Starting phenix.real_space_refine on Sat Jul 4 09:47:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9tak_55749/07_2026/9tak_55749.cif Found real_map, /net/cci-nas-00/data/ceres_data/9tak_55749/07_2026/9tak_55749.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9tak_55749/07_2026/9tak_55749.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9tak_55749/07_2026/9tak_55749.map" model { file = "/net/cci-nas-00/data/ceres_data/9tak_55749/07_2026/9tak_55749.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9tak_55749/07_2026/9tak_55749.cif" } resolution = 2.8 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= 0.039 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: 5 Type Number sf(0) Gaussians P 18 5.49 5 S 121 5.16 5 C 13034 2.51 5 N 2908 2.21 5 O 3356 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 19437 Number of models: 1 Model: "" Number of chains: 21 Chain: "H" Number of atoms: 2404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2404 Classifications: {'peptide': 307} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 292} Chain breaks: 1 Chain: "J" Number of atoms: 1226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1226 Classifications: {'peptide': 162} Link IDs: {'PTRANS': 5, 'TRANS': 156} Chain: "K" Number of atoms: 760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 760 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 1, 'TRANS': 98} Chain: "M" Number of atoms: 3964 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 504, 3953 Classifications: {'peptide': 504} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 482} Conformer: "B" Number of residues, atoms: 504, 3953 Classifications: {'peptide': 504} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 482} bond proxies already assigned to first conformer: 4060 Chain: "A" Number of atoms: 784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 784 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 1, 'TRANS': 96} Chain breaks: 1 Chain: "B" Number of atoms: 731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 731 Classifications: {'peptide': 89} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 82} Chain breaks: 3 Chain: "L" Number of atoms: 4685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 613, 4685 Classifications: {'peptide': 613} Link IDs: {'PTRANS': 18, 'TRANS': 594} Chain: "N" Number of atoms: 3673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 485, 3673 Classifications: {'peptide': 485} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 463} Chain: "H" Number of atoms: 122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 122 Unusual residues: {'3PE': 2, 'LFA': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "J" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 102 Unusual residues: {'3PE': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "M" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 140 Unusual residues: {'3PE': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 13 Chain: "A" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 89 Unusual residues: {'3PE': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 13 Chain: "L" Number of atoms: 359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 359 Unusual residues: {'3PE': 5, 'CDL': 1, 'TRD': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 22 Chain: "N" Number of atoms: 232 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 232 Unusual residues: {'3PE': 2, 'LFA': 1, 'TRD': 1, 'UQ8': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 9 Chain: "H" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 22 Classifications: {'water': 22} Link IDs: {None: 21} Chain: "J" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "K" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "M" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 40 Classifications: {'water': 40} Link IDs: {None: 39} Chain: "A" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "L" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 44 Classifications: {'water': 44} Link IDs: {None: 43} Chain: "N" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 36 Classifications: {'water': 36} Link IDs: {None: 35} Time building chain proxies: 3.76, per 1000 atoms: 0.19 Number of scatterers: 19437 At special positions: 0 Unit cell: (111.375, 149.325, 196.35, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 121 16.00 P 18 15.00 O 3356 8.00 N 2908 7.00 C 13034 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: 1.68 Conformation dependent library (CDL) restraints added in 827.2 milliseconds 4666 Ramachandran restraints generated. 2333 Oldfield, 0 Emsley, 2333 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4300 Finding SS restraints... Secondary structure from input PDB file: 116 helices and 6 sheets defined 79.1% alpha, 1.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'H' and resid 7 through 39 removed outlier: 3.694A pdb=" N LEU H 13 " --> pdb=" O ILE H 9 " (cutoff:3.500A) Processing helix chain 'H' and resid 56 through 69 removed outlier: 3.737A pdb=" N LEU H 60 " --> pdb=" O GLY H 56 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N VAL H 61 " --> pdb=" O SER H 57 " (cutoff:3.500A) Processing helix chain 'H' and resid 81 through 93 Proline residue: H 87 - end of helix Processing helix chain 'H' and resid 95 through 101 removed outlier: 3.751A pdb=" N ILE H 100 " --> pdb=" O ALA H 97 " (cutoff:3.500A) Processing helix chain 'H' and resid 115 through 125 removed outlier: 3.875A pdb=" N PHE H 119 " --> pdb=" O GLY H 115 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU H 120 " --> pdb=" O ILE H 116 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU H 125 " --> pdb=" O MET H 121 " (cutoff:3.500A) Processing helix chain 'H' and resid 126 through 137 removed outlier: 3.935A pdb=" N VAL H 130 " --> pdb=" O ALA H 126 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SER H 137 " --> pdb=" O ALA H 133 " (cutoff:3.500A) Processing helix chain 'H' and resid 139 through 158 Processing helix chain 'H' and resid 159 through 164 removed outlier: 3.917A pdb=" N LEU H 164 " --> pdb=" O LEU H 160 " (cutoff:3.500A) Processing helix chain 'H' and resid 164 through 172 Processing helix chain 'H' and resid 175 through 182 Processing helix chain 'H' and resid 192 through 207 Processing helix chain 'H' and resid 231 through 257 removed outlier: 3.985A pdb=" N GLY H 235 " --> pdb=" O GLY H 231 " (cutoff:3.500A) Processing helix chain 'H' and resid 268 through 285 Processing helix chain 'H' and resid 286 through 288 No H-bonds generated for 'chain 'H' and resid 286 through 288' Processing helix chain 'H' and resid 293 through 304 removed outlier: 3.654A pdb=" N GLY H 301 " --> pdb=" O VAL H 297 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N TRP H 302 " --> pdb=" O MET H 298 " (cutoff:3.500A) Processing helix chain 'H' and resid 305 through 325 removed outlier: 3.582A pdb=" N GLN H 325 " --> pdb=" O LEU H 321 " (cutoff:3.500A) Processing helix chain 'J' and resid 2 through 21 removed outlier: 3.542A pdb=" N TYR J 6 " --> pdb=" O GLU J 2 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N CYS J 8 " --> pdb=" O ALA J 4 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N THR J 21 " --> pdb=" O LEU J 17 " (cutoff:3.500A) Processing helix chain 'J' and resid 24 through 47 Processing helix chain 'J' and resid 48 through 59 removed outlier: 3.595A pdb=" N ILE J 56 " --> pdb=" O GLY J 52 " (cutoff:3.500A) Processing helix chain 'J' and resid 62 through 75 Processing helix chain 'J' and resid 79 through 84 Processing helix chain 'J' and resid 85 through 89 Processing helix chain 'J' and resid 93 through 113 removed outlier: 3.734A pdb=" N GLY J 113 " --> pdb=" O TYR J 109 " (cutoff:3.500A) Processing helix chain 'J' and resid 125 through 134 Processing helix chain 'J' and resid 137 through 158 removed outlier: 3.520A pdb=" N SER J 145 " --> pdb=" O VAL J 141 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N MET J 146 " --> pdb=" O GLU J 142 " (cutoff:3.500A) Processing helix chain 'K' and resid 3 through 25 removed outlier: 3.597A pdb=" N ARG K 25 " --> pdb=" O GLY K 21 " (cutoff:3.500A) Processing helix chain 'K' and resid 27 through 54 Processing helix chain 'K' and resid 56 through 88 Processing helix chain 'K' and resid 91 through 96 removed outlier: 3.905A pdb=" N SER K 96 " --> pdb=" O ASP K 93 " (cutoff:3.500A) Processing helix chain 'M' and resid 4 through 20 Proline residue: M 10 - end of helix Processing helix chain 'M' and resid 21 through 24 Processing helix chain 'M' and resid 27 through 50 Processing helix chain 'M' and resid 84 through 105 removed outlier: 3.614A pdb=" N LEU M 89 " --> pdb=" O GLY M 85 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N MET M 90 " --> pdb=" O LEU M 86 " (cutoff:3.500A) Processing helix chain 'M' and resid 112 through 133 removed outlier: 3.551A pdb=" N PHE M 116 " --> pdb=" O TYR M 112 " (cutoff:3.500A) Processing helix chain 'M' and resid 135 through 144 Processing helix chain 'M' and resid 146 through 157 Processing helix chain 'M' and resid 168 through 201 removed outlier: 3.718A pdb=" N SER M 181 " --> pdb=" O TYR M 177 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLY M 182 " --> pdb=" O THR M 178 " (cutoff:3.500A) Processing helix chain 'M' and resid 216 through 235 removed outlier: 3.727A pdb=" N ALA M 230 " --> pdb=" O GLY M 226 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LYS M 234 " --> pdb=" O ALA M 230 " (cutoff:3.500A) Processing helix chain 'M' and resid 242 through 251 removed outlier: 3.939A pdb=" N ASP M 246 " --> pdb=" O GLY M 242 " (cutoff:3.500A) Processing helix chain 'M' and resid 255 through 260 Processing helix chain 'M' and resid 265 through 275 removed outlier: 3.858A pdb=" N TYR M 269 " --> pdb=" O LYS M 265 " (cutoff:3.500A) Processing helix chain 'M' and resid 279 through 286 Processing helix chain 'M' and resid 286 through 308 