Starting phenix.real_space_refine on Fri Mar 6 06:13:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7rjb_24483/03_2026/7rjb_24483_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rjb_24483/03_2026/7rjb_24483.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7rjb_24483/03_2026/7rjb_24483.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rjb_24483/03_2026/7rjb_24483.map" model { file = "/net/cci-nas-00/data/ceres_data/7rjb_24483/03_2026/7rjb_24483_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rjb_24483/03_2026/7rjb_24483_trim.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.164 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Fe 5 7.16 5 S 44 5.16 5 C 9471 2.51 5 N 2447 2.21 5 O 2742 1.98 5 H 13664 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Residue "D ARG 282": not complete - not flipped Time to flip 25 residue(s): 0.01s 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: 28373 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 6364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 416, 6364 Classifications: {'peptide': 416} Link IDs: {'PTRANS': 8, 'TRANS': 407} Chain: "K" Number of atoms: 6146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 6146 Classifications: {'peptide': 383} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 23, 'TRANS': 359} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "D" Number of atoms: 3736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 3736 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 21, 'TRANS': 222} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'ASP:plan': 2, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 18 Chain: "G" Number of atoms: 1978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 1978 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 7, 'TRANS': 114} Chain: "F" Number of atoms: 1399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 1399 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 4, 'TRANS': 80} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'TYR:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 10 Chain: "H" Number of atoms: 1148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 1148 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 4, 'TRANS': 67} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "I" Number of atoms: 639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 639 Classifications: {'peptide': 39} Link IDs: {'TRANS': 38} Chain: "B" Number of atoms: 5392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 364, 5392 Classifications: {'peptide': 364} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 345} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "M" Number of atoms: 723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 723 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 1, 'TRANS': 48} Chain: "E" Number of atoms: 664 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 664 Classifications: {'peptide': 132} Incomplete info: {'truncation_to_alanine': 103} Link IDs: {'PTRANS': 9, 'TRANS': 122} Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 386 Unresolved non-hydrogen angles: 498 Unresolved non-hydrogen dihedrals: 326 Unresolved non-hydrogen chiralities: 33 Planarities with less than four sites: {'GLU:plan': 10, 'ASN:plan1': 4, 'TRP:plan': 3, 'GLN:plan1': 3, 'PHE:plan': 4, 'ARG:plan': 6, 'HIS:plan': 4, 'ASP:plan': 10, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 209 Chain: "K" Number of atoms: 137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 137 Unusual residues: {'HEM': 2, 'U10': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 90 Unresolved non-hydrogen dihedrals: 60 Planarities with less than four sites: {'U10:plan-5': 2, 'U10:plan-6': 2, 'U10:plan-7': 2, 'U10:plan-8': 2, 'U10:plan-9': 2, 'U10:plan-10': 2, 'U10:plan-11': 2, 'U10:plan-4': 1} Unresolved non-hydrogen planarities: 60 Chain: "D" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEC': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.27, per 1000 atoms: 0.19 Number of scatterers: 28373 At special positions: 0 Unit cell: (117.42, 89.61, 159.65, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 5 26.01 S 44 16.00 O 2742 8.00 N 2447 7.00 C 9471 6.00 H 13664 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS H 89 " - pdb=" SG CYS H 111 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=7, symmetry=0 Number of additional bonds: simple=7, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.64 Conformation dependent library (CDL) restraints added in 957.8 milliseconds 3774 Ramachandran restraints generated. 1887 Oldfield, 0 Emsley, 1887 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3578 Finding SS restraints... Secondary structure from input PDB file: 91 helices and 11 sheets defined 59.7% alpha, 8.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.72 Creating SS restraints... Processing helix chain 'A' and resid 27 through 29 No H-bonds generated for 'chain 'A' and resid 27 through 29' Processing helix chain 'A' and resid 52 through 56 Processing helix chain 'A' and resid 62 through 73 Processing helix chain 'A' and resid 97 through 99 No H-bonds generated for 'chain 'A' and resid 97 through 99' Processing helix chain 'A' and resid 100 through 114 Processing helix chain 'A' and resid 114 through 121 Processing helix chain 'A' and resid 123 through 139 removed outlier: 4.500A pdb=" N HIS A 127 " --> pdb=" O ASP A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 155 Processing helix chain 'A' and resid 158 through 162 Processing helix chain 'A' and resid 167 through 172 removed outlier: 3.817A pdb=" N GLU A 172 " --> pdb=" O THR A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 187 Processing helix chain 'A' and resid 188 through 191 Processing helix chain 'A' and resid 201 through 211 Processing helix chain 'A' and resid 258 through 270 removed outlier: 4.032A pdb=" N TYR A 269 " --> pdb=" O ALA A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 281 removed outlier: 3.912A pdb=" N LYS A 280 " --> pdb=" O THR A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 291 removed outlier: 3.513A pdb=" N SER A 288 " --> pdb=" O PRO A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 322 No H-bonds generated for 'chain 'A' and resid 320 through 322' Processing helix chain 'A' and resid 323 through 339 removed outlier: 3.537A pdb=" N LEU A 338 " --> pdb=" O GLU A 334 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N SER A 339 " --> pdb=" O TRP A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 362 Processing helix chain 'A' and resid 364 through 379 Processing helix chain 'A' and resid 384 through 394 Processing helix chain 'A' and resid 396 through 408 Processing helix chain 'A' and resid 420 through 424 removed outlier: 4.451A pdb=" N ASP A 423 " --> pdb=" O LEU A 420 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 433 removed outlier: 3.865A pdb=" N ASN A 430 " --> pdb=" O ASP A 426 " (cutoff:3.500A) Processing helix chain 'K' and resid 2 through 7 Processing helix chain 'K' and resid 7 through 18 Processing helix chain 'K' and resid 28 through 30 No H-bonds generated for 'chain 'K' and resid 28 through 30' Processing helix chain 'K' and resid 31 through 52 removed outlier: 3.647A pdb=" N MET K 52 " --> pdb=" O VAL K 48 " (cutoff:3.500A) Processing helix chain 'K' and resid 60 through 71 Processing helix chain 'K' and resid 74 through 103 removed outlier: 3.605A pdb=" N ALA K 86 " --> pdb=" O HIS K 82 " (cutoff:3.500A) Processing helix chain 'K' and resid 107 through 109 No H-bonds generated for 'chain 'K' and resid 107 through 109' Processing helix chain 'K' and resid 110 through 136 removed outlier: 3.860A pdb=" N VAL K 135 " --> pdb=" O GLY K 131 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N TYR K 136 " --> pdb=" O TYR K 132 " (cutoff:3.500A) Processing helix chain 'K' and resid 137 through 152 Processing helix chain 'K' and resid 157 through 167 Proline residue: K 163 - end of helix Processing helix chain 'K' and resid 172 through 205 Proline residue: K 187 - end of helix removed outlier: 4.144A pdb=" N HIS K 204 " --> pdb=" O ALA K 200 " (cutoff:3.500A) Processing helix chain 'K' and resid 225 through 245 Processing helix chain 'K' and resid 253 through 258 Processing helix chain 'K' and resid 272 through 274 No H-bonds generated for 'chain 'K' and resid 272 through 274' Processing helix chain 'K' and resid 275 through 285 Processing helix chain 'K' and resid 287 through 309 removed outlier: 5.110A pdb=" N LEU K 302 " --> pdb=" O ALA K 