+03 1.89e+02 bond pdb=" C2D HEC D 301 " pdb=" C3D HEC D 301 " ideal model delta sigma weight residual 1.544 1.332 0.212 2.00e-02 2.50e+03 1.13e+02 bond pdb=" CAB HEC D 301 " pdb=" CBB HEC D 301 " ideal model delta sigma weight residual 1.544 1.332 0.212 2.00e-02 2.50e+03 1.12e+02 bond pdb=" CAC HEC D 301 " pdb=" CBC HEC D 301 " ideal model delta sigma weight residual 1.544 1.336 0.208 2.00e-02 2.50e+03 1.08e+02 bond pdb=" C13 U10 K 404 " pdb=" C14 U10 K 404 " ideal model delta sigma weight residual 1.335 1.475 -0.140 2.00e-02 2.50e+03 4.87e+01 ... (remaining 28778 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.54: 51425 3.54 - 7.09: 194 7.09 - 10.63: 12 10.63 - 14.18: 9 14.18 - 17.72: 4 Bond angle restraints: 51644 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 86.61 17.72 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 88.18 16.15 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 89.77 -14.11 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 51639 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.28: 13352 35.28 - 70.56: 320 70.56 - 105.84: 33 105.84 - 141.12: 0 141.12 - 176.40: 1 Dihedral angle restraints: 13706 sinusoidal: 7061 harmonic: 6645 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 -139.06 16.46 0 2.50e+00 1.60e-01 4.33e+01 dihedral pdb=" C2B HEC D 301 " pdb=" C3B HEC D 301 " pdb=" CAB HEC D 301 " pdb=" CBB HEC D 301 " ideal model delta sinusoidal sigma weight residual -120.00 -168.78 48.78 2 1.00e+01 1.00e-02 2.72e+01 ... (remaining 13703 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.103: 2158 0.103 - 0.206: 105 0.206 - 0.309: 21 0.309 - 0.411: 4 0.411 - 0.514: 2 Chirality restraints: 2290 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 6.61e+00 chirality pdb=" CA TRP E 108 " pdb=" N TRP E 108 " pdb=" C TRP E 108 " pdb=" CB TRP E 108 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.62e+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 3.94e+00 ... (remaining 2287 not shown) Planarity restraints: 4308 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 U10 K 403 " -0.112 2.00e-02 2.50e+03 1.80e-01 9.70e+02 pdb=" C1M U10 K 403 " -0.252 2.00e-02 2.50e+03 pdb=" C2 U10 K 403 " 0.020 2.00e-02 2.50e+03 pdb=" C3 U10 K 403 " 0.148 2.00e-02 2.50e+03 pdb=" C4 U10 K 403 " 0.162 2.00e-02 2.50e+03 pdb=" C5 U10 K 403 " 0.028 2.00e-02 2.50e+03 pdb=" C6 U10 K 403 " -0.100 2.00e-02 2.50e+03 pdb=" C7 U10 K 403 " 0.086 2.00e-02 2.50e+03 pdb=" O2 U10 K 403 " 0.336 2.00e-02 2.50e+03 pdb=" O3 U10 K 403 " -0.217 2.00e-02 2.50e+03 pdb=" O4 U10 K 403 " -0.250 2.00e-02 2.50e+03 pdb=" O5 U10 K 403 " 0.150 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1 U10 K 404 " -0.110 2.00e-02 2.50e+03 1.68e-01 8.44e+02 pdb=" C1M U10 K 404 " -0.227 2.00e-02 2.50e+03 pdb=" C2 U10 K 404 " 0.039 2.00e-02 2.50e+03 pdb=" C3 U10 K 404 " 0.137 2.00e-02 2.50e+03 pdb=" C4 U10 K 404 " 0.132 2.00e-02 2.50e+03 pdb=" C5 U10 K 404 " -0.019 2.00e-02 2.50e+03 pdb=" C6 U10 K 404 " -0.120 2.00e-02 2.50e+03 pdb=" C7 U10 K 404 " 0.188 2.00e-02 2.50e+03 pdb=" O2 U10 K 404 " 0.313 2.00e-02 2.50e+03 pdb=" O3 U10 K 404 " -0.295 2.00e-02 2.50e+03 pdb=" O4 U10 K 404 " -0.014 2.00e-02 2.50e+03 pdb=" O5 U10 K 404 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 U10 K 404 " 0.011 2.00e-02 2.50e+03 6.69e-02 5.60e+01 pdb=" C11 U10 K 404 " -0.066 2.00e-02 2.50e+03 pdb=" C7 U10 K 404 " -0.081 2.00e-02 2.50e+03 pdb=" C8 U10 K 404 " 0.099 2.00e-02 2.50e+03 pdb=" C9 U10 K 404 " 0.037 2.00e-02 2.50e+03 ... (remaining 4305 not shown) Histogram of nonbonded interaction distances: 1.10 - 1.80: 97 1.80 - 2.50: 21122 2.50 - 3.20: 89403 3.20 - 3.90: 116928 3.90 - 4.60: 184778 Nonbonded interactions: 412328 Sorted by model distance: 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=" CB THR E 157 " pdb="FE1 FES E 301 " model vdw 1.342 3.180 nonbonded pdb="HD11 LEU D 261 " pdb=" HG3 MET M 60 " model vdw 1.488 2.440 ... (remaining 412323 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: 2.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.180 Extract box with map and model: 0.400 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 25.200 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5845 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.315 15127 Z= 0.440 Angle : 0.860 17.723 20605 Z= 0.548 Chirality : 0.054 0.514 2290 Planarity : 0.007 0.180 2632 Dihedral : 13.415 176.404 5287 Min Nonbonded Distance : 1.342 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.42 % Allowed : 4.55 % Favored : 95.03 % Rotamer: Outliers : 0.27 % Allowed : 0.40 % Favored : 99.33 % Cbeta Deviations : 0.22 % 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: 0.07 (0.20), residues: 1892 helix: 0.53 (0.17), residues: 970 sheet: -0.85 (0.38), residues: 174 loop : -0.17 (0.24), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 282 TYR 0.023 0.002 TYR K 132 PHE 0.068 0.002 PHE K 184 TRP 0.012 0.001 TRP K 142 HIS 0.037 0.001 HIS K 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00786 / 0.44 (15119) covalent geometry : angle 0.85955 / 0.55 (20603) SS BOND : bond 0.00034 / 0.02 ( 1) SS BOND : angle 0.75220 / 0.41 ( 2) hydrogen bonds : bond 0.14006 / 10.18 ( 833) hydrogen bonds : angle 6.55424 / 4.89 ( 2364) Misc. bond : bond 0.12128 / 6.12 ( 7) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3784 Ramachandran restraints generated. 1892 Oldfield, 0 Emsley, 1892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3784 Ramachandran restraints generated. 