Starting phenix.real_space_refine on Thu Mar 5 10:48:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9n9g_49168/03_2026/9n9g_49168.cif Found real_map, /net/cci-nas-00/data/ceres_data/9n9g_49168/03_2026/9n9g_49168.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9n9g_49168/03_2026/9n9g_49168.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9n9g_49168/03_2026/9n9g_49168.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9n9g_49168/03_2026/9n9g_49168.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9n9g_49168/03_2026/9n9g_49168.map" } resolution = 3.0 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= 0.001 sd= 0.015 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 P 10 5.49 5 Mg 4 5.21 5 S 141 5.16 5 C 13246 2.51 5 N 3525 2.21 5 O 4060 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 39 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 20986 Number of models: 1 Model: "" Number of chains: 15 Chain: "1" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 116 Classifications: {'peptide': 14} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 13} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "A" Number of atoms: 3481 Number of conformers: 1 Conformer: "" Number of residues, atoms: 444, 3481 Classifications: {'peptide': 444} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 423} Chain breaks: 1 Chain: "B" Number of atoms: 3498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3498 Classifications: {'peptide': 445} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 424} Chain: "F" Number of atoms: 1451 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1451 Classifications: {'peptide': 177} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 166} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "N" Number of atoms: 2127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2127 Classifications: {'peptide': 266} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 253} Chain breaks: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "a" Number of atoms: 3481 Number of conformers: 1 Conformer: "" Number of residues, atoms: 444, 3481 Classifications: {'peptide': 444} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 423} Chain breaks: 1 Chain: "b" Number of atoms: 3415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3415 Classifications: {'peptide': 435} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 414} Chain: "f" Number of atoms: 1451 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1451 Classifications: {'peptide': 177} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 166} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "n" Number of atoms: 1718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1718 Classifications: {'peptide': 215} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 11, 'TRANS': 203} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TRP:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 63 Unusual residues: {' MG': 1, 'TA1': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "a" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 34 Unusual residues: {' MG': 2, 'GTP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "b" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 62 Unusual residues: {'TA1': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.10, per 1000 atoms: 0.24 Number of scatterers: 20986 At special positions: 0 Unit cell: (150.342, 144.934, 155.75, 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) S 141 16.00 P 10 15.00 Mg 4 11.99 O 4060 8.00 N 3525 7.00 C 13246 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS F 111 " - pdb=" SG CYS N 137 " distance=2.03 Simple disulfide: pdb=" SG CYS F 134 " - pdb=" SG CYS N 232 " distance=2.04 Simple disulfide: pdb=" SG CYS f 111 " - pdb=" SG CYS n 137 " distance=2.04 Simple disulfide: pdb=" SG CYS f 134 " - pdb=" SG CYS n 232 " distance=2.04 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=0, symmetry=0 Time building additional restraints: 1.80 Conformation dependent library (CDL) restraints added in 1.0 seconds 5186 Ramachandran restraints generated. 2593 Oldfield, 0 Emsley, 2593 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4898 Finding SS restraints... Secondary structure from input PDB file: 121 helices and 10 sheets defined 61.8% alpha, 9.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.57 Creating SS restraints... Processing helix chain '1' and resid 14 through 19 removed outlier: 3.864A pdb=" N GLU 1 18 " --> pdb=" O LEU 1 14 " (cutoff:3.500A) Processing helix chain 'A' and resid 10 through 29 removed outlier: 3.817A pdb=" N ALA A 19 " --> pdb=" O GLN A 15 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 51 removed outlier: 3.691A pdb=" N THR A 51 " --> pdb=" O SER A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 81 Processing helix chain 'A' and resid 102 through 108 Processing helix chain 'A' and resid 110 through 127 removed outlier: 3.923A pdb=" N ILE A 114 " --> pdb=" O ILE A 110 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N ASP A 116 " --> pdb=" O LYS A 112 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N LEU A 117 " --> pdb=" O GLU A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 162 Processing helix chain 'A' and resid 182 through 197 removed outlier: 3.741A pdb=" N ASN A 186 " --> pdb=" O VAL A 182 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N HIS A 192 " --> pdb=" O ILE A 188 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N THR A 193 " --> pdb=" O LEU A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 218 removed outlier: 3.645A pdb=" N ASP A 218 " --> pdb=" O ARG A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 244 removed outlier: 3.786A pdb=" N LEU A 227 " --> pdb=" O THR A 223 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N SER A 241 " --> pdb=" O SER A 237 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N LEU A 242 " --> pdb=" O ILE A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 260 Processing helix chain 'A' and resid 277 through 284 Processing helix chain 'A' and resid 287 through 295 Processing helix chain 'A' and resid 296 through 301 removed outlier: 6.102A pdb=" N ALA A 299 " --> pdb=" O PHE A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 310 Processing helix chain 'A' and resid 324 through 338 removed outlier: 3.527A pdb=" N VAL A 328 " --> pdb=" O VAL A 324 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LYS A 338 " --> pdb=" O THR A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 402 removed outlier: 4.179A pdb=" N ALA A 387 " --> pdb=" O ALA A 383 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N TRP A 388 " --> pdb=" O ILE A 384 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N MET A 398 " --> pdb=" O LYS A 394 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LYS A 401 " --> pdb=" O LEU A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 411 removed outlier: 4.144A pdb=" N TYR A 408 " --> pdb=" O PHE A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 437 removed outlier: 3.899A pdb=" N SER A 419 " --> pdb=" O GLU A 415 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ARG A 422 " --> pdb=" O PHE A 418 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU A 433 " --> pdb=" O GLU A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 450 removed outlier: 4.045A pdb=" N GLY A 442 " --> pdb=" O ASP A 438 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N GLY A 444 " --> pdb=" O VAL A 440 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N GLU A 445 " --> pdb=" O GLU A 441 " (cutoff:3.500A) Processing helix chain 'B' and resid 11 through 29 Processing helix chain 'B' and resid 40 through 48 removed outlier: 3.990A pdb=" N LEU B 44 " --> pdb=" O SER B 40 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N ARG B 48 " --> pdb=" O LEU B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 51 No H-bonds generated for 'chain 'B' and resid 49 through 51' Processing helix chain 'B' and resid 72 through 81 Processing helix chain 'B' and resid 88 through 90 No H-bonds generated for 'chain 'B' and resid 88 through 90' Processing helix chain 'B' and resid 102 through 108 Processing helix chain 'B' and resid 108 through 128 removed outlier: 3.714A pdb=" N ALA B 112 " --> pdb=" O TYR B 108 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N GLU B 113 " --> pdb=" O THR B 109 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N ASP B 116 " --> pdb=" O ALA B 112 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N SER B 117 " --> pdb=" O GLU B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 161 removed outlier: 3.527A pdb=" N GLY B 148 " --> pdb=" O GLY B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 198 removed outlier: 3.550A pdb=" N ASN B 186 " --> pdb=" O VAL B 182 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N HIS B 192 " --> pdb=" O THR B 188 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLN B 193 " --> pdb=" O LEU B 189 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N GLU B 196 " --> pdb=" O HIS B 192 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ASN B 197 " --> pdb=" O GLN B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 216 Processing helix chain 'B' and resid 223 through 244 removed outlier: 3.627A pdb=" N LEU B 227 " --> pdb=" O THR B 223 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N THR B 239 " --> pdb=" O MET B 235 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N CYS B 241 " --> pdb=" O GLY B 237 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N LEU B 242 " --> pdb=" O VAL B 238 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ARG B 243 " --> pdb=" O THR B 239 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N PHE B 244 " --> pdb=" O THR B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 260 Processing helix chain 'B' and resid 287 through 296 Processing helix chain 'B' and resid 297 through 301 removed outlier: 3.605A pdb=" N MET B 301 " --> pdb=" O ALA B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 310 Processing helix chain 'B' and resid 324 through 339 removed outlier: 3.762A pdb=" N VAL B 328 " --> pdb=" O SER B 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 340 through 343 removed outlier: 3.707A pdb=" N PHE B 343 " --> pdb=" O SER B 340 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 340 through 343' Processing helix chain 'B' and resid 383 through 400 removed outlier: 4.018A pdb=" N LEU B 387 " --> pdb=" O ALA B 383 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N PHE B 388 " --> pdb=" O ILE B 384 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE B 391 " --> pdb=" O LEU B 387 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N THR B 396 " --> pdb=" O SER B 392 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 411 removed outlier: 4.078A pdb=" N TYR B 408 " --> pdb=" O PHE B 404 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N GLU B 411 " --> pdb=" O TRP B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 437 removed outlier: 3.585A pdb=" N GLN B 433 " --> pdb=" O VAL B 429 " (cutoff:3.500A) Processing helix chain 'B' and resid 440 through 455 removed outlier: 3.651A pdb=" N GLU B 449 " --> pdb=" O GLU B 445 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLU B 452 " --> pdb=" O GLU B 448 " (cutoff:3.500A) Processing helix chain 'F' and resid 10 through 21 Processing helix chain 'F' and resid 24 through 29 Processing helix chain 'F' and resid 41 through 58 removed outlier: 3.870A pdb=" N LEU F 45 " --> pdb=" O LYS F 41 " (cutoff:3.500A) Processing helix chain 'F' and resid 60 through 64 removed outlier: 3.530A pdb=" N HIS F 63 " --> pdb=" O ARG F 60 " (cutoff:3.500A) Processing helix chain 'F' and resid 75 through 80 removed outlier: 3.713A pdb=" N MET F 79 " --> pdb=" O TYR F 75 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 96 removed outlier: 3.883A pdb=" N SER F 86 " --> pdb=" O PHE F 82 " (cutoff:3.500A) Processing helix chain 'F' and resid 105 through 111 removed outlier: 3.985A pdb=" N ILE F 109 " --> pdb=" O GLU F 105 " (cutoff:3.500A) Processing helix chain 'F' and resid 113 through 177 removed outlier: 3.694A pdb=" N SER F 148 " --> pdb=" O GLN F 144 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N LYS F 151 " --> pdb=" O SER F 147 " (cutoff:3.500A) Proline residue: F 173 - end of helix Processing helix chain 'N' and resid 13 through 22 Processing helix chain 'N' and resid 30 through 34 Processing helix chain 'N' and resid 61 through 67 Processing helix chain 'N' and resid 72 through 78 Processing helix chain 'N' and resid 88 through 106 Processing helix chain 'N' and resid 113 through 119 removed outlier: 3.527A pdb=" N ALA N 119 " --> pdb=" O LYS N 115 " (cutoff:3.500A) Processing helix chain 'N' and resid 121 through 135 removed outlier: 4.123A pdb=" N PHE N 135 " --> pdb=" O PHE N 131 " (cutoff:3.500A) Processing helix chain 'N' and resid 146 through 158 removed outlier: 3.544A pdb=" N GLU N 150 " --> pdb=" O LYS N 146 " (cutoff:3.500A) Proline residue: N 152 - end of helix Processing helix chain 'N' and resid 165 through 171 removed outlier: 3.585A pdb=" N THR N 171 " --> pdb=" O SER N 167 " (cutoff:3.500A) Processing helix chain 'N' and resid 177 through 201 removed outlier: 3.514A pdb=" N ILE N 181 " --> pdb=" O THR N 177 " (cutoff:3.500A) Processing helix chain 'N' and resid 202 through 206 Processing helix chain 'N' and resid 221 through 238 Processing helix chain 'N' and resid 243 through 259 removed outlier: 3.790A pdb=" N ASN N 247 " --> pdb=" O PHE N 243 " (cutoff:3.500A) Processing helix chain 'N' and resid 261 through 289 Processing helix chain 'a' and resid 10 through 29 removed outlier: 3.880A pdb=" N ALA a 19 " --> pdb=" O GLN a 15 " (cutoff:3.500A) Processing helix chain 'a' and resid 47 through 51 Processing helix chain 'a' and resid 72 through 81 Processing helix chain 'a' and resid 88 through 90 No H-bonds generated for 'chain 'a' and resid 88 through 90' Processing helix chain 'a' and resid 102 through 108 Processing helix chain 'a' and resid 110 through 129 removed outlier: 4.764A pdb=" N ASP a 116 " --> pdb=" O LYS a 112 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N LEU a 117 " --> pdb=" O GLU a 113 " (cutoff:3.500A) Processing helix chain 'a' and resid 143 through 161 removed outlier: 3.648A pdb=" N SER a 147 " --> pdb=" O GLY a 143 " (cutoff:3.500A) Processing helix chain 'a' and resid 182 through 197 removed outlier: 3.509A pdb=" N ASN a 186 " --> pdb=" O VAL a 182 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N HIS a 192 " --> pdb=" O ILE a 188 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N THR a 193 " --> pdb=" O LEU a 189 " (cutoff:3.500A) Processing helix chain 'a' and resid 206 through 216 Processing helix chain 'a' and resid 223 through 244 removed outlier: 3.845A pdb=" N LEU a 227 " --> pdb=" O THR a 223 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N SER a 241 " --> pdb=" O SER a 237 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N LEU a 242 " --> pdb=" O ILE a 238 " (cutoff:3.500A) Processing helix chain 'a' and resid 251 through 260 removed outlier: 3.514A pdb=" N PHE a 255 " --> pdb=" O ASP a 251 " (cutoff:3.500A) Processing helix chain 'a' and resid 277 through 284 removed outlier: 4.038A pdb=" N HIS a 283 " --> pdb=" O GLU a 279 " (cutoff:3.500A) Processing helix chain 'a' and resid 287 through 295 removed outlier: 3.606A pdb=" N ILE a 291 " --> pdb=" O SER a 287 " (cutoff:3.500A) Processing helix chain 'a' and resid 297 through 301 Processing helix chain 'a' and resid 306 through 310 Processing helix chain 'a' and resid 324 through 338 removed outlier: 3.614A pdb=" N VAL a 328 " --> pdb=" O VAL a 324 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LYS a 338 " --> pdb=" O THR a 334 " (cutoff:3.500A) Processing helix chain 'a' and resid 382 through 401 removed outlier: 4.119A pdb=" N GLU a 386 " --> pdb=" O THR a 382 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ALA a 387 " --> pdb=" O ALA a 383 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ARG a 390 " --> pdb=" O GLU a 386 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N LEU a 391 " --> pdb=" O ALA a 387 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N MET a 398 " --> pdb=" O LYS a 394 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N LYS a 401 " --> pdb=" O LEU a 397 " (cutoff:3.500A) Processing helix chain 'a' and resid 404 through 412 removed outlier: 4.016A pdb=" N TYR a 408 " --> pdb=" O PHE a 404 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N GLU a 411 " --> pdb=" O TRP a 407 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLY a 412 " --> pdb=" O TYR a 408 " (cutoff:3.500A) Processing helix chain 'a' and resid 414 through 438 removed outlier: 3.938A pdb=" N PHE a 418 " --> pdb=" O GLU a 414 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N ASP a 438 " --> pdb=" O GLU a 434 " (cutoff:3.500A) Processing helix chain 'a' and resid 439 through 451 removed outlier: 3.504A pdb=" N GLU a 449 " --> pdb=" O GLU a 445 " (cutoff:3.500A) Processing helix chain 'b' and resid 10 through 29 Processing helix chain 'b' and resid 40 through 48 removed outlier: 4.118A pdb=" N LEU b 44 " --> pdb=" O SER b 40 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ARG b 48 " --> pdb=" O LEU b 42 " (cutoff:3.500A) Processing helix chain 'b' and resid 49 through 51 No H-bonds generated for 'chain 'b' and resid 49 through 51' Processing helix chain 'b' and resid 71 through 81 removed outlier: 4.587A pdb=" N MET b 75 " --> pdb=" O GLU b 71 " (cutoff:3.500A) Processing helix chain 'b' and resid 88 through 90 No H-bonds generated for 'chain 'b' and resid 88 through 90' Processing helix chain 'b' and resid 102 through 108 Processing helix chain 'b' and resid 109 through 129 removed outlier: 3.888A pdb=" N GLU b 113 " --> pdb=" O THR b 109 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N ASP b 116 " --> pdb=" O ALA b 112 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N SER b 117 " --> pdb=" O GLU b 113 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N CYS b 129 " --> pdb=" O GLU b 125 " (cutoff:3.500A) Processing helix chain 'b' and resid 144 through 161 Processing helix chain 'b' and resid 182 through 198 removed outlier: 3.797A pdb=" N ASN b 186 " --> pdb=" O VAL b 182 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N HIS b 192 " --> pdb=" O THR b 188 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N GLN b 193 " --> pdb=" O LEU b 189 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLU b 196 " --> pdb=" O HIS b 192 " (cutoff:3.500A) Processing helix chain 'b' and resid 205 through 216 Processing helix chain 'b' and resid 223 through 240 removed outlier: 3.588A pdb=" N LEU b 227 " --> pdb=" O THR b 223 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N THR b 239 " --> pdb=" O MET b 235 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N THR b 240 " --> pdb=" O SER b 236 " (cutoff:3.500A) Processing helix chain 'b' and resid 241 through 243 No H-bonds generated for 'chain 'b' and resid 241 through 243' Processing helix chain 'b' and resid 251 through 260 removed outlier: 3.534A pdb=" N VAL b 260 " --> pdb=" O ALA b 256 " (cutoff:3.500A) Processing helix chain 'b' and resid 287 through 296 Processing helix chain 'b' and resid 306 through 310 Processing helix chain 'b' and resid 324 through 339 removed outlier: 3.703A pdb=" N VAL b 328 " --> pdb=" O SER b 324 " (cutoff:3.500A) Processing helix chain 'b' and resid 340 through 343 removed outlier: 3.652A pdb=" N PHE b 343 " --> pdb=" O SER b 340 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 340 through 343' Processing helix chain 'b' and resid 384 through 400 removed outlier: 3.581A pdb=" N PHE b 388 " --> pdb=" O ILE b 384 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ARG b 390 " --> pdb=" O GLU b 386 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N THR b 396 " --> pdb=" O SER b 392 " (cutoff:3.500A) Processing helix chain 'b' and resid 404 through 411 removed outlier: 4.137A pdb=" N TYR b 408 " --> pdb=" O PHE b 404 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N GLU b 411 " --> pdb=" O TRP b 407 " (cutoff:3.500A) Processing helix chain 'b' and resid 414 through 445 removed outlier: 3.978A pdb=" N PHE b 418 " --> pdb=" O ASP b 414 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N THR b 439 " --> pdb=" O TYR b 435 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N ALA b 440 " --> pdb=" O GLN b 436 " (cutoff:3.500A) Processing helix chain 'f' and resid 10 through 22 Processing helix chain 'f' and resid 24 through 31 Processing helix chain 'f' and resid 32 through 36 Processing helix chain 'f' and resid 41 through 58 removed outlier: 3.533A pdb=" N LEU f 45 " --> pdb=" O LYS f 41 " (cutoff:3.500A) Processing helix chain 'f' and resid 60 through 66 removed outlier: 3.793A pdb=" N MET f 66 " --> pdb=" O HIS f 63 " (cutoff:3.500A) Processing helix chain 'f' and resid 75 through 80 removed outlier: 3.578A pdb=" N MET f 79 " --> pdb=" O TYR f 75 " (cutoff:3.500A) Processing helix chain 'f' and resid 82 through 99 removed outlier: 3.810A pdb=" N SER f 86 " --> pdb=" O PHE f 82 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N SER f 94 " --> pdb=" O THR f 90 " (cutoff:3.500A) Proline residue: f 97 - end of helix Processing helix chain 'f' and resid 106 through 111 Processing helix chain 'f' and resid 113 through 178 Proline residue: f 173 - end of helix Processing helix chain 'n' and resid 88 through 107 Processing helix chain 'n' and resid 113 through 118 Processing helix chain 'n' and resid 121 through 135 Processing helix chain 'n' and resid 146 through 158 removed outlier: 3.620A pdb=" N GLU n 150 " --> pdb=" O LYS n 146 " (cutoff:3.500A) Proline residue: n 152 - end of helix Processing helix chain 'n' and resid 165 through 171 Processing helix chain 'n' and resid 177 through 201 Processing helix chain 'n' and resid 221 through 239 Processing helix chain 'n' and resid 243 through 259 removed outlier: 3.524A pdb=" N LYS n 253 " --> pdb=" O GLU n 249 " (cutoff:3.500A) Processing helix chain 'n' and resid 261 through 289 removed outlier: 3.508A pdb=" N GLU n 289 " --> pdb=" O GLU n 285 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 92 through 94 removed outlier: 7.939A pdb=" N ILE A 93 " --> pdb=" O ALA A 65 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N PHE A 67 " --> pdb=" O ILE A 93 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N SER A 6 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 8.048A pdb=" N VAL A 68 " --> pdb=" O SER A 6 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N HIS A 8 " --> pdb=" O VAL A 68 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N SER A 140 " --> pdb=" O VAL A 9 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N PHE A 135 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 7.758A pdb=" N PHE A 169 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N VAL A 137 " --> pdb=" O PHE A 169 " (cutoff:3.500A) removed outlier: 8.037A pdb=" N ILE A 171 " --> pdb=" O VAL A 137 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N HIS A 139 " --> pdb=" O ILE A 171 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N CYS A 200 " --> pdb=" O LYS A 166 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AA3, first strand: chain 'A' and resid 269 through 273 removed outlier: 3.513A pdb=" N ASN A 380 " --> pdb=" O ALA A 314 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ALA A 314 " --> pdb=" O ASN A 380 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 92 through 94 removed outlier: 8.311A pdb=" N VAL B 93 " --> pdb=" O ALA B 65 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N LEU B 67 " --> pdb=" O VAL B 93 " (cutoff:3.500A) removed outlier: 8.426A pdb=" N ILE B 66 " --> pdb=" O ILE B 4 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N HIS B 6 " --> pdb=" O ILE B 66 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N VAL B 68 " --> pdb=" O HIS B 6 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N GLN B 8 " --> pdb=" O VAL B 68 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N GLU B 3 " --> pdb=" O GLY B 134 " (cutoff:3.500A) removed outlier: 7.977A pdb=" N GLN B 136 " --> pdb=" O GLU B 3 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N VAL B 5 " --> pdb=" O GLN B 136 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N THR B 138 " --> pdb=" O VAL B 5 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N ILE B 7 " --> pdb=" O THR B 138 " (cutoff:3.500A) removed outlier: 9.068A pdb=" N SER B 140 " --> pdb=" O ILE B 7 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ILE B 165 " --> pdb=" O GLN B 133 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N MET B 166 " --> pdb=" O GLU B 200 " (cutoff:3.500A) removed outlier: 8.099A pdb=" N TYR B 202 " --> pdb=" O MET B 166 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N THR B 168 " --> pdb=" O TYR B 202 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N ILE B 204 " --> pdb=" O THR B 168 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N SER B 170 " --> pdb=" O ILE B 204 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N THR B 201 " --> pdb=" O PHE B 268 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N CYS B 203 " --> pdb=" O PRO B 270 " (cutoff:3.500A) removed outlier: 10.571A pdb=" N PHE B 272 " --> pdb=" O CYS B 203 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N PHE B 267 " --> pdb=" O SER B 381 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N SER B 381 " --> pdb=" O PHE B 267 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N THR B 314 " --> pdb=" O ASN B 380 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 53 through 56 Processing sheet with id=AA6, first strand: chain 'a' and resid 92 through 94 removed outlier: 8.275A pdb=" N ILE a 93 " --> pdb=" O ALA a 65 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N PHE a 67 " --> pdb=" O ILE a 93 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N SER a 140 " --> pdb=" O VAL a 9 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N PHE a 135 " --> pdb=" O LEU a 167 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N PHE a 169 " --> pdb=" O PHE a 135 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N VAL a 137 " --> pdb=" O PHE a 169 " (cutoff:3.500A) removed outlier: 8.023A pdb=" N ILE a 171 " --> pdb=" O VAL a 137 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N HIS a 139 " --> pdb=" O ILE a 171 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N CYS a 200 " --> pdb=" O LYS a 166 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'a' and resid 53 through 55 Processing sheet with id=AA8, first strand: chain 'a' and resid 269 through 273 removed outlier: 6.655A pdb=" N ALA a 374 " --> pdb=" O TYR a 319 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N TYR a 319 " --> pdb=" O ALA a 374 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N CYS a 376 " --> pdb=" O LEU a 317 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N LEU a 317 " --> pdb=" O CYS a 376 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N LEU a 378 " --> pdb=" O CYS a 315 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N CYS a 315 " --> pdb=" O LEU a 378 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N ASN a 380 " --> pdb=" O MET a 313 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'b' and resid 92 through 94 removed outlier: 8.303A pdb=" N VAL b 93 " --> pdb=" O ALA b 65 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N LEU b 67 " --> pdb=" O VAL b 93 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N GLU b 3 " --> pdb=" O LEU b 132 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N GLY b 134 " --> pdb=" O GLU b 3 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N SER b 140 " --> pdb=" O ALA b 9 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N MET b 166 " --> pdb=" O GLU b 200 " (cutoff:3.500A) removed outlier: 8.221A pdb=" N TYR b 202 " --> pdb=" O MET b 166 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N THR b 168 " --> pdb=" O TYR b 202 " (cutoff:3.500A) removed outlier: 7.873A pdb=" N ILE b 204 " --> pdb=" O THR b 168 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N SER b 170 " --> pdb=" O ILE b 204 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N THR b 201 " --> pdb=" O PHE b 268 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N CYS b 203 " --> pdb=" O PRO b 270 " (cutoff:3.500A) removed outlier: 10.677A pdb=" N PHE b 272 " --> pdb=" O CYS b 203 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N PHE b 267 " --> pdb=" O SER b 381 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N SER b 381 " --> pdb=" O PHE b 267 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N THR b 314 " --> pdb=" O ASN b 380 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'b' and resid 53 through 56 1131 hydrogen bonds defined for protein. 