298 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N LEU K 303 " --> pdb=" O ILE K 299 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N SER K 304 " --> pdb=" O LEU K 300 " (cutoff:3.500A) Proline residue: K 306 - end of helix Processing helix chain 'K' and resid 319 through 342 removed outlier: 3.762A pdb=" N GLN K 341 " --> pdb=" O GLY K 337 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU K 342 " --> pdb=" O ASN K 338 " (cutoff:3.500A) Processing helix chain 'K' and resid 345 through 365 removed outlier: 4.149A pdb=" N GLN K 350 " --> pdb=" O VAL K 346 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N TYR K 363 " --> pdb=" O TYR K 359 " (cutoff:3.500A) Processing helix chain 'K' and resid 365 through 383 Processing helix chain 'D' and resid 44 through 49 Processing helix chain 'D' and resid 67 through 81 Processing helix chain 'D' and resid 82 through 85 Processing helix chain 'D' and resid 92 through 97 Processing helix chain 'D' and resid 102 through 112 Processing helix chain 'D' and resid 142 through 150 Processing helix chain 'D' and resid 157 through 161 removed outlier: 4.215A pdb=" N LEU D 160 " --> pdb=" O ASP D 157 " (cutoff:3.500A) Processing helix chain 'D' and resid 168 through 177 Processing helix chain 'D' and resid 224 through 241 Processing helix chain 'D' and resid 243 through 278 Proline residue: D 275 - end of helix Processing helix chain 'G' and resid 4 through 18 removed outlier: 4.222A pdb=" N ARG G 18 " --> pdb=" O PHE G 14 " (cutoff:3.500A) Processing helix chain 'G' and resid 18 through 37 Proline residue: G 27 - end of helix removed outlier: 4.215A pdb=" N GLY G 37 " --> pdb=" O THR G 33 " (cutoff:3.500A) Processing helix chain 'G' and resid 38 through 42 Processing helix chain 'G' and resid 44 through 48 Processing helix chain 'G' and resid 53 through 62 Processing helix chain 'G' and resid 64 through 85 Processing helix chain 'G' and resid 103 through 122 Processing helix chain 'F' and resid 40 through 82 removed outlier: 3.646A pdb=" N VAL F 46 " --> pdb=" O ALA F 42 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N THR F 49 " --> pdb=" O ALA F 45 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N LEU F 58 " --> pdb=" O LYS F 54 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N TYR F 59 " --> pdb=" O ASN F 55 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N VAL F 60 " --> pdb=" O GLN F 56 " (cutoff:3.500A) Proline residue: F 63 - end of helix Processing helix chain 'F' and resid 86 through 93 Processing helix chain 'H' and resid 64 through 75 removed outlier: 3.743A pdb=" N THR H 68 " --> pdb=" O ASP H 64 " (cutoff:3.500A) Processing helix chain 'H' and resid 79 through 99 removed outlier: 3.650A pdb=" N GLU H 99 " --> pdb=" O LYS H 95 " (cutoff:3.500A) Processing helix chain 'H' and resid 101 through 105 Processing helix chain 'H' and resid 111 through 131 removed outlier: 3.890A pdb=" N CYS H 125 " --> pdb=" O CYS H 121 " (cutoff:3.500A) Proline residue: H 128 - end of helix removed outlier: 4.686A pdb=" N PHE H 131 " --> pdb=" O ALA H 127 " (cutoff:3.500A) Processing helix chain 'H' and resid 132 through 134 No H-bonds generated for 'chain 'H' and resid 132 through 134' Processing helix chain 'I' and resid 18 through 42 removed outlier: 3.712A pdb=" N PHE I 24 " --> pdb=" O PHE I 20 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA I 25 " --> pdb=" O GLY I 21 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N GLU I 39 " --> pdb=" O ASN I 35 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLU I 40 " --> pdb=" O LYS I 36 " (cutoff:3.500A) Processing helix chain 'I' and resid 46 through 55 removed outlier: 5.344A pdb=" N GLY I 52 " --> pdb=" O LYS I 48 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N LYS I 53 " --> pdb=" O ASN I 49 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N PHE I 54 " --> pdb=" O VAL I 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 55 Processing helix chain 'B' and resid 63 through 75 removed outlier: 3.741A pdb=" N ARG B 69 " --> pdb=" O LEU B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 110 removed outlier: 3.561A pdb=" N GLU B 103 " --> pdb=" O PRO B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 122 Processing helix chain 'B' and resid 123 through 136 Processing helix chain 'B' and resid 137 through 151 Processing helix chain 'B' and resid 153 through 157 removed outlier: 3.605A pdb=" N GLY B 156 " --> pdb=" O ARG B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 177 Processing helix chain 'B' and resid 181 through 183 No H-bonds generated for 'chain 'B' and resid 181 through 183' Processing helix chain 'B' and resid 193 through 204 Processing helix chain 'B' and resid 205 through 209 Processing helix chain 'B' and resid 247 through 249 No H-bonds generated for 'chain 'B' and resid 247 through 249' Processing helix chain 'B' and resid 250 through 262 Processing helix chain 'B' and resid 271 through 276 Processing helix chain 'B' and resid 299 through 315 removed outlier: 3.692A pdb=" N GLN B 305 " --> pdb=" O SER B 301 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LYS B 308 " --> pdb=" O ALA B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 325 Processing helix chain 'B' and resid 325 through 337 Processing helix chain 'B' and resid 370 through 374 Processing helix chain 'M' and resid 45 through 80 removed outlier: 4.359A pdb=" N ARG M 50 " --> pdb=" O GLY M 46 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N SER M 78 " --> pdb=" O ALA M 74 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N PHE M 79 " --> pdb=" O PHE M 75 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ALA M 80 " --> pdb=" O LEU M 76 " (cutoff:3.500A) Processing helix chain 'E' and resid 82 through 87 Processing helix chain 'E' and resid 119 through 129 Processing helix chain 'E' and resid 139 through 144 Processing sheet with id=AA1, first strand: chain 'A' and resid 23 through 25 removed outlier: 6.521A pdb=" N THR A 31 " --> pdb=" O ILE A 194 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N ALA A 196 " --> pdb=" O THR A 31 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N ALA A 33 " --> pdb=" O ALA A 196 " (cutoff:3.500A) removed outlier: 8.722A pdb=" N GLY A 198 " --> pdb=" O ALA A 33 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N GLU A 35 " --> pdb=" O GLY A 198 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N VAL A 45 " --> pdb=" O ALA A 94 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 271 through 273 removed outlier: 6.453A pdb=" N SER A 231 " --> pdb=" O ILE A 415 " (cutoff:3.500A) removed outlier: 8.739A pdb=" N GLY A 417 " --> pdb=" O SER A 231 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N VAL A 233 " --> pdb=" O GLY A 417 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'K' and resid 22 through 23 Processing sheet with id=AA4, first strand: chain 'D' and resid 114 through 117 removed outlier: 4.681A pdb=" N ARG D 126 " --> pdb=" O ASP D 117 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 194 through 195 Processing sheet with id=AA6, first strand: chain 'B' and resid 18 through 22 removed outlier: 6.219A pdb=" N LYS B 18 " --> pdb=" O ILE B 187 " (cutoff:3.500A) removed outlier: 7.951A pdb=" N ALA B 189 " --> pdb=" O LYS B 18 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N ALA B 20 " --> pdb=" O ALA B 189 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N PHE B 93 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 18 through 22 removed outlier: 6.219A pdb=" N LYS B 18 " --> pdb=" O ILE B 187 " (cutoff:3.500A) removed outlier: 7.951A pdb=" N ALA B 189 " --> pdb=" O LYS B 18 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N ALA B 20 " --> pdb=" O ALA B 189 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 233 Processing sheet with id=AA9, first strand: chain 'E' and resid 106 through 108 removed outlier: 3.630A pdb=" N ILE E 106 " --> pdb=" O VAL E 113 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ARG E 116 " --> pdb=" O LEU E 150 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU E 150 " --> pdb=" O ARG E 116 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 173 through 175 Processing sheet with id=AB2, first strand: chain 'E' and resid 203 through 204 844 hydrogen bonds defined for protein. 2379 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: 6.39 Time building geometry restraints manager: 3.