Starting phenix.real_space_refine on Fri Mar 6 06:21:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7rjd_24485/03_2026/7rjd_24485_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rjd_24485/03_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 { model { file = "/net/cci-nas-00/data/ceres_data/7rjd_24485/03_2026/7rjd_24485_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rjd_24485/03_2026/7rjd_24485_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7rjd_24485/03_2026/7rjd_24485.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rjd_24485/03_2026/7rjd_24485.map" } 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-5986/lib/python3.9/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: 60 Planarities with less than four sites: {'U10:plan-5': 2, 'U10:plan-6': 2, 'U10:plan-7': 2, 'U10:plan-8': 2, 'U10:plan-9': 2, 'U10:plan-10': 2, 'U10:plan-11': 2, 'U10:plan-4': 1} Unresolved non-hydrogen planarities: 60 Chain: "D" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEC': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.63, per 1000 atoms: 0.16 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: 2.67 Conformation dependent library (CDL) restraints added in 718.7 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: 0.71 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: 6.22 Time building geometry restraints manager: 3.63 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=" C ILE F 30 " pdb=" N SER F 31 " ideal model delta sigma weight residual 1.331 1.234 0.097 1.48e-02 4.57e+03 4.26e+01 ... (remaining 28778 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.54: 51447 3.54 - 7.09: 175 7.09 - 10.63: 9 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: 313 70.56 - 105.84: 35 105.84 - 141.12: 1 141.12 - 176.40: 1 Dihedral angle restraints: 13702 sinusoidal: 7057 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=" C3M U10 K 403 " pdb=" C3 U10 K 403 " pdb=" O3 U10 K 403 " pdb=" C4 U10 K 403 " ideal model delta sinusoidal sigma weight residual 244.38 105.86 138.51 1 2.00e+01 2.50e-03 4.20e+01 ... (remaining 13699 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=" CB HIS K 96 " 0.056 2.00e-02 2.50e+03 4.00e-02 3.60e+01 pdb=" CG HIS K 96 " -0.069 2.00e-02 2.50e+03 pdb=" ND1 HIS K 96 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 HIS K 96 " -0.053 2.00e-02 2.50e+03 pdb=" CE1 HIS K 96 " -0.006 2.00e-02 2.50e+03 pdb=" NE2 HIS K 96 " 0.060 2.00e-02 2.50e+03 pdb=" HD1 HIS K 96 " -0.001 2.00e-02 2.50e+03 pdb=" HD2 HIS K 96 " 0.009 2.00e-02 2.50e+03 pdb=" HE1 HIS K 96 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP E 149 " 0.026 2.00e-02 2.50e+03 5.03e-02 2.53e+01 pdb=" C TRP E 149 " -0.087 2.00e-02 2.50e+03 pdb=" O TRP E 149 " 0.032 2.00e-02 2.50e+03 pdb=" N LEU E 150 " 0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL E 91 " 0.022 2.00e-02 2.50e+03 4.52e-02 2.04e+01 pdb=" C VAL E 91 " -0.078 2.00e-02 2.50e+03 pdb=" O VAL E 91 " 0.029 2.00e-02 2.50e+03 pdb=" N GLU E 92 " 0.028 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: 1.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.110 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 26.460 Find NCS groups from input model: 0.110 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:0.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5709 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.315 15127 Z= 0.393 Angle : 0.839 17.723 20605 Z= 0.545 Chirality : 0.054 0.514 2290 Planarity : 0.005 0.050 2632 Dihedral : 13.566 176.404 5283 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 covalent geometry : bond 0.00681 (15119) covalent geometry : angle 0.83916 (20603) SS BOND : bond 0.00034 ( 1) SS BOND : angle 0.75220 ( 2) hydrogen bonds : bond 0.14006 ( 833) hydrogen bonds : angle 6.55424 ( 2364) Misc. bond : bond 0.12128 ( 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 : 0.688 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: 0.2900 time to fit residues: 150.0953 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 : 0.715 ------------------------------------------------------------------------------- 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: 0.9980 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: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3769 r_free = 0.3769 target = 0.166065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.147256 restraints weight = 50796.824| |-----------------------------------------------------------------------------| r_work (start): 0.3569 rms_B_bonded: 1.64 r_work: 0.3459 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3353 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7379 moved from start: 0.2707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.372 15127 Z= 0.197 Angle : 0.630 20.815 20605 Z= 0.321 Chirality : 0.041 0.159 2290 Planarity : 0.005 0.048 2632 Dihedral : 7.996 174.736 2089 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 1.34 % Allowed : 7.10 % Favored : 91.57 % 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: 0.41 (0.19), residues: 1892 helix: 0.92 (0.16), residues: 978 sheet: -0.86 (0.38), residues: 172 loop : -0.15 (0.24), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 133 TYR 0.016 0.002 TYR D 78 PHE 0.017 0.001 PHE K 227 TRP 0.012 0.001 TRP K 142 HIS 0.007 0.001 HIS K 362 Details of bonding type rmsd covalent geometry : bond 0.00424 (15119) covalent geometry : angle 0.62961 (20603) SS BOND : bond 0.00166 ( 1) SS BOND : angle 0.39343 ( 2) hydrogen bonds : bond 0.04552 ( 833) hydrogen bonds : angle 4.92390 ( 2364) Misc. bond : bond 0.15675 ( 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 294 residues out of total 1611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 274 time to evaluate : 0.682 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: E 90 LYS cc_start: 0.6899 (tttp) cc_final: 0.6620 (tttm) REVERT: A 100 ASN cc_start: 0.7285 (t0) cc_final: 0.6988 (t0) REVERT: A 433 GLU cc_start: 0.7491 (mm-30) cc_final: 0.7026 (mm-30) REVERT: K 69 MET cc_start: 0.8096 (mmm) cc_final: 0.7644 (mmm) REVERT: K 299 ILE cc_start: 0.8625 (mt) cc_final: 0.8344 (mt) REVERT: D 150 ASN cc_start: 0.7642 (m-40) cc_final: 0.7269 (m-40) REVERT: D 194 ASN cc_start: 0.6194 (m-40) cc_final: 0.5686 (t0) REVERT: D 231 ASP cc_start: 0.7993 (m-30) cc_final: 0.7513 (m-30) REVERT: D 265 SER cc_start: 0.8806 (OUTLIER) cc_final: 0.8506 (p) REVERT: G 40 GLU cc_start: 0.7880 (mp0) cc_final: 0.7584 (mm-30) REVERT: F 52 ARG cc_start: 0.5938 (mtm180) cc_final: 0.4568 (mtp85) REVERT: I 40 GLU cc_start: 0.7221 (tm-30) cc_final: 0.6839 (mp0) outliers start: 20 outliers final: 15 residues processed: 283 average time/residue: 0.2472 time to fit residues: 105.8122 Evaluate side-chains 260 residues out of total 1611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 244 time to evaluate : 0.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 77 SER 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 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: 0.9990 chunk 58 optimal weight: 0.5980 chunk 38 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 1 optimal weight: 0.1980 chunk 170 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3634 r_free = 0.3634 target = 0.154243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.137162 restraints weight = 50028.920| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 1.41 r_work: 0.3326 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.3232 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.3929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.308 15127 Z= 0.162 Angle : 0.571 13.716 20605 Z= 0.288 Chirality : 0.040 0.170 2290 Planarity : 0.004 0.070 2632 Dihedral : 7.443 177.539 2089 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 1.81 % Allowed : 8.77 % Favored : 89.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.76 (0.20), residues: 1892 helix: 1.25 (0.16), residues: 986 sheet: -0.97 (0.37), residues: 168 loop : -0.02 (0.25), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 87 TYR 0.016 0.001 TYR K 358 PHE 0.013 0.001 PHE K 90 TRP 0.010 0.001 TRP K 142 HIS 0.007 0.001 HIS K 362 Details of bonding type rmsd covalent geometry : bond 0.00361 (15119) covalent geometry : angle 0.57119 (20603) SS BOND : bond 0.00131 ( 1) SS BOND : angle 0.43624 ( 2) hydrogen bonds : bond 0.04343 ( 833) hydrogen bonds : angle 4.68475 ( 2364) Misc. bond : bond 0.12945 ( 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: 27 poor density : 250 time to evaluate : 0.711 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 THR cc_start: 0.8671 (t) cc_final: 0.8446 (m) REVERT: A 173 ASN cc_start: 0.7381 (t0) cc_final: 0.7125 (t0) REVERT: K 69 MET cc_start: 0.8209 (mmm) cc_final: 0.7753 (mmm) REVERT: K 353 GLN cc_start: 0.7916 (OUTLIER) cc_final: 0.7576 (mt0) REVERT: D 194 ASN cc_start: 0.6974 (m-40) cc_final: 0.6305 (t0) REVERT: D 231 ASP cc_start: 0.8284 (m-30) cc_final: 0.7990 (m-30) REVERT: D 270 ARG cc_start: 0.6314 (mmt180) cc_final: 0.5991 (mmt-90) REVERT: G 47 ASP cc_start: 0.8392 (m-30) cc_final: 0.8106 (m-30) REVERT: G 56 MET cc_start: 0.8747 (tpp) cc_final: 0.8468 (mmm) REVERT: F 52 ARG cc_start: 0.6048 (mtm180) cc_final: 0.4638 (mtp85) REVERT: F 88 GLU cc_start: 0.7444 (tp30) cc_final: 0.7093 (tp30) outliers start: 27 outliers final: 14 residues processed: 263 average time/residue: 0.2321 time to fit residues: 92.8529 Evaluate side-chains 245 residues out of total 1611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 230 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 HIS 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 203 VAL Chi-restraints excluded: chain K residue 206 SER 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 B residue 54 PHE Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 122 ILE 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: 3.9990 chunk 29 optimal weight: 3.9990 chunk 165 optimal weight: 1.9990 chunk 155 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 chunk 44 optimal weight: 1.9990 chunk 115 optimal weight: 0.9990 chunk 117 optimal weight: 0.5980 chunk 157 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 150 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.142295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.124446 restraints weight = 49084.481| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 1.37 r_work: 0.3172 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.3075 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.5089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.290 15127 Z= 0.193 Angle : 0.591 18.853 20605 Z= 0.296 Chirality : 0.040 0.154 2290 Planarity : 0.004 0.084 2632 Dihedral : 7.483 178.438 2089 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.07 % Allowed : 9.30 % Favored : 88.62 % 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: 0.70 (0.20), residues: 1892 helix: 1.28 (0.16), residues: 987 sheet: -0.91 (0.39), residues: 169 loop : -0.19 (0.24), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG F 87 TYR 0.021 0.002 TYR H 107 PHE 0.011 0.001 PHE K 188 TRP 0.011 0.001 TRP I 38 HIS 0.005 0.001 HIS K 362 Details of bonding type rmsd covalent geometry : bond 0.00439 (15119) covalent geometry : angle 0.59093 (20603) SS BOND : bond 0.00081 ( 1) SS BOND : angle 0.38863 ( 2) hydrogen bonds : bond 0.04095 ( 833) hydrogen bonds : angle 4.64706 ( 2364) Misc. bond : bond 0.12032 ( 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 279 residues out of total 1611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 248 time to evaluate : 0.681 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: E 75 PHE cc_start: 0.6752 (OUTLIER) cc_final: 0.6145 (t80) REVERT: A 173 ASN cc_start: 0.7358 (t0) cc_final: 0.7063 (t0) REVERT: K 69 MET cc_start: 0.8510 (mmm) cc_final: 0.8094 (mmm) REVERT: K 112 MET cc_start: 0.7949 (ttp) cc_final: 0.7635 (ttt) REVERT: K 353 GLN cc_start: 0.8330 (OUTLIER) cc_final: 0.8089 (mt0) REVERT: D 231 ASP cc_start: 0.8511 (m-30) cc_final: 0.8285 (m-30) REVERT: G 47 ASP cc_start: 0.8616 (m-30) cc_final: 0.8364 (m-30) REVERT: G 56 MET cc_start: 0.8901 (tpp) cc_final: 0.8683 (mmm) REVERT: G 86 GLN cc_start: 0.8102 (pt0) cc_final: 0.7865 (pt0) REVERT: G 98 GLU cc_start: 0.7705 (OUTLIER) cc_final: 0.7470 (mt-10) REVERT: F 89 GLU cc_start: 0.7987 (tp30) cc_final: 0.7485 (tt0) REVERT: I 40 GLU cc_start: 0.7014 (mp0) cc_final: 0.6730 (mp0) outliers start: 31 outliers final: 20 residues processed: 263 average time/residue: 0.2502 time to fit residues: 99.5656 Evaluate side-chains 252 residues out of total 1611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 229 time to evaluate : 1.041 ------------------------------------------------------------------------------- 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 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 353 GLN Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 221 THR Chi-restraints excluded: chain D residue 226 SER 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 16 SER 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 162 ASN Chi-restraints excluded: chain B residue 246 VAL 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: 5.9990 chunk 97 optimal weight: 0.6980 chunk 69 optimal weight: 0.0970 chunk 176 optimal weight: 0.9990 chunk 39 optimal weight: 0.5980 chunk 55 optimal weight: 1.9990 chunk 173 optimal weight: 1.9990 chunk 144 optimal weight: 2.