3291 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: 3.04 Time building geometry restraints manager: 2.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 4211 1.33 - 1.45: 5263 1.45 - 1.58: 11741 1.58 - 1.70: 24 1.70 - 1.83: 226 Bond restraints: 21465 Sorted by residual: bond pdb=" N ILE N 80 " pdb=" CA ILE N 80 " ideal model delta sigma weight residual 1.456 1.495 -0.039 1.11e-02 8.12e+03 1.25e+01 bond pdb=" N VAL n 172 " pdb=" CA VAL n 172 " ideal model delta sigma weight residual 1.456 1.496 -0.040 1.19e-02 7.06e+03 1.12e+01 bond pdb=" N VAL A 437 " pdb=" CA VAL A 437 " ideal model delta sigma weight residual 1.457 1.497 -0.040 1.19e-02 7.06e+03 1.11e+01 bond pdb=" N VAL n 260 " pdb=" CA VAL n 260 " ideal model delta sigma weight residual 1.458 1.497 -0.039 1.19e-02 7.06e+03 1.06e+01 bond pdb=" N VAL a 303 " pdb=" CA VAL a 303 " ideal model delta sigma weight residual 1.458 1.496 -0.038 1.18e-02 7.18e+03 1.03e+01 ... (remaining 21460 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.01: 27487 2.01 - 4.02: 1487 4.02 - 6.04: 110 6.04 - 8.05: 23 8.05 - 10.06: 5 Bond angle restraints: 29112 Sorted by residual: angle pdb=" C ALA B 440 " pdb=" CA ALA B 440 " pdb=" CB ALA B 440 " ideal model delta sigma weight residual 117.23 109.66 7.57 1.36e+00 5.41e-01 3.10e+01 angle pdb=" N GLU B 448 " pdb=" CA GLU B 448 " pdb=" C GLU B 448 " ideal model delta sigma weight residual 111.07 105.69 5.38 1.07e+00 8.73e-01 2.53e+01 angle pdb=" CA GLY a 10 " pdb=" C GLY a 10 " pdb=" O GLY a 10 " ideal model delta sigma weight residual 122.29 118.23 4.06 8.10e-01 1.52e+00 2.51e+01 angle pdb=" N PHE B 446 " pdb=" CA PHE B 446 " pdb=" C PHE B 446 " ideal model delta sigma weight residual 111.71 106.11 5.60 1.15e+00 7.56e-01 2.37e+01 angle pdb=" N GLN B 443 " pdb=" CA GLN B 443 " pdb=" C GLN B 443 " ideal model delta sigma weight residual 111.82 106.40 5.42 1.16e+00 7.43e-01 2.18e+01 ... (remaining 29107 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.63: 12408 26.63 - 53.25: 487 53.25 - 79.88: 113 79.88 - 106.50: 13 106.50 - 133.13: 6 Dihedral angle restraints: 13027 sinusoidal: 5423 harmonic: 7604 Sorted by residual: dihedral pdb=" C8 GTP a 501 " pdb=" C1' GTP a 501 " pdb=" N9 GTP a 501 " pdb=" O4' GTP a 501 " ideal model delta sinusoidal sigma weight residual 104.59 -28.53 133.13 1 2.00e+01 2.50e-03 4.04e+01 dihedral pdb=" C8 GTP A 501 " pdb=" C1' GTP A 501 " pdb=" N9 GTP A 501 " pdb=" O4' GTP A 501 " ideal model delta sinusoidal sigma weight residual 104.59 -20.89 125.48 1 2.00e+01 2.50e-03 3.79e+01 dihedral pdb=" C5' GTP A 501 " pdb=" O5' GTP A 501 " pdb=" PA GTP A 501 " pdb=" O3A GTP A 501 " ideal model delta sinusoidal sigma weight residual 69.27 -165.31 -125.42 1 2.00e+01 2.50e-03 3.79e+01 ... (remaining 13024 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 2403 0.060 - 0.121: 585 0.121 - 0.181: 136 0.181 - 0.241: 28 0.241 - 0.301: 2 Chirality restraints: 3154 Sorted by residual: chirality pdb=" CB ILE f 14 " pdb=" CA ILE f 14 " pdb=" CG1 ILE f 14 " pdb=" CG2 ILE f 14 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.30 2.00e-01 2.50e+01 2.27e+00 chirality pdb=" CA CYS N 232 " pdb=" N CYS N 232 " pdb=" C CYS N 232 " pdb=" CB CYS N 232 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.51e+00 chirality pdb=" CA GLU B 196 " pdb=" N GLU B 196 " pdb=" C GLU B 196 " pdb=" CB GLU B 196 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.30e+00 ... (remaining 3151 not shown) Planarity restraints: 3797 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG b 311 " -0.279 9.50e-02 1.11e+02 1.25e-01 9.61e+00 pdb=" NE ARG b 311 " 0.017 2.00e-02 2.50e+03 pdb=" CZ ARG b 311 " 0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG b 311 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG b 311 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG N 67 " 0.277 9.50e-02 1.11e+02 1.24e-01 9.47e+00 pdb=" NE ARG N 67 " -0.016 2.00e-02 2.50e+03 pdb=" CZ ARG N 67 " -0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG N 67 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG N 67 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG F 60 " -0.267 9.50e-02 1.11e+02 1.20e-01 8.80e+00 pdb=" NE ARG F 60 " 0.016 2.00e-02 2.50e+03 pdb=" CZ ARG F 60 " 0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG F 60 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG F 60 " -0.010 2.00e-02 2.50e+03 ... (remaining 3794 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 138 2.59 - 3.16: 18204 3.16 - 3.74: 32173 3.74 - 4.32: 43484 4.32 - 4.90: 73305 Nonbonded interactions: 167304 Sorted by model distance: nonbonded pdb=" O1B GTP a 501 " pdb="MG MG a 502 " model vdw 2.008 2.170 nonbonded pdb=" O3G GTP a 501 " pdb="MG MG a 502 " model vdw 2.013 2.170 nonbonded pdb=" O LEU b 313 " pdb=" OG1 THR b 314 " model vdw 2.203 3.040 nonbonded pdb=" O GLY B 10 " pdb=" ND2 ASN B 14 " model vdw 2.214 3.120 nonbonded pdb=" OH TYR a 399 " pdb=" OE1 GLU a 415 " model vdw 2.231 3.040 ... (remaining 167299 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 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'a' and resid 1 through 502) } ncs_group { reference = (chain 'B' and (resid 1 through 445 or resid 503)) selection = (chain 'b' and (resid 1 through 445 or resid 502)) } ncs_group { reference = chain 'F' selection = chain 'f' } 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: 3.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 18.950 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 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 0.057 21469 Z= 0.461 Angle : 0.901 10.059 29120 Z= 0.614 Chirality : 0.058 0.301 3154 Planarity : 0.007 0.125 3797 Dihedral : 15.175 133.126 8117 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 0.71 % Allowed : 10.93 % Favored : 88.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.69 % 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: 0.44 (0.16), residues: 2593 helix: 0.85 (0.14), residues: 1383 sheet: 0.93 (0.30), residues: 274 loop : -0.64 (0.20), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG b 322 TYR 0.014 0.001 TYR n 140 PHE 0.014 0.001 PHE a 255 TRP 0.017 0.002 TRP a 21 HIS 0.005 0.001 HIS F 63 Details of bonding type rmsd covalent geometry : bond 0.00678 (21465) covalent geometry : angle 0.90092 (29112) SS BOND : bond 0.00482 ( 4) SS BOND : angle 1.15417 ( 8) hydrogen bonds : bond 0.17670 ( 1131) hydrogen bonds : angle 6.48706 ( 3291) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5186 Ramachandran restraints generated. 2593 Oldfield, 0 Emsley, 2593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5186 Ramachandran restraints generated. 2593 Oldfield, 0 Emsley, 2593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 468 residues out of total 2271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 452 time to evaluate : 0.720 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 90 GLU cc_start: 0.9312 (mm-30) cc_final: 0.8494 (tm-30) REVERT: A 123 ARG cc_start: 0.9002 (tpp-160) cc_final: 0.8740 (tpp80) REVERT: A 221 ARG cc_start: 0.4308 (tpt170) cc_final: 0.3501 (tpt170) REVERT: A 290 GLU cc_start: 0.8839 (mp0) cc_final: 0.8581 (mp0) REVERT: A 377 MET cc_start: 0.8786 (ttp) cc_final: 0.8585 (ttp) REVERT: B 259 MET cc_start: 0.9028 (mmm) cc_final: 0.8688 (mmt) REVERT: B 431 GLU cc_start: 0.8922 (tt0) cc_final: 0.8721 (mt-10) REVERT: F 17 HIS cc_start: 0.9435 (m-70) cc_final: 0.9032 (m-70) REVERT: F 34 ASN cc_start: 0.9140 (p0) cc_final: 0.8798 (p0) REVERT: F 41 LYS cc_start: 0.9021 (tptt) cc_final: 0.8455 (mmtt) REVERT: F 66 MET cc_start: 0.8789 (mmm) cc_final: 0.7988 (mpp) REVERT: F 80 GLU cc_start: 0.8518 (mt-10) cc_final: 0.8115 (mm-30) REVERT: F 93 ASP cc_start: 0.8672 (t70) cc_final: 0.7998 (m-30) REVERT: F 125 ILE cc_start: 0.9545 (pp) cc_final: 0.9343 (pp) REVERT: F 136 GLU cc_start: 0.9038 (tt0) cc_final: 0.8790 (mm-30) REVERT: F 152 MET cc_start: 0.8736 (tmt) cc_final: 0.8384 (tmm) REVERT: F 156 ASN cc_start: 0.8150 (t0) cc_final: 0.7733 (m110) REVERT: N 92 ILE cc_start: 0.8762 (pt) cc_final: 0.8452 (pp) REVERT: N 95 CYS cc_start: 0.9524 (m) cc_final: 0.9200 (m) REVERT: N 110 HIS cc_start: 0.8116 (t70) cc_final: 0.7634 (m-70) REVERT: N 142 LEU cc_start: 0.8662 (pt) cc_final: 0.8030 (tt) REVERT: N 146 LYS cc_start: 0.9327 (mttt) cc_final: 0.9093 (mmpt) REVERT: N 171 THR cc_start: 0.9249 (t) cc_final: 0.8997 (t) REVERT: N 177 THR cc_start: 0.9324 (OUTLIER) cc_final: 0.9115 (t) REVERT: N 220 MET cc_start: 0.7894 (tpt) cc_final: 0.7244 (tpp) REVERT: N 221 HIS cc_start: 0.8170 (m90) cc_final: 0.6872 (m90) REVERT: N 278 GLN cc_start: 0.9403 (tt0) cc_final: 0.9165 (tp-100) REVERT: a 36 MET cc_start: 0.9057 (ttm) cc_final: 0.8807 (tpp) REVERT: a 91 GLN cc_start: 0.8831 (mt0) cc_final: 0.8622 (mt0) REVERT: a 120 ASP cc_start: 0.9209 (t70) cc_final: 0.8996 (t0) REVERT: a 199 ASP cc_start: 0.8936 (m-30) cc_final: 0.8520 (m-30) REVERT: a 221 ARG cc_start: 0.4050 (tpt170) cc_final: 0.3044 (tpt170) REVERT: a 420 GLU cc_start: 0.8534 (mt-10) cc_final: 0.8333 (pt0) REVERT: b 127 GLU cc_start: 0.8968 (mm-30) cc_final: 0.8634 (mp0) REVERT: b 200 GLU cc_start: 0.8689 (mt-10) cc_final: 0.8457 (mt-10) REVERT: b 323 MET cc_start: 0.9360 (ptp) cc_final: 0.9156 (ptp) REVERT: b 373 MET cc_start: 0.9289 (mtp) cc_final: 0.9084 (mtm) REVERT: b 435 TYR cc_start: 0.8401 (m-10) cc_final: 0.7997 (m-10) REVERT: f 6 PHE cc_start: 0.8229 (m-80) cc_final: 0.7909 (m-10) REVERT: f 47 MET cc_start: 0.8938 (tpt) cc_final: 0.8625 (tpt) REVERT: f 50 MET cc_start: 0.8006 (tmm) cc_final: 0.7540 (tmm) REVERT: f 59 ILE cc_start: 0.8379 (mm) cc_final: 0.8134 (mp) REVERT: f 103 ASP cc_start: 0.8644 (p0) cc_final: 0.8330 (p0) REVERT: f 113 LYS cc_start: 0.7766 (mmmm) cc_final: 0.7102 (tptp) REVERT: f 163 LEU cc_start: 0.6605 (OUTLIER) cc_final: 0.6300 (mm) REVERT: n 95 CYS cc_start: 0.9166 (m) cc_final: 0.8954 (m) REVERT: n 97 ARG cc_start: 0.9467 (ttm110) cc_final: 0.9227 (tpp80) outliers start: 16 outliers final: 11 residues processed: 466 average time/residue: 0.6275 time to fit residues: 330.6470 Evaluate side-chains 317 residues out of total 2271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 304 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 290 GLU Chi-restraints excluded: chain F residue 70 ASN Chi-restraints excluded: chain N residue 177 THR Chi-restraints excluded: chain N residue 189 ILE Chi-restraints excluded: chain a residue 191 THR Chi-restraints excluded: chain a residue 328 VAL Chi-restraints excluded: chain b residue 3 GLU Chi-restraints excluded: chain f residue 21 LYS Chi-restraints excluded: chain f residue 70 ASN Chi-restraints excluded: chain f residue 163 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 197 optimal weight: 0.8980 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 9.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 0.9990 chunk 111 optimal weight: 8.9990 chunk 71 optimal weight: 4.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 64 HIS b 139 HIS b 300 ASN b 424 ASN f 63 HIS n 87 ASN n 93 GLN n 110 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.103154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.068705 restraints weight = 44772.210| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 3.32 r_work: 0.2920 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.1704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 21469 Z= 0.191 Angle : 0.678 10.301 29120 Z= 0.353 Chirality : 0.046 0.251 3154 Planarity : 0.005 0.056 3797 Dihedral : 9.406 131.237 3121 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.30 % Allowed : 15.49 % Favored : 82.