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.12: 13655 1.12 - 1.41: 6289 1.41 - 1.70: 8708 1.70 - 1.98: 72 1.98 - 2.27: 15 Bond restraints: 28739 Sorted by residual: bond pdb=" C CYS D 82 " pdb=" O CYS D 82 " ideal model delta sigma weight residual 1.237 1.076 0.161 1.17e-02 7.31e+03 1.89e+02 bond pdb=" C2D HEC D 301 " pdb=" C3D HEC D 301 " ideal model delta sigma weight residual 1.544 1.332 0.212 2.00e-02 2.50e+03 1.13e+02 bond pdb=" CAB HEC D 301 " pdb=" CBB HEC D 301 " ideal model delta sigma weight residual 1.544 1.332 0.212 2.00e-02 2.50e+03 1.12e+02 bond pdb=" CAC HEC D 301 " pdb=" CBC HEC D 301 " ideal model delta sigma weight residual 1.544 1.336 0.208 2.00e-02 2.50e+03 1.08e+02 bond pdb=" C ILE F 30 " pdb=" N SER F 31 " ideal model delta sigma weight residual 1.331 1.234 0.097 1.48e-02 4.57e+03 4.26e+01 ... (remaining 28734 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.54: 51400 3.54 - 7.08: 161 7.08 - 10.62: 11 10.62 - 14.16: 10 14.16 - 17.70: 3 Bond angle restraints: 51585 Sorted by residual: angle pdb=" S1 FES E 301 " pdb="FE1 FES E 301 " pdb=" S2 FES E 301 " ideal model delta sigma weight residual 104.33 86.63 17.70 1.20e+00 6.94e-01 2.17e+02 angle pdb=" S1 FES E 301 " pdb="FE2 FES E 301 " pdb=" S2 FES E 301 " ideal model delta sigma weight residual 104.33 88.19 16.14 1.14e+00 7.69e-01 2.01e+02 angle pdb="FE1 FES E 301 " pdb=" S2 FES E 301 " pdb="FE2 FES E 301 " ideal model delta sigma weight residual 75.66 89.74 -14.08 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 90.33 -14.67 1.20e+00 6.94e-01 1.50e+02 angle pdb=" CA CYS D 82 " pdb=" C CYS D 82 " pdb=" O CYS D 82 " ideal model delta sigma weight residual 120.55 109.72 10.83 1.06e+00 8.90e-01 1.04e+02 ... (remaining 51580 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.28: 13327 35.28 - 70.56: 315 70.56 - 105.84: 35 105.84 - 141.12: 1 141.12 - 176.40: 1 Dihedral angle restraints: 13679 sinusoidal: 7049 harmonic: 6630 Sorted by residual: dihedral pdb=" CD ARG D 282 " pdb=" NE ARG D 282 " pdb=" CZ ARG D 282 " pdb=" NH1 ARG D 282 " ideal model delta sinusoidal sigma weight residual 0.00 176.40 -176.40 1 1.00e+01 1.00e-02 1.92e+02 dihedral pdb=" C PRO E 192 " pdb=" N PRO E 192 " pdb=" CA PRO E 192 " pdb=" CB PRO E 192 " ideal model delta harmonic sigma weight residual -120.70 -103.51 -17.19 0 2.50e+00 1.60e-01 4.73e+01 dihedral pdb=" C HIS E 117 " pdb=" N HIS E 117 " pdb=" CA HIS E 117 " pdb=" CB HIS E 117 " ideal model delta harmonic sigma weight residual -122.60 -139.00 16.40 0 2.50e+00 1.60e-01 4.30e+01 ... (remaining 13676 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.102: 2148 0.102 - 0.204: 116 0.204 - 0.306: 15 0.306 - 0.408: 4 0.408 - 0.510: 1 Chirality restraints: 2284 Sorted by residual: chirality pdb=" CA HIS E 117 " pdb=" N HIS E 117 " pdb=" C HIS E 117 " pdb=" CB HIS E 117 " both_signs ideal model delta sigma weight residual False 2.51 2.00 0.51 2.00e-01 2.50e+01 6.50e+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 -0.39 2.00e-01 2.50e+01 3.90e+00 chirality pdb=" CA PRO E 192 " pdb=" N PRO E 192 " pdb=" C PRO E 192 " pdb=" CB PRO E 192 " both_signs ideal model delta sigma weight residual False 2.72 3.08 -0.36 2.00e-01 2.50e+01 3.29e+00 ... (remaining 2281 not shown) Planarity restraints: 4301 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG E 189 " -0.041 2.00e-02 2.50e+03 8.10e-02 6.55e+01 pdb=" C ARG E 189 " 0.140 2.00e-02 2.50e+03 pdb=" O ARG E 189 " -0.052 2.00e-02 2.50e+03 pdb=" N LYS E 190 " -0.048 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS K 96 " 0.056 2.00e-02 2.50e+03 4.00e-02 3.60e+01 pdb=" CG HIS K 96 " -0.069 2.00e-02 2.50e+03 pdb=" ND1 HIS K 96 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 HIS K 96 " -0.053 2.00e-02 2.50e+03 pdb=" CE1 HIS K 96 " -0.006 2.00e-02 2.50e+03 pdb=" NE2 HIS K 96 " 0.060 2.00e-02 2.50e+03 pdb=" HD1 HIS K 96 " -0.001 2.00e-02 2.50e+03 pdb=" HD2 HIS K 96 " 0.009 2.00e-02 2.50e+03 pdb=" HE1 HIS K 96 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE K 184 " -0.014 2.00e-02 2.50e+03 2.57e-02 1.98e+01 pdb=" CG PHE K 184 " 0.067 2.00e-02 2.50e+03 pdb=" CD1 PHE K 184 " -0.021 2.00e-02 2.50e+03 pdb=" CD2 PHE K 184 " -0.049 2.00e-02 2.50e+03 pdb=" CE1 PHE K 184 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE K 184 " 0.018 2.00e-02 2.50e+03 pdb=" CZ PHE K 184 " -0.001 2.00e-02 2.50e+03 pdb=" HD1 PHE K 184 " -0.000 2.00e-02 2.50e+03 pdb=" HD2 PHE K 184 " 0.005 2.00e-02 2.50e+03 pdb=" HE1 PHE K 184 " -0.003 2.00e-02 2.50e+03 pdb=" HE2 PHE K 184 " -0.004 2.00e-02 2.50e+03 pdb=" HZ PHE K 184 " 0.004 2.00e-02 2.50e+03 ... (remaining 4298 not shown) Histogram of nonbonded interaction distances: 1.10 - 1.80: 100 1.80 - 2.50: 21129 2.50 - 3.20: 89388 3.20 - 3.90: 116935 3.90 - 4.60: 184749 Nonbonded interactions: 412301 Sorted by model distance: nonbonded pdb=" H LYS F 36 " pdb=" O TYR M 40 " model vdw 1.103 2.450 nonbonded pdb="HD21 ASN K 149 " pdb=" N GLY E 160 " model vdw 1.199 2.600 nonbonded pdb=" HB2 GLN A 156 " pdb=" HG3 GLN M 34 " model vdw 1.227 2.440 nonbonded pdb=" HB THR K 265 " pdb=" CB VAL E 162 " model vdw 1.285 2.920 nonbonded pdb=" HE2 PHE I 30 " pdb="HD12 LEU M 63 " model vdw 1.335 2.270 ... (remaining 412296 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.400 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: 0.170 Extract box with map and model: 0.390 Check model and map are aligned: 0.100 Set scattering table: 0.060 Process input model: 28.380 Find NCS groups from input model: 0.120 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: 0.000 Load rotamer database and sin/cos tables:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6543 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.315 15083 Z= 0.383 Angle : 0.824 17.696 20546 Z= 0.536 Chirality : 0.053 0.510 2284 Planarity : 0.005 0.081 2625 Dihedral : 13.600 176.404 5270 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.32 % Allowed : 4.35 % Favored : 95.34 % Rotamer: Outliers : 0.27 % Allowed : 0.20 % Favored : 99.53 % 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: 0.14 (0.20), residues: 1887 helix: 0.55 (0.17), residues: 970 sheet: -0.60 (0.38), residues: 174 loop : -0.15 (0.24), residues: 743 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 282 TYR 0.023 0.002 TYR K 132 PHE 0.068 0.002 PHE K 184 TRP 0.012 0.001 TRP K 142 HIS 0.037 0.001 HIS K 96 Details of bonding type rmsd covalent geometry : bond 0.00671 (15075) covalent geometry : angle 0.82380 (20544) SS BOND : bond 0.00034 ( 1) SS BOND : angle 0.75220 ( 2) hydrogen bonds : bond 0.14207 ( 836) hydrogen bonds : angle 6.64717 ( 2379) Misc. bond : bond 0.12128 ( 7) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3774 Ramachandran restraints generated. 1887 Oldfield, 0 Emsley, 1887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3774 Ramachandran restraints generated. 1887 Oldfield, 0 Emsley, 1887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 112 is missing expected H atoms. Skipping. Residue LYS 124 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue TYR 43 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue SER 214 is missing expected H atoms. Skipping. Residue LYS 218 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue TYR 32 is missing expected H atoms. Skipping. Evaluate side-chains 372 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 368 time to evaluate : 0.719 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 GLU cc_start: 0.7064 (tm-30) cc_final: 0.6626 (tt0) REVERT: A 126 LYS cc_start: 0.7446 (ttpp) cc_final: 0.7190 (tppt) REVERT: A 174 LEU cc_start: 0.8971 (mt) cc_final: 0.8754 (mt) REVERT: A 252 GLU cc_start: 0.8145 (mm-30) cc_final: 0.7834 (mm-30) REVERT: A 256 SER cc_start: 0.8715 (m) cc_final: 0.8313 (p) REVERT: A 276 SER cc_start: 0.8410 (t) cc_final: 0.8197 (p) REVERT: A 391 LYS cc_start: 0.8051 (ttmm) cc_final: 0.7849 (mtpt) REVERT: A 396 LYS cc_start: 0.7654 (mmtt) cc_final: 0.7351 (mppt) REVERT: K 52 MET cc_start: 0.8702 (mtt) cc_final: 0.8445 (mtm) REVERT: K 60 LEU cc_start: 0.7876 (mt) cc_final: 0.7554 (mt) REVERT: K 261 ASN cc_start: 0.7427 (t0) cc_final: 0.7206 (t0) REVERT: D 79 ARG cc_start: 0.7561 (mtp-110) cc_final: 0.6873 (mtp85) REVERT: D 193 SER cc_start: 0.8023 (m) cc_final: 0.7804 (p) REVERT: D 231 ASP cc_start: 0.8255 (m-30) cc_final: 0.8035 (m-30) REVERT: D 241 GLU cc_start: 0.8412 (mt-10) cc_final: 0.8176 (mt-10) REVERT: D 246 ASP cc_start: 0.7957 (m-30) cc_final: 0.7657 (m-30) REVERT: G 31 LYS cc_start: 0.8125 (ttmm) cc_final: 0.6565 (tmtt) REVERT: G 61 LYS cc_start: 0.7570 (tmmt) cc_final: 0.6931 (ttmt) REVERT: G 92 LYS cc_start: 0.8068 (mtpt) cc_final: 0.7766 (mtmm) REVERT: F 27 GLN cc_start: 0.7690 (mt0) cc_final: 0.7473 (tt0) REVERT: H 91 GLU cc_start: 0.7891 (mm-30) cc_final: 0.7594 (mm-30) REVERT: I 36 LYS cc_start: 0.8176 (ttpp) cc_final: 0.7703 (ttmm) REVERT: I 53 LYS cc_start: 0.8507 (mtpp) cc_final: 0.8209 (mtpt) REVERT: B 113 GLN cc_start: 0.8169 (tt0) cc_final: 0.7904 (tp40) REVERT: B 132 LYS cc_start: 0.7791 (ttpp) cc_final: 0.7590 (ttmt) REVERT: B 152 ARG cc_start: 0.7169 (mtt180) cc_final: 0.6413 (mmm160) REVERT: B 190 GLU cc_start: 0.7230 (mt-10) cc_final: 0.6858 (mt-10) REVERT: B 208 TYR cc_start: 0.5797 (m-80) cc_final: 0.5448 (m-80) REVERT: B 238 SER cc_start: 0.8418 (m) cc_final: 0.8059 (t) REVERT: B 370 TYR cc_start: 0.7765 (m-80) cc_final: 0.7418 (m-80) REVERT: E 86 LEU cc_start: 0.7858 (OUTLIER) cc_final: 0.7594 (mt) outliers start: 4 outliers final: 0 residues processed: 370 average time/residue: 0.2801 time to fit residues: 148.8922 Evaluate side-chains 264 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 263 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 86 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 98 optimal weight: 0.5980 chunk 107 optimal weight: 0.5980 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.1980 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 0.9980 chunk 149 optimal weight: 1.