Processing helix chain 'M' and resid 310 through 331 removed outlier: 3.665A pdb=" N SER M 319 " --> pdb=" O ILE M 315 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N VAL M 320 " --> pdb=" O ALA M 316 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N PHE M 325 " --> pdb=" O SER M 321 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL M 326 " --> pdb=" O HIS M 322 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N TYR M 331 " --> pdb=" O LEU M 327 " (cutoff:3.500A) Processing helix chain 'M' and resid 334 through 367 Processing helix chain 'M' and resid 370 through 374 Processing helix chain 'M' and resid 376 through 380 Processing helix chain 'M' and resid 383 through 396 Processing helix chain 'M' and resid 402 through 416 removed outlier: 4.146A pdb=" N GLN M 416 " --> pdb=" O PHE M 412 " (cutoff:3.500A) Processing helix chain 'M' and resid 418 through 427 removed outlier: 3.771A pdb=" N PHE M 427 " --> pdb=" O VAL M 423 " (cutoff:3.500A) Processing helix chain 'M' and resid 427 through 445 removed outlier: 3.777A pdb=" N PHE M 431 " --> pdb=" O PHE M 427 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N PHE M 445 " --> pdb=" O HIS M 441 " (cutoff:3.500A) Processing helix chain 'M' and resid 450 through 455 removed outlier: 3.560A pdb=" N SER M 454 " --> pdb=" O GLN M 451 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N GLN M 455 " --> pdb=" O ILE M 452 " (cutoff:3.500A) Processing helix chain 'M' and resid 461 through 481 Processing helix chain 'M' and resid 482 through 489 Processing helix chain 'M' and resid 489 through 502 Processing helix chain 'A' and resid 8 through 36 removed outlier: 3.684A pdb=" N CYS A 27 " --> pdb=" O ALA A 23 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLY A 34 " --> pdb=" O MET A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 90 removed outlier: 3.515A pdb=" N VAL A 71 " --> pdb=" O LYS A 67 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA A 72 " --> pdb=" O PHE A 68 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N TYR A 84 " --> pdb=" O VAL A 80 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N LEU A 85 " --> pdb=" O GLU A 81 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N THR A 90 " --> pdb=" O PHE A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 120 removed outlier: 6.148A pdb=" N TRP A 97 " --> pdb=" O ARG A 93 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N VAL A 98 " --> pdb=" O GLU A 94 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLY A 99 " --> pdb=" O SER A 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 39 through 42 Processing helix chain 'B' and resid 43 through 53 Processing helix chain 'B' and resid 108 through 114 Processing helix chain 'B' and resid 163 through 178 removed outlier: 4.193A pdb=" N GLN B 167 " --> pdb=" O GLU B 163 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ALA B 168 " --> pdb=" O ALA B 164 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N LEU B 169 " --> pdb=" O TYR B 165 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N MET B 170 " --> pdb=" O MET B 166 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LEU B 171 " --> pdb=" O GLN B 167 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N LEU B 172 " --> pdb=" O ALA B 168 " (cutoff:3.500A) Processing helix chain 'L' and resid 5 through 22 Proline residue: L 11 - end of helix removed outlier: 3.910A pdb=" N ARG L 22 " --> pdb=" O LEU L 18 " (cutoff:3.500A) Processing helix chain 'L' and resid 26 through 56 removed outlier: 3.822A pdb=" N VAL L 38 " --> pdb=" O GLY L 34 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLY L 56 " --> pdb=" O PHE L 52 " (cutoff:3.500A) Processing helix chain 'L' and resid 82 through 107 removed outlier: 3.997A pdb=" N TRP L 105 " --> pdb=" O MET L 101 " (cutoff:3.500A) Processing helix chain 'L' and resid 112 through 132 Processing helix chain 'L' and resid 135 through 155 removed outlier: 3.570A pdb=" N GLY L 142 " --> pdb=" O LEU L 138 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLY L 155 " --> pdb=" O TYR L 151 " (cutoff:3.500A) Processing helix chain 'L' and resid 160 through 193 removed outlier: 3.573A pdb=" N GLY L 164 " --> pdb=" O ASP L 160 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLY L 177 " --> pdb=" O VAL L 173 " (cutoff:3.500A) Processing helix chain 'L' and resid 196 through 208 Proline residue: L 205 - end of helix Processing helix chain 'L' and resid 212 through 230 removed outlier: 3.508A pdb=" N MET L 216 " --> pdb=" O ASN L 212 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLY L 228 " --> pdb=" O GLY L 224 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LYS L 229 " --> pdb=" O GLY L 225 " (cutoff:3.500A) Processing helix chain 'L' and resid 240 through 245 removed outlier: 4.098A pdb=" N MET L 243 " --> pdb=" O ALA L 240 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ALA L 244 " --> pdb=" O ASP L 241 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N GLY L 245 " --> pdb=" O ALA L 242 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 240 through 245' Processing helix chain 'L' and resid 246 through 256 Processing helix chain 'L' and resid 258 through 269 removed outlier: 4.239A pdb=" N GLY L 262 " --> pdb=" O MET L 258 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N VAL L 263 " --> pdb=" O VAL L 259 " (cutoff:3.500A) Processing helix chain 'L' and resid 269 through 275 removed outlier: 3.715A pdb=" N MET L 275 " --> pdb=" O GLY L 271 " (cutoff:3.500A) Processing helix chain 'L' and resid 276 through 299 Processing helix chain 'L' and resid 303 through 325 Processing helix chain 'L' and resid 327 through 353 removed outlier: 3.866A pdb=" N ALA L 343 " --> pdb=" O ALA L 339 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N SER L 351 " --> pdb=" O LEU L 347 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N VAL L 352 " --> pdb=" O ALA L 348 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ILE L 353 " --> pdb=" O SER L 349 " (cutoff:3.500A) Processing helix chain 'L' and resid 354 through 359 removed outlier: 6.471A pdb=" N HIS L 357 " --> pdb=" O LEU L 354 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLU L 359 " --> pdb=" O CYS L 356 " (cutoff:3.500A) Processing helix chain 'L' and resid 361 through 365 Processing helix chain 'L' and resid 367 through 372 removed outlier: 4.024A pdb=" N SER L 371 " --> pdb=" O GLY L 367 " (cutoff:3.500A) Processing helix chain 'L' and resid 374 through 387 removed outlier: 3.898A pdb=" N CYS L 378 " --> pdb=" O LEU L 374 " (cutoff:3.500A) Processing helix chain 'L' and resid 393 through 409 removed outlier: 4.038A pdb=" N PHE L 397 " --> pdb=" O THR L 393 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ILE L 402 " --> pdb=" O SER L 398 " (cutoff:3.500A) Processing helix chain 'L' and resid 411 through 437 removed outlier: 3.531A pdb=" N MET L 432 " --> pdb=" O TYR L 428 " (cutoff:3.500A) Processing helix chain 'L' and resid 454 through 465 removed outlier: 3.521A pdb=" N THR L 465 " --> pdb=" O LEU L 461 " (cutoff:3.500A) Processing helix chain 'L' and resid 466 through 471 removed outlier: 3.646A pdb=" N ILE L 471 " --> pdb=" O GLY L 468 " (cutoff:3.500A) Processing helix chain 'L' and resid 489 through 496 Processing helix chain 'L' and resid 497 through 512 Processing helix chain 'L' and resid 518 through 524 Processing helix chain 'L' and resid 525 through 537 removed outlier: 3.643A pdb=" N ASN L 537 " --> pdb=" O THR L 533 " (cutoff:3.500A) Processing helix chain 'L' and resid 540 through 549 Processing helix chain 'L' and resid 549 through 560 Processing helix chain 'L' and resid 563 through 570 Processing helix chain 'L' and resid 570 through 584 Processing helix chain 'L' and resid 590 through 613 Processing helix chain 'N' and resid 6 through 11 removed outlier: 4.022A pdb=" N ALA N 10 " --> pdb=" O GLN N 6 " (cutoff:3.500A) Processing helix chain 'N' and resid 11 through 31 Processing helix chain 'N' and resid 33 through 51 Processing helix chain 'N' and resid 51 through 59 Processing helix chain 'N' and resid 70 through 97 removed outlier: 3.518A pdb=" N LEU N 75 " --> pdb=" O GLY N 71 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N TYR N 76 " --> pdb=" O PHE N 72 " (cutoff:3.500A) Proline residue: N 93 - end of helix removed outlier: 4.363A pdb=" N GLY N 97 " --> pdb=" O PRO N 93 " (cutoff:3.500A) Processing helix chain 'N' and resid 103 through 121 removed outlier: 3.736A pdb=" N LEU N 107 " --> pdb=" O ASP N 103 " (cutoff:3.500A) Processing helix chain 'N' and resid 124 through 144 Proline residue: N 138 - end of helix removed outlier: 3.822A pdb=" N GLY N 141 " --> pdb=" O LEU N 137 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLY N 144 " --> pdb=" O PHE N 140 " (cutoff:3.500A) Processing helix chain 'N' and resid 149 through 182 Processing helix chain 'N' and resid 185 through 189 Processing helix chain 'N' and resid 200 through 218 removed outlier: 3.572A pdb=" N PHE N 216 " --> pdb=" O VAL N 212 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N LYS N 217 " --> pdb=" O GLY N 213 " (cutoff:3.500A) Processing helix chain 'N' and resid 226 through 234 Processing helix chain 'N' and resid 235 through 261 removed outlier: 4.151A pdb=" N SER N 246 " --> pdb=" O LEU N 242 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N LYS N 247 " --> pdb=" O ALA N 243 " (cutoff:3.500A) Processing helix chain 'N' and resid 262 through 265 Processing helix chain 'N' and resid 266 through 288 removed outlier: 3.855A pdb=" N ASN N 285 " --> pdb=" O ILE N 281 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA N 288 " --> pdb=" O GLY N 284 " (cutoff:3.500A) Processing helix chain 'N' and resid 293 through 315 removed outlier: 3.547A pdb=" N ILE N 303 " --> pdb=" O GLY N 299 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N SER N 304 " --> pdb=" O TYR N 300 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLY N 307 " --> pdb=" O ILE N 303 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N TYR N 308 " --> pdb=" O SER N 304 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N LEU N 309 " --> pdb=" O HIS N 305 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALA N 312 " --> pdb=" O TYR N 308 " (cutoff:3.500A) Processing helix chain 'N' and resid 321 through 348 removed outlier: 3.584A pdb=" N GLY N 327 " --> pdb=" O MET N 323 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VAL N 328 " --> pdb=" O GLU N 324 " (cutoff:3.500A) Processing helix chain 'N' and resid 364 through 368 Processing helix chain 'N' and resid 369 through 384 Processing helix chain 'N' and resid 389 through 405 Processing helix chain 'N' and resid 407 through 431 removed outlier: 4.110A pdb=" N TYR N 423 " --> pdb=" O ALA N 419 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N TYR N 424 " --> pdb=" O ILE N 420 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL N 428 " --> pdb=" O TYR N 424 " (cutoff:3.500A) Processing helix chain 'N' and resid 447 through 470 Processing helix chain 'N' and resid 471 through 481 Processing sheet with id=AA1, first strand: chain 'M' and resid 65 through 67 removed outlier: 3.862A pdb=" N SER M 65 " --> pdb=" O ILE M 83 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'M' and resid 70 through 72 Processing sheet with id=AA3, first strand: chain 'B' and resid 95 through 96 Processing sheet with id=AA4, first strand: chain 'L' and resid 60 through 62 Processing sheet with id=AA5, first strand: chain 'L' and resid 66 through 70 Processing sheet with id=AA6, first strand: chain 'N' and resid 61 through 63 removed outlier: 3.531A pdb=" N MET N 67 " --> pdb=" O VAL N 63 " (cutoff:3.500A) 1301 hydrogen bonds defined for protein. 3812 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.40 Time building geometry restraints manager: 2.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2763 1.31 - 1.44: 5380 1.44 - 1.56: 11321 1.56 - 1.69: 36 1.69 - 1.82: 229 Bond restraints: 19729 Sorted by residual: bond pdb=" C3 UQ8 N 506 " pdb=" C4 UQ8 N 506 " ideal model delta sigma weight residual 1.339 1.480 -0.141 2.00e-02 2.50e+03 4.97e+01 bond pdb=" C1 UQ8 N 506 " pdb=" C6 UQ8 N 506 " ideal model delta sigma weight residual 1.345 1.481 -0.136 2.00e-02 2.50e+03 4.64e+01 bond pdb=" C21 3PE A 502 " pdb=" O21 3PE A 502 " ideal model delta sigma weight residual 1.316 1.450 -0.134 2.00e-02 2.50e+03 4.50e+01 bond pdb=" C3 UQ8 N 502 " pdb=" C4 UQ8 N 502 " ideal model delta sigma weight residual 1.339 1.468 -0.129 2.00e-02 2.50e+03 4.19e+01 bond pdb=" C1 UQ8 N 502 " pdb=" C6 UQ8 N 502 " ideal model delta sigma weight residual 1.345 1.474 -0.129 2.00e-02 2.50e+03 4.18e+01 ... (remaining 19724 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.54: 26207 2.54 - 5.08: 315 5.08 - 7.62: 66 7.62 - 10.16: 19 10.16 - 12.70: 5 Bond angle restraints: 26612 Sorted by residual: angle pdb=" N ASN L 361 " pdb=" CA ASN L 361 " pdb=" C ASN L 361 " ideal model delta sigma weight residual 109.24 101.92 7.32 1.63e+00 3.76e-01 2.02e+01 angle pdb=" OB3 CDL L 703 " pdb=" PB2 CDL L 703 " pdb=" OB4 CDL L 703 " ideal model delta sigma weight residual 121.80 109.10 12.70 3.00e+00 1.11e-01 1.79e+01 angle pdb=" N PHE H 282 " pdb=" CA PHE H 282 " pdb=" C PHE H 282 " ideal model delta sigma weight residual 113.28 108.15 5.13 1.22e+00 6.72e-01 1.77e+01 angle pdb=" OB2 CDL L 703 " pdb=" PB2 CDL L 703 " pdb=" OB5 CDL L 703 " ideal model delta sigma weight residual 96.70 109.29 -12.59 3.00e+00 1.11e-01 1.76e+01 angle pdb=" C MET H 281 " pdb=" CA MET H 281 " pdb=" CB MET H 281 " ideal model delta sigma weight residual 109.72 101.70 8.02 1.92e+00 2.71e-01 1.74e+01 ... (remaining 26607 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.00: 11049 34.00 - 68.00: 563 68.00 - 102.00: 38 102.00 - 136.00: 6 136.00 - 170.00: 1 Dihedral angle restraints: 11657 sinusoidal: 4932 harmonic: 6725 Sorted by residual: dihedral pdb=" C MET H 281 " pdb=" N MET H 281 " pdb=" CA MET H 281 " pdb=" CB MET H 281 " ideal model delta harmonic sigma weight residual -122.60 -110.94 -11.66 0 2.50e+00 1.60e-01 2.17e+01 dihedral pdb=" O21 3PE M 602 " pdb=" C2 3PE M 602 " pdb=" C3 3PE M 602 " pdb=" O31 3PE M 602 " ideal model delta sinusoidal sigma weight residual 60.47 -109.53 170.00 1 3.00e+01 1.11e-03 2.12e+01 dihedral pdb=" O21 3PE J 202 " pdb=" C2 3PE J 202 " pdb=" C3 3PE J 202 " pdb=" O31 3PE J 202 " ideal model delta sinusoidal sigma weight residual 60.47 178.69 -118.22 1 3.00e+01 1.11e-03 1.57e+01 ... (remaining 11654 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 2362 0.045 - 0.091: 567 0.091 - 0.136: 80 0.136 - 0.181: 3 0.181 - 0.227: 1 Chirality restraints: 3013 Sorted by residual: chirality pdb=" CA MET H 281 " pdb=" N MET H 281 " pdb=" C MET H 281 " pdb=" CB MET H 281 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.28e+00 chirality pdb=" CA PHE H 238 " pdb=" N PHE H 238 " pdb=" C PHE H 238 " pdb=" CB PHE H 238 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.04e-01 chirality pdb=" CA THR N 227 " pdb=" N THR N 227 " pdb=" C THR N 227 " pdb=" CB THR N 227 " both_signs ideal model delta sigma weight residual False 2.53 2.39 0.14 2.00e-01 2.50e+01 4.83e-01 ... (remaining 3010 not shown) Planarity restraints: 3143 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER L 497 " 0.016 2.00e-02 2.50e+03 3.29e-02 1.08e+01 pdb=" C SER L 497 " -0.057 2.00e-02 2.50e+03 pdb=" O SER L 497 " 0.021 2.00e-02 2.50e+03 pdb=" N GLY L 498 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE L 372 " -0.042 5.00e-02 4.00e+02 6.52e-02 6.81e+00 pdb=" N PRO L 373 " 0.113 5.00e-02 4.00e+02 pdb=" CA PRO L 373 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO L 373 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 107 " 0.032 5.00e-02 4.00e+02 4.87e-02 3.80e+00 pdb=" N PRO B 108 " -0.084 5.00e-02 4.00e+02 pdb=" CA PRO B 108 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 108 " 0.028 5.00e-02 4.00e+02 ... (remaining 3140 not shown) Histogram of nonbonded interaction distances: 2.48 - 2.97: 8781 2.97 - 3.45: 20660 3.45 - 3.93: 33469 3.93 - 4.42: 39755 4.42 - 4.90: 63168 Nonbonded interactions: 165833 Sorted by model distance: nonbonded pdb=" O21 3PE L 704 " pdb=" O31 3PE L 704 " model vdw 2.483 2.432 nonbonded pdb=" OB2 CDL L 703 " pdb=" CA2 CDL L 703 " model vdw 2.546 2.752 nonbonded pdb=" O THR L 482 " pdb=" OG1 THR L 483 " model vdw 2.555 3.040 nonbonded pdb=" O21 3PE N 505 " pdb=" O31 3PE N 505 " model vdw 2.560 2.432 nonbonded pdb=" N GLY L 488 " pdb=" N SER L 489 " model vdw 2.563 2.560 ... (remaining 165828 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=0.47 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: 33.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.400 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 16.800 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.050 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:8.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9145 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 0.141 19729 Z= 0.183 Angle : 0.696 12.696 26612 Z= 0.307 Chirality : 0.037 0.227 3013 Planarity : 0.003 0.065 3143 Dihedral : 18.471 170.001 7357 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.29 % Favored : 95.67 % Rotamer: Outliers : 1.47 % Allowed : 18.35 % Favored : 80.18 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.68 (0.18), residues: 2333 helix: 1.89 (0.12), residues: 1713 sheet: -0.22 (1.08), residues: 28 loop : -1.16 (0.27), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG H 80 TYR 0.022 0.001 TYR M 435 PHE 0.023 0.001 PHE L 341 TRP 0.018 0.001 TRP B 122 HIS 0.002 0.000 HIS M 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.18 (19729) covalent geometry : angle 0.69555 / 0.31 (26612) hydrogen bonds : bond 0.15792 / 10.51 ( 1301) hydrogen bonds : angle 5.41281 / 3.81 ( 3812) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4666 Ramachandran restraints generated. 2333 Oldfield, 0 Emsley, 2333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4666 Ramachandran restraints generated. 2333 Oldfield, 0 Emsley, 2333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 277 time to evaluate : 0.670 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 7 GLU cc_start: 0.8978 (mp0) cc_final: 0.8631 (mp0) REVERT: H 71 GLU cc_start: 0.8138 (tt0) cc_final: 0.7118 (mm-30) REVERT: H 286 ARG cc_start: 0.8520 (tpt-90) cc_final: 0.8035 (tpt-90) REVERT: K 94 SER cc_start: 0.9312 (m) cc_final: 0.8933 (p) REVERT: M 22 ARG cc_start: 0.8637 (mtp180) cc_final: 0.7098 (mmt180) REVERT: M 150 MET cc_start: 0.9047 (tpp) cc_final: 0.8835 (mmt) REVERT: M 303 TRP cc_start: 0.9498 (OUTLIER) cc_final: 0.8232 (m-10) REVERT: M 373 MET cc_start: 0.9281 (mmm) cc_final: 0.9080 (mmt) REVERT: B 45 MET cc_start: 0.6185 (OUTLIER) cc_final: 0.5401 (pmm) REVERT: B 47 ASN cc_start: 0.9451 (OUTLIER) cc_final: 0.9202 (m-40) REVERT: B 119 GLU cc_start: 0.8794 (mm-30) cc_final: 0.8491 (tp30) REVERT: B 173 GLN cc_start: 0.8553 (tt0) cc_final: 0.8114 (tm-30) REVERT: B 179 GLU cc_start: 0.8534 (pt0) cc_final: 0.7482 (pm20) REVERT: B 180 ARG cc_start: 0.7455 (mmp80) cc_final: 0.6572 (ppt-90) REVERT: L 58 GLN cc_start: 0.8747 (mt0) cc_final: 0.8414 (mm110) REVERT: L 578 PHE cc_start: 0.8321 (m-10) cc_final: 0.7829 (t80) REVERT: N 104 GLU cc_start: 0.9076 (mp0) cc_final: 0.8861 (mp0) REVERT: N 323 MET cc_start: 0.7832 (ptt) cc_final: 0.7587 (ptp) outliers start: 28 outliers final: 12 residues processed: 295 average time/residue: 0.5991 time to fit residues: 198.1667 Evaluate side-chains 266 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 251 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 245 ILE Chi-restraints excluded: chain J residue 69 PHE Chi-restraints excluded: chain K residue 16 VAL Chi-restraints excluded: chain K residue 46 PHE Chi-restraints excluded: chain M residue 303 TRP Chi-restraints excluded: chain M