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.69 % 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: 0.97 (0.16), residues: 2593 helix: 1.34 (0.14), residues: 1382 sheet: 1.09 (0.32), residues: 256 loop : -0.45 (0.20), residues: 955 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG 1 20 TYR 0.016 0.001 TYR F 65 PHE 0.030 0.001 PHE f 141 TRP 0.014 0.002 TRP A 388 HIS 0.012 0.001 HIS n 110 Details of bonding type rmsd covalent geometry : bond 0.00426 (21465) covalent geometry : angle 0.67703 (29112) SS BOND : bond 0.01098 ( 4) SS BOND : angle 1.82354 ( 8) hydrogen bonds : bond 0.06867 ( 1131) hydrogen bonds : angle 5.02707 ( 3291) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5186 Ramachandran restraints generated. 2593 Oldfield, 0 Emsley, 2593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5186 Ramachandran restraints generated. 2593 Oldfield, 0 Emsley, 2593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 2271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 323 time to evaluate : 0.758 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 90 GLU cc_start: 0.9305 (mm-30) cc_final: 0.8359 (tm-30) REVERT: A 221 ARG cc_start: 0.3836 (tpt170) cc_final: 0.3422 (tpt170) REVERT: A 284 GLU cc_start: 0.8801 (tt0) cc_final: 0.8461 (mp0) REVERT: A 290 GLU cc_start: 0.8910 (OUTLIER) cc_final: 0.8689 (mp0) REVERT: B 290 GLU cc_start: 0.8669 (OUTLIER) cc_final: 0.8369 (mp0) REVERT: B 329 ASP cc_start: 0.8803 (m-30) cc_final: 0.8318 (m-30) REVERT: F 14 ILE cc_start: 0.9583 (pp) cc_final: 0.9360 (pp) REVERT: F 17 HIS cc_start: 0.9445 (m-70) cc_final: 0.8998 (m-70) REVERT: F 47 MET cc_start: 0.9465 (tpp) cc_final: 0.9039 (tpt) REVERT: F 60 ARG cc_start: 0.7900 (ptp-110) cc_final: 0.7610 (ptp90) REVERT: F 66 MET cc_start: 0.8767 (mmm) cc_final: 0.8141 (mpp) REVERT: F 67 MET cc_start: 0.9136 (tpp) cc_final: 0.8845 (tpt) REVERT: F 80 GLU cc_start: 0.8576 (mt-10) cc_final: 0.8263 (mm-30) REVERT: F 139 MET cc_start: 0.9125 (tpp) cc_final: 0.8583 (tpp) REVERT: F 152 MET cc_start: 0.8807 (tmt) cc_final: 0.8420 (tmm) REVERT: F 156 ASN cc_start: 0.8118 (t0) cc_final: 0.7699 (m110) REVERT: N 27 GLN cc_start: 0.5837 (pm20) cc_final: 0.5455 (pm20) REVERT: N 92 ILE cc_start: 0.8602 (pt) cc_final: 0.8400 (pp) REVERT: N 95 CYS cc_start: 0.9486 (m) cc_final: 0.9094 (m) REVERT: N 110 HIS cc_start: 0.8330 (t70) cc_final: 0.7677 (m-70) REVERT: N 142 LEU cc_start: 0.8633 (pt) cc_final: 0.7996 (tt) REVERT: N 146 LYS cc_start: 0.9236 (mttt) cc_final: 0.9014 (mmpt) REVERT: N 171 THR cc_start: 0.9194 (t) cc_final: 0.8958 (t) REVERT: N 220 MET cc_start: 0.8082 (tpt) cc_final: 0.7442 (tpt) REVERT: N 221 HIS cc_start: 0.8359 (m90) cc_final: 0.6707 (m90) REVERT: N 228 TYR cc_start: 0.9259 (t80) cc_final: 0.8952 (t80) REVERT: N 278 GLN cc_start: 0.9442 (tt0) cc_final: 0.9162 (tp-100) REVERT: a 36 MET cc_start: 0.9163 (ttm) cc_final: 0.8795 (tpp) REVERT: a 90 GLU cc_start: 0.9074 (tt0) cc_final: 0.8437 (tt0) REVERT: a 91 GLN cc_start: 0.8935 (mt0) cc_final: 0.8713 (mt0) REVERT: a 123 ARG cc_start: 0.8893 (tpp80) cc_final: 0.8399 (tpp-160) REVERT: a 155 GLU cc_start: 0.8844 (tm-30) cc_final: 0.8483 (pp20) REVERT: a 168 GLU cc_start: 0.9286 (mt-10) cc_final: 0.8831 (mm-30) REVERT: a 203 MET cc_start: 0.9393 (OUTLIER) cc_final: 0.8784 (mmp) REVERT: a 221 ARG cc_start: 0.3709 (tpt170) cc_final: 0.2951 (tpt170) REVERT: a 415 GLU cc_start: 0.7895 (mm-30) cc_final: 0.7487 (mm-30) REVERT: b 127 GLU cc_start: 0.9042 (mm-30) cc_final: 0.8670 (mp0) REVERT: b 200 GLU cc_start: 0.8763 (mt-10) cc_final: 0.8480 (mt-10) REVERT: b 207 GLU cc_start: 0.8464 (pt0) cc_final: 0.8253 (pt0) REVERT: b 323 MET cc_start: 0.9392 (ptp) cc_final: 0.9180 (ptt) REVERT: b 435 TYR cc_start: 0.8074 (m-10) cc_final: 0.7762 (m-10) REVERT: f 47 MET cc_start: 0.9127 (tpt) cc_final: 0.8747 (tpt) REVERT: f 50 MET cc_start: 0.8115 (tmm) cc_final: 0.7599 (tmm) REVERT: f 80 GLU cc_start: 0.9260 (tm-30) cc_final: 0.9023 (tm-30) REVERT: f 103 ASP cc_start: 0.8903 (p0) cc_final: 0.8635 (p0) REVERT: f 108 ASP cc_start: 0.7343 (m-30) cc_final: 0.6791 (m-30) REVERT: f 116 ARG cc_start: 0.8181 (mmm160) cc_final: 0.7851 (mmm160) REVERT: f 130 PHE cc_start: 0.8941 (t80) cc_final: 0.8684 (t80) REVERT: n 95 CYS cc_start: 0.9191 (m) cc_final: 0.8959 (m) REVERT: n 114 MET cc_start: 0.8666 (mmm) cc_final: 0.8338 (mmt) REVERT: n 221 HIS cc_start: 0.8308 (OUTLIER) cc_final: 0.8049 (p90) REVERT: n 233 TYR cc_start: 0.8949 (t80) cc_final: 0.8395 (t80) outliers start: 52 outliers final: 23 residues processed: 358 average time/residue: 0.6526 time to fit residues: 262.0055 Evaluate side-chains 318 residues out of total 2271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 291 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 290 GLU Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 290 GLU Chi-restraints excluded: chain B residue 293 GLN Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain F residue 106 THR Chi-restraints excluded: chain F residue 109 ILE Chi-restraints excluded: chain N residue 100 CYS Chi-restraints excluded: chain N residue 103 LEU Chi-restraints excluded: chain a residue 150 THR Chi-restraints excluded: chain a residue 191 THR Chi-restraints excluded: chain a residue 203 MET Chi-restraints excluded: chain a residue 328 VAL Chi-restraints excluded: chain a residue 367 ASP Chi-restraints excluded: chain b residue 3 GLU Chi-restraints excluded: chain b residue 328 VAL Chi-restraints excluded: chain f residue 137 THR Chi-restraints excluded: chain n residue 100 CYS Chi-restraints excluded: chain n residue 126 LEU Chi-restraints excluded: chain n residue 221 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 21 optimal weight: 0.9990 chunk 161 optimal weight: 4.9990 chunk 195 optimal weight: 5.9990 chunk 151 optimal weight: 6.9990 chunk 3 optimal weight: 4.9990 chunk 221 optimal weight: 5.9990 chunk 237 optimal weight: 0.5980 chunk 32 optimal weight: 5.9990 chunk 60 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 9 optimal weight: 0.3980 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 433 GLN B 436 GLN ** F 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 259 ASN N 272 ASN n 93 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.102986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.068493 restraints weight = 45120.492| |-----------------------------------------------------------------------------| r_work (start): 0.3090 rms_B_bonded: 3.35 r_work: 0.2922 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.2172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 21469 Z= 0.170 Angle : 0.633 11.271 29120 Z= 0.325 Chirality : 0.044 0.197 3154 Planarity : 0.004 0.046 3797 Dihedral : 9.178 130.057 3108 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.74 % Allowed : 16.19 % Favored : 81.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.69 % 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: 1.10 (0.16), residues: 2593 helix: 1.51 (0.14), residues: 1377 sheet: 1.00 (0.32), residues: 261 loop : -0.45 (0.19), residues: 955 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG b 322 TYR 0.035 0.001 TYR F 49 PHE 0.027 0.001 PHE F 141 TRP 0.021 0.002 TRP f 143 HIS 0.006 0.001 HIS B 192 Details of bonding type rmsd covalent geometry : bond 0.00379 (21465) covalent geometry : angle 0.63125 (29112) SS BOND : bond 0.01264 ( 4) SS BOND : angle 2.58350 ( 8) hydrogen bonds : bond 0.05916 ( 1131) hydrogen bonds : angle 4.72252 ( 3291) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5186 Ramachandran restraints generated. 2593 Oldfield, 0 Emsley, 2593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5186 Ramachandran restraints generated. 2593 Oldfield, 0 Emsley, 2593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 2271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 326 time to evaluate : 0.753 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 90 GLU cc_start: 0.9315 (mm-30) cc_final: 0.8389 (tm-30) REVERT: A 221 ARG cc_start: 0.3825 (tpt170) cc_final: 0.3088 (tpt170) REVERT: A 284 GLU cc_start: 0.8867 (tt0) cc_final: 0.8529 (mp0) REVERT: A 290 GLU cc_start: 0.8969 (OUTLIER) cc_final: 0.8616 (mp0) REVERT: A 430 LYS cc_start: 0.9285 (ttmm) cc_final: 0.8754 (tptt) REVERT: B 113 GLU cc_start: 0.8969 (mp0) cc_final: 0.8737 (mp0) REVERT: B 290 GLU cc_start: 0.8729 (OUTLIER) cc_final: 0.8470 (mp0) REVERT: B 329 ASP cc_start: 0.8796 (m-30) cc_final: 0.8289 (m-30) REVERT: B 422 GLU cc_start: 0.8566 (tm-30) cc_final: 0.8357 (tm-30) REVERT: F 17 HIS cc_start: 0.9468 (m-70) cc_final: 0.9017 (m-70) REVERT: F 47 MET cc_start: 0.9446 (tpp) cc_final: 0.9046 (tpt) REVERT: F 49 TYR cc_start: 0.9285 (m-80) cc_final: 0.8901 (m-80) REVERT: F 60 ARG cc_start: 0.7865 (ptp-110) cc_final: 0.7627 (ptp90) REVERT: F 66 MET cc_start: 0.8807 (mmm) cc_final: 0.8204 (mpp) REVERT: F 67 MET cc_start: 0.9174 (tpp) cc_final: 0.8969 (tpt) REVERT: F 80 GLU cc_start: 0.8672 (mt-10) cc_final: 0.8317 (mm-30) REVERT: F 152 MET cc_start: 0.8732 (tmt) cc_final: 0.8298 (tmm) REVERT: F 156 ASN cc_start: 0.8182 (t0) cc_final: 0.7635 (m110) REVERT: N 92 ILE cc_start: 0.8588 (pt) cc_final: 0.8386 (pp) REVERT: N 95 CYS cc_start: 0.9447 (m) cc_final: 0.9087 (m) REVERT: N 110 HIS cc_start: 0.8368 (t70) cc_final: 0.7546 (m-70) REVERT: N 140 TYR cc_start: 0.8679 (t80) cc_final: 0.8132 (t80) REVERT: N 142 LEU cc_start: 0.8645 (pt) cc_final: 0.7760 (tt) REVERT: N 146 LYS cc_start: 0.9220 (mttt) cc_final: 0.8978 (mmpt) REVERT: N 171 THR cc_start: 0.9263 (t) cc_final: 0.9061 (t) REVERT: N 220 MET cc_start: 0.8143 (tpt) cc_final: 0.7353 (tpt) REVERT: N 221 HIS cc_start: 0.8310 (m90) cc_final: 0.6639 (m90) REVERT: N 251 GLN cc_start: 0.9090 (tp-100) cc_final: 0.8662 (tp-100) REVERT: N 259 ASN cc_start: 0.9354 (OUTLIER) cc_final: 0.8909 (m-40) REVERT: N 278 GLN cc_start: 0.9449 (tt0) cc_final: 0.9171 (tp-100) REVERT: a 36 MET cc_start: 0.9161 (ttm) cc_final: 0.8742 (tpp) REVERT: a 90 GLU cc_start: 0.9067 (tt0) cc_final: 0.8506 (tt0) REVERT: a 91 GLN cc_start: 0.8979 (mt0) cc_final: 0.8649 (mt0) REVERT: a 123 ARG cc_start: 0.8877 (tpp80) cc_final: 0.8345 (tpm170) REVERT: a 168 GLU cc_start: 0.9297 (mt-10) cc_final: 0.8637 (mm-30) REVERT: a 203 MET cc_start: 0.9425 (OUTLIER) cc_final: 0.8824 (mmp) REVERT: a 221 ARG cc_start: 0.3718 (tpt170) cc_final: 0.2972 (tpt170) REVERT: a 345 ASP cc_start: 0.8951 (m-30) cc_final: 0.8738 (p0) REVERT: a 415 GLU cc_start: 0.7795 (mm-30) cc_final: 0.7394 (mm-30) REVERT: b 127 GLU cc_start: 0.9061 (mm-30) cc_final: 0.8679 (mp0) REVERT: b 200 GLU cc_start: 0.8715 (mt-10) cc_final: 0.8438 (mt-10) REVERT: b 207 GLU cc_start: 0.8496 (pt0) cc_final: 0.8247 (pt0) REVERT: b 301 MET cc_start: 0.9048 (OUTLIER) cc_final: 0.8829 (mpp) REVERT: b 426 ASN cc_start: 0.9129 (m-40) cc_final: 0.8653 (m110) REVERT: b 435 TYR cc_start: 0.7955 (m-10) cc_final: 0.7702 (m-10) REVERT: f 47 MET cc_start: 0.9143 (tpt) cc_final: 0.8820 (tpt) REVERT: f 50 MET cc_start: 0.8202 (tmm) cc_final: 0.7632 (tmm) REVERT: f 95 PHE cc_start: 0.9382 (t80) cc_final: 0.9111 (t80) REVERT: f 103 ASP cc_start: 0.8909 (p0) cc_final: 0.8683 (p0) REVERT: f 130 PHE cc_start: 0.8950 (t80) cc_final: 0.8353 (t80) REVERT: f 164 MET cc_start: 0.8211 (mmp) cc_final: 0.7368 (mtt) REVERT: n 95 CYS cc_start: 0.9177 (m) cc_final: 0.8947 (m) REVERT: n 97 ARG cc_start: 0.9461 (OUTLIER) cc_final: 0.8886 (ttm110) REVERT: n 221 HIS cc_start: 0.8435 (OUTLIER) cc_final: 0.8119 (p90) REVERT: n 233 TYR cc_start: 0.9032 (t80) cc_final: 0.8448 (t80) outliers start: 62 outliers final: 26 residues processed: 361 average time/residue: 0.5746 time to fit residues: 235.1158 Evaluate side-chains 316 residues out of total 2271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 283 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 290 GLU Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 290 GLU Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain F residue 70 ASN Chi-restraints excluded: chain F residue 109 ILE Chi-restraints excluded: chain N residue 100 CYS Chi-restraints excluded: chain N residue 103 LEU Chi-restraints excluded: chain N residue 117 LEU Chi-restraints excluded: chain N residue 177 THR Chi-restraints excluded: chain N residue 259 ASN Chi-restraints excluded: chain a residue 190 THR Chi-restraints excluded: chain a residue 203 MET Chi-restraints excluded: chain a residue 328 VAL Chi-restraints excluded: chain a residue 367 ASP Chi-restraints excluded: chain b residue 3 GLU Chi-restraints excluded: chain b residue 74 THR Chi-restraints excluded: chain b residue 301 MET Chi-restraints excluded: chain b residue 328 VAL Chi-restraints excluded: chain f residue 89 VAL Chi-restraints excluded: chain f residue 110 LEU Chi-restraints excluded: chain f residue 137 THR Chi-restraints excluded: chain n residue 97 ARG Chi-restraints excluded: chain n residue 100 CYS Chi-restraints excluded: chain n residue 126 LEU Chi-restraints excluded: chain n residue 221 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 167 optimal weight: 9.9990 chunk 148 optimal weight: 5.9990 chunk 251 optimal weight: 6.9990 chunk 245 optimal weight: 0.0770 chunk 8 optimal weight: 5.9990 chunk 49 optimal weight: 5.9990 chunk 207 optimal weight: 7.9990 chunk 190 optimal weight: 7.9990 chunk 125 optimal weight: 30.0000 chunk 241 optimal weight: 2.9990 chunk 253 optimal weight: 6.9990 overall best weight: 4.2146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 192 HIS B 266 HIS ** F 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 111 ASN N 272 ASN a 372 GLN b 350 ASN f 46 HIS n 93 GLN n 111 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.099205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.064845 restraints weight = 45683.897| |-----------------------------------------------------------------------------| r_work (start): 0.3012 rms_B_bonded: 3.33 r_work: 0.2841 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.2589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.057 21469 Z= 0.320 Angle : 0.741 10.048 29120 Z= 0.382 Chirality : 0.049 0.191 3154 Planarity : 0.005 0.056 3797 Dihedral : 9.458 136.251 3105 Min Nonbonded Distance : 1.796 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.32 % Favored : 96.64 % Rotamer: Outliers : 3.45 % Allowed : 17.12 % Favored : 79.