1892 Oldfield, 0 Emsley, 1892 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 363 residues out of total 1611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 359 time to evaluate : 0.752 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 167 THR cc_start: 0.8714 (p) cc_final: 0.8430 (t) REVERT: A 185 LYS cc_start: 0.7333 (tttp) cc_final: 0.7036 (ttpp) REVERT: A 405 LYS cc_start: 0.7164 (mmtt) cc_final: 0.6729 (mttt) REVERT: A 406 SER cc_start: 0.8114 (t) cc_final: 0.7911 (p) REVERT: A 411 ARG cc_start: 0.7726 (mmm-85) cc_final: 0.6689 (mmt-90) REVERT: A 433 GLU cc_start: 0.7015 (mm-30) cc_final: 0.6566 (mm-30) REVERT: K 299 ILE cc_start: 0.7823 (mt) cc_final: 0.7611 (mt) REVERT: D 80 GLU cc_start: 0.7547 (mm-30) cc_final: 0.7076 (mm-30) REVERT: D 194 ASN cc_start: 0.5114 (m-40) cc_final: 0.4245 (t0) REVERT: D 230 LYS cc_start: 0.5994 (ttpt) cc_final: 0.5585 (tttp) REVERT: F 52 ARG cc_start: 0.5231 (mtm180) cc_final: 0.4103 (mtp85) REVERT: I 40 GLU cc_start: 0.7022 (tm-30) cc_final: 0.5987 (mm-30) REVERT: B 362 VAL cc_start: 0.6986 (t) cc_final: 0.6538 (t) REVERT: B 364 ASP cc_start: 0.4918 (t0) cc_final: 0.4560 (t70) outliers start: 4 outliers final: 0 residues processed: 362 average time/residue: 0.2584 time to fit residues: 135.4271 Evaluate side-chains 237 residues out of total 1611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 237 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 20.0000 chunk 66 optimal weight: 0.5980 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 1.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 336 ASN A 381 HIS K 84 ASN K 350 GLN F 56 GLN H 85 HIS I 49 ASN B 157 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.166992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.148724 restraints weight = 50548.126| |-----------------------------------------------------------------------------| r_work (start): 0.3573 rms_B_bonded: 1.61 r_work: 0.3462 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3359 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.2717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.357 15127 Z= 0.196 Angle : 0.622 20.231 20605 Z= 0.318 Chirality : 0.041 0.164 2290 Planarity : 0.005 0.054 2632 Dihedral : 7.866 175.483 2093 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 1.41 % Allowed : 7.10 % Favored : 91.50 % 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: 0.45 (0.19), residues: 1892 helix: 0.94 (0.16), residues: 978 sheet: -0.84 (0.38), residues: 172 loop : -0.12 (0.24), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 72 TYR 0.017 0.002 TYR D 78 PHE 0.016 0.001 PHE D 75 TRP 0.011 0.001 TRP K 142 HIS 0.007 0.001 HIS K 362 Details of bonding type rmsd/Z covalent geometry : bond 0.00413 / 0.19 (15119) covalent geometry : angle 0.62211 / 0.32 (20603) SS BOND : bond 0.00193 / 0.10 ( 1) SS BOND : angle 0.40490 / 0.22 ( 2) hydrogen bonds : bond 0.04532 / 3.41 ( 833) hydrogen bonds : angle 4.88937 / 3.62 ( 2364) Misc. bond : bond 0.15640 / 7.79 ( 7) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3784 Ramachandran restraints generated. 1892 Oldfield, 0 Emsley, 1892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3784 Ramachandran restraints generated. 1892 Oldfield, 0 Emsley, 1892 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 295 residues out of total 1611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 274 time to evaluate : 0.707 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 100 ASN cc_start: 0.7264 (t0) cc_final: 0.6961 (t0) REVERT: A 433 GLU cc_start: 0.7451 (mm-30) cc_final: 0.6988 (mm-30) REVERT: K 69 MET cc_start: 0.8068 (mmm) cc_final: 0.7627 (mmm) REVERT: K 299 ILE cc_start: 0.8616 (mt) cc_final: 0.8335 (mt) REVERT: D 150 ASN cc_start: 0.7590 (m-40) cc_final: 0.7233 (m-40) REVERT: D 194 ASN cc_start: 0.6151 (m-40) cc_final: 0.5651 (t0) REVERT: D 231 ASP cc_start: 0.7990 (m-30) cc_final: 0.7512 (m-30) REVERT: D 265 SER cc_start: 0.8800 (OUTLIER) cc_final: 0.8505 (p) REVERT: G 40 GLU cc_start: 0.7864 (mp0) cc_final: 0.7573 (mm-30) REVERT: F 52 ARG cc_start: 0.5939 (mtm180) cc_final: 0.4566 (mtp85) REVERT: H 110 ASP cc_start: 0.7317 (p0) cc_final: 0.7098 (p0) REVERT: I 40 GLU cc_start: 0.7208 (tm-30) cc_final: 0.6823 (mp0) outliers start: 21 outliers final: 15 residues processed: 283 average time/residue: 0.2163 time to fit residues: 93.5192 Evaluate side-chains 262 residues out of total 1611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 246 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 HIS Chi-restraints excluded: chain A residue 361 GLU Chi-restraints excluded: chain K residue 145 THR Chi-restraints excluded: chain K residue 206 SER Chi-restraints excluded: chain K residue 353 GLN Chi-restraints excluded: chain D residue 157 ASP Chi-restraints excluded: chain D residue 221 THR Chi-restraints excluded: chain D residue 265 SER Chi-restraints excluded: chain G residue 58 THR Chi-restraints excluded: chain G residue 98 GLU Chi-restraints excluded: chain H residue 88 GLU Chi-restraints excluded: chain H residue 104 HIS Chi-restraints excluded: chain B residue 54 PHE Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 299 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 94 optimal weight: 2.9990 chunk 58 optimal weight: 0.5980 chunk 38 optimal weight: 1.9990 chunk 75 optimal weight: 0.5980 chunk 1 optimal weight: 0.4980 chunk 170 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 7 optimal weight: 7.9990 chunk 30 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 57 ASN K 84 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.146462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.128006 restraints weight = 50117.930| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 1.51 r_work: 0.3226 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.3130 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.4399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.345 15127 Z= 0.217 Angle : 0.624 16.237 20605 Z= 0.316 Chirality : 0.041 0.203 2290 Planarity : 0.004 0.080 2632 Dihedral : 7.799 177.030 2093 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 2.14 % Allowed : 8.30 % Favored : 89.