Starting phenix.real_space_refine on Thu Sep 18 05:51:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ud5_64062/09_2025/9ud5_64062.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ud5_64062/09_2025/9ud5_64062.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ud5_64062/09_2025/9ud5_64062.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ud5_64062/09_2025/9ud5_64062.map" model { file = "/net/cci-nas-00/data/ceres_data/9ud5_64062/09_2025/9ud5_64062.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ud5_64062/09_2025/9ud5_64062.cif" } resolution = 2.9 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= -0.000 sd= 0.120 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: 7 Type Number sf(0) Gaussians Ca 1 9.91 5 Fe 4 7.16 5 P 4 5.49 5 S 83 5.16 5 C 9268 2.51 5 N 2415 2.21 5 O 2721 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14496 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 3416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 446, 3416 Classifications: {'peptide': 446} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 422} Chain: "B" Number of atoms: 3177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 412, 3177 Classifications: {'peptide': 412} Link IDs: {'PTRANS': 15, 'TRANS': 396} Chain: "C" Number of atoms: 1902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 251, 1902 Classifications: {'peptide': 251} Link IDs: {'PTRANS': 7, 'TRANS': 243} Chain: "D" Number of atoms: 1580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1580 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 9, 'TRANS': 196} Chain: "E" Number of atoms: 975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 975 Classifications: {'peptide': 198} Incomplete info: {'truncation_to_alanine': 163} Link IDs: {'PTRANS': 7, 'TRANS': 190} Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 570 Unresolved non-hydrogen angles: 738 Unresolved non-hydrogen dihedrals: 472 Unresolved non-hydrogen chiralities: 75 Planarities with less than four sites: {'GLU:plan': 6, 'HIS:plan': 1, 'TYR:plan': 6, 'PHE:plan': 18, 'ASN:plan1': 7, 'ASP:plan': 5, 'GLN:plan1': 3, 'ARG:plan': 4, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 256 Chain: "F" Number of atoms: 3157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 408, 3157 Classifications: {'peptide': 408} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 24, 'TRANS': 383} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "B" Number of atoms: 124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 124 Unusual residues: {'FMN': 1, 'IQT': 1, 'LMT': 1, 'RBF': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' CA': 1, 'FMN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 39 Unusual residues: {'FES': 1, 'LMT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 57 Unusual residues: {'FAD': 1, 'FES': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 19 Classifications: {'water': 19} Link IDs: {None: 18} Chain: "B" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 9319 SG CYS D 112 45.637 74.309 87.618 1.00109.62 S ATOM 10208 SG CYS E 26 43.819 71.701 86.145 1.00105.61 S ATOM 8680 SG CYS D 29 45.212 68.511 90.476 1.00104.33 S ATOM 11832 SG CYS F 111 50.569 89.460 61.700 1.00287.74 S ATOM 11574 SG CYS F 76 45.770 89.844 57.923 1.00299.00 S ATOM 11593 SG CYS F 79 49.378 90.677 58.344 1.00296.98 S Time building chain proxies: 3.73, per 1000 atoms: 0.26 Number of scatterers: 14496 At special positions: 0 Unit cell: (89.76, 124.96, 153.12, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Fe 4 26.01 Ca 1 19.99 S 83 16.00 P 4 15.00 O 2721 8.00 N 2415 7.00 C 9268 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 1.40 Conformation dependent library (CDL) restraints added in 698.1 milliseconds Enol-peptide restraints added in 238.4 nanoseconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES D 302 " pdb="FE1 FES D 302 " - pdb=" SG CYS E 26 " pdb="FE1 FES D 302 " - pdb=" SG CYS D 112 " pdb="FE2 FES D 302 " - pdb=" SG CYS D 29 " pdb=" FES F 501 " pdb="FE1 FES F 501 " - pdb=" SG CYS F 111 " pdb="FE2 FES F 501 " - pdb=" SG CYS F 76 " pdb="FE2 FES F 501 " - pdb=" SG CYS F 79 " Number of angles added : 8 3818 Ramachandran restraints generated. 1909 Oldfield, 0 Emsley, 1909 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3468 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 13 sheets defined 54.6% alpha, 11.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.54 Creating SS restraints... Processing helix chain 'A' and resid 34 through 36 No H-bonds generated for 'chain 'A' and resid 34 through 36' Processing helix chain 'A' and resid 83 through 85 No H-bonds generated for 'chain 'A' and resid 83 through 85' Processing helix chain 'A' and resid 106 through 113 removed outlier: 3.830A pdb=" N LEU A 110 " --> pdb=" O ALA A 107 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N ALA A 111 " --> pdb=" O ASN A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 125 Processing helix chain 'A' and resid 126 through 131 removed outlier: 3.802A pdb=" N THR A 129 " --> pdb=" O GLY A 126 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N PHE A 131 " --> pdb=" O TRP A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 170 removed outlier: 3.644A pdb=" N VAL A 166 " --> pdb=" O GLU A 162 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N GLU A 169 " --> pdb=" O VAL A 165 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLN A 170 " --> pdb=" O VAL A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 185 Processing helix chain 'A' and resid 219 through 228 Processing helix chain 'A' and resid 241 through 254 Processing helix chain 'A' and resid 282 through 287 Processing helix chain 'A' and resid 310 through 314 removed outlier: 3.657A pdb=" N HIS A 313 " --> pdb=" O THR A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 339 Processing helix chain 'A' and resid 351 through 356 removed outlier: 3.867A pdb=" N HIS A 354 " --> pdb=" O PHE A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 383 Processing helix chain 'A' and resid 389 through 400 Processing helix chain 'A' and resid 401 through 409 removed outlier: 3.573A pdb=" N ARG A 407 " --> pdb=" O ASP A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 410 through 413 Processing helix chain 'A' and resid 414 through 417 Processing helix chain 'A' and resid 418 through 424 Processing helix chain 'A' and resid 430 through 446 removed outlier: 4.006A pdb=" N LEU A 434 " --> pdb=" O GLU A 430 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 10 removed outlier: 3.504A pdb=" N GLU B 8 " --> pdb=" O LYS B 4 " (cutoff:3.500A) Processing helix chain 'B' and resid 11 through 14 Processing helix chain 'B' and resid 20 through 22 No H-bonds generated for 'chain 'B' and resid 20 through 22' Processing helix chain 'B' and resid 23 through 35 Processing helix chain 'B' and resid 52 through 64 removed outlier: 3.625A pdb=" N VAL B 60 " --> pdb=" O ILE B 56 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N VAL B 64 " --> pdb=" O VAL B 60 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 87 Processing helix chain 'B' and resid 89 through 99 Processing helix chain 'B' and resid 99 through 108 Processing helix chain 'B' and resid 117 through 151 removed outlier: 3.557A pdb=" N TYR B 128 " --> pdb=" O LEU B 124 " (cutoff:3.500A) Proline residue: B 131 - end of helix removed outlier: 3.514A pdb=" N TRP B 143 " --> pdb=" O VAL B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 169 removed outlier: 3.987A pdb=" N ILE B 164 " --> pdb=" O PHE B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 189 Processing helix chain 'B' and resid 191 through 195 Processing helix chain 'B' and resid 203 through 216 Processing helix chain 'B' and resid 217 through 220 Processing helix chain 'B' and resid 236 through 245 Processing helix chain 'B' and resid 246 through 248 No H-bonds generated for 'chain 'B' and resid 246 through 248' Processing helix chain 'B' and resid 259 through 266 Processing helix chain 'B' and resid 276 through 290 removed outlier: 3.900A pdb=" N PHE B 286 " --> pdb=" O ILE B 282 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ILE B 287 " --> pdb=" O GLY B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 316 Processing helix chain 'B' and resid 320 through 325 removed outlier: 3.619A pdb=" N ASN B 324 " --> pdb=" O ALA B 321 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N MET B 325 " --> pdb=" O MET B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 331 Processing helix chain 'B' and resid 335 through 343 Processing helix chain 'B' and resid 353 through 375 removed outlier: 3.817A pdb=" N TRP B 358 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ALA B 359 " --> pdb=" O SER B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 410 removed outlier: 3.675A pdb=" N LEU B 391 " --> pdb=" O LEU B 387 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N PHE B 392 " --> pdb=" O PHE B 388 " (cutoff:3.500A) Proline residue: B 394 - end of helix Processing helix chain 'C' and resid 7 through 33 removed outlier: 3.737A pdb=" N