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.16), residues: 2593 helix: 1.28 (0.14), residues: 1373 sheet: 0.75 (0.32), residues: 261 loop : -0.67 (0.19), residues: 959 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG b 278 TYR 0.020 0.002 TYR N 228 PHE 0.026 0.002 PHE A 255 TRP 0.025 0.002 TRP f 143 HIS 0.006 0.001 HIS A 266 Details of bonding type rmsd covalent geometry : bond 0.00742 (21465) covalent geometry : angle 0.74028 (29112) SS BOND : bond 0.01093 ( 4) SS BOND : angle 2.61595 ( 8) hydrogen bonds : bond 0.07065 ( 1131) hydrogen bonds : angle 5.00589 ( 3291) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5186 Ramachandran restraints generated. 2593 Oldfield, 0 Emsley, 2593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5186 Ramachandran restraints generated. 2593 Oldfield, 0 Emsley, 2593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 2271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 289 time to evaluate : 0.831 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 90 GLU cc_start: 0.9322 (mm-30) cc_final: 0.8445 (tm-30) REVERT: A 120 ASP cc_start: 0.8785 (OUTLIER) cc_final: 0.8491 (p0) REVERT: A 284 GLU cc_start: 0.8951 (tt0) cc_final: 0.8591 (mp0) REVERT: A 290 GLU cc_start: 0.8990 (OUTLIER) cc_final: 0.8735 (mp0) REVERT: B 113 GLU cc_start: 0.9036 (mp0) cc_final: 0.8714 (mp0) REVERT: B 290 GLU cc_start: 0.8797 (OUTLIER) cc_final: 0.8510 (mp0) REVERT: B 329 ASP cc_start: 0.8855 (m-30) cc_final: 0.8357 (m-30) REVERT: B 422 GLU cc_start: 0.8583 (tm-30) cc_final: 0.8143 (tm-30) REVERT: F 9 TYR cc_start: 0.8832 (m-80) cc_final: 0.8544 (m-80) REVERT: F 17 HIS cc_start: 0.9487 (m-70) cc_final: 0.9108 (m-70) REVERT: F 47 MET cc_start: 0.9472 (tpp) cc_final: 0.9053 (tpt) REVERT: F 49 TYR cc_start: 0.9328 (m-80) cc_final: 0.8995 (m-80) REVERT: F 60 ARG cc_start: 0.8068 (ptp-110) cc_final: 0.7784 (ptp90) REVERT: F 63 HIS cc_start: 0.8527 (OUTLIER) cc_final: 0.8144 (m170) REVERT: F 66 MET cc_start: 0.8915 (mmm) cc_final: 0.8353 (mpp) REVERT: F 80 GLU cc_start: 0.8832 (mt-10) cc_final: 0.8502 (mm-30) REVERT: F 113 LYS cc_start: 0.8360 (tppt) cc_final: 0.7747 (mmmm) REVERT: F 127 PHE cc_start: 0.8779 (t80) cc_final: 0.8500 (t80) REVERT: F 152 MET cc_start: 0.8723 (tmt) cc_final: 0.8374 (tmm) REVERT: F 156 ASN cc_start: 0.8075 (t0) cc_final: 0.7522 (m110) REVERT: N 79 LYS cc_start: 0.9504 (OUTLIER) cc_final: 0.9282 (tmmm) REVERT: N 95 CYS cc_start: 0.9406 (m) cc_final: 0.9064 (m) REVERT: N 110 HIS cc_start: 0.8505 (t70) cc_final: 0.7403 (m-70) REVERT: N 198 MET cc_start: 0.8700 (tpp) cc_final: 0.7809 (ttt) REVERT: N 220 MET cc_start: 0.8238 (tpt) cc_final: 0.7302 (tpt) REVERT: N 221 HIS cc_start: 0.8415 (m90) cc_final: 0.6890 (m90) REVERT: N 228 TYR cc_start: 0.9224 (t80) cc_final: 0.8981 (t80) REVERT: N 259 ASN cc_start: 0.9384 (t0) cc_final: 0.8987 (m-40) REVERT: N 278 GLN cc_start: 0.9475 (tt0) cc_final: 0.9206 (tp-100) REVERT: a 36 MET cc_start: 0.9193 (ttm) cc_final: 0.8747 (tpp) REVERT: a 90 GLU cc_start: 0.9102 (tt0) cc_final: 0.8552 (tt0) REVERT: a 91 GLN cc_start: 0.9037 (mt0) cc_final: 0.8658 (mt0) REVERT: a 123 ARG cc_start: 0.8950 (tpp80) cc_final: 0.8335 (tpp-160) REVERT: a 203 MET cc_start: 0.9540 (OUTLIER) cc_final: 0.8981 (mmp) REVERT: a 221 ARG cc_start: 0.3824 (tpt170) cc_final: 0.3143 (tpt170) REVERT: a 287 SER cc_start: 0.8995 (t) cc_final: 0.8653 (p) REVERT: b 127 GLU cc_start: 0.9109 (mm-30) cc_final: 0.8857 (mm-30) REVERT: b 200 GLU cc_start: 0.8796 (mt-10) cc_final: 0.8511 (mt-10) REVERT: f 47 MET cc_start: 0.8996 (tpt) cc_final: 0.8693 (tpt) REVERT: f 50 MET cc_start: 0.8172 (tmm) cc_final: 0.7573 (tmm) REVERT: f 80 GLU cc_start: 0.9359 (tm-30) cc_final: 0.9049 (tm-30) REVERT: f 95 PHE cc_start: 0.9426 (t80) cc_final: 0.9152 (t80) REVERT: f 130 PHE cc_start: 0.8956 (t80) cc_final: 0.8349 (t80) REVERT: n 95 CYS cc_start: 0.9115 (m) cc_final: 0.8869 (m) REVERT: n 97 ARG cc_start: 0.9479 (OUTLIER) cc_final: 0.9189 (tpp80) REVERT: n 114 MET cc_start: 0.8674 (mmm) cc_final: 0.8448 (mmt) REVERT: n 221 HIS cc_start: 0.8447 (m-70) cc_final: 0.8130 (p90) REVERT: n 233 TYR cc_start: 0.8858 (t80) cc_final: 0.8246 (t80) outliers start: 78 outliers final: 45 residues processed: 345 average time/residue: 0.5573 time to fit residues: 219.5100 Evaluate side-chains 323 residues out of total 2271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 271 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 290 GLU Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 290 GLU Chi-restraints excluded: chain B residue 293 GLN Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain F residue 14 ILE Chi-restraints excluded: chain F residue 22 ILE Chi-restraints excluded: chain F residue 63 HIS Chi-restraints excluded: chain F residue 70 ASN Chi-restraints excluded: chain F residue 92 LEU Chi-restraints excluded: chain F residue 109 ILE Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain F residue 131 ARG Chi-restraints excluded: chain N residue 79 LYS Chi-restraints excluded: chain N residue 100 CYS Chi-restraints excluded: chain N residue 103 LEU Chi-restraints excluded: chain N residue 117 LEU Chi-restraints excluded: chain N residue 172 VAL Chi-restraints excluded: chain N residue 177 THR Chi-restraints excluded: chain N residue 194 ILE Chi-restraints excluded: chain a residue 114 ILE Chi-restraints excluded: chain a residue 122 ILE Chi-restraints excluded: chain a residue 190 THR Chi-restraints excluded: chain a residue 191 THR Chi-restraints excluded: chain a residue 203 MET Chi-restraints excluded: chain a residue 234 ILE Chi-restraints excluded: chain a residue 276 ILE Chi-restraints excluded: chain a residue 328 VAL Chi-restraints excluded: chain a residue 367 ASP Chi-restraints excluded: chain a residue 437 VAL Chi-restraints excluded: chain b residue 3 GLU Chi-restraints excluded: chain b residue 166 MET Chi-restraints excluded: chain b residue 295 MET Chi-restraints excluded: chain b residue 328 VAL Chi-restraints excluded: chain f residue 27 ASP Chi-restraints excluded: chain f residue 89 VAL Chi-restraints excluded: chain f residue 110 LEU Chi-restraints excluded: chain f residue 137 THR Chi-restraints excluded: chain n residue 97 ARG Chi-restraints excluded: chain n residue 100 CYS Chi-restraints excluded: chain n residue 126 LEU Chi-restraints excluded: chain n residue 192 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 33 optimal weight: 2.9990 chunk 201 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 chunk 123 optimal weight: 6.9990 chunk 179 optimal weight: 5.9990 chunk 12 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 48 optimal weight: 0.6980 chunk 186 optimal weight: 0.9990 chunk 63 optimal weight: 0.7980 chunk 7 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 433 GLN F 54 GLN ** F 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 118 GLN n 93 GLN n 98 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.103246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.068813 restraints weight = 44977.637| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 3.37 r_work: 0.2932 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.2770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 21469 Z= 0.139 Angle : 0.635 11.776 29120 Z= 0.322 Chirality : 0.043 0.194 3154 Planarity : 0.004 0.047 3797 Dihedral : 9.063 134.657 3105 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.70 % Allowed : 18.76 % Favored : 78.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.69 % 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: 1.09 (0.16), residues: 2593 helix: 1.56 (0.14), residues: 1363 sheet: 0.89 (0.32), residues: 263 loop : -0.49 (0.19), residues: 967 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG b 278 TYR 0.019 0.001 TYR F 49 PHE 0.019 0.001 PHE F 130 TRP 0.028 0.002 TRP f 143 HIS 0.006 0.001 HIS N 195 Details of bonding type rmsd covalent geometry : bond 0.00291 (21465) covalent geometry : angle 0.63405 (29112) SS BOND : bond 0.01211 ( 4) SS BOND : angle 2.20703 ( 8) hydrogen bonds : bond 0.05307 ( 1131) hydrogen bonds : angle 4.60172 ( 3291) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5186 Ramachandran restraints generated. 2593 Oldfield, 0 Emsley, 2593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5186 Ramachandran restraints generated. 2593 Oldfield, 0 Emsley, 2593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 2271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 321 time to evaluate : 0.647 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 GLU cc_start: 0.9336 (mm-30) cc_final: 0.8441 (tm-30) REVERT: A 120 ASP cc_start: 0.8749 (OUTLIER) cc_final: 0.8475 (p0) REVERT: A 284 GLU cc_start: 0.8908 (tt0) cc_final: 0.8562 (mp0) REVERT: A 290 GLU cc_start: 0.8936 (OUTLIER) cc_final: 0.8594 (mp0) REVERT: A 430 LYS cc_start: 0.9261 (tppp) cc_final: 0.8876 (tmtt) REVERT: B 113 GLU cc_start: 0.9064 (mp0) cc_final: 0.8707 (mp0) REVERT: B 290 GLU cc_start: 0.8727 (OUTLIER) cc_final: 0.8446 (mp0) REVERT: B 329 ASP cc_start: 0.8786 (m-30) cc_final: 0.8269 (m-30) REVERT: B 433 GLN cc_start: 0.8902 (OUTLIER) cc_final: 0.8625 (tp-100) REVERT: F 17 HIS cc_start: 0.9441 (m-70) cc_final: 0.8990 (m-70) REVERT: F 29 LYS cc_start: 0.9650 (mmmm) cc_final: 0.9350 (mmmm) REVERT: F 47 MET cc_start: 0.9454 (tpp) cc_final: 0.9009 (tpt) REVERT: F 49 TYR cc_start: 0.9316 (m-80) cc_final: 0.8904 (m-80) REVERT: F 60 ARG cc_start: 0.8017 (ptp-110) cc_final: 0.7686 (ptp90) REVERT: F 66 MET cc_start: 0.8877 (mmm) cc_final: 0.8400 (mpp) REVERT: F 80 GLU cc_start: 0.8634 (mt-10) cc_final: 0.8302 (mm-30) REVERT: F 93 ASP cc_start: 0.8831 (t0) cc_final: 0.8550 (t0) REVERT: F 113 LYS cc_start: 0.8379 (tppt) cc_final: 0.7821 (mmmm) REVERT: F 152 MET cc_start: 0.8785 (tmt) cc_final: 0.8428 (tmm) REVERT: F 156 ASN cc_start: 0.8030 (t0) cc_final: 0.7490 (m110) REVERT: N 95 CYS cc_start: 0.9420 (m) cc_final: 0.9097 (m) REVERT: N 110 HIS cc_start: 0.8462 (t70) cc_final: 0.7361 (m170) REVERT: N 140 TYR cc_start: 0.8687 (t80) cc_final: 0.8180 (t80) REVERT: N 198 MET cc_start: 0.8555 (tpp) cc_final: 0.7611 (ttt) REVERT: N 220 MET cc_start: 0.8170 (tpt) cc_final: 0.7039 (tpt) REVERT: N 221 HIS cc_start: 0.8440 (m90) cc_final: 0.6924 (m90) REVERT: N 224 LEU cc_start: 0.9353 (OUTLIER) cc_final: 0.9076 (mm) REVERT: N 228 TYR cc_start: 0.9196 (t80) cc_final: 0.8990 (t80) REVERT: N 259 ASN cc_start: 0.9374 (t0) cc_final: 0.8995 (m-40) REVERT: N 278 GLN cc_start: 0.9536 (tt0) cc_final: 0.9280 (tp-100) REVERT: a 36 MET cc_start: 0.9180 (ttm) cc_final: 0.8748 (tpp) REVERT: a 90 GLU cc_start: 0.9056 (tt0) cc_final: 0.8491 (tt0) REVERT: a 91 GLN cc_start: 0.8977 (mt0) cc_final: 0.8639 (mt0) REVERT: a 123 ARG cc_start: 0.8924 (tpp80) cc_final: 0.8340 (tpm170) REVERT: a 168 GLU cc_start: 0.9237 (mt-10) cc_final: 0.8801 (mm-30) REVERT: a 221 ARG cc_start: 0.3384 (tpt170) cc_final: 0.2915 (tpt170) REVERT: a 415 GLU cc_start: 0.7848 (mm-30) cc_final: 0.7551 (mm-30) REVERT: b 47 GLU cc_start: 0.9116 (mm-30) cc_final: 0.8613 (mm-30) REVERT: b 136 GLN cc_start: 0.9146 (pt0) cc_final: 0.8920 (pt0) REVERT: b 200 GLU cc_start: 0.8682 (mt-10) cc_final: 0.8342 (mt-10) REVERT: b 398 MET cc_start: 0.8677 (mtm) cc_final: 0.8462 (mmm) REVERT: b 416 MET cc_start: 0.8682 (ppp) cc_final: 0.8465 (ppp) REVERT: b 426 ASN cc_start: 0.9161 (m-40) cc_final: 0.8938 (m-40) REVERT: f 47 MET cc_start: 0.8974 (tpt) cc_final: 0.8638 (tpt) REVERT: f 50 MET cc_start: 0.8177 (tmm) cc_final: 0.7543 (tmm) REVERT: f 95 PHE cc_start: 0.9426 (t80) cc_final: 0.9140 (t80) REVERT: f 130 PHE cc_start: 0.8932 (t80) cc_final: 0.8278 (t80) REVERT: f 164 MET cc_start: 0.7970 (mmp) cc_final: 0.7108 (mtt) REVERT: n 95 CYS cc_start: 0.9128 (m) cc_final: 0.8912 (m) REVERT: n 97 ARG cc_start: 0.9469 (OUTLIER) cc_final: 0.9194 (tpp80) REVERT: n 114 MET cc_start: 0.8586 (mmm) cc_final: 0.8341 (mmt) REVERT: n 221 HIS cc_start: 0.8338 (m-70) cc_final: 0.8021 (p90) REVERT: n 233 TYR cc_start: 0.8967 (t80) cc_final: 0.8298 (t80) outliers start: 61 outliers final: 20 residues processed: 356 average time/residue: 0.5577 time to fit residues: 225.6499 Evaluate side-chains 310 residues out of total 2271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 284 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 290 GLU Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 290 GLU Chi-restraints excluded: chain B residue 433 GLN Chi-restraints excluded: chain F residue 22 ILE Chi-restraints excluded: chain F residue 70 ASN Chi-restraints excluded: chain F residue 102 ASN Chi-restraints excluded: chain F residue 131 ARG Chi-restraints excluded: chain N residue 117 LEU Chi-restraints excluded: chain N residue 224 LEU Chi-restraints excluded: chain a residue 110 ILE Chi-restraints excluded: chain a residue 159 VAL Chi-restraints excluded: chain a residue 328 VAL Chi-restraints excluded: chain a residue 367 ASP Chi-restraints excluded: chain b residue 3 GLU Chi-restraints excluded: chain f residue 89 VAL Chi-restraints excluded: chain f residue 110 LEU Chi-restraints excluded: chain f residue 137 THR Chi-restraints excluded: chain n residue 97 ARG Chi-restraints excluded: chain n residue 100 CYS Chi-restraints excluded: chain n residue 126 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 99 optimal weight: 0.0970 chunk 218 optimal weight: 2.9990 chunk 191 optimal weight: 3.9990 chunk 55 optimal weight: 0.6980 chunk 249 optimal weight: 20.0000 chunk 27 optimal weight: 4.9990 chunk 151 optimal weight: 4.9990 chunk 126 optimal weight: 5.9990 chunk 157 optimal weight: 0.0670 chunk 145 optimal weight: 6.9990 chunk 94 optimal weight: 3.9990 overall best weight: 1.5720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 11 GLN F 126 ASN F 129 HIS N 111 ASN N 118 GLN N 272 ASN N 284 GLN n 93 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.102644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.068244 restraints weight = 44777.531| |-----------------------------------------------------------------------------| r_work (start): 0.3086 rms_B_bonded: 3.35 r_work: 0.2917 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.2907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 21469 Z= 0.160 Angle : 0.658 11.114 29120 Z= 0.332 Chirality : 0.044 0.192 3154 Planarity : 0.004 0.046 3797 Dihedral : 8.966 134.291 3105 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.48 % Allowed : 19.69 % Favored : 77.