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 ASN D 150 ASN D 151 GLN I 49 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.139413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.122324 restraints weight = 49328.936| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 1.36 r_work: 0.3134 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.3039 rms_B_bonded: 2.84 restraints_weight: 0.2500 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.5717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.257 15127 Z= 0.161 Angle : 0.537 13.074 20605 Z= 0.273 Chirality : 0.039 0.146 2290 Planarity : 0.004 0.045 2632 Dihedral : 7.323 178.660 2089 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 1.54 % Allowed : 11.51 % Favored : 86.95 % 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: 0.84 (0.20), residues: 1892 helix: 1.45 (0.16), residues: 994 sheet: -0.96 (0.39), residues: 171 loop : -0.21 (0.24), residues: 727 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 147 TYR 0.012 0.001 TYR K 358 PHE 0.013 0.001 PHE K 90 TRP 0.012 0.001 TRP K 142 HIS 0.005 0.001 HIS B 117 Details of bonding type rmsd covalent geometry : bond 0.00364 (15119) covalent geometry : angle 0.53696 (20603) SS BOND : bond 0.00165 ( 1) SS BOND : angle 0.49730 ( 2) hydrogen bonds : bond 0.03973 ( 833) hydrogen bonds : angle 4.53171 ( 2364) Misc. bond : bond 0.11356 ( 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 241 residues out of total 1611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 218 time to evaluate : 0.745 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: 0.6885 (OUTLIER) cc_final: 0.6192 (t80) REVERT: E 84 ASP cc_start: 0.7932 (t0) cc_final: 0.7655 (t0) REVERT: A 173 ASN cc_start: 0.7320 (t0) cc_final: 0.7042 (t0) REVERT: K 353 GLN cc_start: 0.8242 (OUTLIER) cc_final: 0.7925 (mt0) REVERT: D 105 GLU cc_start: 0.7366 (mt-10) cc_final: 0.7118 (mt-10) REVERT: D 231 ASP cc_start: 0.8563 (m-30) cc_final: 0.8360 (m-30) REVERT: G 47 ASP cc_start: 0.8654 (m-30) cc_final: 0.8387 (m-30) REVERT: G 57 GLN cc_start: 0.8109 (tp40) cc_final: 0.7803 (mm-40) REVERT: G 86 GLN cc_start: 0.8087 (pt0) cc_final: 0.7868 (pt0) REVERT: F 89 GLU cc_start: 0.7864 (tp30) cc_final: 0.7494 (tt0) REVERT: I 40 GLU cc_start: 0.7035 (mp0) cc_final: 0.6609 (mp0) outliers start: 23 outliers final: 16 residues processed: 228 average time/residue: 0.2360 time to fit residues: 82.4372 Evaluate side-chains 226 residues out of total 1611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 208 time to evaluate : 0.641 ------------------------------------------------------------------------------- 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 A residue 420 LEU Chi-restraints excluded: chain K residue 206 SER 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 D residue 226 SER 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 162 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 30 optimal weight: 2.9990 chunk 102 optimal weight: 0.8980 chunk 108 optimal weight: 0.4980 chunk 12 optimal weight: 8.9990 chunk 56 optimal weight: 0.7980 chunk 62 optimal weight: 0.6980 chunk 61 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 170 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 162 optimal weight: 1.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 428 ASN D 150 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.133599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.115937 restraints weight = 49561.268| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 1.42 r_work: 0.3067 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.2969 rms_B_bonded: 2.90 restraints_weight: 0.2500 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.6382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.250 15127 Z= 0.179 Angle : 0.550 13.836 20605 Z= 0.279 Chirality : 0.039 0.147 2290 Planarity : 0.004 0.047 2632 Dihedral : 7.324 178.512 2089 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 1.87 % Allowed : 11.24 % Favored : 86.88 % 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: 0.84 (0.20), residues: 1892 helix: 1.50 (0.16), residues: 995 sheet: -0.89 (0.40), residues: 165 loop : -0.32 (0.24), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 411 TYR 0.012 0.001 TYR K 358 PHE 0.011 0.001 PHE K 227 TRP 0.011 0.001 TRP K 142 HIS 0.004 0.001 HIS K 362 Details of bonding type rmsd covalent geometry : bond 0.00410 (15119) covalent geometry : angle 0.54970 (20603) SS BOND : bond 0.00142 ( 1) SS BOND : angle 0.48629 ( 2) hydrogen bonds : bond 0.03899 ( 833) hydrogen bonds : angle 4.48346 ( 2364) Misc. bond : bond 0.11642 ( 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 255 residues out of total 1611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 227 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: E 75 PHE cc_start: 0.6876 (OUTLIER) cc_final: 0.6148 (t80) REVERT: E 84 ASP cc_start: 0.8226 (t0) cc_final: 0.8017 (t0) REVERT: A 173 ASN cc_start: 0.7407 (t0) cc_final: 0.7120 (t0) REVERT: A 337 ARG cc_start: 0.8685 (mtp85) cc_final: 0.8132 (ttp80) REVERT: K 69 MET cc_start: 0.8601 (mmm) cc_final: 0.8235 (mmt) REVERT: K 296 PHE cc_start: 0.7997 (m-80) cc_final: 0.7787 (m-80) REVERT: K 353 GLN cc_start: 0.8337 (OUTLIER) cc_final: 0.8100 (mt0) REVERT: D 213 ASP cc_start: 0.7342 (m-30) cc_final: 0.7130 (m-30) REVERT: G 24 ILE cc_start: 0.8456 (mm) cc_final: 0.8119 (mm) REVERT: G 61 LYS cc_start: 0.8636 (ttpt) cc_final: 0.8329 (tttt) REVERT: G 86 GLN cc_start: 0.8172 (pt0) cc_final: 0.7657 (pt0) REVERT: F 89 GLU cc_start: 0.7912 (tp30) cc_final: 0.7445 (tt0) REVERT: H 111 CYS cc_start: 0.7646 (m) cc_final: 0.7145 (m) REVERT: I 40 GLU cc_start: 0.7155 (mp0) cc_final: 0.6724 (mp0) outliers start: 28 outliers final: 19 residues processed: 241 average time/residue: 0.2342 time to fit residues: 86.3491 Evaluate side-chains 235 residues out of total 1611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 214 time to evaluate : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 75 PHE Chi-restraints excluded: chain E residue 78 SER 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 353 GLN Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 221 THR Chi-restraints excluded: chain D residue 226 SER Chi-restraints excluded: chain G residue 60 ILE Chi-restraints excluded: chain H residue 74 THR 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 203 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 157 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 chunk 174 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 93 optimal weight: 0.0870 chunk 96 optimal weight: 0.6980 chunk 87 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 25 optimal weight: 0.3980 chunk 88 optimal weight: 1.9990 overall best weight: 0.8362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 48 HIS ** D 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.141220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.122667 restraints weight = 48409.147| |-----------------------------------------------------------------------------| r_work (start): 0.3162 rms_B_bonded: 1.24 r_work: 0.3100 rms_B_bonded: 1.35 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 2.40 restraints_weight: 0.2500 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.6632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.226 15127 Z= 0.150 Angle : 0.523 12.273 20605 Z= 0.264 Chirality : 0.038 0.147 2290 Planarity : 0.004 0.050 2632 Dihedral : 7.212 179.163 2089 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 1.87 % Allowed : 12.25 % Favored : 85.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.98 (0.20), residues: 1892 helix: 1.60 (0.17), residues: 995 sheet: -0.82 (0.41), 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 0.012 0.001 TYR D 140 PHE 0.012 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 covalent geometry : bond 0.00341 (15119) covalent geometry : angle 0.52339 (20603) SS BOND : bond 0.00143 ( 1) SS BOND : angle 0.62722 ( 2) hydrogen bonds : bond 0.03804 ( 833) hydrogen bonds : angle 4.40648 ( 2364) Misc. bond : bond 0.10764 ( 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 247 residues out of total 1611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 219 time to evaluate : 0.791 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: E 75 PHE cc_start: 0.6831 (OUTLIER) cc_final: 0.6113 (t80) REVERT: A 173 ASN cc_start: 0.7338 (t0) cc_final: 0.7111 (t0) REVERT: K 69 MET cc_start: 0.8625 (mmm) cc_final: 0.8201 (mmm) REVERT: K 353 GLN cc_start: 0.8360 (OUTLIER) cc_final: 0.8127 (mt0) REVERT: K 375 ASN cc_start: 0.8226 (m-40) cc_final: 0.7877 (m-40) REVERT: D 213 ASP cc_start: 0.7333 (m-30) cc_final: 0.7125 (m-30) REVERT: G 30 GLN cc_start: 0.8412 (OUTLIER) cc_final: 0.7636 (mt0) REVERT: G 61 LYS cc_start: 0.8519 (ttpt) cc_final: 0.8231 (tttt) REVERT: G 86 GLN cc_start: 0.8199 (pt0) cc_final: 0.7743 (pt0) REVERT: G 98 GLU cc_start: 0.7812 (OUTLIER) cc_final: 0.7549 (mt-10) REVERT: F 89 GLU cc_start: 0.7691 (tp30) cc_final: 0.7479 (tt0) REVERT: I 40 GLU cc_start: 0.7120 (mp0) cc_final: 0.6718 (mp0) outliers start: 28 outliers final: 22 residues processed: 236 average time/residue: 0.2420 time to fit residues: 87.7393 Evaluate side-chains 235 residues out of total 1611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 209 time to evaluate : 0.