ILE C 25 " --> pdb=" O VAL C 21 " (cutoff:3.500A) Processing helix chain 'C' and resid 33 through 53 removed outlier: 3.635A pdb=" N LYS C 45 " --> pdb=" O ALA C 41 " (cutoff:3.500A) Processing helix chain 'C' and resid 59 through 70 removed outlier: 3.556A pdb=" N ASN C 68 " --> pdb=" O VAL C 64 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 91 removed outlier: 3.521A pdb=" N ASN C 90 " --> pdb=" O ASP C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 97 Processing helix chain 'C' and resid 177 through 181 removed outlier: 3.716A pdb=" N VAL C 180 " --> pdb=" O GLY C 177 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 187 Processing helix chain 'C' and resid 188 through 190 No H-bonds generated for 'chain 'C' and resid 188 through 190' Processing helix chain 'C' and resid 224 through 239 removed outlier: 3.697A pdb=" N SER C 228 " --> pdb=" O ALA C 224 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLY C 230 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 254 Processing helix chain 'D' and resid 6 through 17 Proline residue: D 14 - end of helix Processing helix chain 'D' and resid 27 through 34 removed outlier: 3.900A pdb=" N ALA D 31 " --> pdb=" O GLY D 27 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 62 Processing helix chain 'D' and resid 70 through 94 Processing helix chain 'D' and resid 94 through 102 Processing helix chain 'D' and resid 103 through 109 removed outlier: 3.688A pdb=" N LEU D 107 " --> pdb=" O PHE D 104 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 121 removed outlier: 3.977A pdb=" N MET D 115 " --> pdb=" O ASN D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 125 removed outlier: 3.559A pdb=" N SER D 125 " --> pdb=" O ALA D 122 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 122 through 125' Processing helix chain 'D' and resid 126 through 158 removed outlier: 3.698A pdb=" N PHE D 151 " --> pdb=" O THR D 147 " (cutoff:3.500A) Processing helix chain 'D' and resid 178 through 183 Processing helix chain 'D' and resid 184 through 202 removed outlier: 3.866A pdb=" N PHE D 188 " --> pdb=" O ALA D 184 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N PHE D 189 " --> pdb=" O PRO D 185 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 206 Processing helix chain 'E' and resid 2 through 13 Processing helix chain 'E' and resid 24 through 31 Processing helix chain 'E' and resid 34 through 63 Proline residue: E 54 - end of helix Processing helix chain 'E' and resid 75 through 77 No H-bonds generated for 'chain 'E' and resid 75 through 77' Processing helix chain 'E' and resid 78 through 99 Processing helix chain 'E' and resid 105 through 110 removed outlier: 4.269A pdb=" N LEU E 109 " --> pdb=" O LEU E 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 111 through 116 removed outlier: 3.875A pdb=" N LEU E 115 " --> pdb=" O ILE E 111 " (cutoff:3.500A) Processing helix chain 'E' and resid 119 through 133 removed outlier: 3.905A pdb=" N PHE E 123 " --> pdb=" O ASN E 119 " (cutoff:3.500A) Processing helix chain 'E' and resid 135 through 164 Processing helix chain 'E' and resid 165 through 167 No H-bonds generated for 'chain 'E' and resid 165 through 167' Processing helix chain 'E' and resid 175 through 191 removed outlier: 3.530A pdb=" N THR E 179 " --> pdb=" O GLY E 175 " (cutoff:3.500A) Processing helix chain 'E' and resid 192 through 194 No H-bonds generated for 'chain 'E' and resid 192 through 194' Processing helix chain 'F' and resid 2 through 30 removed outlier: 3.633A pdb=" N LYS F 28 " --> pdb=" O PHE F 24 " (cutoff:3.500A) Processing helix chain 'F' and resid 54 through 62 removed outlier: 4.439A pdb=" N ALA F 58 " --> pdb=" O LYS F 54 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU F 59 " --> pdb=" O LEU F 55 " (cutoff:3.500A) Processing helix chain 'F' and resid 91 through 97 removed outlier: 3.823A pdb=" N ASP F 96 " --> pdb=" O THR F 93 " (cutoff:3.500A) Processing helix chain 'F' and resid 99 through 104 removed outlier: 3.678A pdb=" N ARG F 104 " --> pdb=" O LYS F 100 " (cutoff:3.500A) Processing helix chain 'F' and resid 126 through 130 Processing helix chain 'F' and resid 180 through 182 No H-bonds generated for 'chain 'F' and resid 180 through 182' Processing helix chain 'F' and resid 185 through 190 Processing helix chain 'F' and resid 191 through 194 removed outlier: 3.774A pdb=" N LYS F 194 " --> pdb=" O ASP F 191 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 191 through 194' Processing helix chain 'F' and resid 196 through 199 Processing helix chain 'F' and resid 243 through 252 removed outlier: 3.570A pdb=" N TYR F 248 " --> pdb=" O GLN F 244 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LEU F 252 " --> pdb=" O TYR F 248 " (cutoff:3.500A) Processing helix chain 'F' and resid 284 through 298 removed outlier: 3.891A pdb=" N MET F 288 " --> pdb=" O GLY F 284 " (cutoff:3.500A) Processing helix chain 'F' and resid 313 through 317 Processing helix chain 'F' and resid 319 through 330 Processing helix chain 'F' and resid 354 through 363 Processing helix chain 'F' and resid 364 through 367 Processing helix chain 'F' and resid 369 through 373 Processing helix chain 'F' and resid 380 through 394 removed outlier: 4.214A pdb=" N ILE F 388 " --> pdb=" O ASN F 384 " (cutoff:3.500A) Processing helix chain 'F' and resid 397 through 399 No H-bonds generated for 'chain 'F' and resid 397 through 399' Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 3 removed outlier: 6.361A pdb=" N ILE A 2 " --> pdb=" O ASP A 212 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 17 through 22 removed outlier: 3.815A pdb=" N LEU A 274 " --> pdb=" O SER A 17 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N VAL A 19 " --> pdb=" O LEU A 274 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N ARG A 276 " --> pdb=" O VAL A 19 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N SER A 21 " --> pdb=" O ARG A 276 " (cutoff:3.500A) removed outlier: 9.747A pdb=" N VAL A 278 " --> pdb=" O SER A 21 " (cutoff:3.500A) removed outlier: 8.189A pdb=" N VAL A 323 " --> pdb=" O VAL A 261 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N SER A 263 " --> pdb=" O VAL A 323 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N VAL A 325 " --> pdb=" O SER A 263 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ALA A 265 " --> pdb=" O VAL A 325 " (cutoff:3.500A) removed outlier: 9.158A pdb=" N ARG A 327 " --> pdb=" O ALA A 265 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N GLN A 322 " --> pdb=" O GLY A 301 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 28 through 32 removed outlier: 6.744A pdb=" N LEU A 87 " --> pdb=" O ARG A 81 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ARG A 81 " --> pdb=" O LEU A 87 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N SER A 89 " --> pdb=" O ILE A 79 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N ILE A 79 " --> pdb=" O SER A 89 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N VAL A 91 " --> pdb=" O VAL A 77 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 41 through 43 removed outlier: 7.083A pdb=" N PHE A 68 " --> pdb=" O LEU A 57 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 250 through 251 Processing sheet with id=AA6, first strand: chain 'C' and resid 82 through 84 removed outlier: 3.742A pdb=" N ASP C 82 " --> pdb=" O ASP C 77 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N LEU C 75 " --> pdb=" O VAL C 84 " (cutoff:3.500A) removed outlier: 14.866A pdb=" N VAL C 121 " --> pdb=" O HIS C 141 " (cutoff:3.500A) removed outlier: 12.698A pdb=" N HIS C 141 " --> pdb=" O VAL C 121 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N VAL C 123 " --> pdb=" O PRO C 139 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LYS C 135 " --> pdb=" O VAL C 127 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N ASP C 129 " --> pdb=" O THR C 133 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N THR C 133 " --> pdb=" O ASP C 129 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N MET C 148 " --> pdb=" O GLU C 169 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N GLU C 169 " --> pdb=" O MET C 148 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N TYR C 150 " --> pdb=" O TYR C 167 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N TYR C 167 " --> pdb=" O TYR C 150 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N PHE C 152 " --> pdb=" O LEU C 165 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N LEU C 165 " --> pdb=" O PHE C 152 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N ALA C 154 " --> pdb=" O SER C 163 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 103 through 105 Processing sheet with id=AA8, first strand: chain 'C' and resid 204 through 206 Processing sheet with id=AA9, first strand: chain 'D' and resid 159 through 160 Processing sheet with id=AB1, first strand: chain 'F' and resid 47 through 49 removed outlier: 8.038A pdb=" N LEU F 121 " --> pdb=" O THR F 36 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N SER F 38 " --> pdb=" O LEU F 121 