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 HIS A 255 ASN K 14 ASN K 84 ASN ** K 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 150 ASN B 15 ASN B 223 ASN B 287 GLN M 34 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.163084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.144120 restraints weight = 52452.875| |-----------------------------------------------------------------------------| r_work (start): 0.3585 rms_B_bonded: 1.95 r_work: 0.3470 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3354 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.2196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.348 15083 Z= 0.160 Angle : 0.596 12.007 20546 Z= 0.306 Chirality : 0.040 0.160 2284 Planarity : 0.004 0.051 2625 Dihedral : 8.014 175.651 2086 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 0.60 % Allowed : 6.38 % Favored : 93.02 % 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: 0.58 (0.20), residues: 1887 helix: 1.00 (0.16), residues: 984 sheet: -0.58 (0.39), residues: 173 loop : -0.06 (0.25), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 92 TYR 0.016 0.001 TYR B 254 PHE 0.014 0.001 PHE K 227 TRP 0.012 0.001 TRP K 142 HIS 0.008 0.001 HIS K 96 Details of bonding type rmsd covalent geometry : bond 0.00354 (15075) covalent geometry : angle 0.59611 (20544) SS BOND : bond 0.00185 ( 1) SS BOND : angle 0.42478 ( 2) hydrogen bonds : bond 0.04664 ( 836) hydrogen bonds : angle 4.96308 ( 2379) Misc. bond : bond 0.15563 ( 7) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3774 Ramachandran restraints generated. 1887 Oldfield, 0 Emsley, 1887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3774 Ramachandran restraints generated. 1887 Oldfield, 0 Emsley, 1887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 112 is missing expected H atoms. Skipping. Residue LYS 124 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue TYR 43 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue SER 214 is missing expected H atoms. Skipping. Residue LYS 218 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue TYR 32 is missing expected H atoms. Skipping. Evaluate side-chains 281 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 272 time to evaluate : 0.722 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 GLU cc_start: 0.7877 (tm-30) cc_final: 0.7524 (tt0) REVERT: A 252 GLU cc_start: 0.8282 (mm-30) cc_final: 0.7987 (mm-30) REVERT: K 152 SER cc_start: 0.7748 (t) cc_final: 0.7473 (p) REVERT: K 218 ARG cc_start: 0.8913 (mtt-85) cc_final: 0.8696 (mtt180) REVERT: D 79 ARG cc_start: 0.8091 (mtp-110) cc_final: 0.7603 (mtp85) REVERT: D 105 GLU cc_start: 0.8761 (mt-10) cc_final: 0.8478 (mt-10) REVERT: D 144 GLN cc_start: 0.8511 (tp40) cc_final: 0.8262 (tm-30) REVERT: D 243 GLU cc_start: 0.8110 (pm20) cc_final: 0.7580 (pm20) REVERT: G 61 LYS cc_start: 0.8141 (tmmt) cc_final: 0.7765 (ttmt) REVERT: F 27 GLN cc_start: 0.8317 (mt0) cc_final: 0.8115 (tt0) REVERT: I 36 LYS cc_start: 0.8442 (ttpp) cc_final: 0.8010 (ttmm) REVERT: B 152 ARG cc_start: 0.8035 (mtt180) cc_final: 0.6545 (mmm160) REVERT: B 208 TYR cc_start: 0.6135 (m-80) cc_final: 0.5768 (m-80) REVERT: B 225 PHE cc_start: 0.7234 (m-80) cc_final: 0.6779 (m-10) REVERT: B 238 SER cc_start: 0.8624 (m) cc_final: 0.8424 (t) REVERT: B 356 LYS cc_start: 0.8690 (mmmt) cc_final: 0.8348 (mmmm) REVERT: B 370 TYR cc_start: 0.8534 (m-80) cc_final: 0.7989 (m-80) outliers start: 9 outliers final: 8 residues processed: 278 average time/residue: 0.2872 time to fit residues: 114.6508 Evaluate side-chains 242 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 234 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 288 SER Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain E residue 82 SER Chi-restraints excluded: chain E residue 86 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 1 optimal weight: 2.9990 chunk 74 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 37 optimal weight: 0.5980 chunk 9 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 186 optimal weight: 30.0000 chunk 146 optimal weight: 1.9990 chunk 182 optimal weight: 20.0000 chunk 127 optimal weight: 6.9990 chunk 156 optimal weight: 0.6980 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 HIS K 84 ASN ** K 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 375 ASN ** D 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 84 HIS B 287 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.130545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.110565 restraints weight = 54070.432| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 2.05 r_work: 0.3091 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2974 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.3167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.340 15083 Z= 0.216 Angle : 0.606 11.000 20546 Z= 0.311 Chirality : 0.041 0.156 2284 Planarity : 0.004 0.047 2625 Dihedral : 7.674 178.961 2086 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 1.34 % Allowed : 7.92 % Favored : 90.73 % 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: 0.67 (0.20), residues: 1887 helix: 1.29 (0.17), residues: 972 sheet: -0.92 (0.38), residues: 170 loop : -0.25 (0.24), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 92 TYR 0.019 0.002 TYR K 358 PHE 0.017 0.001 PHE K 278 TRP 0.018 0.001 TRP K 142 HIS 0.009 0.002 HIS D 48 Details of bonding type rmsd covalent geometry : bond 0.00493 (15075) covalent geometry : angle 0.60647 (20544) SS BOND : bond 0.00155 ( 1) SS BOND : angle 0.32611 ( 2) hydrogen bonds : bond 0.04451 ( 836) hydrogen bonds : angle 4.69415 ( 2379) Misc. bond : bond 0.14700 ( 7) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3774 Ramachandran restraints generated. 1887 Oldfield, 0 Emsley, 1887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3774 Ramachandran restraints generated. 1887 Oldfield, 0 Emsley, 1887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 112 is missing expected H atoms. Skipping. Residue LYS 124 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue TYR 43 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue SER 214 is missing expected H atoms. Skipping. Residue LYS 218 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue TYR 32 is missing expected H atoms. Skipping. Evaluate side-chains 271 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 251 time to evaluate : 0.749 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 GLU cc_start: 0.7921 (tm-30) cc_final: 0.7533 (tt0) REVERT: A 210 GLU cc_start: 0.8111 (tm-30) cc_final: 0.7622 (tp30) REVERT: A 252 GLU cc_start: 0.8586 (mm-30) cc_final: 0.8217 (mm-30) REVERT: A 396 LYS cc_start: 0.8157 (mppt) cc_final: 0.7752 (mtmm) REVERT: D 79 ARG cc_start: 0.8083 (mtp-110) cc_final: 0.7531 (mtp85) REVERT: D 131 LYS cc_start: 0.8042 (ptpt) cc_final: 0.7447 (pttm) REVERT: D 144 GLN cc_start: 0.8608 (tp40) cc_final: 0.8333 (tm-30) REVERT: F 54 LYS cc_start: 0.8252 (tttp) cc_final: 0.7731 (tppt) REVERT: H 67 ASP cc_start: 0.7236 (m-30) cc_final: 0.6951 (m-30) REVERT: I 36 LYS cc_start: 0.8615 (ttpp) cc_final: 0.8186 (ttmm) REVERT: I 53 LYS cc_start: 0.8484 (mtpt) cc_final: 0.8270 (mtpt) REVERT: B 152 ARG cc_start: 0.8456 (mtt180) cc_final: 0.6661 (mmm160) REVERT: B 190 GLU cc_start: 0.7670 (mt-10) cc_final: 0.7418 (mt-10) REVERT: B 193 ASN cc_start: 0.8028 (t0) cc_final: 0.7748 (t0) REVERT: B 204 SER cc_start: 0.8504 (p) cc_final: 0.8220 (p) REVERT: B 208 TYR cc_start: 0.6421 (m-80) cc_final: 0.5823 (m-80) REVERT: B 225 PHE cc_start: 0.7478 (m-80) cc_final: 0.7080 (m-10) REVERT: B 238 SER cc_start: 0.8938 (m) cc_final: 0.8591 (t) REVERT: B 356 LYS cc_start: 0.8842 (mmmt) cc_final: 0.8515 (mmmm) outliers start: 20 outliers final: 14 residues processed: 264 average time/residue: 0.2801 time to fit residues: 106.5980 Evaluate side-chains 252 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 238 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 288 SER Chi-restraints excluded: chain G residue 60 ILE Chi-restraints excluded: chain I residue 40 GLU Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 199 LYS Chi-restraints excluded: chain B residue 229 GLU Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain E residue 82 SER Chi-restraints excluded: chain E residue 86 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 109 optimal weight: 0.5980 chunk 21 optimal weight: 2.9990 chunk 178 optimal weight: 5.9990 chunk 8 optimal weight: 2.9990 chunk 99 optimal weight: 0.9990 chunk 101 optimal weight: 1.9990 chunk 133 optimal weight: 0.9990 chunk 105 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 162 optimal weight: 1.9990 chunk 157 optimal weight: 1.9990 overall best weight: 1.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 HIS A 156 GLN K 57 ASN ** K 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 47 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.128285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.108591 restraints weight = 54653.222| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 2.08 r_work: 0.3118 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3001 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.3640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.264 15083 Z= 0.205 Angle : 0.566 9.767 20546 Z= 0.293 Chirality : 0.040 0.153 2284 Planarity : 0.004 0.038 2625 Dihedral : 7.532 178.000 2086 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.21 % Allowed : 8.87 % Favored : 89.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.20), residues: 1887 helix: 1.34 (0.16), residues: 975 sheet: -0.96 (0.39), residues: 168 loop : -0.24 (0.24), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 279 TYR 0.014 0.001 TYR K 279 PHE 0.013 0.001 PHE A 48 TRP 0.016 0.001 TRP K 142 HIS 0.008 0.001 HIS K 197 Details of bonding type rmsd covalent geometry : bond 0.00468 (15075) covalent geometry : angle 0.56616 (20544) SS BOND : bond 0.00128 ( 1) SS BOND : angle 0.43266 ( 2) hydrogen bonds : bond 0.04079 ( 836) hydrogen bonds : angle 4.59622 ( 2379) Misc. bond : bond 0.13316 ( 7) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3774 Ramachandran restraints generated. 1887 Oldfield, 0 Emsley, 1887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3774 Ramachandran restraints generated. 1887 Oldfield, 0 Emsley, 1887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 112 is missing expected H atoms. Skipping. Residue LYS 124 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue TYR 43 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue SER 214 is missing expected H atoms. Skipping. Residue LYS 218 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue TYR 32 is missing expected H atoms. Skipping. Evaluate side-chains 261 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 243 time to evaluate : 0.751 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 GLU cc_start: 0.7922 (tm-30) cc_final: 0.7540 (tt0) REVERT: A 396 LYS cc_start: 0.8184 (mppt) cc_final: 0.7768 (mtmm) REVERT: D 79 ARG cc_start: 0.8052 (mtp-110) cc_final: 0.7569 (mtp85) REVERT: D 144 GLN cc_start: 0.8622 (tp40) cc_final: 0.8360 (tm-30) REVERT: D 151 GLN cc_start: 0.8715 (mp10) cc_final: 0.8299 (mp10) REVERT: G 109 GLU cc_start: 0.7851 (tp30) cc_final: 0.7272 (mt-10) REVERT: F 54 LYS cc_start: 0.8206 (tttp) cc_final: 0.7722 (tppt) REVERT: H 67 ASP cc_start: 0.7279 (m-30) cc_final: 0.6978 (m-30) REVERT: I 36 LYS cc_start: 0.8652 (ttpp) cc_final: 0.8219 (ttmm) REVERT: B 152 ARG cc_start: 0.8560 (mtt180) cc_final: 0.6671 (mmm160) REVERT: B 190 GLU cc_start: 0.7924 (mt-10) cc_final: 0.7596 (mt-10) REVERT: B 204 SER cc_start: 0.8673 (p) cc_final: 0.8445 (p) REVERT: B 225 PHE cc_start: 0.7628 (m-80) cc_final: 0.7240 (m-10) REVERT: B 238 SER cc_start: 0.8963 (m) cc_final: 0.8595 (t) REVERT: B 356 LYS cc_start: 0.8782 (mmmt) cc_final: 0.8460 (mmmm) REVERT: M 60 MET cc_start: 0.8761 (ttm) cc_final: 0.8496 (ttm) outliers start: 18 outliers final: 16 residues processed: 254 average time/residue: 0.2849 time to fit residues: 104.5336 Evaluate side-chains 251 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 235 time to evaluate : 0.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain K residue 152 SER Chi-restraints excluded: chain K residue 364 ILE Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain G residue 60 ILE Chi-restraints excluded: chain I residue 32 VAL Chi-restraints excluded: chain I residue 40 GLU Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain E residue 82 SER Chi-restraints excluded: chain E residue 86 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 80 optimal weight: 0.0020 chunk 186 optimal weight: 30.0000 chunk 24 optimal weight: 1.9990 chunk 143 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 18 optimal weight: 0.5980 chunk 42 optimal weight: 1.9990 chunk 124 optimal weight: 4.9990 chunk 167 optimal weight: 2.9990 chunk 170 optimal weight: 3.9990 chunk 183 optimal weight: 20.0000 overall best weight: 1.3194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 HIS ** K 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 150 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.125757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.106608 restraints weight = 55046.281| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 2.06 r_work: 0.3091 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2975 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.3908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.285 15083 Z= 0.210 Angle : 0.564 10.030 20546 Z= 0.291 Chirality : 0.040 0.152 2284 Planarity : 0.004 0.037 2625 Dihedral : 7.460 178.884 2086 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 1.41 % Allowed : 9.67 % Favored : 88.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.74 (0.20), residues: 1887 helix: 1.40 (0.17), residues: 976 sheet: -1.04 (0.38), residues: 175 loop : -0.23 (0.24), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 279 TYR 0.019 0.001 TYR H 107 PHE 0.014 0.001 PHE K 278 TRP 0.016 0.001 TRP K 142 HIS 0.006 0.001 HIS K 197 Details of bonding type rmsd covalent geometry : bond 0.00484 (15075) covalent geometry : angle 0.56374 (20544) SS BOND : bond 0.00004 ( 1) SS BOND : angle 0.28014 ( 2) hydrogen bonds : bond 0.04095 ( 836) hydrogen bonds : angle 4.56948 ( 2379) Misc. bond : bond 0.13181 ( 7) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3774 Ramachandran restraints generated. 1887 Oldfield, 0 Emsley, 1887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3774 Ramachandran restraints generated. 1887 Oldfield, 0 Emsley, 1887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 112 is missing expected H atoms. Skipping. Residue LYS 124 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue TYR 43 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue SER 214 is missing expected H atoms. Skipping. Residue LYS 218 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue TYR 32 is missing expected H atoms. Skipping. Evaluate side-chains 263 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 242 time to evaluate : 0.882 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 GLU cc_start: 0.7974 (tm-30) cc_final: 0.7588 (tt0) REVERT: A 396 LYS cc_start: 0.8212 (mppt) cc_final: 0.7976 (mtmm) REVERT: K 7 ASN cc_start: 0.8099 (t0) cc_final: 0.7870 (t0) REVERT: D 79 ARG cc_start: 0.8137 (mtp-110) cc_final: 0.7667 (mtp85) REVERT: D 143 GLU cc_start: 0.8282 (tt0) cc_final: 0.8043 (tt0) REVERT: D 144 GLN cc_start: 0.8633 (tp40) cc_final: 0.8394 (tm-30) REVERT: D 151 GLN cc_start: 0.8699 (mp10) cc_final: 0.8257 (mp10) REVERT: G 98 GLU cc_start: 0.7804 (mt-10) cc_final: 0.7492 (mt-10) REVERT: G 109 GLU cc_start: 0.7863 (tp30) cc_final: 0.7437 (tp30) REVERT: F 54 LYS cc_start: 0.8157 (tttp) cc_final: 0.7701 (tppt) REVERT: H 67 ASP cc_start: 0.7255 (m-30) cc_final: 0.6928 (m-30) REVERT: I 36 LYS cc_start: 0.8720 (ttpp) cc_final: 0.8322 (ttmm) REVERT: B 152 ARG cc_start: 0.8637 (mtt180) cc_final: 0.6673 (mmm160) REVERT: B 190 GLU cc_start: 0.7949 (mt-10) cc_final: 0.7651 (mt-10) REVERT: B 204 SER cc_start: 0.8702 (p) cc_final: 0.8453 (p) REVERT: B 356 LYS cc_start: 0.8815 (mmmt) cc_final: 0.8507 (mmmm) REVERT: M 60 MET cc_start: 0.8840 (ttm) cc_final: 0.8442 (ttp) outliers start: 21 outliers final: 18 residues processed: 255 average time/residue: 0.2892 time to fit residues: 106.4631 Evaluate side-chains 251 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 233 time to evaluate : 0.