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.20), residues: 1892 helix: 1.12 (0.16), residues: 981 sheet: -0.99 (0.38), residues: 173 loop : -0.17 (0.25), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 87 TYR 0.020 0.002 TYR K 358 PHE 0.014 0.001 PHE K 240 TRP 0.013 0.001 TRP K 142 HIS 0.016 0.001 HIS D 48 Details of bonding type rmsd/Z covalent geometry : bond 0.00488 / 0.22 (15119) covalent geometry : angle 0.62373 / 0.32 (20603) SS BOND : bond 0.00066 / 0.03 ( 1) SS BOND : angle 0.15906 / 0.09 ( 2) hydrogen bonds : bond 0.04586 / 3.44 ( 833) hydrogen bonds : angle 4.81119 / 3.56 ( 2364) Misc. bond : bond 0.14533 / 7.20 ( 7) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3784 Ramachandran restraints generated. 1892 Oldfield, 0 Emsley, 1892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3784 Ramachandran restraints generated. 1892 Oldfield, 0 Emsley, 1892 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 277 residues out of total 1611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 245 time to evaluate : 0.808 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: E 75 PHE cc_start: 0.6882 (OUTLIER) cc_final: 0.6275 (t80) REVERT: A 173 ASN cc_start: 0.7438 (t0) cc_final: 0.7202 (t0) REVERT: K 69 MET cc_start: 0.8414 (mmm) cc_final: 0.7901 (mmm) REVERT: K 179 PHE cc_start: 0.8701 (m-10) cc_final: 0.8480 (m-10) REVERT: K 353 GLN cc_start: 0.8120 (OUTLIER) cc_final: 0.7812 (mt0) REVERT: K 356 THR cc_start: 0.8600 (m) cc_final: 0.8400 (m) REVERT: D 231 ASP cc_start: 0.8359 (m-30) cc_final: 0.8104 (m-30) REVERT: G 40 GLU cc_start: 0.8083 (mp0) cc_final: 0.7867 (mm-30) REVERT: G 47 ASP cc_start: 0.8571 (m-30) cc_final: 0.8311 (m-30) REVERT: G 56 MET cc_start: 0.8849 (tpp) cc_final: 0.8623 (mmm) REVERT: G 86 GLN cc_start: 0.8036 (pt0) cc_final: 0.7582 (pt0) REVERT: F 88 GLU cc_start: 0.7266 (tp30) cc_final: 0.6905 (tp30) REVERT: I 40 GLU cc_start: 0.7339 (tm-30) cc_final: 0.7060 (mp0) outliers start: 32 outliers final: 18 residues processed: 262 average time/residue: 0.2437 time to fit residues: 99.1937 Evaluate side-chains 243 residues out of total 1611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 223 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 75 PHE Chi-restraints excluded: chain A residue 57 HIS Chi-restraints excluded: chain A residue 343 SER Chi-restraints excluded: chain A residue 361 GLU Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 406 SER Chi-restraints excluded: chain K residue 145 THR Chi-restraints excluded: chain K residue 206 SER Chi-restraints excluded: chain K residue 312 ILE Chi-restraints excluded: chain K residue 353 GLN Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain D residue 221 THR Chi-restraints excluded: chain G residue 60 ILE Chi-restraints excluded: chain G residue 98 GLU Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain B residue 52 SER Chi-restraints excluded: chain B residue 54 PHE Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 246 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 0 optimal weight: 3.9990 chunk 166 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 chunk 165 optimal weight: 1.9990 chunk 155 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 chunk 44 optimal weight: 0.9990 chunk 115 optimal weight: 0.9990 chunk 117 optimal weight: 0.6980 chunk 157 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 150 ASN D 151 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.150854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.131835 restraints weight = 48584.895| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 1.32 r_work: 0.3174 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.3082 rms_B_bonded: 2.72 restraints_weight: 0.2500 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.5326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.269 15127 Z= 0.167 Angle : 0.556 15.466 20605 Z= 0.281 Chirality : 0.039 0.148 2290 Planarity : 0.004 0.050 2632 Dihedral : 7.791 179.490 2093 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.81 % Allowed : 9.97 % Favored : 88.22 % 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: 0.72 (0.20), residues: 1892 helix: 1.33 (0.16), residues: 985 sheet: -0.97 (0.38), residues: 169 loop : -0.21 (0.24), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 411 TYR 0.014 0.001 TYR K 279 PHE 0.012 0.001 PHE H 86 TRP 0.010 0.001 TRP K 142 HIS 0.004 0.001 HIS D 59 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.17 (15119) covalent geometry : angle 0.55619 / 0.28 (20603) SS BOND : bond 0.00165 / 0.09 ( 1) SS BOND : angle 0.53737 / 0.29 ( 2) hydrogen bonds : bond 0.03964 / 3.01 ( 833) hydrogen bonds : angle 4.58924 / 3.40 ( 2364) Misc. bond : bond 0.11564 / 5.72 ( 7) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3784 Ramachandran restraints generated. 1892 Oldfield, 0 Emsley, 1892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3784 Ramachandran restraints generated. 