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ASP F 120 " --> pdb=" O LYS F 84 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N LYS F 82 " --> pdb=" O GLU F 122 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 208 through 213 removed outlier: 6.594A pdb=" N TYR F 167 " --> pdb=" O PRO F 263 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N GLU F 171 " --> pdb=" O THR F 259 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N THR F 259 " --> pdb=" O GLU F 171 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N VAL F 137 " --> pdb=" O ALA F 153 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N ALA F 153 " --> pdb=" O VAL F 137 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N SER F 139 " --> pdb=" O LYS F 151 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 176 through 178 Processing sheet with id=AB4, first strand: chain 'F' and resid 351 through 352 removed outlier: 4.395A pdb=" N TYR F 351 " --> pdb=" O CYS F 337 " (cutoff:3.500A) removed outlier: 8.689A pdb=" N HIS F 336 " --> pdb=" O MET F 305 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N TYR F 307 " --> pdb=" O HIS F 336 " (cutoff:3.500A) removed outlier: 8.110A pdb=" N ALA F 338 " --> pdb=" O TYR F 307 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N TYR F 309 " --> pdb=" O ALA F 338 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N TYR F 375 " --> pdb=" O LEU F 402 " (cutoff:3.500A) 746 hydrogen bonds defined for protein. 2097 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: 2.24 Time building geometry restraints manager: 1.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.40: 5964 1.40 - 1.60: 8659 1.60 - 1.80: 114 1.80 - 2.00: 30 2.00 - 2.20: 8 Bond restraints: 14775 Sorted by residual: bond pdb=" C4 FMN C 302 " pdb=" C4A FMN C 302 " ideal model delta sigma weight residual 1.485 1.387 0.098 2.00e-02 2.50e+03 2.38e+01 bond pdb=" C4 FMN B 501 " pdb=" C4A FMN B 501 " ideal model delta sigma weight residual 1.485 1.388 0.097 2.00e-02 2.50e+03 2.36e+01 bond pdb=" CG MET E 25 " pdb=" SD MET E 25 " ideal model delta sigma weight residual 1.803 1.902 -0.099 2.50e-02 1.60e+03 1.57e+01 bond pdb=" C4A FMN B 501 " pdb=" N5 FMN B 501 " ideal model delta sigma weight residual 1.300 1.378 -0.078 2.00e-02 2.50e+03 1.53e+01 bond pdb=" C4A FMN C 302 " pdb=" N5 FMN C 302 " ideal model delta sigma weight residual 1.300 1.378 -0.078 2.00e-02 2.50e+03 1.51e+01 ... (remaining 14770 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.33: 19968 3.33 - 6.67: 96 6.67 - 10.00: 12 10.00 - 13.33: 0 13.33 - 16.67: 1 Bond angle restraints: 20077 Sorted by residual: angle pdb=" CG MET E 25 " pdb=" SD MET E 25 " pdb=" CE MET E 25 " ideal model delta sigma weight residual 100.90 117.57 -16.67 2.20e+00 2.07e-01 5.74e+01 angle pdb=" CG MET F 377 " pdb=" SD MET F 377 " pdb=" CE MET F 377 " ideal model delta sigma weight residual 100.90 91.87 9.03 2.20e+00 2.07e-01 1.69e+01 angle pdb=" CA GLN F 169 " pdb=" CB GLN F 169 " pdb=" CG GLN F 169 " ideal model delta sigma weight residual 114.10 121.36 -7.26 2.00e+00 2.50e-01 1.32e+01 angle pdb=" C GLN D 24 " pdb=" N VAL D 25 " pdb=" CA VAL D 25 " ideal model delta sigma weight residual 122.59 118.71 3.88 1.10e+00 8.26e-01 1.25e+01 angle pdb=" C PRO F 155 " pdb=" N ASP F 156 " pdb=" CA ASP F 156 " ideal model delta sigma weight residual 121.54 128.05 -6.51 1.91e+00 2.74e-01 1.16e+01 ... (remaining 20072 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 8062 17.95 - 35.91: 573 35.91 - 53.86: 107 53.86 - 71.81: 29 71.81 - 89.76: 15 Dihedral angle restraints: 8786 sinusoidal: 3355 harmonic: 5431 Sorted by residual: dihedral pdb=" CA ASN F 40 " pdb=" C ASN F 40 " pdb=" N GLY F 41 " pdb=" CA GLY F 41 " ideal model delta harmonic sigma weight residual 180.00 121.77 58.23 0 5.00e+00 4.00e-02 1.36e+02 dihedral pdb=" CA GLU B 274 " pdb=" C GLU B 274 " pdb=" N VAL B 275 " pdb=" CA VAL B 275 " ideal model delta harmonic sigma weight residual -180.00 -156.09 -23.91 0 5.00e+00 4.00e-02 2.29e+01 dihedral pdb=" CA GLU F 134 " pdb=" C GLU F 134 " pdb=" N CYS F 135 " pdb=" CA CYS F 135 " ideal model delta harmonic sigma weight residual -180.00 -156.91 -23.09 0 5.00e+00 4.00e-02 2.13e+01 ... (remaining 8783 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 1489 0.036 - 0.071: 538 0.071 - 0.107: 192 0.107 - 0.143: 52 0.143 - 0.178: 6 Chirality restraints: 2277 Sorted by residual: chirality pdb=" CA TRP B 103 " pdb=" N TRP B 103 " pdb=" C TRP B 103 " pdb=" CB TRP B 103 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.95e-01 chirality pdb=" CA ILE C 205 " pdb=" N ILE C 205 " pdb=" C ILE C 205 " pdb=" CB ILE C 205 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.37e-01 chirality pdb=" CA ASP F 96 " pdb=" N ASP F 96 " pdb=" C ASP F 96 " pdb=" CB ASP F 96 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.85e-01 ... (remaining 2274 not shown) Planarity restraints: 2554 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR E 106 " 0.013 2.00e-02 2.50e+03 2.55e-02 6.51e+00 pdb=" C TYR E 106 " -0.044 2.00e-02 2.50e+03 pdb=" O TYR E 106 " 0.017 2.00e-02 2.50e+03 pdb=" N ASN E 107 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 6 " -0.007 2.00e-02 2.50e+03 1.67e-02 4.86e+00 pdb=" CG PHE B 6 " 0.036 2.00e-02 2.50e+03 pdb=" CD1 PHE B 6 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 PHE B 6 " -0.020 2.00e-02 2.50e+03 pdb=" CE1 PHE B 6 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE B 6 " 0.003 2.00e-02 2.50e+03 pdb=" CZ PHE B 6 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN F 50 " 0.029 5.00e-02 4.00e+02 4.39e-02 3.08e+00 pdb=" N PRO F 51 " -0.076 5.00e-02 4.00e+02 pdb=" CA PRO F 51 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO F 51 " 0.024 5.00e-02 4.00e+02 ... (remaining 2551 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1439 2.75 - 3.29: 14403 3.29 - 3.82: 23527 3.82 - 4.36: 28320 4.36 - 4.90: 49346 Nonbonded interactions: 117035 Sorted by model distance: nonbonded pdb=" O ASN B 375 " pdb=" O HOH B 601 " model vdw 2.209 3.040 nonbonded pdb=" OG SER D 30 " pdb=" OH TYR D 141 " model vdw 2.209 3.040 nonbonded pdb=" O HOH A 511 " pdb=" O HOH A 519 " model vdw 2.222 3.040 nonbonded pdb=" O TYR B 378 " pdb=" O HOH B 601 " model vdw 2.231 3.040 nonbonded pdb=" N SER F 246 " pdb=" O2P FAD F 502 " model vdw 2.254 3.120 ... (remaining 117030 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 16.500 Find NCS groups from input model: 0.100 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:6.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6616 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 : 0.004 0.099 14781 Z= 0.182 Angle : 0.665 16.667 20085 Z= 0.347 Chirality : 0.044 0.178 2277 Planarity : 0.004 0.044 2554 Dihedral : 13.903 89.764 5318 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.21 % Allowed : 2.62 % Favored : 97.17 % Rotamer: Outliers : 0.07 % Allowed : 11.83 % Favored : 88.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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 aren not related in a simple way. whole: 0.30 (0.19), residues: 1909 helix: 1.17 (0.18), residues: 869 sheet: -0.25 (0.36), residues: 184 loop : -0.67 (0.20), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 210 TYR 0.022 0.002 TYR F 309 PHE 0.036 0.002 PHE B 6 TRP 0.018 0.002 TRP B 70 HIS 0.019 0.001 HIS F 97 Details of bonding type rmsd covalent geometry : bond 0.00371 (14775) covalent geometry : angle 0.65993 (20077) hydrogen bonds : bond 0.13336 ( 746) hydrogen bonds : angle 5.52755 ( 2097) metal coordination : bond 0.00906 ( 6) metal coordination : angle 4.18688 ( 8) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3818 Ramachandran restraints generated. 1909 Oldfield, 0 Emsley, 1909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3818 Ramachandran restraints generated. 1909 Oldfield, 0 Emsley, 1909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 231 time to evaluate : 0.