residue 418 VAL Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 47 ASN Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 258 MET Chi-restraints excluded: chain L residue 472 VAL Chi-restraints excluded: chain N residue 253 VAL Chi-restraints excluded: chain N residue 430 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 216 optimal weight: 0.3980 chunk 98 optimal weight: 0.6980 chunk 194 optimal weight: 0.9980 chunk 227 optimal weight: 2.9990 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 2.9990 chunk 200 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 323 GLN J 115 ASN M 206 ASN L 481 GLN N 317 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.087781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.066583 restraints weight = 38623.776| |-----------------------------------------------------------------------------| r_work (start): 0.2852 rms_B_bonded: 2.20 r_work: 0.2736 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2619 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2619 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2624 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2624 r_free = 0.2624 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2624 r_free = 0.2624 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.2624 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8856 moved from start: 0.0845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 19729 Z= 0.140 Angle : 0.522 7.479 26612 Z= 0.265 Chirality : 0.038 0.148 3013 Planarity : 0.004 0.067 3143 Dihedral : 15.785 169.596 3470 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 2.89 % Allowed : 19.61 % Favored : 77.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.03 (0.18), residues: 2333 helix: 2.07 (0.12), residues: 1753 sheet: -0.12 (1.09), residues: 28 loop : -1.01 (0.28), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 91 TYR 0.021 0.001 TYR M 435 PHE 0.024 0.001 PHE L 341 TRP 0.013 0.001 TRP L 143 HIS 0.004 0.001 HIS L 411 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.14 (19729) covalent geometry : angle 0.52189 / 0.26 (26612) hydrogen bonds : bond 0.04799 / 3.19 ( 1301) hydrogen bonds : angle 4.19080 / 2.94 ( 3812) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4666 Ramachandran restraints generated. 2333 Oldfield, 0 Emsley, 2333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4666 Ramachandran restraints generated. 2333 Oldfield, 0 Emsley, 2333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 269 time to evaluate : 0.665 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 7 GLU cc_start: 0.8933 (mp0) cc_final: 0.8726 (mp0) REVERT: H 71 GLU cc_start: 0.7821 (tt0) cc_final: 0.6651 (mm-30) REVERT: K 94 SER cc_start: 0.8788 (m) cc_final: 0.8322 (p) REVERT: M 22 ARG cc_start: 0.8703 (mtp180) cc_final: 0.6870 (mmt180) REVERT: M 36 MET cc_start: 0.8953 (OUTLIER) cc_final: 0.8508 (mmm) REVERT: M 150 MET cc_start: 0.8841 (tpp) cc_final: 0.8466 (mmt) REVERT: M 303 TRP cc_start: 0.9208 (OUTLIER) cc_final: 0.8039 (m-10) REVERT: M 373 MET cc_start: 0.8964 (mmm) cc_final: 0.8726 (mmt) REVERT: B 45 MET cc_start: 0.6497 (mmt) cc_final: 0.5742 (pmm) REVERT: B 91 ARG cc_start: 0.8234 (mmt180) cc_final: 0.7946 (mmt180) REVERT: B 119 GLU cc_start: 0.8594 (mm-30) cc_final: 0.7961 (tp30) REVERT: B 122 TRP cc_start: 0.8747 (m-90) cc_final: 0.8455 (m-90) REVERT: B 173 GLN cc_start: 0.8421 (tt0) cc_final: 0.7883 (tm-30) REVERT: B 179 GLU cc_start: 0.8607 (pt0) cc_final: 0.7455 (tm-30) REVERT: B 180 ARG cc_start: 0.7330 (mmp80) cc_final: 0.6516 (ppt-90) REVERT: B 181 ARG cc_start: 0.7675 (tpp-160) cc_final: 0.6696 (tpt-90) REVERT: L 58 GLN cc_start: 0.8605 (mt0) cc_final: 0.7993 (mm110) REVERT: L 275 MET cc_start: 0.9124 (mtt) cc_final: 0.8895 (mtt) REVERT: L 359 GLU cc_start: 0.6959 (OUTLIER) cc_final: 0.6624 (pm20) REVERT: L 578 PHE cc_start: 0.8112 (m-10) cc_final: 0.7221 (t80) REVERT: N 104 GLU cc_start: 0.9263 (mp0) cc_final: 0.8672 (mp0) outliers start: 55 outliers final: 18 residues processed: 301 average time/residue: 0.5770 time to fit residues: 195.6274 Evaluate side-chains 274 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 253 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 245 ILE Chi-restraints excluded: chain J residue 69 PHE Chi-restraints excluded: chain K residue 46 PHE Chi-restraints excluded: chain M residue 25 VAL Chi-restraints excluded: chain M residue 36 MET Chi-restraints excluded: chain M residue 212 ASN Chi-restraints excluded: chain M residue 303 TRP Chi-restraints excluded: chain M residue 407 GLU Chi-restraints excluded: chain B residue 44 ASP Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain L residue 214 MET Chi-restraints excluded: chain L residue 247 THR Chi-restraints excluded: chain L residue 359 GLU Chi-restraints excluded: chain L residue 598 MET Chi-restraints excluded: chain L residue 599 SER Chi-restraints excluded: chain N residue 135 ILE Chi-restraints excluded: chain N residue 197 MET Chi-restraints excluded: chain N residue 257 LEU Chi-restraints excluded: chain N residue 477 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 74 optimal weight: 0.7980 chunk 69 optimal weight: 0.8980 chunk 133 optimal weight: 0.5980 chunk 71 optimal weight: 0.7980 chunk 166 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 210 optimal weight: 0.9980 chunk 1 optimal weight: 0.7980 chunk 78 optimal weight: 0.7980 chunk 49 optimal weight: 0.5980 chunk 179 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... J 115 ASN N 317 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.087894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.066529 restraints weight = 39469.325| |-----------------------------------------------------------------------------| r_work (start): 0.2816 rms_B_bonded: 2.24 r_work: 0.2694 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2575 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2575 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2617 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2617 r_free = 0.2617 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2617 r_free = 0.2617 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.2617 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8824 moved from start: 0.0989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 19729 Z= 0.134 Angle : 0.508 7.836 26612 Z= 0.256 Chirality : 0.038 0.149 3013 Planarity : 0.004 0.052 3143 Dihedral : 15.356 169.351 3455 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 2.68 % Allowed : 20.56 % Favored : 76.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.11 (0.18), residues: 2333 helix: 2.15 (0.12), residues: 1750 sheet: -0.20 (1.06), residues: 28 loop : -1.03 (0.28), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 91 TYR 0.022 0.001 TYR M 435 PHE 0.024 0.001 PHE L 341 TRP 0.013 0.001 TRP L 143 HIS 0.003 0.001 HIS N 124 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.13 (19729) covalent geometry : angle 0.50821 / 0.26 (26612) hydrogen bonds : bond 0.04403 / 2.93 ( 1301) hydrogen bonds : angle 4.03284 / 2.83 ( 3812) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4666 Ramachandran restraints generated. 2333 Oldfield, 0 Emsley, 2333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4666 Ramachandran restraints generated. 2333 Oldfield, 0 Emsley, 2333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 262 time to evaluate : 0.530 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 71 GLU cc_start: 0.7775 (tt0) cc_final: 0.6618 (mm-30) REVERT: H 88 MET cc_start: 0.8655 (mtp) cc_final: 0.8446 (mtm) REVERT: H 286 ARG cc_start: 0.8075 (tpt-90) cc_final: 0.7658 (tpt-90) REVERT: K 94 SER cc_start: 0.8772 (m) cc_final: 0.8334 (p) REVERT: M 22 ARG cc_start: 0.8688 (mtp180) cc_final: 0.6865 (mmt180) REVERT: M 144 GLU cc_start: 0.9152 (OUTLIER) cc_final: 0.7970 (mt-10) REVERT: M 150 MET cc_start: 0.8820 (tpp) cc_final: 0.8421 (mmt) REVERT: M 303 TRP cc_start: 0.9193 (OUTLIER) cc_final: 0.8034 (m-10) REVERT: M 373 MET cc_start: 0.8924 (mmm) cc_final: 0.8657 (mmt) REVERT: B 45 MET cc_start: 0.6551 (mmt) cc_final: 0.5737 (pmm) REVERT: B 91 ARG cc_start: 0.8264 (mmt180) cc_final: 0.7915 (mmt180) REVERT: B 119 GLU cc_start: 0.8571 (mm-30) cc_final: 0.7946 (tp30) REVERT: B 122 TRP cc_start: 0.8711 (m-90) cc_final: 0.8421 (m-90) REVERT: B 171 LEU cc_start: 0.9476 (mp) cc_final: 0.8982 (tm) REVERT: B 173 GLN cc_start: 0.8399 (tt0) cc_final: 0.7863 (tm-30) REVERT: B 179 GLU cc_start: 0.8578 (pt0) cc_final: 0.6957 (pm20) REVERT: B 180 ARG cc_start: 0.7332 (mmp80) cc_final: 0.6465 (ppt-90) REVERT: B 181 ARG cc_start: 0.7636 (tpp-160) cc_final: 0.7362 (tpt-90) REVERT: L 58 GLN cc_start: 0.8551 (mt0) cc_final: 0.7916 (mm110) REVERT: L 111 GLU cc_start: 0.7681 (OUTLIER) cc_final: 0.7472 (pm20) REVERT: L 359 GLU cc_start: 0.6882 (OUTLIER) cc_final: 0.6572 (pm20) REVERT: L 578 PHE cc_start: 0.8081 (m-10) cc_final: 0.7197 (t80) REVERT: N 104 GLU cc_start: 0.9253 (mp0) cc_final: 0.8627 (mp0) outliers start: 51 outliers final: 26 residues processed: 293 average time/residue: 0.5800 time to fit residues: 191.3449 Evaluate side-chains 276 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 246 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 67 MET Chi-restraints excluded: chain H residue 245 ILE Chi-restraints excluded: chain J residue 69 PHE Chi-restraints excluded: chain J residue 91 GLN Chi-restraints excluded: chain K residue 16 VAL Chi-restraints excluded: chain K residue 46 PHE Chi-restraints excluded: chain M residue 25 VAL Chi-restraints excluded: chain M residue 144 GLU Chi-restraints excluded: chain M residue 212 ASN Chi-restraints excluded: chain M residue 303 TRP Chi-restraints excluded: chain M residue 407 GLU Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain L residue 111 GLU Chi-restraints excluded: chain L residue 214 MET Chi-restraints excluded: chain L residue 247 THR Chi-restraints excluded: chain L residue 359 GLU Chi-restraints excluded: chain L residue 568 MET Chi-restraints excluded: chain L residue 598 MET Chi-restraints excluded: chain L residue 599 SER Chi-restraints excluded: chain N residue 51 SER Chi-restraints excluded: chain N residue 135 ILE Chi-restraints excluded: chain N residue 197 MET Chi-restraints excluded: chain N residue 257 LEU Chi-restraints excluded: chain N residue 355 ASP Chi-restraints excluded: chain N residue 477 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 11 optimal weight: 0.5980 chunk 133 optimal weight: 0.7980 chunk 167 optimal weight: 10.0000 chunk 69 optimal weight: 0.5980 chunk 204 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 chunk 71 optimal weight: 0.9990 chunk 118 optimal weight: 0.4980 chunk 49 optimal weight: 0.5980 chunk 230 optimal weight: 0.9990 chunk 104 optimal weight: 0.0000 overall best weight: 0.