1892 Oldfield, 0 Emsley, 1892 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 274 residues out of total 1611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 247 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: E 84 ASP cc_start: 0.7904 (t0) cc_final: 0.7619 (t0) REVERT: A 173 ASN cc_start: 0.7320 (t0) cc_final: 0.7048 (t0) REVERT: K 69 MET cc_start: 0.8472 (mmm) cc_final: 0.8008 (mmt) REVERT: K 112 MET cc_start: 0.7912 (ttp) cc_final: 0.7590 (ttt) REVERT: K 299 ILE cc_start: 0.8774 (mt) cc_final: 0.8533 (mp) REVERT: K 353 GLN cc_start: 0.8370 (OUTLIER) cc_final: 0.7979 (mt0) REVERT: D 231 ASP cc_start: 0.8443 (m-30) cc_final: 0.8239 (m-30) REVERT: G 47 ASP cc_start: 0.8582 (m-30) cc_final: 0.8354 (m-30) REVERT: G 56 MET cc_start: 0.8882 (tpp) cc_final: 0.8666 (mmm) REVERT: G 86 GLN cc_start: 0.8106 (pt0) cc_final: 0.7880 (pt0) REVERT: F 88 GLU cc_start: 0.7343 (tp30) cc_final: 0.7029 (tp30) REVERT: H 67 ASP cc_start: 0.7268 (m-30) cc_final: 0.7008 (m-30) REVERT: B 343 LEU cc_start: 0.8305 (OUTLIER) cc_final: 0.7884 (mp) outliers start: 27 outliers final: 16 residues processed: 260 average time/residue: 0.2258 time to fit residues: 90.1026 Evaluate side-chains 244 residues out of total 1611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 226 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 HIS Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 361 GLU Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain K residue 206 SER Chi-restraints excluded: chain K residue 353 GLN Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 226 SER Chi-restraints excluded: chain G residue 60 ILE Chi-restraints excluded: chain B residue 52 SER Chi-restraints excluded: chain B residue 54 PHE Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 312 SER Chi-restraints excluded: chain B residue 343 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 22 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 134 optimal weight: 1.9990 chunk 132 optimal weight: 4.9990 chunk 97 optimal weight: 1.9990 chunk 69 optimal weight: 3.9990 chunk 176 optimal weight: 3.9990 chunk 39 optimal weight: 0.8980 chunk 55 optimal weight: 1.9990 chunk 173 optimal weight: 1.9990 chunk 144 optimal weight: 3.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 428 ASN D 150 ASN I 49 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.131364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.113722 restraints weight = 49967.045| |-----------------------------------------------------------------------------| r_work (start): 0.3138 rms_B_bonded: 1.44 r_work: 0.3019 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.2921 rms_B_bonded: 2.94 restraints_weight: 0.2500 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.6325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.302 15127 Z= 0.290 Angle : 0.642 14.485 20605 Z= 0.330 Chirality : 0.043 0.149 2290 Planarity : 0.005 0.076 2632 Dihedral : 7.748 176.831 2093 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 2.14 % Allowed : 10.71 % Favored : 87.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.19), residues: 1892 helix: 1.05 (0.16), residues: 993 sheet: -1.13 (0.39), residues: 165 loop : -0.50 (0.24), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 411 TYR 0.017 0.002 TYR K 16 PHE 0.015 0.002 PHE K 90 TRP 0.012 0.002 TRP K 142 HIS 0.007 0.001 HIS K 362 Details of bonding type rmsd/Z covalent geometry : bond 0.00667 / 0.29 (15119) covalent geometry : angle 0.64154 / 0.33 (20603) SS BOND : bond 0.00143 / 0.08 ( 1) SS BOND : angle 0.38005 / 0.20 ( 2) hydrogen bonds : bond 0.04581 / 3.46 ( 833) hydrogen bonds : angle 4.82173 / 3.58 ( 2364) Misc. bond : bond 0.13101 / 6.48 ( 7) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3784 Ramachandran restraints generated. 1892 Oldfield, 0 Emsley, 1892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3784 Ramachandran restraints generated. 1892 Oldfield, 0 Emsley, 1892 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 255 residues out of total 1611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 223 time to evaluate : 0.756 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: E 75 PHE cc_start: 0.6869 (OUTLIER) cc_final: 0.6088 (t80) REVERT: E 84 ASP cc_start: 0.8318 (t0) cc_final: 0.8027 (t0) REVERT: A 173 ASN cc_start: 0.7448 (t0) cc_final: 0.7169 (t0) REVERT: A 222 GLU cc_start: 0.7962 (mp0) cc_final: 0.7725 (mp0) REVERT: A 341 SER cc_start: 0.8645 (m) cc_final: 0.8365 (t) REVERT: K 353 GLN cc_start: 0.8434 (OUTLIER) cc_final: 0.8190 (mt0) REVERT: K 365 ILE cc_start: 0.8680 (mm) cc_final: 0.8372 (mt) REVERT: D 231 ASP cc_start: 0.8730 (m-30) cc_final: 0.8523 (m-30) REVERT: G 30 GLN cc_start: 0.8559 (OUTLIER) cc_final: 0.7788 (mt0) REVERT: G 47 ASP cc_start: 0.8756 (m-30) cc_final: 0.8456 (m-30) REVERT: G 57 GLN cc_start: 0.8358 (tp40) cc_final: 0.8151 (mm-40) REVERT: G 86 GLN cc_start: 0.8162 (pt0) cc_final: 0.7697 (pt0) REVERT: B 343 LEU cc_start: 0.8462 (OUTLIER) cc_final: 0.7991 (mp) REVERT: M 56 MET cc_start: 0.7965 (mmm) cc_final: 0.7717 (mmt) outliers start: 32 outliers final: 22 residues processed: 242 average time/residue: 0.2284 time to fit residues: 84.0002 Evaluate side-chains 236 residues out of total 1611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 210 time to evaluate : 0.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 75 PHE Chi-restraints excluded: chain A residue 57 HIS Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 343 SER Chi-restraints excluded: chain A residue 406 SER Chi-restraints excluded: chain K residue 145 THR Chi-restraints excluded: chain K residue 206 SER Chi-restraints excluded: chain K residue 312 ILE Chi-restraints excluded: chain K residue 353 GLN Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain D residue 206 MET Chi-restraints excluded: chain G residue 30 GLN Chi-restraints excluded: chain G residue 60 ILE Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 104 HIS Chi-restraints excluded: chain B residue 15 ASN Chi-restraints excluded: chain B residue 52 SER Chi-restraints excluded: chain B residue 54 PHE Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 312 SER Chi-restraints excluded: chain B residue 343 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 30 optimal weight: 1.9990 chunk 102 optimal weight: 0.6980 