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 LYS cc_start: 0.7648 (mtmt) cc_final: 0.7336 (mtmm) REVERT: A 40 ARG cc_start: 0.6217 (mmp80) cc_final: 0.5926 (mmp80) REVERT: A 75 LYS cc_start: 0.6732 (ttmm) cc_final: 0.6120 (ttpp) REVERT: A 142 ILE cc_start: 0.7268 (pt) cc_final: 0.6925 (mp) REVERT: A 172 GLU cc_start: 0.6123 (mp0) cc_final: 0.5590 (tt0) REVERT: A 238 SER cc_start: 0.7754 (t) cc_final: 0.7461 (m) REVERT: A 259 GLN cc_start: 0.7022 (mm-40) cc_final: 0.6778 (mp10) REVERT: A 284 GLU cc_start: 0.6786 (tt0) cc_final: 0.6390 (tp30) REVERT: A 290 GLU cc_start: 0.6572 (mm-30) cc_final: 0.6171 (mm-30) REVERT: A 308 LYS cc_start: 0.7360 (ttpt) cc_final: 0.6502 (tttm) REVERT: A 344 LYS cc_start: 0.7728 (mttm) cc_final: 0.7515 (mttm) REVERT: A 349 ARG cc_start: 0.6969 (mtm180) cc_final: 0.6648 (mtm-85) REVERT: A 356 PHE cc_start: 0.6708 (m-80) cc_final: 0.6454 (m-80) REVERT: A 384 MET cc_start: 0.7564 (tpp) cc_final: 0.7362 (mmm) REVERT: B 42 LYS cc_start: 0.6926 (ptpp) cc_final: 0.6348 (pttm) REVERT: B 72 MET cc_start: 0.6898 (mtp) cc_final: 0.6681 (mtp) REVERT: B 199 ARG cc_start: 0.7204 (mtt90) cc_final: 0.6998 (mtt-85) REVERT: B 250 ILE cc_start: 0.7093 (tt) cc_final: 0.6629 (mt) REVERT: B 267 ASN cc_start: 0.7581 (m-40) cc_final: 0.7207 (m-40) REVERT: B 406 LYS cc_start: 0.5793 (mtmt) cc_final: 0.4889 (mptt) REVERT: C 45 LYS cc_start: 0.5366 (tmmm) cc_final: 0.4873 (tppt) REVERT: C 109 GLU cc_start: 0.6856 (pm20) cc_final: 0.6656 (pm20) REVERT: C 204 LYS cc_start: 0.5819 (tppt) cc_final: 0.5533 (mttt) REVERT: D 99 LYS cc_start: 0.6977 (ttpt) cc_final: 0.6010 (mmtm) REVERT: D 115 MET cc_start: 0.6268 (tpp) cc_final: 0.5466 (tmm) REVERT: F 81 VAL cc_start: 0.4827 (m) cc_final: 0.4321 (p) REVERT: F 107 GLU cc_start: 0.5834 (tt0) cc_final: 0.5565 (tm-30) REVERT: F 109 LEU cc_start: 0.4105 (mp) cc_final: 0.3891 (tp) REVERT: F 122 GLU cc_start: 0.5278 (mm-30) cc_final: 0.5027 (mm-30) REVERT: F 156 ASP cc_start: 0.2401 (p0) cc_final: 0.2059 (t0) REVERT: F 219 GLU cc_start: 0.5927 (mt-10) cc_final: 0.5347 (mp0) REVERT: F 245 MET cc_start: 0.2608 (ttp) cc_final: 0.1480 (pmm) REVERT: F 317 MET cc_start: 0.6606 (ptp) cc_final: 0.5348 (ppp) REVERT: F 319 TYR cc_start: 0.5922 (m-10) cc_final: 0.5718 (m-80) REVERT: F 377 MET cc_start: 0.4767 (tmm) cc_final: 0.4317 (tmm) outliers start: 1 outliers final: 1 residues processed: 232 average time/residue: 0.6541 time to fit residues: 166.0105 Evaluate side-chains 175 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 174 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 402 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 0.5980 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 0.7980 chunk 149 optimal weight: 1.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 GLN B 243 GLN C 188 GLN D 88 GLN F 140 ASN ** F 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.183409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.126571 restraints weight = 14398.172| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 1.49 r_work: 0.3159 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3054 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.1151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 14781 Z= 0.192 Angle : 0.635 10.623 20085 Z= 0.331 Chirality : 0.047 0.175 2277 Planarity : 0.005 0.063 2554 Dihedral : 7.508 59.289 2274 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.30 % Favored : 97.54 % Rotamer: Outliers : 2.92 % Allowed : 11.83 % Favored : 85.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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 aren not related in a simple way. whole: 0.19 (0.19), residues: 1909 helix: 0.98 (0.18), residues: 878 sheet: 0.01 (0.37), residues: 180 loop : -0.70 (0.20), residues: 851 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 209 TYR 0.019 0.002 TYR F 167 PHE 0.021 0.002 PHE F 354 TRP 0.023 0.002 TRP B 103 HIS 0.008 0.001 HIS F 97 Details of bonding type rmsd covalent geometry : bond 0.00464 (14775) covalent geometry : angle 0.63239 (20077) hydrogen bonds : bond 0.05660 ( 746) hydrogen bonds : angle 4.88429 ( 2097) metal coordination : bond 0.00540 ( 6) metal coordination : angle 3.00876 ( 8) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3818 Ramachandran restraints generated. 1909 Oldfield, 0 Emsley, 1909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3818 Ramachandran restraints generated. 1909 Oldfield, 0 Emsley, 1909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 185 time to evaluate : 0.558 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.8746 (OUTLIER) cc_final: 0.8451 (ttp) REVERT: A 6 LYS cc_start: 0.8884 (mtmt) cc_final: 0.8629 (mtmm) REVERT: A 75 LYS cc_start: 0.8261 (ttmm) cc_final: 0.7920 (tttp) REVERT: A 168 ASN cc_start: 0.8427 (m-40) cc_final: 0.8218 (m-40) REVERT: A 172 GLU cc_start: 0.7553 (mp0) cc_final: 0.7276 (tt0) REVERT: A 259 GLN cc_start: 0.8286 (mm-40) cc_final: 0.8065 (mp10) REVERT: A 372 ARG cc_start: 0.9112 (OUTLIER) cc_final: 0.8587 (mmt90) REVERT: A 396 ASP cc_start: 0.8454 (m-30) cc_final: 0.8251 (m-30) REVERT: B 42 LYS cc_start: 0.7702 (ptpp) cc_final: 0.7208 (pttm) REVERT: B 406 LYS cc_start: 0.8136 (mtmt) cc_final: 0.7368 (mppt) REVERT: C 204 LYS cc_start: 0.7207 (tppt) cc_final: 0.7006 (mttt) REVERT: F 81 VAL cc_start: 0.6715 (m) cc_final: 0.6084 (p) REVERT: F 122 GLU cc_start: 0.6135 (mm-30) cc_final: 0.5854 (mm-30) REVERT: F 219 GLU cc_start: 0.6107 (mt-10) cc_final: 0.5501 (mp0) REVERT: F 245 MET cc_start: 0.3019 (ttp) cc_final: 0.1775 (pmm) REVERT: F 309 TYR cc_start: 0.6656 (t80) cc_final: 0.6234 (t80) REVERT: F 317 MET cc_start: 0.6636 (ptp) cc_final: 0.5826 (mtm) REVERT: F 319 TYR cc_start: 0.6662 (m-10) cc_final: 0.6420 (m-80) REVERT: F 339 LEU cc_start: 0.6814 (mm) cc_final: 0.6600 (mm) REVERT: F 377 MET cc_start: 0.6268 (tmm) cc_final: 0.5904 (tmt) REVERT: F 399 GLU cc_start: 0.6813 (OUTLIER) cc_final: 0.5634 (pm20) outliers start: 41 outliers final: 16 residues processed: 211 average time/residue: 0.5846 time to fit residues: 136.1239 Evaluate side-chains 186 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 167 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 372 ARG Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 96 ASP Chi-restraints excluded: chain F residue 13 LEU Chi-restraints excluded: chain F residue 113 VAL Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain F residue 382 MET Chi-restraints excluded: chain F residue 399 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 44 optimal weight: 8.9990 chunk 31 optimal weight: 1.9990 chunk 132 optimal weight: 4.9990 chunk 176 optimal weight: 9.9990 chunk 77 optimal weight: 3.9990 chunk 154 optimal weight: 10.0000 chunk 130 optimal weight: 9.9990 chunk 175 optimal weight: 10.0000 chunk 8 optimal weight: 1.9990 chunk 103 optimal weight: 7.9990 chunk 109 optimal weight: 2.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 GLN B 313 ASN C 79 ASN C 90 ASN C 188 GLN ** F 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.180160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.123227 restraints weight = 14666.454| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 1.49 r_work: 0.3141 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3040 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.1701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.055 14781 Z= 0.283 Angle : 0.702 8.206 20085 Z= 0.361 Chirality : 0.051 0.174 2277 Planarity : 0.006 0.071 2554 Dihedral : 8.058 56.537 2272 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.67 % Favored : 97.22 % Rotamer: Outliers : 3.71 % Allowed : 11.40 % Favored : 84.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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 aren not related in a simple way. whole: -0.27 (0.19), residues: 1909 helix: 0.54 (0.17), residues: 883 sheet: 0.05 (0.39), residues: 172 loop : -0.92 (0.20), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 395 TYR 0.014 0.002 TYR A 257 PHE 0.023 0.003 PHE D 104 TRP 0.024 0.003 TRP B 103 HIS 0.007 0.002 HIS B 330 Details of bonding type rmsd covalent geometry : bond 0.00702 (14775) covalent geometry : angle 0.69812 (20077) hydrogen bonds : bond 0.06772 ( 746) hydrogen bonds : angle 5.05115 ( 2097) metal coordination : bond 0.01005 ( 6) metal coordination : angle 3.71224 ( 8) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3818 Ramachandran restraints generated. 1909 Oldfield, 0 Emsley, 1909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3818 Ramachandran restraints generated. 1909 Oldfield, 0 Emsley, 1909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 169 time to evaluate : 0.566 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 75 LYS cc_start: 0.8326 (ttmm) cc_final: 0.7964 (tttp) REVERT: A 172 GLU cc_start: 0.7544 (mp0) cc_final: 0.7291 (tt0) REVERT: A 200 ARG cc_start: 0.8444 (mtp85) cc_final: 0.8239 (mtp85) REVERT: A 259 GLN cc_start: 0.8259 (mm-40) cc_final: 0.8026 (mp10) REVERT: A 284 GLU cc_start: 0.8027 (OUTLIER) cc_final: 0.7346 (tp30) REVERT: A 349 ARG cc_start: 0.8847 (OUTLIER) cc_final: 0.7622 (mtt-85) REVERT: A 372 ARG cc_start: 0.9112 (OUTLIER) cc_final: 0.8908 (mmt180) REVERT: B 42 LYS cc_start: 0.7954 (ptpp) cc_final: 0.7400 (pttm) REVERT: B 152 LYS cc_start: 0.8364 (mtmm) cc_final: 0.8111 (mttp) REVERT: B 406 LYS cc_start: 0.8120 (OUTLIER) cc_final: 0.7450 (mptt) REVERT: C 45 LYS cc_start: 0.7206 (OUTLIER) cc_final: 0.6575 (ttmt) REVERT: C 80 THR cc_start: 0.8166 (p) cc_final: 0.7949 (t) REVERT: C 204 LYS cc_start: 0.7339 (tppt) cc_final: 0.7112 (mptt) REVERT: F 10 MET cc_start: 0.8266 (mmp) cc_final: 0.7698 (mmt) REVERT: F 122 GLU cc_start: 0.6058 (mm-30) cc_final: 0.5786 (mm-30) REVERT: F 219 GLU cc_start: 0.6142 (mt-10) cc_final: 0.5558 (mp0) REVERT: F 245 MET cc_start: 0.2956 (OUTLIER) cc_final: 0.1616 (mtp) REVERT: F 302 LYS cc_start: 0.6769 (mmmt) cc_final: 0.6549 (mmtm) REVERT: F 305 MET cc_start: 0.7699 (OUTLIER) cc_final: 0.7434 (mtm) REVERT: F 309 TYR cc_start: 0.6728 (t80) cc_final: 0.6078 (t80) REVERT: F 317 MET cc_start: 0.6705 (ptp) cc_final: 0.5871 (mtm) REVERT: F 319 TYR cc_start: 0.6860 (m-10) cc_final: 0.6449 (m-80) REVERT: F 339 LEU cc_start: 0.6895 (mm) cc_final: 0.6682 (mm) REVERT: F 377 MET cc_start: 0.6465 (tmm) cc_final: 0.6078 (tmt) REVERT: F 399 GLU cc_start: 0.6892 (OUTLIER) cc_final: 0.5667 (pm20) outliers start: 52 outliers final: 22 residues processed: 201 average time/residue: 0.5835 time to fit residues: 129.6370 Evaluate side-chains 188 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 158 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 284 GLU Chi-restraints excluded: chain A residue 349 ARG Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 372 ARG Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 383 MET Chi-restraints excluded: chain B residue 406 LYS Chi-restraints excluded: chain C residue 45 LYS Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 96 ASP Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain F residue 13 LEU Chi-restraints excluded: chain F residue 113 VAL Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 230 ILE Chi-restraints excluded: chain F residue 245 MET Chi-restraints excluded: chain F residue 285 MET Chi-restraints excluded: chain F residue 305 MET Chi-restraints excluded: chain F residue 399 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 127 optimal weight: 0.7980 chunk 73 optimal weight: 1.9990 chunk 133 optimal weight: 9.9990 chunk 28 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 51 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 chunk 117 optimal weight: 0.5980 chunk 140 optimal weight: 20.0000 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 GLN B 313 ASN C 188 GLN ** F 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.185865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.130188 restraints weight = 14468.718| |-----------------------------------------------------------------------------| r_work (start): 0.3443 rms_B_bonded: 1.59 r_work: 0.3229 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3126 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.1754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 14781 Z= 0.119 Angle : 0.533 7.593 20085 Z= 0.279 Chirality : 0.043 0.186 2277 Planarity : 0.004 0.039 2554 Dihedral : 7.374 59.584 2272 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.25 % Favored : 97.64 % Rotamer: Outliers : 2.28 % Allowed : 13.26 % Favored : 84.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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 aren not related in a simple way. whole: 0.22 (0.19), residues: 1909 helix: 1.08 (0.18), residues: 866 sheet: 0.01 (0.38), residues: 181 loop : -0.74 (0.20), residues: 862 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 408 TYR 0.020 0.001 TYR F 167 PHE 0.013 0.001 PHE D 50 TRP 0.019 0.001 TRP B 103 HIS 0.005 0.001 HIS B 12 Details of bonding type rmsd covalent geometry : bond 0.00262 (14775) covalent geometry : angle 0.53048 (20077) hydrogen bonds : bond 0.04574 ( 746) hydrogen bonds : angle 4.62723 ( 2097) metal coordination : bond 0.00361 ( 6) metal coordination : angle 2.70825 ( 8) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3818 Ramachandran restraints generated. 1909 Oldfield, 0 Emsley, 1909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3818 Ramachandran restraints generated. 1909 Oldfield, 0 Emsley, 1909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 162 time to evaluate : 0.590 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 ARG cc_start: 0.7971 (ptp90) cc_final: 0.7598 (ptp90) REVERT: A 75 LYS cc_start: 0.8295 (ttmm) cc_final: 0.7935 (tttp) REVERT: A 172 GLU cc_start: 0.7513 (mp0) cc_final: 0.7308 (tt0) REVERT: A 259 GLN cc_start: 0.8277 (mm-40) cc_final: 0.8054 (mp10) REVERT: A 284 GLU cc_start: 0.8029 (OUTLIER) cc_final: 0.7393 (tp30) REVERT: A 290 GLU cc_start: 0.7972 (OUTLIER) cc_final: 0.7221 (mm-30) REVERT: A 372 ARG cc_start: 0.9089 (OUTLIER) cc_final: 0.8849 (mmt180) REVERT: B 42 LYS cc_start: 0.7832 (ptpp) cc_final: 0.7236 (pttm) REVERT: B 152 LYS cc_start: 0.8291 (mtmm) cc_final: 0.8053 (mttp) REVERT: B 406 LYS cc_start: 0.8058 (OUTLIER) cc_final: 0.7365 (mppt) REVERT: C 45 LYS cc_start: 0.7185 (OUTLIER) cc_final: 0.6589 (ttmt) REVERT: F 10 MET cc_start: 0.8243 (mmp) cc_final: 0.7746 (mmp) REVERT: F 109 LEU cc_start: 0.5425 (mp) cc_final: 0.4839 (tp) REVERT: F 122 GLU cc_start: 0.6012 (mm-30) cc_final: 0.5779 (mm-30) REVERT: F 219 GLU cc_start: 0.5963 (mt-10) cc_final: 0.5477 (mp0) REVERT: F 245 MET cc_start: 0.2978 (OUTLIER) cc_final: 0.1637 (mtp) REVERT: F 309 TYR cc_start: 0.6676 (t80) cc_final: 0.6032 (t80) REVERT: F 317 MET cc_start: 0.6690 (ptp) cc_final: 0.5788 (mtm) REVERT: F 319 TYR cc_start: 0.6737 (m-10) cc_final: 0.6500 (m-80) REVERT: F 339 LEU cc_start: 0.6798 (mm) cc_final: 0.5949 (pp) REVERT: F 399 GLU cc_start: 0.6878 (OUTLIER) cc_final: 0.5671 (pm20) outliers start: 32 outliers final: 12 residues processed: 183 average time/residue: 0.6225 time to fit residues: 125.2938 Evaluate side-chains 171 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 152 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 284 GLU Chi-restraints excluded: chain A residue 290 GLU Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 372 ARG Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 406 LYS Chi-restraints excluded: chain C residue 45 LYS Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 96 ASP Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain F residue 113 VAL Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 245 MET Chi-restraints excluded: chain F residue 285 MET Chi-restraints excluded: chain F residue 382 MET Chi-restraints excluded: chain F residue 399 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 109 optimal weight: 3.9990 chunk 157 optimal weight: 40.0000 chunk 38 optimal weight: 3.9990 chunk 145 optimal weight: 9.9990 chunk 119 optimal weight: 4.9990 chunk 23 optimal weight: 3.9990 chunk 169 optimal weight: 30.0000 chunk 40 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 132 optimal weight: 10.0000 chunk 118 optimal weight: 1.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 GLN B 313 ASN C 188 GLN ** F 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.181636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.126661 restraints weight = 14504.578| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 1.70 r_work: 0.3163 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3061 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.1968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.060 14781 Z= 0.296 Angle : 0.687 8.572 20085 Z= 0.354 Chirality : 0.051 0.192 2277 Planarity : 0.005 0.059 2554 Dihedral : 7.962 58.484 2272 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.88 % Favored : 97.01 % Rotamer: Outliers : 3.78 % Allowed : 12.69 % Favored : 83.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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 aren not related in a simple way. whole: -0.28 (0.18), residues: 1909 helix: 0.59 (0.18), residues: 871 sheet: -0.03 (0.38), residues: 175 loop : -0.98 (0.20), residues: 863 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 395 TYR 0.019 0.002 TYR F 167 PHE 0.023 0.003 PHE D 104 TRP 0.020 0.003 TRP B 103 HIS 0.007 0.002 HIS B 330 Details of bonding type rmsd covalent geometry : bond 0.00739 (14775) covalent geometry : angle 0.68339 (20077) hydrogen bonds : bond 0.06662 ( 746) hydrogen bonds : angle 5.00999 ( 2097) metal coordination : bond 0.01020 ( 6) metal coordination : angle 3.76413 ( 8) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3818 Ramachandran restraints generated. 1909 Oldfield, 0 Emsley, 1909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3818 Ramachandran restraints generated. 1909 Oldfield, 0 Emsley, 1909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 157 time to evaluate : 0.397 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.8684 (OUTLIER) cc_final: 0.7790 (tpp) REVERT: A 75 LYS cc_start: 0.8352 (ttmm) cc_final: 0.7975 (tttp) REVERT: A 172 GLU cc_start: 0.7617 (mp0) cc_final: 0.7370 (tt0) REVERT: A 212 ASP cc_start: 0.8408 (t0) cc_final: 0.8174 (m-30) REVERT: A 259 GLN cc_start: 0.8277 (mm-40) cc_final: 0.8058 (mp10) REVERT: A 284 GLU cc_start: 0.8097 (OUTLIER) cc_final: 0.7435 (tp30) REVERT: A 290 GLU cc_start: 0.8094 (OUTLIER) cc_final: 0.7398 (mm-30) REVERT: A 349 ARG cc_start: 0.8896 (OUTLIER) cc_final: 0.7695 (mtt-85) REVERT: A 372 ARG cc_start: 0.9138 (OUTLIER) cc_final: 0.8936 (mmt-90) REVERT: B 42 LYS cc_start: 0.8035 (OUTLIER) cc_final: 0.7416 (pttm) REVERT: B 152 LYS cc_start: 0.8420 (mtmm) cc_final: 0.8176 (mttp) REVERT: B 406 LYS cc_start: 0.8174 (OUTLIER) cc_final: 0.7528 (mptt) REVERT: C 45 LYS cc_start: 0.7293 (OUTLIER) cc_final: 0.6703 (ttmt) REVERT: F 10 MET cc_start: 0.8264 (mmp) cc_final: 0.7770 (mmt) REVERT: F 122 GLU cc_start: 0.6039 (mm-30) cc_final: 0.5780 (mm-30) REVERT: F 219 GLU cc_start: 0.6041 (mt-10) cc_final: 0.5573 (mp0) REVERT: F 245 MET cc_start: 0.2996 (OUTLIER) cc_final: 0.1539 (mtp) REVERT: F 309 TYR cc_start: 0.6709 (t80) cc_final: 0.6267 (t80) REVERT: F 317 MET cc_start: 0.6784 (ptp) cc_final: 0.5948 (mtm) REVERT: F 319 TYR cc_start: 0.6943 (m-10) cc_final: 0.6563 (m-80) REVERT: F 339 LEU cc_start: 0.6849 (mm) cc_final: 0.5974 (pp) REVERT: F 377 MET cc_start: 0.6335 (tmt) cc_final: 0.5754 (ptp) REVERT: F 399 GLU cc_start: 0.6978 (OUTLIER) cc_final: 0.5721 (pm20) outliers start: 53 outliers final: 24 residues processed: 194 average time/residue: 0.6093 time to fit residues: 130.1926 Evaluate side-chains 187 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 153 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 284 GLU Chi-restraints excluded: chain A residue 290 GLU Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 349 ARG Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 372 ARG Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain B residue 42 LYS Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 318 ASP Chi-restraints excluded: chain B residue 406 LYS Chi-restraints excluded: chain C residue 45 LYS Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 160 ASN Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 96 ASP Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain F residue 113 VAL Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 230 ILE Chi-restraints excluded: chain F residue 245 MET Chi-restraints excluded: chain F residue 285 MET Chi-restraints excluded: chain F residue 399 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 149 optimal weight: 4.9990 chunk 78 optimal weight: 0.9990 chunk 61 optimal weight: 0.9990 chunk 26 optimal weight: 0.5980 chunk 31 optimal weight: 0.9990 chunk 37 optimal weight: 0.9980 chunk 110 optimal weight: 0.0030 chunk 14 optimal weight: 0.7980 chunk 81 optimal weight: 0.7980 chunk 184 optimal weight: 6.9990 chunk 39 optimal weight: 0.7980 overall best weight: 0.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 GLN B 313 ASN C 188 GLN ** F 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.186687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.132152 restraints weight = 14432.086| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 1.69 r_work: 0.3249 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3148 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.1985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 14781 Z= 0.104 Angle : 0.511 7.903 20085 Z= 0.267 Chirality : 0.042 0.165 2277 Planarity : 0.004 0.042 2554 Dihedral : 7.156 59.036 2272 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.89 % Favored : 98.01 % Rotamer: Outliers : 2.21 % Allowed : 14.47 % Favored : 83.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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 aren not related in a simple way. whole: 0.28 (0.19), residues: 1909 helix: 1.14 (0.18), residues: 866 sheet: 0.17 (0.39), residues: 170 loop : -0.75 (0.20), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 104 TYR 0.018 0.001 TYR F 167 PHE 0.013 0.001 PHE D 50 TRP 0.018 0.001 TRP B 103 HIS 0.004 0.001 HIS B 12 Details of bonding type rmsd covalent geometry : bond 0.00221 (14775) covalent geometry : angle 0.50921 (20077) hydrogen bonds : bond 0.04203 ( 746) hydrogen bonds : angle 4.53974 ( 2097) metal coordination : bond 0.00278 ( 6) metal coordination : angle 2.30017 ( 8) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3818 Ramachandran restraints generated. 1909 Oldfield, 0 Emsley, 1909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3818 Ramachandran restraints generated. 1909 Oldfield, 0 Emsley, 1909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 162 time to evaluate : 0.555 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 ARG cc_start: 0.7975 (ptp90) cc_final: 0.7585 (ptp90) REVERT: A 75 LYS cc_start: 0.8283 (ttmm) cc_final: 0.7911 (tttp) REVERT: A 259 GLN cc_start: 0.8186 (mm-40) cc_final: 0.7937 (mp10) REVERT: A 284 GLU cc_start: 0.7985 (OUTLIER) cc_final: 0.7349 (tp30) REVERT: A 290 GLU cc_start: 0.7966 (OUTLIER) cc_final: 0.7203 (mm-30) REVERT: A 372 ARG cc_start: 0.9080 (OUTLIER) cc_final: 0.8850 (mmt180) REVERT: B 42 LYS cc_start: 0.7796 (ptpp) cc_final: 0.7179 (pttm) REVERT: B 152 LYS cc_start: 0.8311 (OUTLIER) cc_final: 0.8080 (mttp) REVERT: B 406 LYS cc_start: 0.8026 (mtmt) cc_final: 0.7329 (mppt) REVERT: C 45 LYS cc_start: 0.7158 (OUTLIER) cc_final: 0.6597 (ttmt) REVERT: C 84 VAL cc_start: 0.8395 (OUTLIER) cc_final: 0.8169 (m) REVERT: F 10 MET cc_start: 0.8244 (mmp) cc_final: 0.7818 (mmp) REVERT: F 109 LEU cc_start: 0.5395 (mp) cc_final: 0.4841 (tp) REVERT: F 122 GLU cc_start: 0.6011 (mm-30) cc_final: 0.5743 (mm-30) REVERT: F 219 GLU cc_start: 0.5826 (mt-10) cc_final: 0.5434 (mp0) REVERT: F 245 MET cc_start: 0.2888 (OUTLIER) cc_final: 0.1450 (mtp) REVERT: F 276 MET cc_start: 0.8012 (OUTLIER) cc_final: 0.7644 (mtp) REVERT: F 317 MET cc_start: 0.6778 (ptp) cc_final: 0.6011 (mtm) REVERT: F 319 TYR cc_start: 0.6747 (m-10) cc_final: 0.6540 (m-80) REVERT: F 339 LEU cc_start: 0.6811 (mm) cc_final: 0.5950 (pp) REVERT: F 377 MET cc_start: 0.6241 (tmt) cc_final: 0.5705 (ptp) REVERT: F 399 GLU cc_start: 0.6868 (OUTLIER) cc_final: 0.5660 (pm20) REVERT: F 402 LEU cc_start: 0.6932 (mp) cc_final: 0.6588 (mm) outliers start: 31 outliers final: 9 residues processed: 180 average time/residue: 0.6242 time to fit residues: 123.6125 Evaluate side-chains 170 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 152 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 284 GLU Chi-restraints excluded: chain A residue 290 GLU Chi-restraints excluded: chain A residue 372 ARG Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 152 LYS Chi-restraints excluded: chain B residue 318 ASP Chi-restraints excluded: chain C residue 45 LYS Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain D residue 96 ASP Chi-restraints excluded: chain D residue 119 GLU Chi-restraints excluded: chain F residue 113 VAL Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 245 MET Chi-restraints excluded: chain F residue 276 MET Chi-restraints excluded: chain F residue 285 MET Chi-restraints excluded: chain F residue 382 MET Chi-restraints excluded: chain F residue 399 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 47 optimal weight: 3.9990 chunk 86 optimal weight: 4.9990 chunk 183 optimal weight: 6.9990 chunk 19 optimal weight: 2.9990 chunk 164 optimal weight: 0.0170 chunk 140 optimal weight: 20.0000 chunk 97 optimal weight: 6.9990 chunk 88 optimal weight: 4.9990 chunk 102 optimal weight: 3.9990 chunk 125 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 overall best weight: 2.4026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 GLN B 20 HIS C 188 GLN F 332 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.183022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.127884 restraints weight = 14351.734| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 1.66 r_work: 0.3187 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3085 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.2086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 14781 Z= 0.218 Angle : 0.612 7.688 20085 Z= 0.316 Chirality : 0.047 0.163 2277 Planarity : 0.005 0.046 2554 Dihedral : 7.603 59.398 2272 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.57 % Favored : 97.33 % Rotamer: Outliers : 3.06 % Allowed : 14.04 % Favored : 82.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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 aren not related in a simple way. whole: 0.03 (0.19), residues: 1909 helix: 0.92 (0.18), residues: 864 sheet: 0.14 (0.38), residues: 173 loop : -0.90 (0.20), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 395 TYR 0.015 0.002 TYR D 141 PHE 0.020 0.002 PHE D 104 TRP 0.019 0.002 TRP B 103 HIS 0.006 0.001 HIS B 330 Details of bonding type rmsd covalent geometry : bond 0.00539 (14775) covalent geometry : angle 0.60896 (20077) hydrogen bonds : bond 0.05747 ( 746) hydrogen bonds : angle 4.78972 ( 2097) metal coordination : bond 0.00713 ( 6) metal coordination : angle 3.29332 ( 8) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3818 Ramachandran restraints generated. 1909 Oldfield, 0 Emsley, 1909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3818 Ramachandran restraints generated. 