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.69 % 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: 1.10 (0.16), residues: 2593 helix: 1.57 (0.14), residues: 1370 sheet: 0.83 (0.32), residues: 264 loop : -0.47 (0.20), residues: 959 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG f 119 TYR 0.030 0.001 TYR N 233 PHE 0.035 0.001 PHE n 236 TRP 0.015 0.001 TRP f 143 HIS 0.005 0.001 HIS N 195 Details of bonding type rmsd covalent geometry : bond 0.00361 (21465) covalent geometry : angle 0.65741 (29112) SS BOND : bond 0.01206 ( 4) SS BOND : angle 2.33818 ( 8) hydrogen bonds : bond 0.05436 ( 1131) hydrogen bonds : angle 4.59707 ( 3291) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5186 Ramachandran restraints generated. 2593 Oldfield, 0 Emsley, 2593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5186 Ramachandran restraints generated. 2593 Oldfield, 0 Emsley, 2593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 2271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 292 time to evaluate : 0.731 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 GLU cc_start: 0.9335 (mm-30) cc_final: 0.8448 (tm-30) REVERT: A 120 ASP cc_start: 0.8798 (OUTLIER) cc_final: 0.8523 (p0) REVERT: A 284 GLU cc_start: 0.8941 (tt0) cc_final: 0.8594 (mp0) REVERT: A 290 GLU cc_start: 0.8958 (OUTLIER) cc_final: 0.8582 (mp0) REVERT: A 430 LYS cc_start: 0.9301 (tppp) cc_final: 0.8912 (tmtt) REVERT: B 113 GLU cc_start: 0.9090 (mp0) cc_final: 0.8724 (mp0) REVERT: B 290 GLU cc_start: 0.8748 (OUTLIER) cc_final: 0.8458 (mp0) REVERT: B 329 ASP cc_start: 0.8825 (m-30) cc_final: 0.8319 (m-30) REVERT: B 422 GLU cc_start: 0.8485 (tm-30) cc_final: 0.8234 (tm-30) REVERT: F 9 TYR cc_start: 0.8708 (m-80) cc_final: 0.8407 (m-80) REVERT: F 17 HIS cc_start: 0.9428 (m-70) cc_final: 0.8993 (m-70) REVERT: F 47 MET cc_start: 0.9421 (tpp) cc_final: 0.8967 (tpt) REVERT: F 49 TYR cc_start: 0.9323 (m-80) cc_final: 0.8883 (m-80) REVERT: F 60 ARG cc_start: 0.8085 (ptp-110) cc_final: 0.7762 (ptp90) REVERT: F 63 HIS cc_start: 0.8504 (OUTLIER) cc_final: 0.8185 (m170) REVERT: F 66 MET cc_start: 0.8895 (mmm) cc_final: 0.8404 (mpp) REVERT: F 80 GLU cc_start: 0.8648 (mt-10) cc_final: 0.8250 (mm-30) REVERT: F 93 ASP cc_start: 0.8847 (t0) cc_final: 0.8553 (t0) REVERT: F 113 LYS cc_start: 0.8359 (tppt) cc_final: 0.7841 (mmmm) REVERT: F 127 PHE cc_start: 0.8187 (t80) cc_final: 0.7971 (t80) REVERT: F 152 MET cc_start: 0.8769 (tmt) cc_final: 0.8400 (tmm) REVERT: F 156 ASN cc_start: 0.8061 (t0) cc_final: 0.7532 (m110) REVERT: N 79 LYS cc_start: 0.9514 (OUTLIER) cc_final: 0.8993 (tppt) REVERT: N 95 CYS cc_start: 0.9426 (m) cc_final: 0.9091 (m) REVERT: N 110 HIS cc_start: 0.8481 (t70) cc_final: 0.7377 (m170) REVERT: N 198 MET cc_start: 0.8567 (tpp) cc_final: 0.7586 (ttp) REVERT: N 220 MET cc_start: 0.8264 (tpt) cc_final: 0.7047 (tpt) REVERT: N 221 HIS cc_start: 0.8461 (m90) cc_final: 0.6956 (m90) REVERT: N 224 LEU cc_start: 0.9344 (OUTLIER) cc_final: 0.9066 (mm) REVERT: N 259 ASN cc_start: 0.9384 (t0) cc_final: 0.9025 (m-40) REVERT: a 36 MET cc_start: 0.9186 (ttm) cc_final: 0.8756 (tpp) REVERT: a 90 GLU cc_start: 0.9063 (tt0) cc_final: 0.8505 (tt0) REVERT: a 91 GLN cc_start: 0.8981 (mt0) cc_final: 0.8688 (mt0) REVERT: a 112 LYS cc_start: 0.8718 (pptt) cc_final: 0.8469 (pptt) REVERT: a 123 ARG cc_start: 0.8926 (tpp80) cc_final: 0.8337 (tpm170) REVERT: a 155 GLU cc_start: 0.8973 (tm-30) cc_final: 0.8549 (pp20) REVERT: a 168 GLU cc_start: 0.9216 (mt-10) cc_final: 0.8818 (mm-30) REVERT: a 221 ARG cc_start: 0.3278 (tpt170) cc_final: 0.2766 (tpt170) REVERT: b 47 GLU cc_start: 0.9131 (mm-30) cc_final: 0.8646 (mm-30) REVERT: b 110 GLU cc_start: 0.9020 (OUTLIER) cc_final: 0.8655 (mp0) REVERT: b 127 GLU cc_start: 0.8463 (mm-30) cc_final: 0.8196 (mm-30) REVERT: b 136 GLN cc_start: 0.9164 (pt0) cc_final: 0.8950 (pt0) REVERT: b 200 GLU cc_start: 0.8722 (mt-10) cc_final: 0.8390 (mt-10) REVERT: b 426 ASN cc_start: 0.9162 (m-40) cc_final: 0.8949 (m-40) REVERT: f 29 LYS cc_start: 0.9582 (mmmm) cc_final: 0.9305 (pptt) REVERT: f 47 MET cc_start: 0.8981 (tpt) cc_final: 0.8653 (tpt) REVERT: f 50 MET cc_start: 0.8201 (tmm) cc_final: 0.7577 (tmm) REVERT: f 67 MET cc_start: 0.8626 (ppp) cc_final: 0.8399 (ttm) REVERT: f 95 PHE cc_start: 0.9451 (t80) cc_final: 0.9185 (t80) REVERT: f 103 ASP cc_start: 0.8949 (p0) cc_final: 0.8744 (p0) REVERT: f 108 ASP cc_start: 0.7800 (m-30) cc_final: 0.7308 (m-30) REVERT: f 116 ARG cc_start: 0.8243 (mmm160) cc_final: 0.7930 (mmm160) REVERT: f 130 PHE cc_start: 0.8864 (t80) cc_final: 0.8221 (t80) REVERT: f 164 MET cc_start: 0.7912 (mmp) cc_final: 0.7118 (mtt) REVERT: n 95 CYS cc_start: 0.9137 (m) cc_final: 0.8890 (m) REVERT: n 97 ARG cc_start: 0.9471 (OUTLIER) cc_final: 0.9199 (tpp80) REVERT: n 114 MET cc_start: 0.8610 (mmm) cc_final: 0.8349 (mmt) REVERT: n 221 HIS cc_start: 0.8378 (m-70) cc_final: 0.8056 (p90) REVERT: n 233 TYR cc_start: 0.8928 (t80) cc_final: 0.8255 (t80) outliers start: 56 outliers final: 26 residues processed: 326 average time/residue: 0.5868 time to fit residues: 216.8060 Evaluate side-chains 316 residues out of total 2271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 282 time to evaluate : 0.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 290 GLU Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 290 GLU Chi-restraints excluded: chain F residue 22 ILE Chi-restraints excluded: chain F residue 63 HIS Chi-restraints excluded: chain F residue 126 ASN Chi-restraints excluded: chain F residue 131 ARG Chi-restraints excluded: chain N residue 69 SER Chi-restraints excluded: chain N residue 79 LYS Chi-restraints excluded: chain N residue 100 CYS Chi-restraints excluded: chain N residue 117 LEU Chi-restraints excluded: chain N residue 224 LEU Chi-restraints excluded: chain a residue 287 SER Chi-restraints excluded: chain a residue 328 VAL Chi-restraints excluded: chain a residue 367 ASP Chi-restraints excluded: chain b residue 3 GLU Chi-restraints excluded: chain b residue 110 GLU Chi-restraints excluded: chain b residue 166 MET Chi-restraints excluded: chain b residue 205 ASP Chi-restraints excluded: chain f residue 77 HIS Chi-restraints excluded: chain f residue 89 VAL Chi-restraints excluded: chain f residue 110 LEU Chi-restraints excluded: chain f residue 137 THR Chi-restraints excluded: chain n residue 97 ARG Chi-restraints excluded: chain n residue 100 CYS Chi-restraints excluded: chain n residue 126 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 6 optimal weight: 8.9990 chunk 187 optimal weight: 0.8980 chunk 253 optimal weight: 5.9990 chunk 248 optimal weight: 0.8980 chunk 109 optimal weight: 0.0970 chunk 144 optimal weight: 0.9980 chunk 36 optimal weight: 3.9990 chunk 128 optimal weight: 9.9990 chunk 83 optimal weight: 2.9990 chunk 208 optimal weight: 1.9990 chunk 164 optimal weight: 0.7980 overall best weight: 0.7378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 433 GLN F 126 ASN N 111 ASN N 118 GLN a 372 GLN f 154 GLN n 93 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.103891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.069558 restraints weight = 44909.706| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 3.33 r_work: 0.2955 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.3080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 21469 Z= 0.129 Angle : 0.643 11.502 29120 Z= 0.319 Chirality : 0.043 0.202 3154 Planarity : 0.004 0.047 3797 Dihedral : 8.727 134.699 3105 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.26 % Allowed : 20.31 % Favored : 77.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.24 (0.17), residues: 2593 helix: 1.67 (0.14), residues: 1382 sheet: 0.98 (0.32), residues: 260 loop : -0.43 (0.20), residues: 951 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG f 119 TYR 0.024 0.001 TYR F 138 PHE 0.031 0.001 PHE F 95 TRP 0.033 0.002 TRP f 143 HIS 0.004 0.001 HIS F 129 Details of bonding type rmsd covalent geometry : bond 0.00275 (21465) covalent geometry : angle 0.64198 (29112) SS BOND : bond 0.01220 ( 4) SS BOND : angle 2.30450 ( 8) hydrogen bonds : bond 0.04813 ( 1131) hydrogen bonds : angle 4.48310 ( 3291) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5186 Ramachandran restraints generated. 2593 Oldfield, 0 Emsley, 2593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5186 Ramachandran restraints generated. 2593 Oldfield, 0 Emsley, 2593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 2271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 307 time to evaluate : 0.787 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 GLU cc_start: 0.9336 (mm-30) cc_final: 0.8424 (tm-30) REVERT: A 120 ASP cc_start: 0.8776 (OUTLIER) cc_final: 0.8520 (p0) REVERT: A 275 VAL cc_start: 0.9055 (OUTLIER) cc_final: 0.8844 (m) REVERT: A 284 GLU cc_start: 0.8908 (tt0) cc_final: 0.8566 (mp0) REVERT: A 290 GLU cc_start: 0.8934 (OUTLIER) cc_final: 0.8562 (mp0) REVERT: A 430 LYS cc_start: 0.9268 (tppp) cc_final: 0.8854 (tmtt) REVERT: B 113 GLU cc_start: 0.9088 (mp0) cc_final: 0.8723 (mp0) REVERT: B 290 GLU cc_start: 0.8677 (OUTLIER) cc_final: 0.8386 (mp0) REVERT: B 329 ASP cc_start: 0.8803 (m-30) cc_final: 0.8275 (m-30) REVERT: B 422 GLU cc_start: 0.8376 (tm-30) cc_final: 0.8149 (tm-30) REVERT: B 433 GLN cc_start: 0.9001 (OUTLIER) cc_final: 0.8690 (tp-100) REVERT: F 17 HIS cc_start: 0.9394 (m-70) cc_final: 0.8933 (m-70) REVERT: F 47 MET cc_start: 0.9437 (tpp) cc_final: 0.8964 (tpt) REVERT: F 49 TYR cc_start: 0.9335 (m-80) cc_final: 0.8872 (m-80) REVERT: F 60 ARG cc_start: 0.8036 (ptp-110) cc_final: 0.7737 (ptp90) REVERT: F 62 GLU cc_start: 0.8538 (tm-30) cc_final: 0.8071 (tm-30) REVERT: F 66 MET cc_start: 0.8831 (mmm) cc_final: 0.8244 (mpp) REVERT: F 80 GLU cc_start: 0.8591 (mt-10) cc_final: 0.8208 (mm-30) REVERT: F 93 ASP cc_start: 0.8797 (t0) cc_final: 0.8507 (t0) REVERT: F 108 ASP cc_start: 0.8895 (m-30) cc_final: 0.8635 (m-30) REVERT: F 113 LYS cc_start: 0.8372 (tppt) cc_final: 0.7898 (mmmm) REVERT: F 152 MET cc_start: 0.8762 (tmt) cc_final: 0.8401 (tmm) REVERT: F 156 ASN cc_start: 0.7859 (t0) cc_final: 0.7374 (m110) REVERT: N 79 LYS cc_start: 0.9513 (OUTLIER) cc_final: 0.9006 (tppt) REVERT: N 95 CYS cc_start: 0.9407 (m) cc_final: 0.9078 (m) REVERT: N 110 HIS cc_start: 0.8466 (t70) cc_final: 0.7391 (m170) REVERT: N 198 MET cc_start: 0.8494 (tpp) cc_final: 0.7529 (ttp) REVERT: N 220 MET cc_start: 0.8264 (tpt) cc_final: 0.7055 (tpt) REVERT: N 221 HIS cc_start: 0.8434 (m90) cc_final: 0.6975 (m90) REVERT: N 224 LEU cc_start: 0.9279 (OUTLIER) cc_final: 0.9017 (mm) REVERT: N 259 ASN cc_start: 0.9375 (t0) cc_final: 0.9034 (m-40) REVERT: a 36 MET cc_start: 0.9170 (ttm) cc_final: 0.8754 (tpp) REVERT: a 90 GLU cc_start: 0.9097 (tt0) cc_final: 0.8572 (tt0) REVERT: a 91 GLN cc_start: 0.8964 (mt0) cc_final: 0.8694 (mt0) REVERT: a 123 ARG cc_start: 0.8883 (tpp80) cc_final: 0.8282 (tpm170) REVERT: a 168 GLU cc_start: 0.9210 (mt-10) cc_final: 0.8837 (mm-30) REVERT: a 203 MET cc_start: 0.9432 (OUTLIER) cc_final: 0.8767 (mmp) REVERT: a 221 ARG cc_start: 0.3307 (tpt170) cc_final: 0.2364 (tpt170) REVERT: a 398 MET cc_start: 0.8625 (mtp) cc_final: 0.8320 (ttm) REVERT: b 47 GLU cc_start: 0.9126 (mm-30) cc_final: 0.8603 (mm-30) REVERT: b 110 GLU cc_start: 0.8968 (OUTLIER) cc_final: 0.8643 (mp0) REVERT: b 127 GLU cc_start: 0.8498 (mm-30) cc_final: 0.8155 (mp0) REVERT: b 136 GLN cc_start: 0.9048 (pt0) cc_final: 0.8813 (pt0) REVERT: b 200 GLU cc_start: 0.8701 (mt-10) cc_final: 0.8317 (mt-10) REVERT: b 398 MET cc_start: 0.8726 (mtm) cc_final: 0.8517 (mtm) REVERT: b 426 ASN cc_start: 0.9183 (m-40) cc_final: 0.8956 (m-40) REVERT: f 6 PHE cc_start: 0.8417 (m-80) cc_final: 0.8167 (m-80) REVERT: f 47 MET cc_start: 0.8945 (tpt) cc_final: 0.8663 (tpt) REVERT: f 50 MET cc_start: 0.8173 (tmm) cc_final: 0.7543 (tmm) REVERT: f 95 PHE cc_start: 0.9443 (t80) cc_final: 0.9191 (t80) REVERT: f 103 ASP cc_start: 0.8981 (p0) cc_final: 0.8428 (p0) REVERT: f 108 ASP cc_start: 0.7949 (m-30) cc_final: 0.7312 (m-30) REVERT: f 116 ARG cc_start: 0.8206 (mmm160) cc_final: 0.7787 (mmm160) REVERT: f 130 PHE cc_start: 0.8890 (t80) cc_final: 0.8234 (t80) REVERT: f 164 MET cc_start: 0.7885 (mmp) cc_final: 0.7094 (mtt) REVERT: n 79 LYS cc_start: 0.9156 (mmmt) cc_final: 0.8689 (mmmt) REVERT: n 95 CYS cc_start: 0.9120 (m) cc_final: 0.8902 (m) REVERT: n 97 ARG cc_start: 0.9444 (OUTLIER) cc_final: 0.9230 (tpp80) REVERT: n 114 MET cc_start: 0.8524 (mmm) cc_final: 0.8251 (mmt) REVERT: n 221 HIS cc_start: 0.8333 (m-70) cc_final: 0.8037 (p90) REVERT: n 233 TYR cc_start: 0.8936 (t80) cc_final: 0.8270 (t80) outliers start: 51 outliers final: 27 residues processed: 339 average time/residue: 0.5797 time to fit residues: 222.9897 Evaluate side-chains 319 residues out of total 2271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 282 time to evaluate : 0.