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 75 PHE Chi-restraints excluded: chain E residue 78 SER 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 206 SER Chi-restraints excluded: chain K residue 208 ASN Chi-restraints excluded: chain K residue 353 GLN Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 206 MET Chi-restraints excluded: chain D residue 221 THR Chi-restraints excluded: chain D residue 226 SER 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 G residue 98 GLU 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 203 GLU 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: 0.5980 chunk 103 optimal weight: 0.4980 chunk 175 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 121 optimal weight: 0.4980 chunk 174 optimal weight: 0.9980 chunk 29 optimal weight: 0.7980 chunk 155 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 129 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 ASN K 253 HIS D 59 HIS M 47 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.132948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.114537 restraints weight = 49751.908| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 1.47 r_work: 0.3057 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.2957 rms_B_bonded: 3.03 restraints_weight: 0.2500 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.6852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.208 15127 Z= 0.136 Angle : 0.516 12.444 20605 Z= 0.261 Chirality : 0.038 0.146 2290 Planarity : 0.004 0.050 2632 Dihedral : 7.081 179.498 2089 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 1.54 % Allowed : 12.58 % Favored : 85.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.14 (0.20), residues: 1892 helix: 1.75 (0.17), residues: 995 sheet: -0.78 (0.41), residues: 167 loop : -0.17 (0.25), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 411 TYR 0.010 0.001 TYR K 358 PHE 0.011 0.001 PHE A 327 TRP 0.012 0.001 TRP F 14 HIS 0.004 0.001 HIS K 183 Details of bonding type rmsd covalent geometry : bond 0.00313 (15119) covalent geometry : angle 0.51643 (20603) SS BOND : bond 0.00168 ( 1) SS BOND : angle 0.60768 ( 2) hydrogen bonds : bond 0.03692 ( 833) hydrogen bonds : angle 4.31325 ( 2364) Misc. bond : bond 0.09812 ( 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 247 residues out of total 1611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 224 time to evaluate : 0.610 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 ASP cc_start: 0.8359 (t0) cc_final: 0.8111 (t0) REVERT: A 173 ASN cc_start: 0.7420 (t0) cc_final: 0.7164 (t0) REVERT: A 337 ARG cc_start: 0.8678 (mtp85) cc_final: 0.8160 (ttp80) REVERT: K 69 MET cc_start: 0.8637 (mmm) cc_final: 0.8318 (mmt) REVERT: K 353 GLN cc_start: 0.8371 (OUTLIER) cc_final: 0.8149 (mt0) REVERT: D 213 ASP cc_start: 0.7406 (m-30) cc_final: 0.7199 (m-30) REVERT: D 240 SER cc_start: 0.9123 (t) cc_final: 0.8850 (m) REVERT: G 30 GLN cc_start: 0.8433 (OUTLIER) cc_final: 0.7682 (mt0) REVERT: G 61 LYS cc_start: 0.8592 (ttpt) cc_final: 0.8290 (tttt) REVERT: G 86 GLN cc_start: 0.8215 (pt0) cc_final: 0.7776 (pt0) REVERT: G 98 GLU cc_start: 0.7803 (OUTLIER) cc_final: 0.7513 (mt-10) REVERT: F 89 GLU cc_start: 0.7725 (tp30) cc_final: 0.7499 (tt0) REVERT: H 114 GLU cc_start: 0.7543 (mp0) cc_final: 0.7042 (mp0) REVERT: I 40 GLU cc_start: 0.7108 (mp0) cc_final: 0.6726 (mp0) REVERT: B 351 GLU cc_start: 0.6941 (tp30) cc_final: 0.6740 (tp30) outliers start: 23 outliers final: 19 residues processed: 236 average time/residue: 0.2341 time to fit residues: 84.0147 Evaluate side-chains 241 residues out of total 1611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 219 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 78 SER 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 A residue 420 LEU 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 44 THR Chi-restraints excluded: chain D residue 48 HIS Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 226 SER Chi-restraints excluded: chain G residue 30 GLN Chi-restraints excluded: chain G residue 60 ILE Chi-restraints excluded: chain G residue 98 GLU 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 235 