1909 Oldfield, 0 Emsley, 1909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 152 time to evaluate : 0.572 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 75 LYS cc_start: 0.8325 (ttmm) cc_final: 0.7935 (tttp) REVERT: A 259 GLN cc_start: 0.8207 (mm-40) cc_final: 0.7979 (mp10) REVERT: A 284 GLU cc_start: 0.8052 (OUTLIER) cc_final: 0.7398 (tp30) REVERT: A 290 GLU cc_start: 0.8047 (OUTLIER) cc_final: 0.7339 (mm-30) REVERT: A 349 ARG cc_start: 0.8865 (OUTLIER) cc_final: 0.7631 (mtt-85) REVERT: A 372 ARG cc_start: 0.9118 (OUTLIER) cc_final: 0.8859 (mmt180) REVERT: B 42 LYS cc_start: 0.7969 (OUTLIER) cc_final: 0.7325 (pttm) REVERT: B 152 LYS cc_start: 0.8403 (mtmm) cc_final: 0.8162 (mttp) REVERT: B 406 LYS cc_start: 0.8123 (OUTLIER) cc_final: 0.7441 (mppt) REVERT: C 45 LYS cc_start: 0.7246 (OUTLIER) cc_final: 0.6645 (ttmt) REVERT: C 84 VAL cc_start: 0.8424 (OUTLIER) cc_final: 0.8201 (m) REVERT: C 193 LYS cc_start: 0.8749 (OUTLIER) cc_final: 0.8278 (mmtt) REVERT: F 5 ILE cc_start: 0.7722 (OUTLIER) cc_final: 0.7415 (mt) REVERT: F 10 MET cc_start: 0.8217 (mmp) cc_final: 0.7801 (mmt) REVERT: F 109 LEU cc_start: 0.5501 (mp) cc_final: 0.4870 (tp) REVERT: F 219 GLU cc_start: 0.5941 (mt-10) cc_final: 0.5447 (mp0) REVERT: F 245 MET cc_start: 0.2913 (OUTLIER) cc_final: 0.2532 (ttm) REVERT: F 276 MET cc_start: 0.8052 (OUTLIER) cc_final: 0.7780 (mtp) REVERT: F 285 MET cc_start: 0.6074 (OUTLIER) cc_final: 0.5846 (mtt) REVERT: F 309 TYR cc_start: 0.6568 (t80) cc_final: 0.5971 (t80) REVERT: F 317 MET cc_start: 0.6690 (ptp) cc_final: 0.5786 (mtm) REVERT: F 339 LEU cc_start: 0.6841 (mm) cc_final: 0.5971 (pp) REVERT: F 377 MET cc_start: 0.6158 (tmt) cc_final: 0.5782 (ptp) REVERT: F 399 GLU cc_start: 0.6982 (OUTLIER) cc_final: 0.5697 (pm20) REVERT: F 402 LEU cc_start: 0.6774 (mp) cc_final: 0.6462 (mm) outliers start: 43 outliers final: 20 residues processed: 182 average time/residue: 0.6267 time to fit residues: 125.8877 Evaluate side-chains 186 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 152 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 284 GLU Chi-restraints excluded: chain A residue 290 GLU Chi-restraints excluded: chain A residue 349 ARG Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 372 ARG Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain B residue 42 LYS Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 318 ASP Chi-restraints excluded: chain B residue 406 LYS Chi-restraints excluded: chain C residue 45 LYS Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 193 LYS Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 96 ASP Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain F residue 5 ILE Chi-restraints excluded: chain F residue 35 ILE Chi-restraints excluded: chain F residue 113 VAL Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 245 MET Chi-restraints excluded: chain F residue 276 MET Chi-restraints excluded: chain F residue 285 MET Chi-restraints excluded: chain F residue 382 MET Chi-restraints excluded: chain F residue 399 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 29 optimal weight: 3.9990 chunk 117 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 140 optimal weight: 20.0000 chunk 164 optimal weight: 20.0000 chunk 96 optimal weight: 0.0170 chunk 121 optimal weight: 6.9990 chunk 145 optimal weight: 10.0000 chunk 160 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 overall best weight: 2.2026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 GLN B 313 ASN C 188 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.183135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.127841 restraints weight = 14398.515| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 1.64 r_work: 0.3187 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3085 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.2157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 14781 Z= 0.204 Angle : 0.602 8.747 20085 Z= 0.311 Chirality : 0.046 0.160 2277 Planarity : 0.005 0.043 2554 Dihedral : 7.666 59.952 2272 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.62 % Favored : 97.28 % Rotamer: Outliers : 3.14 % Allowed : 14.33 % Favored : 82.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % 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 aren not related in a simple way. whole: -0.07 (0.19), residues: 1909 helix: 0.83 (0.18), residues: 870 sheet: 0.09 (0.38), residues: 173 loop : -0.94 (0.20), residues: 866 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 395 TYR 0.018 0.002 TYR F 167 PHE 0.018 0.002 PHE D 104 TRP 0.018 0.002 TRP B 103 HIS 0.006 0.001 HIS B 330 Details of bonding type rmsd covalent geometry : bond 0.00499 (14775) covalent geometry : angle 0.59933 (20077) hydrogen bonds : bond 0.05545 ( 746) hydrogen bonds : angle 4.78602 ( 2097) metal coordination : bond 0.00585 ( 6) metal coordination : angle 2.87329 ( 8) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3818 Ramachandran restraints generated. 1909 Oldfield, 0 Emsley, 1909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3818 Ramachandran restraints generated. 1909 Oldfield, 0 Emsley, 1909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 150 time to evaluate : 0.713 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 75 LYS cc_start: 0.8332 (ttmm) cc_final: 0.7916 (tttp) REVERT: A 168 ASN cc_start: 0.8634 (m110) cc_final: 0.8065 (m110) REVERT: A 259 GLN cc_start: 0.8185 (mm-40) cc_final: 0.7931 (mp10) REVERT: A 284 GLU cc_start: 0.8044 (OUTLIER) cc_final: 0.7391 (tp30) REVERT: A 290 GLU cc_start: 0.8005 (OUTLIER) cc_final: 0.7321 (mm-30) REVERT: A 333 GLU cc_start: 0.8093 (OUTLIER) cc_final: 0.7892 (mt-10) REVERT: A 372 ARG cc_start: 0.9116 (OUTLIER) cc_final: 0.8871 (mmt180) REVERT: B 42 LYS cc_start: 0.7968 (OUTLIER) cc_final: 0.7333 (pttm) REVERT: B 152 LYS cc_start: 0.8386 (mtmm) cc_final: 0.8154 (mttp) REVERT: B 406 LYS cc_start: 0.8120 (OUTLIER) cc_final: 0.7431 (mppt) REVERT: C 45 LYS cc_start: 0.7233 (OUTLIER) cc_final: 0.6630 (ttmt) REVERT: C 84 VAL cc_start: 0.8395 (OUTLIER) cc_final: 0.8179 (m) REVERT: C 193 LYS cc_start: 0.8749 (OUTLIER) cc_final: 0.8297 (mmtt) REVERT: F 5 ILE cc_start: 0.7737 (OUTLIER) cc_final: 0.7435 (mt) REVERT: F 10 MET cc_start: 0.8207 (mmp) cc_final: 0.7805 (mmt) REVERT: F 109 LEU cc_start: 0.5474 (mp) cc_final: 0.4775 (tp) REVERT: F 219 GLU cc_start: 0.5928 (mt-10) cc_final: 0.5470 (mp0) REVERT: F 245 MET cc_start: 0.2871 (OUTLIER) cc_final: 0.2595 (ttm) REVERT: F 276 MET cc_start: 0.8052 (OUTLIER) cc_final: 0.7791 (mtp) REVERT: F 309 TYR cc_start: 0.6536 (t80) cc_final: 0.5906 (t80) REVERT: F 317 MET cc_start: 0.6693 (ptp) cc_final: 0.5829 (mtm) REVERT: F 339 LEU cc_start: 0.6759 (mm) cc_final: 0.5945 (pp) REVERT: F 377 MET cc_start: 0.6183 (tmt) cc_final: 0.5763 (ptp) REVERT: F 399 GLU cc_start: 0.6935 (OUTLIER) cc_final: 0.5665 (pm20) REVERT: F 402 LEU cc_start: 0.6748 (mp) cc_final: 0.6445 (mm) outliers start: 44 outliers final: 22 residues processed: 182 average time/residue: 0.6210 time to fit residues: 124.6719 Evaluate side-chains 181 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 146 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 284 GLU Chi-restraints excluded: chain A residue 290 GLU Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 333 GLU Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 372 ARG Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain B residue 42 LYS Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 318 ASP Chi-restraints excluded: chain B residue 406 LYS Chi-restraints excluded: chain C residue 45 LYS Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 193 LYS Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 96 ASP Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain F residue 5 ILE Chi-restraints excluded: chain F residue 35 ILE Chi-restraints excluded: chain F residue 113 VAL Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 245 MET Chi-restraints excluded: chain F residue 276 MET Chi-restraints excluded: chain F residue 382 MET Chi-restraints excluded: chain F residue 399 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 46 optimal weight: 3.9990 chunk 95 optimal weight: 1.9990 chunk 123 optimal weight: 4.9990 chunk 21 optimal weight: 0.7980 chunk 1 optimal weight: 0.0050 chunk 124 optimal weight: 4.9990 chunk 150 optimal weight: 4.9990 chunk 91 optimal weight: 2.9990 chunk 65 optimal weight: 0.6980 chunk 178 optimal weight: 5.9990 chunk 107 optimal weight: 0.8980 overall best weight: 0.8796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 GLN B 313 ASN C 188 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.185957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.130830 restraints weight = 14478.290| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 1.69 r_work: 0.3233 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3132 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.2188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14781 Z= 0.117 Angle : 0.523 8.068 20085 Z= 0.272 Chirality : 0.042 0.157 2277 Planarity : 0.004 0.042 2554 Dihedral : 7.143 59.359 2272 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.36 % Favored : 97.54 % Rotamer: Outliers : 2.42 % Allowed : 15.04 % Favored : 82.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % 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 aren not related in a simple way. whole: 0.34 (0.19), residues: 1909 helix: 1.25 (0.18), residues: 859 sheet: 0.19 (0.39), residues: 171 loop : -0.77 (0.20), residues: 879 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 349 TYR 0.013 0.001 TYR B 360 PHE 0.014 0.001 PHE B 213 TRP 0.018 0.001 TRP B 100 HIS 0.004 0.001 HIS B 330 Details of bonding type rmsd covalent geometry : bond 0.00263 (14775) covalent geometry : angle 0.52082 (20077) hydrogen bonds : bond 0.04319 ( 746) hydrogen bonds : angle 4.50653 ( 2097) metal coordination : bond 0.00222 ( 6) metal coordination : angle 2.26119 ( 8) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3818 Ramachandran restraints generated. 