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... J 115 ASN L 481 GLN N 317 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.088816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.067347 restraints weight = 42327.741| |-----------------------------------------------------------------------------| r_work (start): 0.2836 rms_B_bonded: 2.32 r_work: 0.2713 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2594 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2594 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2639 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2639 r_free = 0.2639 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2639 r_free = 0.2639 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (7 function evaluations) r_final: 0.2639 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8791 moved from start: 0.1157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 19729 Z= 0.113 Angle : 0.490 7.641 26612 Z= 0.249 Chirality : 0.038 0.149 3013 Planarity : 0.004 0.054 3143 Dihedral : 14.912 169.103 3455 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 2.47 % Allowed : 21.29 % Favored : 76.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.21 (0.18), residues: 2333 helix: 2.24 (0.12), residues: 1751 sheet: -0.26 (1.04), residues: 28 loop : -1.05 (0.28), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 209 TYR 0.023 0.001 TYR M 435 PHE 0.023 0.001 PHE L 341 TRP 0.013 0.001 TRP L 143 HIS 0.002 0.000 HIS H 210 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.11 (19729) covalent geometry : angle 0.49022 / 0.25 (26612) hydrogen bonds : bond 0.04006 / 2.66 ( 1301) hydrogen bonds : angle 3.89436 / 2.74 ( 3812) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4666 Ramachandran restraints generated. 2333 Oldfield, 0 Emsley, 2333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4666 Ramachandran restraints generated. 2333 Oldfield, 0 Emsley, 2333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 262 time to evaluate : 0.692 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 71 GLU cc_start: 0.7736 (tt0) cc_final: 0.6610 (mm-30) REVERT: H 141 TYR cc_start: 0.7498 (m-80) cc_final: 0.7117 (m-10) REVERT: H 286 ARG cc_start: 0.8074 (tpt-90) cc_final: 0.7724 (tpt-90) REVERT: K 94 SER cc_start: 0.8715 (m) cc_final: 0.8270 (p) REVERT: M 22 ARG cc_start: 0.8684 (mtp180) cc_final: 0.6858 (mmt180) REVERT: M 115 PHE cc_start: 0.7582 (t80) cc_final: 0.7176 (m-80) REVERT: M 146 MET cc_start: 0.8932 (pmm) cc_final: 0.8690 (pmt) REVERT: M 150 MET cc_start: 0.8796 (tpp) cc_final: 0.8347 (mmt) REVERT: M 303 TRP cc_start: 0.9155 (OUTLIER) cc_final: 0.8100 (m-10) REVERT: M 373 MET cc_start: 0.8903 (mmm) cc_final: 0.8665 (mmt) REVERT: B 45 MET cc_start: 0.6476 (mmt) cc_final: 0.5768 (pmm) REVERT: B 91 ARG cc_start: 0.8315 (mmt180) cc_final: 0.7841 (mmt180) REVERT: B 119 GLU cc_start: 0.8566 (mm-30) cc_final: 0.7958 (tp30) REVERT: B 122 TRP cc_start: 0.8700 (m-90) cc_final: 0.8431 (m-90) REVERT: B 171 LEU cc_start: 0.9471 (mp) cc_final: 0.8977 (tm) REVERT: B 173 GLN cc_start: 0.8378 (tt0) cc_final: 0.7842 (tm-30) REVERT: B 179 GLU cc_start: 0.8602 (pt0) cc_final: 0.7462 (tm-30) REVERT: B 180 ARG cc_start: 0.7365 (mmp80) cc_final: 0.6602 (ppt-90) REVERT: B 181 ARG cc_start: 0.7629 (tpp-160) cc_final: 0.6820 (tpt-90) REVERT: L 58 GLN cc_start: 0.8552 (mt0) cc_final: 0.7894 (mm110) REVERT: L 359 GLU cc_start: 0.6844 (OUTLIER) cc_final: 0.6503 (pm20) REVERT: L 578 PHE cc_start: 0.8139 (m-10) cc_final: 0.7202 (t80) REVERT: N 104 GLU cc_start: 0.9254 (mp0) cc_final: 0.8604 (mp0) outliers start: 47 outliers final: 22 residues processed: 289 average time/residue: 0.6411 time to fit residues: 208.0644 Evaluate side-chains 272 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 248 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain H residue 245 ILE Chi-restraints excluded: chain J residue 69 PHE Chi-restraints excluded: chain J residue 138 VAL Chi-restraints excluded: chain K residue 16 VAL Chi-restraints excluded: chain K residue 46 PHE Chi-restraints excluded: chain M residue 25 VAL Chi-restraints excluded: chain M residue 212 ASN Chi-restraints excluded: chain M residue 237 VAL Chi-restraints excluded: chain M residue 303 TRP Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain L residue 247 THR Chi-restraints excluded: chain L residue 359 GLU Chi-restraints excluded: chain L residue 568 MET Chi-restraints excluded: chain L residue 598 MET Chi-restraints excluded: chain L residue 599 SER Chi-restraints excluded: chain N residue 135 ILE Chi-restraints excluded: chain N residue 197 MET Chi-restraints excluded: chain N residue 257 LEU Chi-restraints excluded: chain N residue 263 VAL Chi-restraints excluded: chain N residue 477 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 5 optimal weight: 0.0570 chunk 67 optimal weight: 0.4980 chunk 11 optimal weight: 1.9990 chunk 231 optimal weight: 2.9990 chunk 61 optimal weight: 4.9990 chunk 229 optimal weight: 0.9990 chunk 162 optimal weight: 3.9990 chunk 72 optimal weight: 5.9990 chunk 120 optimal weight: 4.9990 chunk 49 optimal weight: 1.9990 chunk 127 optimal weight: 3.9990 overall best weight: 1.1104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... J 115 ASN L 481 GLN N 317 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.086426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.064484 restraints weight = 47566.132| |-----------------------------------------------------------------------------| r_work (start): 0.2812 rms_B_bonded: 2.43 r_work: 0.2691 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2691 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2686 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2686 r_free = 0.2686 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2686 r_free = 0.2686 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.2686 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8829 moved from start: 0.1216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 19729 Z= 0.173 Angle : 0.538 8.746 26612 Z= 0.271 Chirality : 0.039 0.162 3013 Planarity : 0.004 0.055 3143 Dihedral : 14.913 168.944 3455 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 2.68 % Allowed : 21.19 % Favored : 76.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.17 (0.18), residues: 2333 helix: 2.20 (0.12), residues: 1750 sheet: -0.40 (1.01), residues: 28 loop : -1.03 (0.28), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 209 TYR 0.021 0.001 TYR M 435 PHE 0.024 0.001 PHE L 341 TRP 0.013 0.001 TRP L 143 HIS 0.004 0.001 HIS N 124 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.17 (19729) covalent geometry : angle 0.53846 / 0.27 (26612) hydrogen bonds : bond 0.04465 / 2.97 ( 1301) hydrogen bonds : angle 3.98109 / 2.80 ( 3812) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4666 Ramachandran restraints generated. 2333 Oldfield, 0 Emsley, 2333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4666 Ramachandran restraints generated. 2333 Oldfield, 0 Emsley, 2333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 250 time to evaluate : 0.797 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 71 GLU cc_start: 0.7721 (tt0) cc_final: 0.6583 (mm-30) REVERT: H 141 TYR cc_start: 0.7597 (m-80) cc_final: 0.7244 (m-10) REVERT: H 281 MET cc_start: 0.8590 (tpp) cc_final: 0.8360 (mpp) REVERT: H 294 TYR cc_start: 0.8560 (t80) cc_final: 0.8325 (t80) REVERT: K 94 SER cc_start: 0.8805 (m) cc_final: 0.8323 (p) REVERT: M 22 ARG cc_start: 0.8638 (mtp180) cc_final: 0.6877 (mmt180) REVERT: M 115 PHE cc_start: 0.7598 (t80) cc_final: 0.7234 (m-80) REVERT: M 146 MET cc_start: 0.8893 (pmm) cc_final: 0.8658 (pmt) REVERT: M 150 MET cc_start: 0.8781 (tpp) cc_final: 0.8316 (mmt) REVERT: M 303 TRP cc_start: 0.9159 (OUTLIER) cc_final: 0.8005 (m-10) REVERT: M 373 MET cc_start: 0.8921 (mmm) cc_final: 0.8677 (mmt) REVERT: B 45 MET cc_start: 0.6452 (mmt) cc_final: 0.5697 (pmm) REVERT: B 91 ARG cc_start: 0.8275 (mmt180) cc_final: 0.7739 (mmt180) REVERT: B 116 GLN cc_start: 0.7500 (OUTLIER) cc_final: 0.7103 (mp10) REVERT: B 119 GLU cc_start: 0.8463 (mm-30) cc_final: 0.7968 (tp30) REVERT: B 122 TRP cc_start: 0.8648 (m-90) cc_final: 0.8354 (m-90) REVERT: B 173 GLN cc_start: 0.8415 (tt0) cc_final: 0.7883 (tm-30) REVERT: B 179 GLU cc_start: 0.8574 (pt0) cc_final: 0.7468 (tm-30) REVERT: B 180 ARG cc_start: 0.7422 (mmp80) cc_final: 0.6676 (ppt-90) REVERT: L 58 GLN cc_start: 0.8500 (mt0) cc_final: 0.7859 (mm110) REVERT: L 359 GLU cc_start: 0.6795 (OUTLIER) cc_final: 0.6413 (pm20) REVERT: L 547 LYS cc_start: 0.8830 (OUTLIER) cc_final: 0.8558 (mptm) REVERT: L 578 PHE cc_start: 0.8100 (m-10) cc_final: 0.7216 (t80) REVERT: N 104 GLU cc_start: 0.9215 (mp0) cc_final: 0.8625 (mp0) REVERT: N 200 GLU cc_start: 0.8587 (OUTLIER) cc_final: 0.8097 (tm-30) outliers start: 51 outliers final: 26 residues processed: 283 average time/residue: 0.6434 time to fit residues: 204.2803 Evaluate side-chains 276 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 