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 93 optimal weight: 0.0970 chunk 81 optimal weight: 0.9980 chunk 74 optimal weight: 0.8980 chunk 114 optimal weight: 1.9990 chunk 138 optimal weight: 3.9990 chunk 39 optimal weight: 0.8980 chunk 68 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 179 optimal weight: 0.6980 chunk 90 optimal weight: 0.5980 chunk 50 optimal weight: 0.8980 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 ASN D 237 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.133614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.115991 restraints weight = 49271.622| |-----------------------------------------------------------------------------| r_work (start): 0.3172 rms_B_bonded: 1.38 r_work: 0.3063 rms_B_bonded: 1.62 restraints_weight: 0.5000 r_work: 0.2966 rms_B_bonded: 2.83 restraints_weight: 0.2500 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.7014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.196 15127 Z= 0.130 Angle : 0.510 12.124 20605 Z= 0.256 Chirality : 0.038 0.148 2290 Planarity : 0.004 0.058 2632 Dihedral : 7.005 179.451 2089 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 1.54 % Allowed : 12.78 % Favored : 85.68 % 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: 1.24 (0.20), residues: 1892 helix: 1.83 (0.17), residues: 998 sheet: -0.75 (0.41), residues: 166 loop : -0.12 (0.25), 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 0.011 0.001 PHE A 327 TRP 0.010 0.001 TRP K 142 HIS 0.004 0.001 HIS K 362 Details of bonding type rmsd covalent geometry : bond 0.00298 (15119) covalent geometry : angle 0.51037 (20603) SS BOND : bond 0.00152 ( 1) SS BOND : angle 0.60501 ( 2) hydrogen bonds : bond 0.03672 ( 833) hydrogen bonds : angle 4.23471 ( 2364) Misc. bond : bond 0.09649 ( 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 250 residues out of total 1611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 227 time to evaluate : 0.727 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: E 75 PHE cc_start: 0.6718 (OUTLIER) cc_final: 0.5936 (t80) REVERT: A 123 ASP cc_start: 0.8376 (t0) cc_final: 0.8111 (t0) REVERT: A 173 ASN cc_start: 0.7354 (t0) cc_final: 0.7075 (t0) REVERT: A 337 ARG cc_start: 0.8647 (mtp85) cc_final: 0.8118 (ttp80) REVERT: A 422 GLU cc_start: 0.8349 (tt0) cc_final: 0.7636 (tm-30) REVERT: K 69 MET cc_start: 0.8654 (mmm) cc_final: 0.8289 (mmm) REVERT: K 353 GLN cc_start: 0.8347 (OUTLIER) cc_final: 0.8111 (mt0) REVERT: D 240 SER cc_start: 0.9132 (t) cc_final: 0.8854 (m) REVERT: G 30 GLN cc_start: 0.8442 (OUTLIER) cc_final: 0.7718 (mt0) REVERT: G 61 LYS cc_start: 0.8565 (ttpt) cc_final: 0.8265 (tttt) REVERT: G 86 GLN cc_start: 0.8233 (pt0) cc_final: 0.7851 (pt0) REVERT: G 98 GLU cc_start: 0.7749 (OUTLIER) cc_final: 0.7452 (mt-10) REVERT: H 114 GLU cc_start: 0.7634 (mp0) cc_final: 0.7086 (mp0) REVERT: I 40 GLU cc_start: 0.7084 (mp0) cc_final: 0.6679 (mp0) outliers start: 23 outliers final: 19 residues processed: 239 average time/residue: 0.2488 time to fit residues: 90.1927 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 : 0.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 75 PHE Chi-restraints excluded: chain E residue 78 SER 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 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 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 30 GLN Chi-restraints excluded: chain G residue 60 ILE Chi-restraints excluded: chain G residue 98 GLU 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 235 SER Chi-restraints excluded: chain B residue 312 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 108 optimal weight: 0.4980 chunk 27 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 119 optimal weight: 1.9990 chunk 133 optimal weight: 0.9980 chunk 138 optimal weight: 3.9990 chunk 65 optimal weight: 0.5980 chunk 156 optimal weight: 0.9980 chunk 170 optimal weight: 1.9990 chunk 106 optimal weight: 0.0170 chunk 91 optimal weight: 0.9990 overall best weight: 0.6218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.132979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.115235 restraints weight = 49334.054| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 1.38 r_work: 0.3060 rms_B_bonded: 1.63 restraints_weight: 0.5000 r_work: 0.2963 rms_B_bonded: 2.86 restraints_weight: 0.2500 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.7137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.191 15127 Z= 0.130 Angle : 0.519 12.130 20605 Z= 0.259 Chirality : 0.038 0.156 