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 290 GLU Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 290 GLU Chi-restraints excluded: chain B residue 433 GLN Chi-restraints excluded: chain F residue 22 ILE Chi-restraints excluded: chain F residue 131 ARG Chi-restraints excluded: chain N residue 69 SER Chi-restraints excluded: chain N residue 79 LYS Chi-restraints excluded: chain N residue 100 CYS Chi-restraints excluded: chain N residue 117 LEU Chi-restraints excluded: chain N residue 224 LEU Chi-restraints excluded: chain a residue 191 THR Chi-restraints excluded: chain a residue 194 THR Chi-restraints excluded: chain a residue 203 MET Chi-restraints excluded: chain a residue 328 VAL Chi-restraints excluded: chain a residue 367 ASP Chi-restraints excluded: chain a residue 375 VAL Chi-restraints excluded: chain a residue 432 TYR Chi-restraints excluded: chain b residue 3 GLU Chi-restraints excluded: chain b residue 110 GLU Chi-restraints excluded: chain b residue 166 MET Chi-restraints excluded: chain b residue 205 ASP Chi-restraints excluded: chain f residue 77 HIS Chi-restraints excluded: chain f residue 89 VAL Chi-restraints excluded: chain f residue 110 LEU Chi-restraints excluded: chain f residue 137 THR Chi-restraints excluded: chain n residue 97 ARG Chi-restraints excluded: chain n residue 100 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 83 optimal weight: 0.6980 chunk 53 optimal weight: 0.5980 chunk 81 optimal weight: 8.9990 chunk 145 optimal weight: 0.6980 chunk 210 optimal weight: 0.9990 chunk 99 optimal weight: 10.0000 chunk 253 optimal weight: 0.4980 chunk 174 optimal weight: 0.8980 chunk 6 optimal weight: 8.9990 chunk 235 optimal weight: 10.0000 chunk 51 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 ASN B 433 GLN F 126 ASN N 111 ASN N 118 GLN a 372 GLN f 154 GLN n 93 GLN ** n 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.104738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.070471 restraints weight = 44737.768| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 3.36 r_work: 0.2962 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.3230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 21469 Z= 0.129 Angle : 0.661 11.567 29120 Z= 0.328 Chirality : 0.043 0.272 3154 Planarity : 0.004 0.046 3797 Dihedral : 8.588 133.305 3105 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.04 % Allowed : 20.75 % Favored : 77.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.69 % 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: 1.31 (0.17), residues: 2593 helix: 1.70 (0.14), residues: 1392 sheet: 1.00 (0.32), residues: 272 loop : -0.40 (0.20), residues: 929 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG F 168 TYR 0.027 0.001 TYR N 228 PHE 0.045 0.001 PHE F 130 TRP 0.016 0.001 TRP f 143 HIS 0.004 0.001 HIS n 176 Details of bonding type rmsd covalent geometry : bond 0.00277 (21465) covalent geometry : angle 0.65986 (29112) SS BOND : bond 0.01161 ( 4) SS BOND : angle 2.13596 ( 8) hydrogen bonds : bond 0.04687 ( 1131) hydrogen bonds : angle 4.42919 ( 3291) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5186 Ramachandran restraints generated. 2593 Oldfield, 0 Emsley, 2593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5186 Ramachandran restraints generated. 2593 Oldfield, 0 Emsley, 2593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 2271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 303 time to evaluate : 0.844 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 GLU cc_start: 0.9327 (mm-30) cc_final: 0.8414 (tm-30) REVERT: A 120 ASP cc_start: 0.8795 (OUTLIER) cc_final: 0.8532 (p0) REVERT: A 275 VAL cc_start: 0.9036 (OUTLIER) cc_final: 0.8823 (m) REVERT: A 284 GLU cc_start: 0.8905 (tt0) cc_final: 0.8566 (mp0) REVERT: A 290 GLU cc_start: 0.8937 (OUTLIER) cc_final: 0.8677 (mp0) REVERT: A 339 ARG cc_start: 0.7792 (tpp80) cc_final: 0.7553 (tpp-160) REVERT: A 430 LYS cc_start: 0.9265 (tppp) cc_final: 0.8879 (tmtt) REVERT: B 113 GLU cc_start: 0.9091 (mp0) cc_final: 0.8827 (mp0) REVERT: B 127 GLU cc_start: 0.8115 (pp20) cc_final: 0.7668 (pp20) REVERT: B 290 GLU cc_start: 0.8673 (OUTLIER) cc_final: 0.8438 (mp0) REVERT: B 329 ASP cc_start: 0.8829 (m-30) cc_final: 0.8404 (m-30) REVERT: B 422 GLU cc_start: 0.8364 (tm-30) cc_final: 0.8119 (tm-30) REVERT: B 433 GLN cc_start: 0.8883 (OUTLIER) cc_final: 0.8617 (tp-100) REVERT: F 17 HIS cc_start: 0.9433 (m-70) cc_final: 0.8997 (m-70) REVERT: F 47 MET cc_start: 0.9438 (tpp) cc_final: 0.8958 (tpt) REVERT: F 49 TYR cc_start: 0.9319 (m-80) cc_final: 0.8847 (m-80) REVERT: F 60 ARG cc_start: 0.8031 (ptp-110) cc_final: 0.7761 (ptp90) REVERT: F 62 GLU cc_start: 0.8584 (tm-30) cc_final: 0.8194 (tm-30) REVERT: F 66 MET cc_start: 0.8824 (mmm) cc_final: 0.8229 (mpp) REVERT: F 80 GLU cc_start: 0.8581 (mt-10) cc_final: 0.8174 (mm-30) REVERT: F 93 ASP cc_start: 0.8765 (t0) cc_final: 0.8463 (t0) REVERT: F 113 LYS cc_start: 0.8328 (tppt) cc_final: 0.7892 (mmmm) REVERT: F 152 MET cc_start: 0.8711 (tmt) cc_final: 0.8378 (tmm) REVERT: F 156 ASN cc_start: 0.7910 (t0) cc_final: 0.7388 (m110) REVERT: N 79 LYS cc_start: 0.9508 (OUTLIER) cc_final: 0.9131 (tmtt) REVERT: N 95 CYS cc_start: 0.9426 (m) cc_final: 0.9100 (m) REVERT: N 110 HIS cc_start: 0.8466 (t70) cc_final: 0.7404 (m170) REVERT: N 198 MET cc_start: 0.8508 (tpp) cc_final: 0.7699 (ttm) REVERT: N 220 MET cc_start: 0.8277 (tpt) cc_final: 0.7445 (tpt) REVERT: N 221 HIS cc_start: 0.8480 (m90) cc_final: 0.7243 (m90) REVERT: N 224 LEU cc_start: 0.9325 (OUTLIER) cc_final: 0.9072 (mm) REVERT: N 228 TYR cc_start: 0.9182 (t80) cc_final: 0.8891 (t80) REVERT: N 259 ASN cc_start: 0.9373 (t0) cc_final: 0.9081 (m-40) REVERT: a 36 MET cc_start: 0.9174 (ttm) cc_final: 0.8761 (tpp) REVERT: a 84 ARG cc_start: 0.8815 (ptt-90) cc_final: 0.8540 (pmm-80) REVERT: a 90 GLU cc_start: 0.9072 (tt0) cc_final: 0.8563 (tt0) REVERT: a 91 GLN cc_start: 0.8965 (mt0) cc_final: 0.8745 (mt0) REVERT: a 123 ARG cc_start: 0.8881 (tpp80) cc_final: 0.8275 (tpm170) REVERT: a 168 GLU cc_start: 0.9188 (mt-10) cc_final: 0.8854 (mm-30) REVERT: a 203 MET cc_start: 0.9423 (OUTLIER) cc_final: 0.8701 (mmp) REVERT: a 221 ARG cc_start: 0.3257 (tpt170) cc_final: 0.2313 (tpt170) REVERT: a 398 MET cc_start: 0.8579 (mtp) cc_final: 0.8349 (ttm) REVERT: b 47 GLU cc_start: 0.9119 (mm-30) cc_final: 0.8579 (mm-30) REVERT: b 127 GLU cc_start: 0.8521 (mm-30) cc_final: 0.8135 (mp0) REVERT: b 136 GLN cc_start: 0.9032 (pt0) cc_final: 0.8797 (pt0) REVERT: b 200 GLU cc_start: 0.8703 (mt-10) cc_final: 0.8355 (mt-10) REVERT: b 426 ASN cc_start: 0.9192 (m-40) cc_final: 0.8965 (m-40) REVERT: f 47 MET cc_start: 0.8937 (tpt) cc_final: 0.8662 (tpt) REVERT: f 50 MET cc_start: 0.8169 (tmm) cc_final: 0.7541 (tmm) REVERT: f 95 PHE cc_start: 0.9437 (t80) cc_final: 0.9205 (t80) REVERT: f 108 ASP cc_start: 0.7925 (m-30) cc_final: 0.7276 (m-30) REVERT: f 130 PHE cc_start: 0.8884 (t80) cc_final: 0.8226 (t80) REVERT: f 164 MET cc_start: 0.7813 (mmp) cc_final: 0.7037 (mtt) REVERT: n 79 LYS cc_start: 0.8953 (mmmt) cc_final: 0.8720 (mmmt) REVERT: n 95 CYS cc_start: 0.9131 (m) cc_final: 0.8901 (m) REVERT: n 97 ARG cc_start: 0.9431 (OUTLIER) cc_final: 0.8906 (ttm110) REVERT: n 118 GLN cc_start: 0.9243 (mm-40) cc_final: 0.8977 (mm110) REVERT: n 221 HIS cc_start: 0.8322 (m-70) cc_final: 0.8076 (p90) REVERT: n 233 TYR cc_start: 0.8914 (t80) cc_final: 0.8284 (t80) outliers start: 46 outliers final: 25 residues processed: 332 average time/residue: 0.5600 time to fit residues: 211.8443 Evaluate side-chains 317 residues out of total 2271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 283 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 290 GLU Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 290 GLU Chi-restraints excluded: chain B residue 433 GLN Chi-restraints excluded: chain F residue 22 ILE Chi-restraints excluded: chain F residue 131 ARG Chi-restraints excluded: chain N residue 69 SER Chi-restraints excluded: chain N residue 79 LYS Chi-restraints excluded: chain N residue 100 CYS Chi-restraints excluded: chain N residue 103 LEU Chi-restraints excluded: chain N residue 117 LEU Chi-restraints excluded: chain N residue 224 LEU Chi-restraints excluded: chain a residue 191 THR Chi-restraints excluded: chain a residue 194 THR Chi-restraints excluded: chain a residue 203 MET Chi-restraints excluded: chain a residue 328 VAL Chi-restraints excluded: chain a residue 367 ASP Chi-restraints excluded: chain a residue 375 VAL Chi-restraints excluded: chain b residue 3 GLU Chi-restraints excluded: chain b residue 120 ASP Chi-restraints excluded: chain b residue 166 MET Chi-restraints excluded: chain b residue 205 ASP Chi-restraints excluded: chain f residue 89 VAL Chi-restraints excluded: chain n residue 97 ARG Chi-restraints excluded: chain n residue 100 CYS Chi-restraints excluded: chain n residue 126 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 127 optimal weight: 0.9990 chunk 221 optimal weight: 9.9990 chunk 225 optimal weight: 4.9990 chunk 65 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 76 optimal weight: 3.9990 chunk 182 optimal weight: 0.9990 chunk 149 optimal weight: 0.0010 chunk 123 optimal weight: 6.9990 chunk 208 optimal weight: 0.0980 chunk 80 optimal weight: 0.9990 overall best weight: 0.6192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 111 ASN N 118 GLN N 272 ASN a 372 GLN f 154 GLN n 93 GLN n 176 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.105482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.071237 restraints weight = 44775.830| |-----------------------------------------------------------------------------| r_work (start): 0.3143 rms_B_bonded: 3.36 r_work: 0.2980 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.3339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 21469 Z= 0.131 Angle : 0.687 11.769 29120 Z= 0.339 Chirality : 0.044 0.349 3154 Planarity : 0.004 0.046 3797 Dihedral : 8.474 131.642 3105 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.86 % Allowed : 21.64 % Favored : 76.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.69 % 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: 1.32 (0.17), residues: 2593 helix: 1.67 (0.14), residues: 1398 sheet: 1.23 (0.32), residues: 263 loop : -0.40 (0.21), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG f 119 TYR 0.027 0.001 TYR F 138 PHE 0.051 0.001 PHE F 130 TRP 0.042 0.002 TRP f 143 HIS 0.004 0.001 HIS f 77 Details of bonding type rmsd covalent geometry : bond 0.00286 (21465) covalent geometry : angle 0.68571 (29112) SS BOND : bond 0.01245 ( 4) SS BOND : angle 2.32861 ( 8) hydrogen bonds : bond 0.04598 ( 1131) hydrogen bonds : angle 4.41072 ( 3291) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5186 Ramachandran restraints generated. 2593 Oldfield, 0 Emsley, 2593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5186 Ramachandran restraints generated. 