245 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 64 MET Chi-restraints excluded: chain H residue 67 MET Chi-restraints excluded: chain H residue 245 ILE Chi-restraints excluded: chain J residue 69 PHE Chi-restraints excluded: chain J residue 91 GLN Chi-restraints excluded: chain J residue 138 VAL Chi-restraints excluded: chain K residue 16 VAL Chi-restraints excluded: chain K residue 46 PHE Chi-restraints excluded: chain M residue 25 VAL Chi-restraints excluded: chain M residue 212 ASN Chi-restraints excluded: chain M residue 237 VAL Chi-restraints excluded: chain M residue 303 TRP Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 116 GLN Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain L residue 247 THR Chi-restraints excluded: chain L residue 359 GLU Chi-restraints excluded: chain L residue 547 LYS Chi-restraints excluded: chain L residue 568 MET Chi-restraints excluded: chain L residue 599 SER Chi-restraints excluded: chain N residue 51 SER Chi-restraints excluded: chain N residue 135 ILE Chi-restraints excluded: chain N residue 197 MET Chi-restraints excluded: chain N residue 200 GLU Chi-restraints excluded: chain N residue 227 THR Chi-restraints excluded: chain N residue 246 SER Chi-restraints excluded: chain N residue 263 VAL Chi-restraints excluded: chain N residue 355 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 164 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 223 optimal weight: 0.6980 chunk 203 optimal weight: 0.9980 chunk 104 optimal weight: 1.9990 chunk 165 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 144 optimal weight: 0.7980 chunk 79 optimal weight: 0.5980 chunk 54 optimal weight: 2.9990 chunk 148 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 62 GLN L 481 GLN N 46 ASN N 317 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.087516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.065651 restraints weight = 47359.233| |-----------------------------------------------------------------------------| r_work (start): 0.2797 rms_B_bonded: 2.44 r_work: 0.2671 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.2671 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2709 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2709 r_free = 0.2709 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2709 r_free = 0.2709 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2709 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8782 moved from start: 0.1290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 19729 Z= 0.138 Angle : 0.518 8.651 26612 Z= 0.261 Chirality : 0.038 0.160 3013 Planarity : 0.004 0.059 3143 Dihedral : 14.689 169.057 3455 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 2.21 % Allowed : 21.92 % Favored : 75.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.21 (0.18), residues: 2333 helix: 2.23 (0.12), residues: 1753 sheet: -0.43 (1.01), residues: 28 loop : -1.00 (0.28), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 209 TYR 0.022 0.001 TYR M 435 PHE 0.024 0.001 PHE L 341 TRP 0.014 0.001 TRP L 143 HIS 0.003 0.001 HIS N 124 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 (19729) covalent geometry : angle 0.51837 / 0.26 (26612) hydrogen bonds : bond 0.04189 / 2.79 ( 1301) hydrogen bonds : angle 3.92103 / 2.76 ( 3812) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4666 Ramachandran restraints generated. 2333 Oldfield, 0 Emsley, 2333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4666 Ramachandran restraints generated. 2333 Oldfield, 0 Emsley, 2333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 253 time to evaluate : 0.686 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 71 GLU cc_start: 0.7678 (tt0) cc_final: 0.6534 (mm-30) REVERT: H 141 TYR cc_start: 0.7493 (m-80) cc_final: 0.7273 (m-10) REVERT: K 94 SER cc_start: 0.8741 (m) cc_final: 0.8297 (p) REVERT: M 22 ARG cc_start: 0.8652 (mtp180) cc_final: 0.6871 (mmt180) REVERT: M 115 PHE cc_start: 0.7536 (t80) cc_final: 0.7154 (m-80) REVERT: M 146 MET cc_start: 0.8866 (pmm) cc_final: 0.8652 (pmt) REVERT: M 150 MET cc_start: 0.8734 (tpp) cc_final: 0.8223 (mmt) REVERT: M 303 TRP cc_start: 0.9122 (OUTLIER) cc_final: 0.7975 (m-10) REVERT: M 373 MET cc_start: 0.8881 (mmm) cc_final: 0.8640 (mmt) REVERT: B 45 MET cc_start: 0.6425 (mmt) cc_final: 0.5712 (pmm) REVERT: B 91 ARG cc_start: 0.8252 (mmt180) cc_final: 0.7712 (mmt180) REVERT: B 116 GLN cc_start: 0.7475 (OUTLIER) cc_final: 0.7137 (mp10) REVERT: B 119 GLU cc_start: 0.8456 (mm-30) cc_final: 0.7952 (tp30) REVERT: B 122 TRP cc_start: 0.8633 (m-90) cc_final: 0.8368 (m-90) REVERT: B 171 LEU cc_start: 0.9473 (mp) cc_final: 0.8970 (tm) REVERT: B 173 GLN cc_start: 0.8395 (tt0) cc_final: 0.7863 (tm-30) REVERT: B 179 GLU cc_start: 0.8606 (pt0) cc_final: 0.7503 (tm-30) REVERT: B 180 ARG cc_start: 0.7360 (mmp80) cc_final: 0.6539 (ppt-90) REVERT: B 192 VAL cc_start: 0.7496 (m) cc_final: 0.7247 (t) REVERT: L 58 GLN cc_start: 0.8471 (mt0) cc_final: 0.7808 (mm110) REVERT: L 354 LEU cc_start: 0.7930 (mt) cc_final: 0.7512 (pp) REVERT: L 547 LYS cc_start: 0.8791 (OUTLIER) cc_final: 0.8528 (mptm) REVERT: L 578 PHE cc_start: 0.8074 (m-10) cc_final: 0.7190 (t80) REVERT: N 104 GLU cc_start: 0.9213 (mp0) cc_final: 0.8462 (mp0) REVERT: N 200 GLU cc_start: 0.8574 (OUTLIER) cc_final: 0.7566 (tm-30) outliers start: 42 outliers final: 27 residues processed: 278 average time/residue: 0.6072 time to fit residues: 190.4667 Evaluate side-chains 275 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 244 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 64 MET Chi-restraints excluded: chain H residue 67 MET Chi-restraints excluded: chain H residue 245 ILE Chi-restraints excluded: chain H residue 279 MET Chi-restraints excluded: chain J residue 69 PHE Chi-restraints excluded: chain J residue 138 VAL Chi-restraints excluded: chain K residue 16 VAL Chi-restraints excluded: chain K residue 46 PHE Chi-restraints excluded: chain M residue 25 VAL Chi-restraints excluded: chain M residue 212 ASN Chi-restraints excluded: chain M residue 237 VAL Chi-restraints excluded: chain M residue 303 TRP Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 116 GLN Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain L residue 214 MET Chi-restraints excluded: chain L residue 247 THR Chi-restraints excluded: chain L residue 547 LYS Chi-restraints excluded: chain L residue 568 MET Chi-restraints excluded: chain L residue 599 SER Chi-restraints excluded: chain N residue 51 SER Chi-restraints excluded: chain N residue 135 ILE Chi-restraints excluded: chain N residue 197 MET Chi-restraints excluded: chain N residue 200 GLU Chi-restraints excluded: chain N residue 246 SER Chi-restraints excluded: chain N residue 257 LEU Chi-restraints excluded: chain N residue 263 VAL Chi-restraints excluded: chain N residue 355 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 177 optimal weight: 0.9990 chunk 131 optimal weight: 1.9990 chunk 67 optimal weight: 0.8980 chunk 206 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 117 optimal weight: 6.9990 chunk 223 optimal weight: 0.9980 chunk 158 optimal weight: 0.0670 chunk 186 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 175 optimal weight: 1.9990 overall best weight: 0.7318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 481 GLN N 317 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.088325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.066757 restraints weight = 47430.830| |-----------------------------------------------------------------------------| r_work (start): 0.2841 rms_B_bonded: 2.40 r_work: 0.2717 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.2717 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2713 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2713 r_free = 0.2713 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2713 r_free = 0.2713 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.2713 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8884 moved from start: 0.1314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 19729 Z= 0.135 Angle : 0.522 8.895 26612 Z= 0.264 Chirality : 0.038 0.159 3013 Planarity : 0.004 0.060 3143 Dihedral : 14.522 169.248 3455 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 2.31 % Allowed : 21.92 % Favored : 75.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.24 (0.18), residues: 2333 helix: 2.25 (0.12), residues: 1754 sheet: -0.42 (1.01), residues: 28 loop : -1.00 (0.28), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 209 TYR 0.023 0.001 TYR M 435 PHE 0.023 0.001 PHE L 341 TRP 0.013 0.001 TRP L 143 HIS 0.003 0.001 HIS N 124 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.13 (19729) covalent geometry : angle 0.52152 / 0.26 (26612) hydrogen bonds : bond 0.04133 / 2.75 ( 1301) hydrogen bonds : angle 3.89419 / 2.74 ( 3812) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4666 Ramachandran restraints generated. 2333 Oldfield, 0 Emsley, 2333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4666 Ramachandran restraints generated. 