2290 Planarity : 0.004 0.059 2632 Dihedral : 6.967 179.439 2089 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 1.47 % Allowed : 13.45 % Favored : 85.07 % 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: 1.27 (0.20), residues: 1892 helix: 1.86 (0.17), residues: 998 sheet: -0.77 (0.41), residues: 166 loop : -0.13 (0.25), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG K 310 TYR 0.011 0.001 TYR F 82 PHE 0.011 0.001 PHE A 327 TRP 0.010 0.001 TRP K 142 HIS 0.003 0.001 HIS K 183 Details of bonding type rmsd covalent geometry : bond 0.00301 (15119) covalent geometry : angle 0.51850 (20603) SS BOND : bond 0.00169 ( 1) SS BOND : angle 0.59266 ( 2) hydrogen bonds : bond 0.03627 ( 833) hydrogen bonds : angle 4.21905 ( 2364) Misc. bond : bond 0.09267 ( 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 240 residues out of total 1611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 218 time to evaluate : 0.612 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: 0.6720 (OUTLIER) cc_final: 0.5940 (t80) REVERT: A 123 ASP cc_start: 0.8386 (t0) cc_final: 0.8144 (t0) REVERT: A 173 ASN cc_start: 0.7338 (t0) cc_final: 0.7062 (t0) REVERT: A 337 ARG cc_start: 0.8643 (mtp85) cc_final: 0.8115 (ttp80) REVERT: K 69 MET cc_start: 0.8660 (mmm) cc_final: 0.8301 (mmm) REVERT: K 353 GLN cc_start: 0.8357 (OUTLIER) cc_final: 0.8148 (mt0) REVERT: K 375 ASN cc_start: 0.8226 (m-40) cc_final: 0.7991 (m-40) REVERT: D 240 SER cc_start: 0.9127 (t) cc_final: 0.8861 (m) REVERT: G 30 GLN cc_start: 0.8435 (OUTLIER) cc_final: 0.7746 (mt0) REVERT: G 61 LYS cc_start: 0.8553 (ttpt) cc_final: 0.8266 (tttt) REVERT: G 86 GLN cc_start: 0.8253 (pt0) cc_final: 0.7881 (pt0) REVERT: G 98 GLU cc_start: 0.7743 (OUTLIER) cc_final: 0.7445 (mt-10) REVERT: F 89 GLU cc_start: 0.7431 (tt0) cc_final: 0.7216 (tt0) REVERT: H 114 GLU cc_start: 0.7733 (mp0) cc_final: 0.7186 (mp0) REVERT: I 40 GLU cc_start: 0.7065 (mp0) cc_final: 0.6658 (mp0) REVERT: B 202 SER cc_start: 0.8477 (p) cc_final: 0.8238 (m) outliers start: 22 outliers final: 18 residues processed: 229 average time/residue: 0.2460 time to fit residues: 85.6153 Evaluate side-chains 236 residues out of total 1611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 214 time to evaluate : 0.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 75 PHE Chi-restraints excluded: chain E residue 78 SER 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 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 48 HIS Chi-restraints excluded: chain D residue 88 LEU 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 98 GLU 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 235 SER Chi-restraints excluded: chain B residue 312 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 74 optimal weight: 0.9980 chunk 86 optimal weight: 0.7980 chunk 19 optimal weight: 2.9990 chunk 129 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 116 optimal weight: 0.9980 chunk 59 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 chunk 130 optimal weight: 1.9990 chunk 166 optimal weight: 2.9990 chunk 81 optimal weight: 0.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.130685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.112860 restraints weight = 50014.103| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 1.40 r_work: 0.3028 rms_B_bonded: 1.64 restraints_weight: 0.5000 r_work: 0.2931 rms_B_bonded: 2.88 restraints_weight: 0.2500 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.7345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.201 15127 Z= 0.163 Angle : 0.529 12.079 20605 Z= 0.267 Chirality : 0.039 0.146 2290 Planarity : 0.004 0.054 2632 Dihedral : 7.021 178.706 2089 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 1.61 % Allowed : 13.39 % Favored : 85.01 % 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: 1.18 (0.20), residues: 1892 helix: 1.80 (0.17), residues: 998 sheet: -0.83 (0.41), residues: 166 loop : -0.17 (0.24), residues: 728 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 0.012 0.001 PHE K 90 TRP 0.010 0.001 TRP K 142 HIS 0.005 0.001 HIS K 362 Details of bonding type rmsd covalent geometry : bond 0.00376 (15119) covalent geometry : angle 0.52912 (20603) SS BOND : bond 0.00291 ( 1) SS BOND : angle 0.79815 ( 2) hydrogen bonds : bond 0.03785 ( 833) hydrogen bonds : angle 4.28024 ( 2364) Misc. bond : bond 0.10063 ( 7) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6175.56 seconds wall clock time: 105 minutes 35.50 seconds (6335.50 seconds total)