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain K residue 152 SER Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain G residue 60 ILE Chi-restraints excluded: chain I residue 32 VAL Chi-restraints excluded: chain I residue 40 GLU Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 118 GLU Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain E residue 82 SER Chi-restraints excluded: chain E residue 86 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 94 optimal weight: 1.9990 chunk 135 optimal weight: 1.9990 chunk 57 optimal weight: 0.0970 chunk 183 optimal weight: 9.9990 chunk 52 optimal weight: 0.9980 chunk 84 optimal weight: 1.9990 chunk 121 optimal weight: 0.6980 chunk 165 optimal weight: 1.9990 chunk 181 optimal weight: 20.0000 chunk 70 optimal weight: 1.9990 chunk 147 optimal weight: 1.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 HIS ** A 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 398 ASN ** K 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 86 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.125915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.106197 restraints weight = 54619.871| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 2.21 r_work: 0.3152 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3032 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.4099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.290 15083 Z= 0.189 Angle : 0.556 9.791 20546 Z= 0.284 Chirality : 0.039 0.150 2284 Planarity : 0.004 0.036 2625 Dihedral : 7.338 178.589 2086 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 1.48 % Allowed : 10.21 % Favored : 88.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.80 (0.20), residues: 1887 helix: 1.45 (0.17), residues: 976 sheet: -1.07 (0.37), residues: 175 loop : -0.21 (0.24), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 429 TYR 0.013 0.001 TYR F 82 PHE 0.016 0.001 PHE K 121 TRP 0.016 0.001 TRP K 142 HIS 0.006 0.001 HIS K 197 Details of bonding type rmsd covalent geometry : bond 0.00436 (15075) covalent geometry : angle 0.55576 (20544) SS BOND : bond 0.00077 ( 1) SS BOND : angle 0.45092 ( 2) hydrogen bonds : bond 0.04003 ( 836) hydrogen bonds : angle 4.49753 ( 2379) Misc. bond : bond 0.14375 ( 7) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3774 Ramachandran restraints generated. 1887 Oldfield, 0 Emsley, 1887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3774 Ramachandran restraints generated. 1887 Oldfield, 0 Emsley, 1887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 112 is missing expected H atoms. Skipping. Residue LYS 124 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue TYR 43 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue SER 214 is missing expected H atoms. Skipping. Residue LYS 218 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue TYR 32 is missing expected H atoms. Skipping. Evaluate side-chains 265 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 243 time to evaluate : 0.718 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 GLU cc_start: 0.8021 (tm-30) cc_final: 0.7632 (tt0) REVERT: A 396 LYS cc_start: 0.8212 (mppt) cc_final: 0.7877 (mtmm) REVERT: D 79 ARG cc_start: 0.8110 (mtp-110) cc_final: 0.7652 (mtp85) REVERT: D 143 GLU cc_start: 0.8265 (tt0) cc_final: 0.7904 (tt0) REVERT: D 144 GLN cc_start: 0.8652 (tp40) cc_final: 0.8409 (tm-30) REVERT: D 151 GLN cc_start: 0.8725 (mp10) cc_final: 0.8258 (mp10) REVERT: G 98 GLU cc_start: 0.7842 (mt-10) cc_final: 0.7522 (mt-10) REVERT: G 109 GLU cc_start: 0.7909 (tp30) cc_final: 0.7484 (tp30) REVERT: F 54 LYS cc_start: 0.8151 (tttp) cc_final: 0.7690 (tppt) REVERT: H 67 ASP cc_start: 0.7290 (m-30) cc_final: 0.6953 (m-30) REVERT: I 36 LYS cc_start: 0.8723 (ttpp) cc_final: 0.8324 (ttmm) REVERT: B 152 ARG cc_start: 0.8630 (mtt180) cc_final: 0.6722 (mmm160) REVERT: B 190 GLU cc_start: 0.7941 (mt-10) cc_final: 0.7636 (mt-10) REVERT: B 204 SER cc_start: 0.8738 (p) cc_final: 0.8482 (p) REVERT: B 238 SER cc_start: 0.9005 (m) cc_final: 0.8634 (t) REVERT: B 356 LYS cc_start: 0.8819 (mmmt) cc_final: 0.8502 (mmmm) REVERT: M 60 MET cc_start: 0.8840 (ttm) cc_final: 0.8506 (ttp) outliers start: 22 outliers final: 19 residues processed: 258 average time/residue: 0.2823 time to fit residues: 104.7523 Evaluate side-chains 250 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 231 time to evaluate : 0.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 288 SER Chi-restraints excluded: chain K residue 152 SER Chi-restraints excluded: chain G residue 60 ILE Chi-restraints excluded: chain I residue 32 VAL Chi-restraints excluded: chain I residue 40 GLU Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 118 GLU Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain E residue 82 SER Chi-restraints excluded: chain E residue 86 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 184 optimal weight: 8.9990 chunk 97 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 52 optimal weight: 0.4980 chunk 122 optimal weight: 2.9990 chunk 182 optimal weight: 20.0000 chunk 76 optimal weight: 1.9990 chunk 133 optimal weight: 0.9990 chunk 149 optimal weight: 1.9990 chunk 68 optimal weight: 0.6980 chunk 137 optimal weight: 1.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 HIS ** A 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 149 ASN ** 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 = 0.3365 r_free = 0.3365 target = 0.126211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.105868 restraints weight = 54235.203| |-----------------------------------------------------------------------------| r_work (start): 0.3499 rms_B_bonded: 2.38 r_work: 0.3359 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3237 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.4256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.260 15083 Z= 0.176 Angle : 0.550 9.665 20546 Z= 0.281 Chirality : 0.039 0.149 2284 Planarity : 0.004 0.072 2625 Dihedral : 7.177 171.747 2086 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 1.48 % Allowed : 10.68 % Favored : 87.84 % 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: 0.86 (0.20), residues: 1887 helix: 1.51 (0.17), residues: 977 sheet: -1.05 (0.38), residues: 175 loop : -0.18 (0.24), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 282 TYR 0.013 0.001 TYR F 82 PHE 0.013 0.001 PHE K 121 TRP 0.016 0.001 TRP K 142 HIS 0.005 0.001 HIS K 197 Details of bonding type rmsd covalent geometry : bond 0.00404 (15075) covalent geometry : angle 0.55037 (20544) SS BOND : bond 0.00045 ( 1) SS BOND : angle 0.46742 ( 2) hydrogen bonds : bond 0.03946 ( 836) hydrogen bonds : angle 4.44873 ( 2379) Misc. bond : bond 0.13318 ( 7) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3774 Ramachandran restraints generated. 1887 Oldfield, 0 Emsley, 1887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3774 Ramachandran restraints generated. 