2333 Oldfield, 0 Emsley, 2333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 248 time to evaluate : 0.608 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 71 GLU cc_start: 0.7778 (tt0) cc_final: 0.6621 (mm-30) REVERT: H 141 TYR cc_start: 0.7565 (m-80) cc_final: 0.7231 (m-10) REVERT: H 214 GLN cc_start: 0.8744 (mt0) cc_final: 0.7802 (pp30) REVERT: K 94 SER cc_start: 0.8859 (m) cc_final: 0.8395 (p) REVERT: M 22 ARG cc_start: 0.8629 (mtp180) cc_final: 0.6889 (mmt180) REVERT: M 115 PHE cc_start: 0.7599 (t80) cc_final: 0.7215 (m-80) REVERT: M 150 MET cc_start: 0.8796 (tpp) cc_final: 0.8299 (mmt) REVERT: M 303 TRP cc_start: 0.9238 (OUTLIER) cc_final: 0.8056 (m-10) REVERT: M 373 MET cc_start: 0.8977 (mmm) cc_final: 0.8732 (mmt) REVERT: B 45 MET cc_start: 0.6436 (mmt) cc_final: 0.5738 (pmm) REVERT: B 91 ARG cc_start: 0.8314 (mmt180) cc_final: 0.7695 (mmt180) REVERT: B 116 GLN cc_start: 0.7523 (OUTLIER) cc_final: 0.7148 (mp10) REVERT: B 119 GLU cc_start: 0.8515 (mm-30) cc_final: 0.8035 (tp30) REVERT: B 122 TRP cc_start: 0.8736 (m-90) cc_final: 0.8512 (m-90) REVERT: B 171 LEU cc_start: 0.9440 (mp) cc_final: 0.8888 (tm) REVERT: B 173 GLN cc_start: 0.8430 (tt0) cc_final: 0.7897 (tm-30) REVERT: B 179 GLU cc_start: 0.8616 (pt0) cc_final: 0.7503 (tm-30) REVERT: B 180 ARG cc_start: 0.7445 (mmp80) cc_final: 0.6713 (ppt-90) REVERT: B 192 VAL cc_start: 0.7618 (m) cc_final: 0.7310 (t) REVERT: L 58 GLN cc_start: 0.8526 (mt0) cc_final: 0.7874 (mm110) REVERT: L 547 LYS cc_start: 0.8872 (OUTLIER) cc_final: 0.8617 (mptm) REVERT: L 578 PHE cc_start: 0.8130 (m-10) cc_final: 0.7281 (t80) REVERT: N 104 GLU cc_start: 0.9241 (mp0) cc_final: 0.8569 (mp0) REVERT: N 207 PHE cc_start: 0.9137 (OUTLIER) cc_final: 0.8134 (t80) outliers start: 44 outliers final: 31 residues processed: 274 average time/residue: 0.6078 time to fit residues: 187.5282 Evaluate side-chains 278 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 243 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 64 MET Chi-restraints excluded: chain H residue 67 MET Chi-restraints excluded: chain H residue 245 ILE Chi-restraints excluded: chain H residue 279 MET Chi-restraints excluded: chain J residue 69 PHE Chi-restraints excluded: chain J residue 91 GLN Chi-restraints excluded: chain J residue 138 VAL Chi-restraints excluded: chain K residue 16 VAL Chi-restraints excluded: chain K residue 46 PHE Chi-restraints excluded: chain M residue 25 VAL Chi-restraints excluded: chain M residue 212 ASN Chi-restraints excluded: chain M residue 237 VAL Chi-restraints excluded: chain M residue 303 TRP Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 116 GLN Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain L residue 3 MET Chi-restraints excluded: chain L residue 214 MET Chi-restraints excluded: chain L residue 247 THR Chi-restraints excluded: chain L residue 547 LYS Chi-restraints excluded: chain L residue 568 MET Chi-restraints excluded: chain L residue 599 SER Chi-restraints excluded: chain N residue 51 SER Chi-restraints excluded: chain N residue 135 ILE Chi-restraints excluded: chain N residue 197 MET Chi-restraints excluded: chain N residue 207 PHE Chi-restraints excluded: chain N residue 227 THR Chi-restraints excluded: chain N residue 246 SER Chi-restraints excluded: chain N residue 257 LEU Chi-restraints excluded: chain N residue 263 VAL Chi-restraints excluded: chain N residue 323 MET Chi-restraints excluded: chain N residue 355 ASP Chi-restraints excluded: chain N residue 477 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 140 optimal weight: 1.9990 chunk 115 optimal weight: 10.0000 chunk 198 optimal weight: 0.9990 chunk 105 optimal weight: 0.5980 chunk 181 optimal weight: 2.9990 chunk 11 optimal weight: 0.7980 chunk 224 optimal weight: 2.9990 chunk 142 optimal weight: 0.5980 chunk 19 optimal weight: 2.9990 chunk 201 optimal weight: 2.9990 chunk 193 optimal weight: 0.7980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... N 317 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.088451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.067469 restraints weight = 38661.072| |-----------------------------------------------------------------------------| r_work (start): 0.2864 rms_B_bonded: 2.18 r_work: 0.2748 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2634 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2634 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2619 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2619 r_free = 0.2619 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2619 r_free = 0.2619 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.2619 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8927 moved from start: 0.1359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 19729 Z= 0.137 Angle : 0.530 9.095 26612 Z= 0.266 Chirality : 0.039 0.160 3013 Planarity : 0.004 0.064 3143 Dihedral : 14.417 169.554 3455 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 2.37 % Allowed : 21.71 % Favored : 75.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.24 (0.18), residues: 2333 helix: 2.25 (0.12), residues: 1750 sheet: -0.43 (1.01), residues: 28 loop : -0.98 (0.28), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 209 TYR 0.022 0.001 TYR M 435 PHE 0.023 0.001 PHE L 341 TRP 0.013 0.001 TRP L 143 HIS 0.003 0.001 HIS N 124 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 (19729) covalent geometry : angle 0.53021 / 0.27 (26612) hydrogen bonds : bond 0.04136 / 2.75 ( 1301) hydrogen bonds : angle 3.89961 / 2.75 ( 3812) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4666 Ramachandran restraints generated. 2333 Oldfield, 0 Emsley, 2333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4666 Ramachandran restraints generated. 2333 Oldfield, 0 Emsley, 2333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 253 time to evaluate : 0.698 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 71 GLU cc_start: 0.7856 (tt0) cc_final: 0.6671 (mm-30) REVERT: H 79 ASP cc_start: 0.8396 (m-30) cc_final: 0.8142 (m-30) REVERT: H 141 TYR cc_start: 0.7612 (m-80) cc_final: 0.7292 (m-10) REVERT: H 214 GLN cc_start: 0.8763 (mt0) cc_final: 0.7729 (pp30) REVERT: K 94 SER cc_start: 0.8894 (m) cc_final: 0.8442 (p) REVERT: M 22 ARG cc_start: 0.8670 (mtp180) cc_final: 0.6894 (mmt180) REVERT: M 115 PHE cc_start: 0.7741 (t80) cc_final: 0.7314 (m-80) REVERT: M 150 MET cc_start: 0.8898 (tpp) cc_final: 0.8430 (mmt) REVERT: M 303 TRP cc_start: 0.9289 (OUTLIER) cc_final: 0.8109 (m-10) REVERT: M 373 MET cc_start: 0.9024 (mmm) cc_final: 0.8793 (mmt) REVERT: B 45 MET cc_start: 0.6506 (mmt) cc_final: 0.5747 (pmm) REVERT: B 91 ARG cc_start: 0.8375 (mmt180) cc_final: 0.7785 (mmt180) REVERT: B 116 GLN cc_start: 0.7576 (OUTLIER) cc_final: 0.7172 (mp10) REVERT: B 119 GLU cc_start: 0.8581 (mm-30) cc_final: 0.8105 (tp30) REVERT: B 171 LEU cc_start: 0.9441 (mp) cc_final: 0.8908 (tm) REVERT: B 173 GLN cc_start: 0.8453 (tt0) cc_final: 0.7922 (tm-30) REVERT: B 179 GLU cc_start: 0.8643 (pt0) cc_final: 0.7570 (tm-30) REVERT: B 180 ARG cc_start: 0.7439 (mmp80) cc_final: 0.6677 (ppt-90) REVERT: B 192 VAL cc_start: 0.7602 (m) cc_final: 0.7289 (t) REVERT: L 58 GLN cc_start: 0.8585 (mt0) cc_final: 0.7913 (mm110) REVERT: L 354 LEU cc_start: 0.7988 (mt) cc_final: 0.7573 (pp) REVERT: L 547 LYS cc_start: 0.8873 (OUTLIER) cc_final: 0.8633 (mptm) REVERT: L 578 PHE cc_start: 0.8201 (m-10) cc_final: 0.7308 (t80) REVERT: N 104 GLU cc_start: 0.9310 (mp0) cc_final: 0.8651 (mp0) REVERT: N 207 PHE cc_start: 0.9179 (OUTLIER) cc_final: 0.8177 (t80) outliers start: 45 outliers final: 31 residues processed: 279 average time/residue: 0.5933 time to fit residues: 185.7498 Evaluate side-chains 282 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 247 time to evaluate : 0.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 64 MET Chi-restraints excluded: chain H residue 67 MET Chi-restraints excluded: chain H residue 245 ILE Chi-restraints excluded: chain H residue 279 MET Chi-restraints excluded: chain J residue 69 PHE Chi-restraints excluded: chain J residue 91 GLN Chi-restraints excluded: chain J residue 138 VAL Chi-restraints excluded: chain K residue 16 VAL Chi-restraints excluded: chain K residue 46 PHE Chi-restraints excluded: chain M residue 25 VAL Chi-restraints excluded: chain M residue 38 LEU Chi-restraints excluded: chain M residue 146 MET Chi-restraints excluded: chain M residue 212 ASN Chi-restraints excluded: chain M residue 237 VAL Chi-restraints excluded: chain M residue 303 TRP Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 116 GLN Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain L residue 3 MET Chi-restraints excluded: chain L residue 214 MET Chi-restraints excluded: chain L residue 247 THR Chi-restraints excluded: chain L residue 547 LYS Chi-restraints excluded: chain L residue 568 MET Chi-restraints excluded: chain L residue 599 SER Chi-restraints excluded: chain N residue 51 SER Chi-restraints excluded: chain N residue 135 ILE Chi-restraints excluded: chain N residue 197 MET Chi-restraints excluded: chain N residue 207 PHE Chi-restraints excluded: chain N residue 227 THR Chi-restraints excluded: chain N residue 257 LEU Chi-restraints excluded: chain N residue 263 VAL Chi-restraints excluded: chain N residue 477 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 0 optimal weight: 7.9990 chunk 9 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 125 optimal weight: 0.8980 chunk 218 optimal weight: 1.9990 chunk 42 optimal weight: 0.0470 chunk 219 optimal weight: 3.9990 chunk 97 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 166 optimal weight: 0.7980 chunk 145 optimal weight: 2.9990 overall best weight: 1.1482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 481 GLN N 317 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.086868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.065381 restraints weight = 49733.881| |-----------------------------------------------------------------------------| r_work (start): 0.2823 rms_B_bonded: 2.45 r_work: 0.2696 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.2696 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2687 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2687 r_free = 0.2687 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2687 r_free = 0.2687 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2687 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8898 moved from start: 0.1394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 19729 Z= 0.177 Angle : 0.557 9.239 26612 Z= 0.281 Chirality : 0.040 0.165 3013 Planarity : 0.004 0.065 3143 Dihedral : 14.472 169.974 3455 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 2.26 % Allowed : 21.92 % Favored : 75.