chunk 108 optimal weight: 0.6980 chunk 12 optimal weight: 4.9990 chunk 56 optimal weight: 0.9990 chunk 62 optimal weight: 0.0570 chunk 61 optimal weight: 0.9990 chunk 94 optimal weight: 1.9990 chunk 170 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 162 optimal weight: 1.9990 overall best weight: 0.6902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 253 HIS B 59 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.133851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.116105 restraints weight = 49212.090| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 1.37 r_work: 0.3066 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.2969 rms_B_bonded: 2.84 restraints_weight: 0.2500 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.6605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.273 15127 Z= 0.136 Angle : 0.530 12.684 20605 Z= 0.267 Chirality : 0.038 0.150 2290 Planarity : 0.004 0.045 2632 Dihedral : 7.525 179.650 2093 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 1.81 % Allowed : 12.58 % Favored : 85.61 % 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: 0.71 (0.20), residues: 1892 helix: 1.37 (0.16), residues: 993 sheet: -0.95 (0.40), residues: 162 loop : -0.33 (0.24), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 411 TYR 0.012 0.001 TYR D 140 PHE 0.012 0.001 PHE A 327 TRP 0.012 0.001 TRP K 142 HIS 0.004 0.001 HIS K 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.13 (15119) covalent geometry : angle 0.52965 / 0.27 (20603) SS BOND : bond 0.00190 / 0.10 ( 1) SS BOND : angle 0.63320 / 0.33 ( 2) hydrogen bonds : bond 0.03898 / 2.95 ( 833) hydrogen bonds : angle 4.50231 / 3.33 ( 2364) Misc. bond : bond 0.12584 / 6.20 ( 7) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3784 Ramachandran restraints generated. 1892 Oldfield, 0 Emsley, 1892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3784 Ramachandran restraints generated. 1892 Oldfield, 0 Emsley, 1892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 112 is missing expected H atoms. Skipping. Residue LYS 124 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue TYR 43 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue SER 214 is missing expected H atoms. Skipping. Residue LYS 218 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue TYR 32 is missing expected H atoms. Skipping. Evaluate side-chains 251 residues out of total 1611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 224 time to evaluate : 0.600 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 ASN cc_start: 0.7399 (t0) cc_final: 0.7161 (t0) REVERT: A 341 SER cc_start: 0.8701 (m) cc_final: 0.8312 (t) REVERT: K 353 GLN cc_start: 0.8332 (OUTLIER) cc_final: 0.8086 (mt0) REVERT: K 375 ASN cc_start: 0.8154 (m-40) cc_final: 0.7910 (m-40) REVERT: D 105 GLU cc_start: 0.7671 (OUTLIER) cc_final: 0.7439 (tt0) REVERT: D 231 ASP cc_start: 0.8729 (m-30) cc_final: 0.8322 (m-30) REVERT: G 86 GLN cc_start: 0.8225 (pt0) cc_final: 0.7781 (pt0) REVERT: F 89 GLU cc_start: 0.7677 (tp30) cc_final: 0.7243 (tt0) REVERT: B 343 LEU cc_start: 0.8424 (OUTLIER) cc_final: 0.7974 (mp) outliers start: 27 outliers final: 22 residues processed: 236 average time/residue: 0.2413 time to fit residues: 87.5815 Evaluate side-chains 235 residues out of total 1611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 210 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 57 HIS Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 406 SER Chi-restraints excluded: chain A residue 428 ASN Chi-restraints excluded: chain K residue 208 ASN Chi-restraints excluded: chain K residue 353 GLN Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 105 GLU Chi-restraints excluded: chain D residue 206 MET Chi-restraints excluded: chain D residue 226 SER Chi-restraints excluded: chain G residue 10 LYS Chi-restraints excluded: chain G residue 60 ILE Chi-restraints excluded: chain H residue 104 HIS Chi-restraints excluded: chain H residue 106 HIS Chi-restraints excluded: chain B residue 52 SER Chi-restraints excluded: chain B residue 54 PHE Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 80 SER Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 181 SER Chi-restraints excluded: chain B residue 203 GLU Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 276 ILE Chi-restraints excluded: chain B residue 343 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 157 optimal weight: 0.9980 chunk 105 optimal weight: 1.9990 chunk 174 optimal weight: 0.5980 chunk 36 optimal weight: 2.9990 chunk 93 optimal weight: 0.3980 chunk 96 optimal weight: 3.9990 chunk 87 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 88 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 237 ASN ** 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 = 0.3386 r_free = 0.3386 target = 0.132178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.114352 restraints weight = 49487.991| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 1.39 r_work: 0.3048 rms_B_bonded: 1.63 restraints_weight: 0.5000 r_work: 0.2951 rms_B_bonded: 2.85 restraints_weight: 0.2500 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.6869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.233 15127 Z= 0.154 Angle : 0.533 13.481 20605 Z= 0.268 Chirality : 0.039 0.148 2290 Planarity : 0.004 0.052 2632 Dihedral : 7.302 178.865 2093 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 1.61 % Allowed : 12.45 % Favored : 85.94 % 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: 0.90 (0.20), residues: 1892 helix: 1.54 (0.17), residues: 995 sheet: -0.97 (0.40), residues: 167 loop : -0.23 (0.24), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 411 TYR 0.011 0.001 TYR K 358 PHE 0.012 0.001 PHE K 90 TRP 0.012 0.001 TRP K 142 HIS 0.004 0.001 HIS D 48 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.15 (15119) covalent geometry : angle 0.53273 / 0.27 (20603) SS BOND : bond 0.00186 / 0.10 ( 1) SS BOND : angle 0.46797 / 0.25 ( 2) hydrogen bonds : bond 0.03877 / 2.93 ( 833) hydrogen bonds : angle 4.42816 / 3.28 ( 2364) Misc. bond : bond 0.10914 / 5.37 ( 7) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3784 Ramachandran restraints generated. 