1887 Oldfield, 0 Emsley, 1887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 112 is missing expected H atoms. Skipping. Residue LYS 124 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue TYR 43 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue SER 214 is missing expected H atoms. Skipping. Residue LYS 218 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue TYR 32 is missing expected H atoms. Skipping. Evaluate side-chains 261 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 239 time to evaluate : 0.737 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 GLU cc_start: 0.8089 (tm-30) cc_final: 0.7708 (tt0) REVERT: A 396 LYS cc_start: 0.8278 (mppt) cc_final: 0.8002 (mtmm) REVERT: D 79 ARG cc_start: 0.8190 (mtp-110) cc_final: 0.7767 (mtp85) REVERT: D 143 GLU cc_start: 0.8173 (tt0) cc_final: 0.7833 (tt0) REVERT: D 151 GLN cc_start: 0.8665 (mp10) cc_final: 0.8261 (mp10) REVERT: G 98 GLU cc_start: 0.7897 (mt-10) cc_final: 0.7617 (mt-10) REVERT: G 109 GLU cc_start: 0.7975 (tp30) cc_final: 0.7731 (tp30) REVERT: F 54 LYS cc_start: 0.8200 (tttp) cc_final: 0.7816 (tppt) REVERT: H 67 ASP cc_start: 0.7194 (m-30) cc_final: 0.6885 (m-30) REVERT: H 102 TYR cc_start: 0.8017 (t80) cc_final: 0.7115 (t80) REVERT: I 36 LYS cc_start: 0.8756 (ttpp) cc_final: 0.8393 (ttmm) REVERT: B 152 ARG cc_start: 0.8634 (mtt180) cc_final: 0.6765 (mmm160) REVERT: B 190 GLU cc_start: 0.7917 (mt-10) cc_final: 0.7648 (mt-10) REVERT: B 204 SER cc_start: 0.8785 (p) cc_final: 0.8555 (p) REVERT: B 238 SER cc_start: 0.8949 (m) cc_final: 0.8635 (t) REVERT: B 356 LYS cc_start: 0.8776 (mmmt) cc_final: 0.8496 (mmmm) REVERT: M 60 MET cc_start: 0.8855 (ttm) cc_final: 0.8598 (ttp) outliers start: 22 outliers final: 21 residues processed: 253 average time/residue: 0.2986 time to fit residues: 106.9913 Evaluate side-chains 254 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 233 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 288 SER Chi-restraints excluded: chain K residue 152 SER Chi-restraints excluded: chain K residue 226 ILE Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain G residue 18 ARG Chi-restraints excluded: chain G residue 60 ILE Chi-restraints excluded: chain I residue 32 VAL Chi-restraints excluded: chain I residue 40 GLU Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 118 GLU Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain E residue 82 SER Chi-restraints excluded: chain E residue 86 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 81 optimal weight: 0.5980 chunk 18 optimal weight: 1.9990 chunk 91 optimal weight: 0.9990 chunk 153 optimal weight: 0.9990 chunk 109 optimal weight: 0.0060 chunk 60 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 156 optimal weight: 0.5980 chunk 75 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 HIS ** A 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 149 ASN ** 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 = 0.3370 r_free = 0.3370 target = 0.126820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.107030 restraints weight = 54245.510| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 2.23 r_work: 0.3113 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2996 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.4353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.206 15083 Z= 0.134 Angle : 0.527 9.484 20546 Z= 0.268 Chirality : 0.038 0.150 2284 Planarity : 0.004 0.059 2625 Dihedral : 7.065 173.343 2086 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 1.88 % Allowed : 10.88 % Favored : 87.24 % 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: 1.00 (0.20), residues: 1887 helix: 1.64 (0.17), residues: 982 sheet: -1.04 (0.38), residues: 175 loop : -0.13 (0.24), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 282 TYR 0.012 0.001 TYR F 82 PHE 0.014 0.001 PHE A 327 TRP 0.014 0.001 TRP K 142 HIS 0.003 0.001 HIS D 59 Details of bonding type rmsd covalent geometry : bond 0.00308 (15075) covalent geometry : angle 0.52677 (20544) SS BOND : bond 0.00075 ( 1) SS BOND : angle 0.53921 ( 2) hydrogen bonds : bond 0.03760 ( 836) hydrogen bonds : angle 4.34463 ( 2379) Misc. bond : bond 0.10860 ( 7) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3774 Ramachandran restraints generated. 1887 Oldfield, 0 Emsley, 1887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3774 Ramachandran restraints generated. 1887 Oldfield, 0 Emsley, 1887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 112 is missing expected H atoms. Skipping. Residue LYS 124 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue TYR 43 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue SER 214 is missing expected H atoms. Skipping. Residue LYS 218 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue TYR 32 is missing expected H atoms. Skipping. Evaluate side-chains 274 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 246 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: A 35 GLU cc_start: 0.8031 (tm-30) cc_final: 0.7662 (tt0) REVERT: A 191 ASN cc_start: 0.8728 (t0) cc_final: 0.7976 (t0) REVERT: A 236 ARG cc_start: 0.8332 (OUTLIER) cc_final: 0.7250 (ttt90) REVERT: A 396 LYS cc_start: 0.8212 (mppt) cc_final: 0.7981 (mtmm) REVERT: K 162 VAL cc_start: 0.8510 (OUTLIER) cc_final: 0.8276 (t) REVERT: D 79 ARG cc_start: 0.8123 (mtp-110) cc_final: 0.7634 (mtp85) REVERT: D 143 GLU cc_start: 0.8290 (tt0) cc_final: 0.7856 (tt0) REVERT: D 151 GLN cc_start: 0.8680 (mp10) cc_final: 0.8202 (mp10) REVERT: G 98 GLU cc_start: 0.7867 (mt-10) cc_final: 0.7581 (mt-10) REVERT: G 109 GLU cc_start: 0.7852 (tp30) cc_final: 0.7205 (mt-10) REVERT: F 54 LYS cc_start: 0.8169 (tttp) cc_final: 0.7712 (tppt) REVERT: H 67 ASP cc_start: 0.7296 (m-30) cc_final: 0.6970 (m-30) REVERT: I 36 LYS cc_start: 0.8752 (ttpp) cc_final: 0.8356 (ttmm) REVERT: B 152 ARG cc_start: 0.8520 (mtt180) cc_final: 0.6630 (mmm160) REVERT: B 204 SER cc_start: 0.8759 (p) cc_final: 0.8507 (p) REVERT: B 238 SER cc_start: 0.8947 (m) cc_final: 0.8580 (t) REVERT: B 356 LYS cc_start: 0.8817 (mmmt) cc_final: 0.8498 (mmmm) REVERT: M 60 MET cc_start: 0.8822 (ttm) cc_final: 0.8564 (ttp) outliers start: 28 outliers final: 23 residues processed: 265 average time/residue: 0.3000 time to fit residues: 113.9163 Evaluate side-chains 262 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 237 time to evaluate : 0.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 236 ARG Chi-restraints excluded: chain A residue 288 SER Chi-restraints excluded: chain K residue 152 SER Chi-restraints excluded: chain K residue 162 VAL Chi-restraints excluded: chain K residue 226 ILE Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain D residue 118 GLU Chi-restraints excluded: chain G residue 18 ARG Chi-restraints excluded: chain G residue 60 ILE Chi-restraints excluded: chain I residue 32 VAL Chi-restraints excluded: chain I residue 40 GLU Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 118 GLU Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain E residue 82 SER Chi-restraints excluded: chain E residue 86 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 133 optimal weight: 0.7980 chunk 46 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 chunk 61 optimal weight: 0.9980 chunk 51 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 HIS ** A 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 149 ASN ** 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 = 0.3344 r_free = 0.3344 target = 0.124822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.105099 restraints weight = 54248.925| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 2.20 r_work: 0.3107 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2988 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.4479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.242 15083 Z= 0.193 Angle : 0.561 9.555 20546 Z= 0.288 Chirality : 0.039 0.150 2284 Planarity : 0.004 0.071 2625 Dihedral : 7.149 171.961 2086 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 1.61 % Allowed : 11.55 % Favored : 86.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.20), residues: 1887 helix: 1.59 (0.17), residues: 978 sheet: -1.09 (0.38), residues: 177 loop : -0.17 (0.24), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 282 TYR 0.024 0.001 TYR H 102 PHE 0.012 0.001 PHE K 278 TRP 0.016 0.001 TRP K 142 HIS 0.006 0.001 HIS K 197 Details of bonding type rmsd covalent geometry : bond 0.00445 (15075) covalent geometry : angle 0.56071 (20544) SS BOND : bond 0.00002 ( 1) SS BOND : angle 0.53016 ( 2) hydrogen bonds : bond 0.03950 ( 836) hydrogen bonds : angle 4.38774 ( 2379) Misc. bond : bond 0.12568 ( 7) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3774 Ramachandran restraints generated. 1887 Oldfield, 0 Emsley, 1887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3774 Ramachandran restraints generated. 