1909 Oldfield, 0 Emsley, 1909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3818 Ramachandran restraints generated. 1909 Oldfield, 0 Emsley, 1909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 155 time to evaluate : 0.563 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 ARG cc_start: 0.8048 (ptp90) cc_final: 0.7647 (ptp90) REVERT: A 75 LYS cc_start: 0.8275 (ttmm) cc_final: 0.7861 (tttp) REVERT: A 168 ASN cc_start: 0.8583 (m110) cc_final: 0.8086 (m110) REVERT: A 259 GLN cc_start: 0.8127 (mm-40) cc_final: 0.7890 (mp10) REVERT: A 290 GLU cc_start: 0.7924 (OUTLIER) cc_final: 0.7097 (mm-30) REVERT: B 42 LYS cc_start: 0.7823 (OUTLIER) cc_final: 0.7210 (pttm) REVERT: B 152 LYS cc_start: 0.8319 (mtmm) cc_final: 0.8092 (mttp) REVERT: B 406 LYS cc_start: 0.8028 (OUTLIER) cc_final: 0.7331 (mppt) REVERT: C 45 LYS cc_start: 0.7133 (OUTLIER) cc_final: 0.6545 (ttmt) REVERT: C 58 LYS cc_start: 0.8185 (ptpp) cc_final: 0.7958 (mtmm) REVERT: C 193 LYS cc_start: 0.8730 (OUTLIER) cc_final: 0.8252 (mmtt) REVERT: F 10 MET cc_start: 0.8210 (mmp) cc_final: 0.7863 (mmp) REVERT: F 109 LEU cc_start: 0.5501 (mp) cc_final: 0.4817 (tp) REVERT: F 120 ASP cc_start: 0.5633 (t0) cc_final: 0.5219 (p0) REVERT: F 219 GLU cc_start: 0.5819 (mt-10) cc_final: 0.5405 (mp0) REVERT: F 245 MET cc_start: 0.2864 (OUTLIER) cc_final: 0.2486 (ttm) REVERT: F 309 TYR cc_start: 0.6564 (t80) cc_final: 0.6043 (t80) REVERT: F 317 MET cc_start: 0.6653 (ptp) cc_final: 0.5901 (mtm) REVERT: F 339 LEU cc_start: 0.6752 (OUTLIER) cc_final: 0.5973 (pp) REVERT: F 377 MET cc_start: 0.6086 (tmt) cc_final: 0.5758 (ptp) REVERT: F 399 GLU cc_start: 0.6921 (OUTLIER) cc_final: 0.5684 (pm20) REVERT: F 402 LEU cc_start: 0.6774 (mp) cc_final: 0.6496 (mm) outliers start: 34 outliers final: 16 residues processed: 177 average time/residue: 0.5947 time to fit residues: 116.3960 Evaluate side-chains 175 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 151 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 290 GLU Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain B residue 42 LYS Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 318 ASP Chi-restraints excluded: chain B residue 406 LYS Chi-restraints excluded: chain C residue 45 LYS Chi-restraints excluded: chain C residue 193 LYS Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 96 ASP Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain F residue 35 ILE Chi-restraints excluded: chain F residue 113 VAL Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 245 MET Chi-restraints excluded: chain F residue 339 LEU Chi-restraints excluded: chain F residue 382 MET Chi-restraints excluded: chain F residue 399 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 63 optimal weight: 0.9990 chunk 110 optimal weight: 5.9990 chunk 148 optimal weight: 9.9990 chunk 56 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 13 optimal weight: 0.5980 chunk 22 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 88 optimal weight: 3.9990 chunk 125 optimal weight: 1.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 GLN C 188 GLN F 40 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.184663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.129594 restraints weight = 14431.619| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 1.75 r_work: 0.3214 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3112 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.2224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 14781 Z= 0.157 Angle : 0.562 7.961 20085 Z= 0.291 Chirality : 0.044 0.155 2277 Planarity : 0.004 0.041 2554 Dihedral : 7.304 59.968 2272 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.57 % Favored : 97.33 % Rotamer: Outliers : 1.92 % Allowed : 15.82 % Favored : 82.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % 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 aren not related in a simple way. whole: 0.27 (0.19), residues: 1909 helix: 1.15 (0.18), residues: 865 sheet: 0.16 (0.38), residues: 180 loop : -0.78 (0.20), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 408 TYR 0.015 0.001 TYR F 167 PHE 0.017 0.002 PHE B 213 TRP 0.017 0.002 TRP B 100 HIS 0.005 0.001 HIS B 330 Details of bonding type rmsd covalent geometry : bond 0.00376 (14775) covalent geometry : angle 0.56038 (20077) hydrogen bonds : bond 0.04879 ( 746) hydrogen bonds : angle 4.59100 ( 2097) metal coordination : bond 0.00464 ( 6) metal coordination : angle 2.48363 ( 8) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3818 Ramachandran restraints generated. 1909 Oldfield, 0 Emsley, 1909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3818 Ramachandran restraints generated. 1909 Oldfield, 0 Emsley, 1909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 149 time to evaluate : 0.581 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 75 LYS cc_start: 0.8332 (ttmm) cc_final: 0.7918 (tttp) REVERT: A 168 ASN cc_start: 0.8599 (m110) cc_final: 0.8090 (m110) REVERT: A 259 GLN cc_start: 0.8148 (mm-40) cc_final: 0.7916 (mp10) REVERT: A 290 GLU cc_start: 0.7957 (OUTLIER) cc_final: 0.7189 (mm-30) REVERT: B 42 LYS cc_start: 0.7885 (OUTLIER) cc_final: 0.7286 (pttm) REVERT: B 152 LYS cc_start: 0.8357 (mtmm) cc_final: 0.8125 (mttp) REVERT: B 406 LYS cc_start: 0.8115 (OUTLIER) cc_final: 0.7444 (mppt) REVERT: C 45 LYS cc_start: 0.7177 (OUTLIER) cc_final: 0.6598 (ttmt) REVERT: C 58 LYS cc_start: 0.8166 (ptpp) cc_final: 0.7934 (mtmm) REVERT: C 193 LYS cc_start: 0.8738 (OUTLIER) cc_final: 0.8280 (mmtt) REVERT: F 10 MET cc_start: 0.8226 (mmp) cc_final: 0.7862 (mmt) REVERT: F 109 LEU cc_start: 0.5439 (mp) cc_final: 0.4774 (tp) REVERT: F 120 ASP cc_start: 0.5660 (t0) cc_final: 0.5233 (p0) REVERT: F 219 GLU cc_start: 0.5840 (mt-10) cc_final: 0.5463 (mp0) REVERT: F 245 MET cc_start: 0.2887 (OUTLIER) cc_final: 0.2500 (ttm) REVERT: F 309 TYR cc_start: 0.6551 (t80) cc_final: 0.6061 (t80) REVERT: F 317 MET cc_start: 0.6665 (ptp) cc_final: 0.5937 (mtm) REVERT: F 339 LEU cc_start: 0.6778 (OUTLIER) cc_final: 0.5983 (pp) REVERT: F 377 MET cc_start: 0.6193 (tmt) cc_final: 0.5847 (ptp) REVERT: F 399 GLU cc_start: 0.7005 (OUTLIER) cc_final: 0.5755 (pm20) REVERT: F 402 LEU cc_start: 0.6839 (mp) cc_final: 0.6548 (mm) outliers start: 27 outliers final: 15 residues processed: 168 average time/residue: 0.6176 time to fit residues: 114.7776 Evaluate side-chains 172 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 149 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 290 GLU Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain B residue 42 LYS Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 318 ASP Chi-restraints excluded: chain B residue 406 LYS Chi-restraints excluded: chain C residue 45 LYS Chi-restraints excluded: chain C residue 193 LYS Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 96 ASP Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain F residue 113 VAL Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 245 MET Chi-restraints excluded: chain F residue 339 LEU Chi-restraints excluded: chain F residue 382 MET Chi-restraints excluded: chain F residue 399 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 70 optimal weight: 0.0050 chunk 29 optimal weight: 4.9990 chunk 93 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 111 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 182 optimal weight: 8.9990 chunk 68 optimal weight: 3.9990 chunk 118 optimal weight: 4.9990 chunk 84 optimal weight: 1.9990 chunk 107 optimal weight: 4.9990 overall best weight: 1.7800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 GLN B 313 ASN C 188 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.183891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.128712 restraints weight = 14435.575| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 1.70 r_work: 0.3199 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3096 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.2266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 14781 Z= 0.174 Angle : 0.578 8.243 20085 Z= 0.300 Chirality : 0.045 0.153 2277 Planarity : 0.004 0.041 2554 Dihedral : 7.437 59.933 2272 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.78 % Favored : 97.12 % Rotamer: Outliers : 2.00 % Allowed : 15.82 % Favored : 82.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % 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 aren not related in a simple way. whole: 0.16 (0.19), residues: 1909 helix: 1.06 (0.18), residues: 863 sheet: 0.14 (0.38), residues: 174 loop : -0.84 (0.20), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 408 TYR 0.014 0.001 TYR F 319 PHE 0.017 0.002 PHE D 104 TRP 0.016 0.002 TRP B 100 HIS 0.005 0.001 HIS B 330 Details of bonding type rmsd covalent geometry : bond 0.00422 (14775) covalent geometry : angle 0.57612 (20077) hydrogen bonds : bond 0.05185 ( 746) hydrogen bonds : angle 4.66226 ( 2097) metal coordination : bond 0.00531 ( 6) metal coordination : angle 2.66438 ( 8) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5275.80 seconds wall clock time: 90 minutes 38.80 seconds (5438.80 seconds total)