1892 Oldfield, 0 Emsley, 1892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3784 Ramachandran restraints generated. 1892 Oldfield, 0 Emsley, 1892 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 241 residues out of total 1611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 217 time to evaluate : 0.669 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 ASN cc_start: 0.7380 (t0) cc_final: 0.7143 (t0) REVERT: A 222 GLU cc_start: 0.7832 (mp0) cc_final: 0.7592 (mp0) REVERT: A 341 SER cc_start: 0.8769 (m) cc_final: 0.8445 (t) REVERT: D 240 SER cc_start: 0.9140 (t) cc_final: 0.8836 (m) REVERT: G 61 LYS cc_start: 0.8602 (ttpt) cc_final: 0.8273 (tttt) REVERT: G 86 GLN cc_start: 0.8216 (pt0) cc_final: 0.7838 (pt0) REVERT: F 89 GLU cc_start: 0.7683 (tp30) cc_final: 0.7268 (tt0) REVERT: H 114 GLU cc_start: 0.7529 (mp0) cc_final: 0.7138 (mp0) REVERT: B 343 LEU cc_start: 0.8421 (OUTLIER) cc_final: 0.7999 (mp) outliers start: 24 outliers final: 19 residues processed: 228 average time/residue: 0.2504 time to fit residues: 87.2986 Evaluate side-chains 226 residues out of total 1611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 206 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 HIS Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 343 SER Chi-restraints excluded: chain A residue 406 SER Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 428 ASN Chi-restraints excluded: chain K residue 208 ASN Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 206 MET Chi-restraints excluded: chain G residue 10 LYS Chi-restraints excluded: chain G residue 60 ILE Chi-restraints excluded: chain H residue 104 HIS Chi-restraints excluded: chain H residue 106 HIS Chi-restraints excluded: chain B residue 52 SER Chi-restraints excluded: chain B residue 54 PHE Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 343 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 135 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 103 optimal weight: 0.5980 chunk 175 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 121 optimal weight: 0.8980 chunk 174 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 155 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 129 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 59 HIS D 237 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.130582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.112713 restraints weight = 49913.334| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 1.41 r_work: 0.3026 rms_B_bonded: 1.63 restraints_weight: 0.5000 r_work: 0.2928 rms_B_bonded: 2.87 restraints_weight: 0.2500 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.7102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.224 15127 Z= 0.179 Angle : 0.540 12.387 20605 Z= 0.274 Chirality : 0.039 0.148 2290 Planarity : 0.004 0.051 2632 Dihedral : 7.401 179.087 2093 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.67 % Allowed : 12.85 % Favored : 85.48 % 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: 0.85 (0.20), residues: 1892 helix: 1.50 (0.17), residues: 996 sheet: -1.10 (0.40), residues: 167 loop : -0.24 (0.24), residues: 729 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 411 TYR 0.012 0.001 TYR K 358 PHE 0.016 0.001 PHE K 90 TRP 0.011 0.001 TRP K 142 HIS 0.004 0.001 HIS K 362 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.18 (15119) covalent geometry : angle 0.53953 / 0.27 (20603) SS BOND : bond 0.00214 / 0.11 ( 1) SS BOND : angle 0.56267 / 0.30 ( 2) hydrogen bonds : bond 0.03923 / 2.96 ( 833) hydrogen bonds : angle 4.41874 / 3.27 ( 2364) Misc. bond : bond 0.10886 / 5.34 ( 7) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3784 Ramachandran restraints generated. 1892 Oldfield, 0 Emsley, 1892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3784 Ramachandran restraints generated. 1892 Oldfield, 0 Emsley, 1892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 112 is missing expected H atoms. Skipping. Residue LYS 124 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue TYR 43 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue SER 214 is missing expected H atoms. Skipping. Residue LYS 218 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue TYR 32 is missing expected H atoms. Skipping. Evaluate side-chains 240 residues out of total 1611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 215 time to evaluate : 0.688 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 ASP cc_start: 0.8386 (t0) cc_final: 0.8142 (t0) REVERT: A 173 ASN cc_start: 0.7449 (t0) cc_final: 0.7160 (t0) REVERT: A 222 GLU cc_start: 0.7948 (mp0) cc_final: 0.7712 (mp0) REVERT: A 341 SER cc_start: 0.8755 (m) cc_final: 0.8500 (t) REVERT: D 231 ASP cc_start: 0.8768 (m-30) cc_final: 0.8484 (m-30) REVERT: D 240 SER cc_start: 0.9140 (t) cc_final: 0.8838 (m) REVERT: G 30 GLN cc_start: 0.8451 (OUTLIER) cc_final: 0.7774 (mt0) REVERT: G 61 LYS cc_start: 0.8617 (ttpt) cc_final: 0.8285 (tttt) REVERT: G 86 GLN cc_start: 0.8212 (pt0) cc_final: 0.7887 (pt0) REVERT: F 89 GLU cc_start: 0.7755 (tp30) cc_final: 0.7364 (tt0) REVERT: H 114 GLU cc_start: 0.7691 (mp0) cc_final: 0.7221 (mp0) REVERT: B 202 SER cc_start: 0.8551 (p) cc_final: 0.8285 (m) REVERT: B 343 LEU cc_start: 0.8442 (OUTLIER) cc_final: 0.8016 (mp) outliers start: 25 outliers final: 21 residues