2593 Oldfield, 0 Emsley, 2593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 2271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 298 time to evaluate : 0.823 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 GLU cc_start: 0.9319 (mm-30) cc_final: 0.8410 (tm-30) REVERT: A 120 ASP cc_start: 0.8822 (OUTLIER) cc_final: 0.8561 (p0) REVERT: A 275 VAL cc_start: 0.9054 (OUTLIER) cc_final: 0.8842 (m) REVERT: A 284 GLU cc_start: 0.8906 (tt0) cc_final: 0.8565 (mp0) REVERT: A 290 GLU cc_start: 0.8952 (OUTLIER) cc_final: 0.8720 (mp0) REVERT: A 413 MET cc_start: 0.9004 (ttp) cc_final: 0.8664 (ptm) REVERT: A 430 LYS cc_start: 0.9261 (tppp) cc_final: 0.8810 (tmtt) REVERT: B 113 GLU cc_start: 0.9097 (mp0) cc_final: 0.8722 (mp0) REVERT: B 290 GLU cc_start: 0.8686 (OUTLIER) cc_final: 0.8449 (mp0) REVERT: B 329 ASP cc_start: 0.8845 (m-30) cc_final: 0.8417 (m-30) REVERT: B 422 GLU cc_start: 0.8337 (tm-30) cc_final: 0.8110 (tm-30) REVERT: F 17 HIS cc_start: 0.9409 (m-70) cc_final: 0.8990 (m-70) REVERT: F 47 MET cc_start: 0.9429 (tpp) cc_final: 0.8894 (tpt) REVERT: F 49 TYR cc_start: 0.9316 (m-80) cc_final: 0.8830 (m-80) REVERT: F 60 ARG cc_start: 0.7993 (ptp-110) cc_final: 0.7715 (ptp90) REVERT: F 62 GLU cc_start: 0.8604 (tm-30) cc_final: 0.8206 (tm-30) REVERT: F 66 MET cc_start: 0.8823 (mmm) cc_final: 0.8122 (mpp) REVERT: F 79 MET cc_start: 0.8967 (mmm) cc_final: 0.8680 (mmm) REVERT: F 80 GLU cc_start: 0.8545 (mt-10) cc_final: 0.8124 (mm-30) REVERT: F 93 ASP cc_start: 0.8782 (t0) cc_final: 0.8494 (t0) REVERT: F 113 LYS cc_start: 0.8290 (tppt) cc_final: 0.7878 (mmmm) REVERT: F 152 MET cc_start: 0.8643 (tmt) cc_final: 0.8342 (tmm) REVERT: F 156 ASN cc_start: 0.7911 (t0) cc_final: 0.7436 (m110) REVERT: N 79 LYS cc_start: 0.9509 (OUTLIER) cc_final: 0.9144 (tmtt) REVERT: N 95 CYS cc_start: 0.9410 (m) cc_final: 0.9076 (m) REVERT: N 110 HIS cc_start: 0.8452 (t70) cc_final: 0.7436 (m170) REVERT: N 142 LEU cc_start: 0.8719 (pt) cc_final: 0.7999 (tt) REVERT: N 198 MET cc_start: 0.8483 (tpp) cc_final: 0.7664 (ttm) REVERT: N 220 MET cc_start: 0.8253 (tpt) cc_final: 0.7478 (tpt) REVERT: N 221 HIS cc_start: 0.8452 (m90) cc_final: 0.7245 (m90) REVERT: N 224 LEU cc_start: 0.9320 (OUTLIER) cc_final: 0.9064 (mm) REVERT: N 228 TYR cc_start: 0.9212 (t80) cc_final: 0.8979 (t80) REVERT: N 259 ASN cc_start: 0.9387 (t0) cc_final: 0.9030 (m-40) REVERT: a 36 MET cc_start: 0.9176 (ttm) cc_final: 0.8765 (tpp) REVERT: a 77 GLU cc_start: 0.9515 (mt-10) cc_final: 0.9313 (tm-30) REVERT: a 84 ARG cc_start: 0.8750 (ptt-90) cc_final: 0.8511 (pmm-80) REVERT: a 90 GLU cc_start: 0.9068 (tt0) cc_final: 0.8548 (tt0) REVERT: a 91 GLN cc_start: 0.8965 (mt0) cc_final: 0.8759 (mt0) REVERT: a 123 ARG cc_start: 0.8882 (tpp80) cc_final: 0.8296 (tpm170) REVERT: a 155 GLU cc_start: 0.8950 (tm-30) cc_final: 0.8675 (pp20) REVERT: a 203 MET cc_start: 0.9426 (OUTLIER) cc_final: 0.8700 (mmp) REVERT: a 221 ARG cc_start: 0.3265 (tpt170) cc_final: 0.2322 (tpt170) REVERT: a 255 PHE cc_start: 0.9228 (p90) cc_final: 0.9021 (p90) REVERT: a 398 MET cc_start: 0.8605 (mtp) cc_final: 0.8314 (ttm) REVERT: a 413 MET cc_start: 0.8122 (mtp) cc_final: 0.7845 (mtp) REVERT: b 47 GLU cc_start: 0.9114 (mm-30) cc_final: 0.8594 (mm-30) REVERT: b 127 GLU cc_start: 0.8553 (mm-30) cc_final: 0.8136 (mp0) REVERT: b 136 GLN cc_start: 0.9023 (pt0) cc_final: 0.8799 (pt0) REVERT: b 200 GLU cc_start: 0.8756 (mt-10) cc_final: 0.8441 (mt-10) REVERT: b 426 ASN cc_start: 0.9192 (m-40) cc_final: 0.8963 (m-40) REVERT: f 47 MET cc_start: 0.8934 (tpt) cc_final: 0.8659 (tpt) REVERT: f 50 MET cc_start: 0.8170 (tmm) cc_final: 0.7543 (tmm) REVERT: f 95 PHE cc_start: 0.9455 (t80) cc_final: 0.9214 (t80) REVERT: f 103 ASP cc_start: 0.8995 (p0) cc_final: 0.8464 (p0) REVERT: f 108 ASP cc_start: 0.7625 (m-30) cc_final: 0.7220 (m-30) REVERT: f 116 ARG cc_start: 0.8165 (mmm160) cc_final: 0.7901 (mmm160) REVERT: f 130 PHE cc_start: 0.8882 (t80) cc_final: 0.8213 (t80) REVERT: f 137 THR cc_start: 0.8713 (OUTLIER) cc_final: 0.8340 (p) REVERT: f 164 MET cc_start: 0.7714 (mmp) cc_final: 0.6961 (mtt) REVERT: n 79 LYS cc_start: 0.9058 (mmmt) cc_final: 0.8820 (mmmt) REVERT: n 95 CYS cc_start: 0.9140 (m) cc_final: 0.8914 (m) REVERT: n 97 ARG cc_start: 0.9430 (OUTLIER) cc_final: 0.8918 (ttm110) REVERT: n 118 GLN cc_start: 0.9250 (mm-40) cc_final: 0.8989 (mm110) REVERT: n 233 TYR cc_start: 0.8908 (t80) cc_final: 0.8266 (t80) outliers start: 42 outliers final: 26 residues processed: 325 average time/residue: 0.5623 time to fit residues: 207.8320 Evaluate side-chains 325 residues out of total 2271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 290 time to evaluate : 0.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 290 GLU Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 290 GLU Chi-restraints excluded: chain F residue 22 ILE Chi-restraints excluded: chain F residue 131 ARG Chi-restraints excluded: chain N residue 69 SER Chi-restraints excluded: chain N residue 79 LYS Chi-restraints excluded: chain N residue 100 CYS Chi-restraints excluded: chain N residue 117 LEU Chi-restraints excluded: chain N residue 224 LEU Chi-restraints excluded: chain a residue 191 THR Chi-restraints excluded: chain a residue 194 THR Chi-restraints excluded: chain a residue 203 MET Chi-restraints excluded: chain a residue 287 SER Chi-restraints excluded: chain a residue 328 VAL Chi-restraints excluded: chain a residue 367 ASP Chi-restraints excluded: chain a residue 375 VAL Chi-restraints excluded: chain a residue 432 TYR Chi-restraints excluded: chain b residue 3 GLU Chi-restraints excluded: chain b residue 166 MET Chi-restraints excluded: chain b residue 205 ASP Chi-restraints excluded: chain f residue 77 HIS Chi-restraints excluded: chain f residue 89 VAL Chi-restraints excluded: chain f residue 137 THR Chi-restraints excluded: chain n residue 97 ARG Chi-restraints excluded: chain n residue 100 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 153 optimal weight: 0.0870 chunk 213 optimal weight: 4.9990 chunk 167 optimal weight: 4.9990 chunk 123 optimal weight: 5.9990 chunk 243 optimal weight: 0.0270 chunk 51 optimal weight: 2.9990 chunk 55 optimal weight: 4.9990 chunk 139 optimal weight: 5.9990 chunk 231 optimal weight: 1.9990 chunk 161 optimal weight: 0.5980 chunk 145 optimal weight: 0.6980 overall best weight: 0.6818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 111 ASN N 118 GLN f 154 GLN n 93 GLN n 176 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.105784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.071676 restraints weight = 45075.264| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 3.37 r_work: 0.2985 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.3445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 21469 Z= 0.132 Angle : 0.689 13.183 29120 Z= 0.341 Chirality : 0.044 0.336 3154 Planarity : 0.004 0.062 3797 Dihedral : 8.349 130.025 3105 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.81 % Allowed : 21.77 % Favored : 76.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.69 % 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: 1.31 (0.17), residues: 2593 helix: 1.66 (0.14), residues: 1398 sheet: 1.22 (0.32), residues: 264 loop : -0.41 (0.21), residues: 931 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG F 168 TYR 0.026 0.001 TYR F 138 PHE 0.044 0.001 PHE F 130 TRP 0.016 0.001 TRP F 143 HIS 0.005 0.001 HIS f 159 Details of bonding type rmsd covalent geometry : bond 0.00289 (21465) covalent geometry : angle 0.68823 (29112) SS BOND : bond 0.01194 ( 4) SS BOND : angle 2.14681 ( 8) hydrogen bonds : bond 0.04552 ( 1131) hydrogen bonds : angle 4.40010 ( 3291) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5186 Ramachandran restraints generated. 2593 Oldfield, 0 Emsley, 2593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5186 Ramachandran restraints generated. 2593 Oldfield, 0 Emsley, 2593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 2271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 309 time to evaluate : 0.699 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 90 GLU cc_start: 0.9314 (mm-30) cc_final: 0.8408 (tm-30) REVERT: A 120 ASP cc_start: 0.8771 (OUTLIER) cc_final: 0.8488 (p0) REVERT: A 275 VAL cc_start: 0.9047 (OUTLIER) cc_final: 0.8833 (m) REVERT: A 284 GLU cc_start: 0.8897 (tt0) cc_final: 0.8552 (mp0) REVERT: A 290 GLU cc_start: 0.8953 (OUTLIER) cc_final: 0.8728 (mp0) REVERT: A 430 LYS cc_start: 0.9276 (tppp) cc_final: 0.8825 (tmtt) REVERT: B 113 GLU cc_start: 0.9123 (mp0) cc_final: 0.8882 (mp0) REVERT: B 290 GLU cc_start: 0.8672 (OUTLIER) cc_final: 0.8384 (mp0) REVERT: B 329 ASP cc_start: 0.8925 (m-30) cc_final: 0.8484 (m-30) REVERT: B 422 GLU cc_start: 0.8351 (tm-30) cc_final: 0.8095 (tm-30) REVERT: F 17 HIS cc_start: 0.9380 (m-70) cc_final: 0.8964 (m-70) REVERT: F 47 MET cc_start: 0.9376 (tpp) cc_final: 0.8868 (tpt) REVERT: F 49 TYR cc_start: 0.9319 (m-80) cc_final: 0.8788 (m-80) REVERT: F 60 ARG cc_start: 0.7982 (ptp-110) cc_final: 0.7679 (ptp90) REVERT: F 62 GLU cc_start: 0.8615 (tm-30) cc_final: 0.8223 (tm-30) REVERT: F 66 MET cc_start: 0.8798 (mmm) cc_final: 0.8093 (mpp) REVERT: F 79 MET cc_start: 0.8972 (mmm) cc_final: 0.8751 (mmm) REVERT: F 80 GLU cc_start: 0.8503 (mt-10) cc_final: 0.8084 (mm-30) REVERT: F 93 ASP cc_start: 0.8791 (t0) cc_final: 0.8501 (t0) REVERT: F 113 LYS cc_start: 0.8244 (tppt) cc_final: 0.7914 (mmmm) REVERT: F 152 MET cc_start: 0.8669 (tmt) cc_final: 0.8366 (tmm) REVERT: F 156 ASN cc_start: 0.7903 (t0) cc_final: 0.7437 (m110) REVERT: N 79 LYS cc_start: 0.9502 (OUTLIER) cc_final: 0.9133 (tmtt) REVERT: N 95 CYS cc_start: 0.9392 (m) cc_final: 0.9062 (m) REVERT: N 110 HIS cc_start: 0.8436 (t70) cc_final: 0.7428 (m170) REVERT: N 142 LEU cc_start: 0.8715 (pt) cc_final: 0.8001 (tt) REVERT: N 198 MET cc_start: 0.8446 (tpp) cc_final: 0.7598 (ttm) REVERT: N 220 MET cc_start: 0.8251 (tpt) cc_final: 0.7465 (tpt) REVERT: N 221 HIS cc_start: 0.8485 (m90) cc_final: 0.7249 (m90) REVERT: N 224 LEU cc_start: 0.9283 (OUTLIER) cc_final: 0.9030 (mm) REVERT: N 228 TYR cc_start: 0.9233 (t80) cc_final: 0.8999 (t80) REVERT: N 259 ASN cc_start: 0.9407 (t0) cc_final: 0.9077 (m-40) REVERT: a 36 MET cc_start: 0.9180 (ttm) cc_final: 0.8769 (tpp) REVERT: a 77 GLU cc_start: 0.9519 (mt-10) cc_final: 0.9304 (tm-30) REVERT: a 90 GLU cc_start: 0.9069 (tt0) cc_final: 0.8548 (tt0) REVERT: a 91 GLN cc_start: 0.8969 (mt0) cc_final: 0.8724 (mt0) REVERT: a 123 ARG cc_start: 0.8888 (tpp80) cc_final: 0.8294 (tpm170) REVERT: a 155 GLU cc_start: 0.8966 (tm-30) cc_final: 0.8676 (pp20) REVERT: a 203 MET cc_start: 0.9436 (OUTLIER) cc_final: 0.8795 (mmp) REVERT: a 221 ARG cc_start: 0.3240 (tpt170) cc_final: 0.2301 (tpt170) REVERT: a 398 MET cc_start: 0.8603 (mtp) cc_final: 0.8337 (ttm) REVERT: a 413 MET cc_start: 0.8053 (mtp) cc_final: 0.7773 (mtp) REVERT: a 417 GLU cc_start: 0.8814 (mm-30) cc_final: 0.8003 (mp0) REVERT: a 424 ASP cc_start: 0.8731 (m-30) cc_final: 0.8438 (m-30) REVERT: b 47 GLU cc_start: 0.9102 (mm-30) cc_final: 0.8577 (mm-30) REVERT: b 127 GLU cc_start: 0.8589 (mm-30) cc_final: 0.8112 (mp0) REVERT: b 136 GLN cc_start: 0.9027 (pt0) cc_final: 0.8778 (pt0) REVERT: b 200 GLU cc_start: 0.8781 (mt-10) cc_final: 0.8468 (mt-10) REVERT: b 259 MET cc_start: 0.8859 (mmm) cc_final: 0.8626 (mmp) REVERT: b 426 ASN cc_start: 0.9189 (m-40) cc_final: 0.8957 (m-40) REVERT: f 47 MET cc_start: 0.8892 (tpt) cc_final: 0.8600 (tpt) REVERT: f 50 MET cc_start: 0.8168 (tmm) cc_final: 0.7538 (tmm) REVERT: f 95 PHE cc_start: 0.9434 (t80) cc_final: 0.9184 (t80) REVERT: f 130 PHE cc_start: 0.8878 (t80) cc_final: 0.8209 (t80) REVERT: f 137 THR cc_start: 0.8750 (OUTLIER) cc_final: 0.8386 (p) REVERT: f 164 MET cc_start: 0.7448 (mmp) cc_final: 0.6618 (mtt) REVERT: n 95 CYS cc_start: 0.9135 (m) cc_final: 0.8919 (m) REVERT: n 97 ARG cc_start: 0.9426 (OUTLIER) cc_final: 0.8907 (ttm110) REVERT: n 118 GLN cc_start: 0.9253 (mm-40) cc_final: 0.8997 (mm110) REVERT: n 233 TYR cc_start: 0.8888 (t80) cc_final: 0.8242 (t80) outliers start: 41 outliers final: 25 residues processed: 336 average time/residue: 0.5851 time to fit residues: 222.7309 Evaluate side-chains 323 residues out of total 2271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 289 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 290 GLU Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 290 GLU Chi-restraints excluded: chain F residue 22 ILE Chi-restraints excluded: chain F residue 131 ARG Chi-restraints excluded: chain N residue 69 SER Chi-restraints excluded: chain N residue 79 LYS Chi-restraints excluded: chain N residue 100 CYS Chi-restraints excluded: chain N residue 224 LEU Chi-restraints excluded: chain a residue 191 THR Chi-restraints excluded: chain a residue 194 THR Chi-restraints excluded: chain a residue 203 MET Chi-restraints excluded: chain a residue 287 SER Chi-restraints excluded: chain a residue 328 VAL Chi-restraints excluded: chain a residue 367 ASP Chi-restraints excluded: chain a residue 375 VAL Chi-restraints excluded: chain a residue 432 TYR Chi-restraints excluded: chain b residue 3 GLU Chi-restraints excluded: chain b residue 166 MET Chi-restraints excluded: chain b residue 205 ASP Chi-restraints excluded: chain f residue 77 HIS Chi-restraints excluded: chain f residue 89 VAL Chi-restraints excluded: chain f residue 137 THR Chi-restraints excluded: chain n residue 97 ARG Chi-restraints excluded: chain n residue 100 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 72 optimal weight: 0.5980 chunk 250 optimal weight: 10.0000 chunk 109 optimal weight: 2.9990 chunk 197 optimal weight: 0.5980 chunk 195 optimal weight: 2.9990 chunk 188 optimal weight: 0.9990 chunk 79 optimal weight: 0.9980 chunk 134 optimal weight: 0.9990 chunk 45 optimal weight: 4.9990 chunk 237 optimal weight: 0.8980 chunk 182 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 111 ASN N 118 GLN a 18 ASN b 133 GLN n 93 GLN n 176 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.105117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.070974 restraints weight = 44893.695| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 3.33 r_work: 0.2985 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.3546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 21469 Z= 0.135 Angle : 0.701 12.833 29120 Z= 0.345 Chirality : 0.044 0.322 3154 Planarity : 0.004 0.047 3797 Dihedral : 8.277 129.022 3105 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 1.99 % Allowed : 21.99 % Favored : 76.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.69 % 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: 1.31 (0.17), residues: 2593 helix: 1.65 (0.14), residues: 1398 sheet: 1.22 (0.32), residues: 266 loop : -0.40 (0.21), residues: 929 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG F 168 TYR 0.021 0.001 TYR N 228 PHE 0.042 0.001 PHE F 130 TRP 0.048 0.002 TRP f 143 HIS 0.008 0.001 HIS f 159 Details of bonding type rmsd covalent geometry : bond 0.00300 (21465) covalent geometry : angle 0.69989 (29112) SS BOND : bond 0.01095 ( 4) SS BOND : angle 2.01868 ( 8) hydrogen bonds : bond 0.04553 ( 1131) hydrogen bonds : angle 4.39037 ( 3291) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7558.49 seconds wall clock time: 129 minutes 15.04 seconds (7755.04 seconds total)