1887 Oldfield, 0 Emsley, 1887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 112 is missing expected H atoms. Skipping. Residue LYS 124 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue TYR 43 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue SER 214 is missing expected H atoms. Skipping. Residue LYS 218 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue TYR 32 is missing expected H atoms. Skipping. Evaluate side-chains 264 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 240 time to evaluate : 0.691 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 GLU cc_start: 0.8059 (tm-30) cc_final: 0.7646 (tt0) REVERT: A 236 ARG cc_start: 0.8327 (OUTLIER) cc_final: 0.7292 (ttt90) REVERT: A 396 LYS cc_start: 0.8208 (mppt) cc_final: 0.7990 (mtmm) REVERT: K 162 VAL cc_start: 0.8543 (OUTLIER) cc_final: 0.8317 (t) REVERT: D 79 ARG cc_start: 0.8110 (mtp-110) cc_final: 0.7611 (mtp85) REVERT: D 143 GLU cc_start: 0.8301 (tt0) cc_final: 0.7758 (tt0) REVERT: D 151 GLN cc_start: 0.8696 (mp10) cc_final: 0.8185 (mp10) REVERT: D 243 GLU cc_start: 0.8488 (pm20) cc_final: 0.7198 (pm20) REVERT: G 98 GLU cc_start: 0.7862 (mt-10) cc_final: 0.7587 (mt-10) REVERT: G 109 GLU cc_start: 0.7912 (tp30) cc_final: 0.7231 (mt-10) REVERT: F 54 LYS cc_start: 0.8171 (tttp) cc_final: 0.7678 (tppt) REVERT: H 67 ASP cc_start: 0.7387 (m-30) cc_final: 0.7052 (m-30) REVERT: I 36 LYS cc_start: 0.8783 (ttpp) cc_final: 0.8399 (ttmm) REVERT: B 152 ARG cc_start: 0.8530 (mtt180) cc_final: 0.6613 (mmm160) REVERT: B 190 GLU cc_start: 0.7985 (mt-10) cc_final: 0.7670 (mt-10) REVERT: B 204 SER cc_start: 0.8771 (p) cc_final: 0.8523 (p) REVERT: B 238 SER cc_start: 0.8998 (m) cc_final: 0.8605 (t) REVERT: B 356 LYS cc_start: 0.8739 (mmmt) cc_final: 0.8444 (mmmm) REVERT: M 50 ARG cc_start: 0.6800 (tpt170) cc_final: 0.5314 (ptp90) REVERT: M 60 MET cc_start: 0.8840 (ttm) cc_final: 0.8610 (ttp) outliers start: 24 outliers final: 21 residues processed: 257 average time/residue: 0.3041 time to fit residues: 110.7559 Evaluate side-chains 254 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 231 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 236 ARG Chi-restraints excluded: chain A residue 288 SER Chi-restraints excluded: chain K residue 152 SER Chi-restraints excluded: chain K residue 162 VAL Chi-restraints excluded: chain K residue 226 ILE Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain D residue 118 GLU Chi-restraints excluded: chain G residue 18 ARG Chi-restraints excluded: chain G residue 60 ILE Chi-restraints excluded: chain G residue 66 GLU Chi-restraints excluded: chain I residue 32 VAL Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 118 GLU Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain E residue 82 SER Chi-restraints excluded: chain E residue 86 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 101 optimal weight: 1.9990 chunk 170 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 174 optimal weight: 0.5980 chunk 122 optimal weight: 0.6980 chunk 9 optimal weight: 1.9990 chunk 169 optimal weight: 1.9990 chunk 49 optimal weight: 0.0980 chunk 29 optimal weight: 0.7980 chunk 138 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 HIS ** A 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 149 ASN ** 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 = 0.3364 r_free = 0.3364 target = 0.126457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.106518 restraints weight = 53994.725| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 2.34 r_work: 0.3144 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3021 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.4535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.205 15083 Z= 0.133 Angle : 0.530 9.443 20546 Z= 0.270 Chirality : 0.038 0.148 2284 Planarity : 0.004 0.072 2625 Dihedral : 7.015 171.785 2086 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 1.41 % Allowed : 11.89 % Favored : 86.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.04 (0.20), residues: 1887 helix: 1.68 (0.17), residues: 983 sheet: -1.00 (0.38), residues: 175 loop : -0.15 (0.24), residues: 729 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 282 TYR 0.023 0.001 TYR H 102 PHE 0.013 0.001 PHE A 327 TRP 0.015 0.001 TRP K 142 HIS 0.003 0.001 HIS K 343 Details of bonding type rmsd covalent geometry : bond 0.00305 (15075) covalent geometry : angle 0.52956 (20544) SS BOND : bond 0.00070 ( 1) SS BOND : angle 0.64669 ( 2) hydrogen bonds : bond 0.03742 ( 836) hydrogen bonds : angle 4.27784 ( 2379) Misc. bond : bond 0.10656 ( 7) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3774 Ramachandran restraints generated. 1887 Oldfield, 0 Emsley, 1887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3774 Ramachandran restraints generated. 1887 Oldfield, 0 Emsley, 1887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 112 is missing expected H atoms. Skipping. Residue LYS 124 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue TYR 43 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue SER 214 is missing expected H atoms. Skipping. Residue LYS 218 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue TYR 32 is missing expected H atoms. Skipping. Evaluate side-chains 261 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 240 time to evaluate : 0.775 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 GLU cc_start: 0.8133 (tm-30) cc_final: 0.7784 (tt0) REVERT: A 396 LYS cc_start: 0.8210 (mppt) cc_final: 0.8000 (mtmm) REVERT: K 162 VAL cc_start: 0.8576 (OUTLIER) cc_final: 0.8342 (t) REVERT: D 79 ARG cc_start: 0.8114 (mtp-110) cc_final: 0.7637 (mtp85) REVERT: D 143 GLU cc_start: 0.8279 (tt0) cc_final: 0.7782 (tt0) REVERT: D 243 GLU cc_start: 0.8307 (pm20) cc_final: 0.7053 (pm20) REVERT: G 86 GLN cc_start: 0.8220 (pt0) cc_final: 0.7979 (pt0) REVERT: G 98 GLU cc_start: 0.7852 (mt-10) cc_final: 0.7590 (mt-10) REVERT: G 109 GLU cc_start: 0.7893 (tp30) cc_final: 0.7246 (mt-10) REVERT: F 54 LYS cc_start: 0.8216 (tttp) cc_final: 0.7681 (tppt) REVERT: H 67 ASP cc_start: 0.7409 (m-30) cc_final: 0.7063 (m-30) REVERT: I 36 LYS cc_start: 0.8794 (ttpp) cc_final: 0.8415 (ttmm) REVERT: B 97 ASP cc_start: 0.8598 (m-30) cc_final: 0.8264 (m-30) REVERT: B 152 ARG cc_start: 0.8476 (mtt180) cc_final: 0.6581 (mmm160) REVERT: B 204 SER cc_start: 0.8814 (p) cc_final: 0.8565 (p) REVERT: B 238 SER cc_start: 0.8966 (m) cc_final: 0.8601 (t) REVERT: M 50 ARG cc_start: 0.6766 (tpt170) cc_final: 0.5311 (ptp90) REVERT: M 60 MET cc_start: 0.8852 (ttm) cc_final: 0.8617 (ttp) outliers start: 21 outliers final: 19 residues processed: 255 average time/residue: 0.3030 time to fit residues: 110.0743 Evaluate side-chains 254 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 234 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 288 SER Chi-restraints excluded: chain K residue 152 SER Chi-restraints excluded: chain K residue 162 VAL Chi-restraints excluded: chain K residue 226 ILE Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain D residue 118 GLU Chi-restraints excluded: chain G residue 18 ARG Chi-restraints excluded: chain G residue 60 ILE Chi-restraints excluded: chain I residue 32 VAL Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 118 GLU Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain E residue 82 SER Chi-restraints excluded: chain E residue 86 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 168 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 181 optimal weight: 20.0000 chunk 183 optimal weight: 9.9990 chunk 77 optimal weight: 0.3980 chunk 150 optimal weight: 2.9990 chunk 155 optimal weight: 2.9990 chunk 175 optimal weight: 20.0000 chunk 161 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 overall best weight: 2.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 HIS ** A 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 150 ASN B 179 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.122014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.101910 restraints weight = 55283.413| |-----------------------------------------------------------------------------| r_work (start): 0.3139 rms_B_bonded: 2.24 r_work: 0.3016 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2899 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.4707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.284 15083 Z= 0.306 Angle : 0.632 9.846 20546 Z= 0.330 Chirality : 0.042 0.155 2284 Planarity : 0.004 0.056 2625 Dihedral : 7.425 173.715 2086 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 1.34 % Allowed : 12.09 % Favored : 86.57 % 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: 0.66 (0.20), residues: 1887 helix: 1.36 (0.17), residues: 977 sheet: -1.16 (0.37), residues: 183 loop : -0.29 (0.24), residues: 727 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 282 TYR 0.024 0.002 TYR H 102 PHE 0.017 0.002 PHE K 278 TRP 0.018 0.002 TRP K 142 HIS 0.008 0.002 HIS K 222 Details of bonding type rmsd covalent geometry : bond 0.00704 (15075) covalent geometry : angle 0.63180 (20544) SS BOND : bond 0.00056 ( 1) SS BOND : angle 0.53700 ( 2) hydrogen bonds : bond 0.04337 ( 836) hydrogen bonds : angle 4.54647 ( 2379) Misc. bond : bond 0.15074 ( 7) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6187.77 seconds wall clock time: 105 minutes 42.15 seconds (6342.15 seconds total)