processed: 229 average time/residue: 0.2500 time to fit residues: 87.9674 Evaluate side-chains 229 residues out of total 1611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 206 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 HIS Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 343 SER Chi-restraints excluded: chain A residue 406 SER Chi-restraints excluded: chain A residue 428 ASN Chi-restraints excluded: chain K residue 145 THR Chi-restraints excluded: chain K residue 208 ASN Chi-restraints excluded: chain D residue 48 HIS Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 206 MET Chi-restraints excluded: chain G residue 10 LYS Chi-restraints excluded: chain G residue 30 GLN Chi-restraints excluded: chain G residue 60 ILE Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain H residue 104 HIS Chi-restraints excluded: chain H residue 106 HIS Chi-restraints excluded: chain B residue 52 SER Chi-restraints excluded: chain B residue 54 PHE Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 312 SER Chi-restraints excluded: chain B residue 343 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 93 optimal weight: 0.0570 chunk 81 optimal weight: 1.9990 chunk 74 optimal weight: 0.5980 chunk 114 optimal weight: 1.9990 chunk 138 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 179 optimal weight: 2.9990 chunk 90 optimal weight: 0.5980 chunk 50 optimal weight: 0.8980 overall best weight: 0.8300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... M 47 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.133823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.113982 restraints weight = 49529.838| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 1.42 r_work: 0.3039 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.2944 rms_B_bonded: 2.68 restraints_weight: 0.2500 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.7274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.221 15127 Z= 0.150 Angle : 0.528 12.636 20605 Z= 0.265 Chirality : 0.039 0.148 2290 Planarity : 0.004 0.056 2632 Dihedral : 7.336 179.632 2093 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 1.54 % Allowed : 13.79 % Favored : 84.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.99 (0.20), residues: 1892 helix: 1.62 (0.17), residues: 997 sheet: -1.10 (0.40), residues: 167 loop : -0.18 (0.24), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 411 TYR 0.011 0.001 TYR K 358 PHE 0.026 0.001 PHE K 121 TRP 0.012 0.001 TRP K 142 HIS 0.004 0.001 HIS K 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.15 (15119) covalent geometry : angle 0.52767 / 0.27 (20603) SS BOND : bond 0.00282 / 0.15 ( 1) SS BOND : angle 0.74586 / 0.40 ( 2) hydrogen bonds : bond 0.03805 / 2.87 ( 833) hydrogen bonds : angle 4.35064 / 3.22 ( 2364) Misc. bond : bond 0.10753 / 5.28 ( 7) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3784 Ramachandran restraints generated. 1892 Oldfield, 0 Emsley, 1892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3784 Ramachandran restraints generated. 1892 Oldfield, 0 Emsley, 1892 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 242 residues out of total 1611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 219 time to evaluate : 0.766 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 ASP cc_start: 0.8359 (t0) cc_final: 0.8116 (t0) REVERT: A 173 ASN cc_start: 0.7421 (t0) cc_final: 0.7143 (t0) REVERT: A 222 GLU cc_start: 0.7954 (mp0) cc_final: 0.7680 (mp0) REVERT: A 341 SER cc_start: 0.8743 (m) cc_final: 0.8498 (t) REVERT: D 231 ASP cc_start: 0.8678 (m-30) cc_final: 0.8353 (m-30) REVERT: D 240 SER cc_start: 0.9108 (t) cc_final: 0.8824 (m) REVERT: G 61 LYS cc_start: 0.8585 (ttpt) cc_final: 0.8274 (tttt) REVERT: G 86 GLN cc_start: 0.8157 (pt0) cc_final: 0.7846 (pt0) REVERT: F 89 GLU cc_start: 0.7720 (tp30) cc_final: 0.7379 (tt0) REVERT: H 114 GLU cc_start: 0.7718 (mp0) cc_final: 0.7244 (mp0) REVERT: B 202 SER cc_start: 0.8518 (p) cc_final: 0.8285 (m) REVERT: B 343 LEU cc_start: 0.8430 (OUTLIER) cc_final: 0.8019 (mp) outliers start: 23 outliers final: 20 residues processed: 231 average time/residue: 0.2428 time to fit residues: 85.3957 Evaluate side-chains 227 residues out of total 1611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 206 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 HIS Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 343 SER Chi-restraints excluded: chain A residue 406 SER Chi-restraints excluded: chain A residue 428 ASN Chi-restraints excluded: chain K residue 27 ASN Chi-restraints excluded: chain K residue 208 ASN Chi-restraints excluded: chain D residue 48 HIS Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 206 MET Chi-restraints excluded: chain D residue 226 SER Chi-restraints excluded: chain G residue 10 LYS Chi-restraints excluded: chain G residue 60 ILE Chi-restraints excluded: chain H residue 104 HIS Chi-restraints excluded: chain B residue 52 SER Chi-restraints excluded: chain B residue 54 PHE Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 312 SER Chi-restraints excluded: chain B residue 343 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 108 optimal weight: 0.8980 chunk 27 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 119 optimal weight: 1.9990 chunk 133 optimal weight: 1.9990 chunk 138 optimal weight: 2.9990 chunk 65 optimal weight: 0.8980 chunk 156 optimal weight: 0.7980 chunk 170 optimal weight: 1.9990 chunk 106 optimal weight: 0.0270 chunk 91 optimal weight: 0.9980 overall best weight: 0.7238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.134141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.114401 restraints weight = 49255.932| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 1.40 r_work: 0.3049 rms_B_bonded: 1.51 restraints_weight: 0.5000 r_work: 0.2954 rms_B_bonded: 2.67 restraints_weight: 0.2500 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.7342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.210 15127 Z= 0.142 Angle : 0.522 12.407 20605 Z= 0.262 Chirality : 0.038 0.148 2290 Planarity : 0.004 0.057 2632 Dihedral : 7.297 179.677 2093 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 1.41 % Allowed : 13.99 % Favored : 84.61 % 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: 1.03 (0.20), residues: 1892 helix: 1.68 (0.17), residues: 996 sheet: -1.13 (0.40), residues: 167 loop : -0.16 (0.24), residues: 729 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG K 310 TYR 0.011 0.001 TYR K 358 PHE 0.013 0.001 PHE K 90 TRP 0.012 0.001 TRP K 142 HIS 0.004 0.001 HIS K 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.14 (15119) covalent geometry : angle 0.52159 / 0.26 (20603) SS BOND : bond 0.00236 / 0.12 ( 1) SS BOND : angle 0.68427 / 0.37 ( 2) hydrogen bonds : bond 0.03756 / 2.84 ( 833) hydrogen bonds : angle 4.31431 / 3.19 ( 2364) Misc. bond : bond 0.10356 / 5.08 ( 7) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3784 Ramachandran restraints generated. 1892 Oldfield, 0 Emsley, 1892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3784 Ramachandran restraints generated. 1892 Oldfield, 0 Emsley, 1892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 112 is missing expected H atoms. Skipping. Residue LYS 124 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue TYR 43 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue SER 214 is missing expected H atoms. Skipping. Residue LYS 218 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue TYR 32 is missing expected H atoms. Skipping. Evaluate side-chains 231 residues out of total 1611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 210 time to evaluate : 0.717 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 ASP cc_start: 0.8358 (t0) cc_final: 0.8134 (t0) REVERT: A 173 ASN cc_start: 0.7392 (t0) cc_final: 0.7122 (t0) REVERT: A 222 GLU cc_start: 0.7927 (mp0) cc_final: 0.7670 (mp0) REVERT: A 341 SER cc_start: 0.8737 (m) cc_final: 0.8511 (t) REVERT: D 105 GLU cc_start: 0.7655 (tt0) cc_final: 0.7223 (tt0) REVERT: D 231 ASP cc_start: 0.8681 (m-30) cc_final: 0.8374 (m-30) REVERT: G 30 GLN cc_start: 0.8411 (OUTLIER) cc_final: 0.7784 (mt0) REVERT: G 61 LYS cc_start: 0.8576 (ttpt) cc_final: 0.8265 (tttt) REVERT: G 86 GLN cc_start: 0.8095 (pt0) cc_final: 0.7795 (pt0) REVERT: F 89 GLU cc_start: 0.7700 (tp30) cc_final: 0.7398 (tt0) REVERT: H 114 GLU cc_start: 0.7784 (mp0) cc_final: 0.7291 (mp0) REVERT: B 202 SER cc_start: 0.8544 (p) cc_final: 0.8318 (m) REVERT: B 343 LEU cc_start: 0.8436 (OUTLIER) cc_final: 0.8027 (mp) outliers start: 21 outliers final: 19 residues processed: 221 average time/residue: 0.2392 time to fit residues: 81.5760 Evaluate side-chains 227 residues out of total 1611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 206 time to evaluate : 0.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 HIS Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 343 SER Chi-restraints excluded: chain A residue 406 SER Chi-restraints excluded: chain A residue 428 ASN Chi-restraints excluded: chain K residue 208 ASN Chi-restraints excluded: chain D residue 48 HIS Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 206 MET Chi-restraints excluded: chain D residue 226 SER Chi-restraints excluded: chain G residue 10 LYS Chi-restraints excluded: chain G residue 30 GLN Chi-restraints excluded: chain G residue 60 ILE Chi-restraints excluded: chain H residue 104 HIS Chi-restraints excluded: chain B residue 52 SER Chi-restraints excluded: chain B residue 54 PHE Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 312 SER Chi-restraints excluded: chain B residue 343 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 74 optimal weight: 0.8980 chunk 86 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 129 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 116 optimal weight: 2.9990 chunk 59 optimal weight: 0.8980 chunk 45 optimal weight: 2.9990 chunk 130 optimal weight: 1.9990 chunk 166 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.127729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.109965 restraints weight = 50594.751| |-----------------------------------------------------------------------------| r_work (start): 0.3107 rms_B_bonded: 1.42 r_work: 0.2995 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.2897 rms_B_bonded: 2.91 restraints_weight: 0.2500 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.7518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.229 15127 Z= 0.211 Angle : 0.563 12.691 20605 Z= 0.286 Chirality : 0.040 0.147 2290 Planarity : 0.004 0.054 2632 Dihedral : 7.395 179.394 2093 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 1.74 % Allowed : 13.79 % Favored : 84.47 % 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: 0.85 (0.20), residues: 1892 helix: 1.54 (0.17), residues: 997 sheet: -1.21 (0.40), residues: 168 loop : -0.27 (0.24), residues: 727 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 411 TYR 0.013 0.002 TYR K 358 PHE 0.016 0.001 PHE K 90 TRP 0.012 0.001 TRP K 142 HIS 0.006 0.001 HIS K 362 Details of bonding type rmsd/Z covalent geometry : bond 0.00486 / 0.21 (15119) covalent geometry : angle 0.56265 / 0.29 (20603) SS BOND : bond 0.00284 / 0.15 ( 1) SS BOND : angle 0.67487 / 0.36 ( 2) hydrogen bonds : bond 0.04048 / 3.06 ( 833) hydrogen bonds : angle 4.44346 / 3.28 ( 2364) Misc. bond : bond 0.11413 / 5.59 ( 7) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5963.88 seconds wall clock time: 102 minutes 8.49 seconds (6128.49 seconds total)