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.13 (0.18), residues: 2333 helix: 2.17 (0.12), residues: 1756 sheet: -0.43 (1.01), residues: 28 loop : -1.05 (0.28), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 80 TYR 0.026 0.001 TYR H 242 PHE 0.024 0.001 PHE L 341 TRP 0.015 0.001 TRP B 122 HIS 0.004 0.001 HIS N 124 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.18 (19729) covalent geometry : angle 0.55727 / 0.28 (26612) hydrogen bonds : bond 0.04447 / 2.96 ( 1301) hydrogen bonds : angle 3.98110 / 2.81 ( 3812) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4666 Ramachandran restraints generated. 2333 Oldfield, 0 Emsley, 2333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4666 Ramachandran restraints generated. 2333 Oldfield, 0 Emsley, 2333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 247 time to evaluate : 0.479 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 71 GLU cc_start: 0.7872 (tt0) cc_final: 0.6691 (mm-30) REVERT: H 79 ASP cc_start: 0.8389 (m-30) cc_final: 0.8134 (m-30) REVERT: H 141 TYR cc_start: 0.7631 (m-80) cc_final: 0.7314 (m-10) REVERT: H 214 GLN cc_start: 0.8771 (mt0) cc_final: 0.7752 (pp30) REVERT: H 294 TYR cc_start: 0.8584 (t80) cc_final: 0.8365 (t80) REVERT: K 94 SER cc_start: 0.8892 (m) cc_final: 0.8424 (p) REVERT: M 22 ARG cc_start: 0.8655 (mtp180) cc_final: 0.6896 (mmt180) REVERT: M 115 PHE cc_start: 0.7659 (t80) cc_final: 0.7265 (m-80) REVERT: M 150 MET cc_start: 0.8792 (tpp) cc_final: 0.8305 (mmt) REVERT: M 303 TRP cc_start: 0.9241 (OUTLIER) cc_final: 0.8076 (m-10) REVERT: M 373 MET cc_start: 0.8977 (mmm) cc_final: 0.8736 (mmt) REVERT: B 45 MET cc_start: 0.6417 (mmt) cc_final: 0.5723 (pmm) REVERT: B 91 ARG cc_start: 0.8301 (mmt180) cc_final: 0.7779 (mmt180) REVERT: B 116 GLN cc_start: 0.7556 (OUTLIER) cc_final: 0.7195 (mp10) REVERT: B 119 GLU cc_start: 0.8535 (mm-30) cc_final: 0.8037 (tp30) REVERT: B 122 TRP cc_start: 0.8678 (m-90) cc_final: 0.8466 (m-90) REVERT: B 171 LEU cc_start: 0.9455 (mp) cc_final: 0.8923 (tm) REVERT: B 173 GLN cc_start: 0.8438 (tt0) cc_final: 0.7879 (tm-30) REVERT: B 179 GLU cc_start: 0.8625 (pt0) cc_final: 0.7138 (pm20) REVERT: B 180 ARG cc_start: 0.7454 (mmp80) cc_final: 0.6641 (ppt-90) REVERT: B 192 VAL cc_start: 0.7638 (m) cc_final: 0.7344 (t) REVERT: L 58 GLN cc_start: 0.8527 (mt0) cc_final: 0.7874 (mm110) REVERT: L 354 LEU cc_start: 0.7994 (mt) cc_final: 0.7598 (pp) REVERT: L 547 LYS cc_start: 0.8857 (OUTLIER) cc_final: 0.8602 (mptm) REVERT: L 578 PHE cc_start: 0.8130 (m-10) cc_final: 0.7285 (t80) REVERT: N 104 GLU cc_start: 0.9228 (mp0) cc_final: 0.8498 (mp0) REVERT: N 255 MET cc_start: 0.9150 (tpt) cc_final: 0.8813 (tpt) outliers start: 43 outliers final: 32 residues processed: 272 average time/residue: 0.6069 time to fit residues: 185.1677 Evaluate side-chains 279 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 244 time to evaluate : 0.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 64 MET Chi-restraints excluded: chain H residue 67 MET Chi-restraints excluded: chain H residue 241 GLU Chi-restraints excluded: chain H residue 245 ILE Chi-restraints excluded: chain H residue 279 MET Chi-restraints excluded: chain H residue 285 ILE Chi-restraints excluded: chain J residue 69 PHE Chi-restraints excluded: chain J residue 138 VAL Chi-restraints excluded: chain K residue 16 VAL Chi-restraints excluded: chain K residue 46 PHE Chi-restraints excluded: chain M residue 25 VAL Chi-restraints excluded: chain M residue 38 LEU Chi-restraints excluded: chain M residue 146 MET Chi-restraints excluded: chain M residue 212 ASN Chi-restraints excluded: chain M residue 237 VAL Chi-restraints excluded: chain M residue 303 TRP Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 116 GLN Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain L residue 247 THR Chi-restraints excluded: chain L residue 547 LYS Chi-restraints excluded: chain L residue 568 MET Chi-restraints excluded: chain L residue 599 SER Chi-restraints excluded: chain N residue 51 SER Chi-restraints excluded: chain N residue 135 ILE Chi-restraints excluded: chain N residue 197 MET Chi-restraints excluded: chain N residue 227 THR Chi-restraints excluded: chain N residue 246 SER Chi-restraints excluded: chain N residue 257 LEU Chi-restraints excluded: chain N residue 263 VAL Chi-restraints excluded: chain N residue 355 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 13 optimal weight: 0.9990 chunk 160 optimal weight: 0.8980 chunk 66 optimal weight: 0.7980 chunk 170 optimal weight: 2.9990 chunk 204 optimal weight: 0.9990 chunk 188 optimal weight: 0.5980 chunk 227 optimal weight: 0.6980 chunk 20 optimal weight: 3.9990 chunk 134 optimal weight: 0.6980 chunk 179 optimal weight: 0.8980 chunk 69 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... N 317 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.088303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.067251 restraints weight = 42630.879| |-----------------------------------------------------------------------------| r_work (start): 0.2846 rms_B_bonded: 2.28 r_work: 0.2726 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2610 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2610 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2609 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2609 r_free = 0.2609 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2609 r_free = 0.2609 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (6 function evaluations) r_final: 0.2609 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8927 moved from start: 0.1440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 19729 Z= 0.134 Angle : 0.537 9.280 26612 Z= 0.271 Chirality : 0.039 0.159 3013 Planarity : 0.004 0.069 3143 Dihedral : 14.288 170.483 3455 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 1.89 % Allowed : 22.50 % Favored : 75.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.22 (0.18), residues: 2333 helix: 2.24 (0.12), residues: 1754 sheet: -0.45 (1.00), residues: 28 loop : -1.01 (0.28), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG H 209 TYR 0.027 0.001 TYR H 242 PHE 0.023 0.001 PHE L 341 TRP 0.014 0.001 TRP L 143 HIS 0.003 0.001 HIS H 210 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.13 (19729) covalent geometry : angle 0.53699 / 0.27 (26612) hydrogen bonds : bond 0.04138 / 2.76 ( 1301) hydrogen bonds : angle 3.91592 / 2.76 ( 3812) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4666 Ramachandran restraints generated. 2333 Oldfield, 0 Emsley, 2333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4666 Ramachandran restraints generated. 2333 Oldfield, 0 Emsley, 2333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 248 time to evaluate : 0.683 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 71 GLU cc_start: 0.7888 (tt0) cc_final: 0.6709 (mm-30) REVERT: H 79 ASP cc_start: 0.8423 (m-30) cc_final: 0.8183 (m-30) REVERT: H 214 GLN cc_start: 0.8764 (mt0) cc_final: 0.7777 (pp30) REVERT: K 1 MET cc_start: 0.7362 (pmt) cc_final: 0.7145 (pmm) REVERT: K 94 SER cc_start: 0.8896 (m) cc_final: 0.8455 (p) REVERT: M 22 ARG cc_start: 0.8664 (mtp180) cc_final: 0.6885 (mmt180) REVERT: M 115 PHE cc_start: 0.7736 (t80) cc_final: 0.7307 (m-80) REVERT: M 150 MET cc_start: 0.8872 (tpp) cc_final: 0.8398 (mmt) REVERT: M 303 TRP cc_start: 0.9289 (OUTLIER) cc_final: 0.8122 (m-10) REVERT: M 373 MET cc_start: 0.9024 (mmm) cc_final: 0.8795 (mmt) REVERT: B 45 MET cc_start: 0.6480 (mmt) cc_final: 0.5719 (pmm) REVERT: B 91 ARG cc_start: 0.8358 (mmt180) cc_final: 0.7787 (mmt180) REVERT: B 116 GLN cc_start: 0.7543 (OUTLIER) cc_final: 0.7089 (mp10) REVERT: B 119 GLU cc_start: 0.8617 (mm-30) cc_final: 0.8153 (tp30) REVERT: B 171 LEU cc_start: 0.9461 (mp) cc_final: 0.8919 (tm) REVERT: B 173 GLN cc_start: 0.8456 (tt0) cc_final: 0.7902 (tm-30) REVERT: B 179 GLU cc_start: 0.8493 (pt0) cc_final: 0.7000 (pt0) REVERT: B 180 ARG cc_start: 0.7377 (mmp80) cc_final: 0.6737 (ppt-90) REVERT: B 192 VAL cc_start: 0.7545 (m) cc_final: 0.7318 (t) REVERT: L 58 GLN cc_start: 0.8584 (mt0) cc_final: 0.7913 (mm110) REVERT: L 354 LEU cc_start: 0.7987 (mt) cc_final: 0.7565 (pp) REVERT: L 547 LYS cc_start: 0.8871 (OUTLIER) cc_final: 0.8631 (mptm) REVERT: L 578 PHE cc_start: 0.8221 (m-10) cc_final: 0.7322 (t80) REVERT: N 104 GLU cc_start: 0.9333 (mp0) cc_final: 0.8622 (mp0) REVERT: N 255 MET cc_start: 0.9138 (tpt) cc_final: 0.8829 (tpt) outliers start: 36 outliers final: 30 residues processed: 271 average time/residue: 0.6200 time to fit residues: 188.7867 Evaluate side-chains 276 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 243 time to evaluate : 0.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 64 MET Chi-restraints excluded: chain H residue 241 GLU Chi-restraints excluded: chain H residue 245 ILE Chi-restraints excluded: chain H residue 279 MET Chi-restraints excluded: chain H residue 285 ILE Chi-restraints excluded: chain J residue 69 PHE Chi-restraints excluded: chain J residue 138 VAL Chi-restraints excluded: chain K residue 16 VAL Chi-restraints excluded: chain K residue 46 PHE Chi-restraints excluded: chain M residue 25 VAL Chi-restraints excluded: chain M residue 38 LEU Chi-restraints excluded: chain M residue 146 MET Chi-restraints excluded: chain M residue 212 ASN Chi-restraints excluded: chain M residue 237 VAL Chi-restraints excluded: chain M residue 303 TRP Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 116 GLN Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain L residue 247 THR Chi-restraints excluded: chain L residue 547 LYS Chi-restraints excluded: chain L residue 568 MET Chi-restraints excluded: chain L residue 599 SER Chi-restraints excluded: chain N residue 51 SER Chi-restraints excluded: chain N residue 135 ILE Chi-restraints excluded: chain N residue 197 MET Chi-restraints excluded: chain N residue 227 THR Chi-restraints excluded: chain N residue 246 SER Chi-restraints excluded: chain N residue 257 LEU Chi-restraints excluded: chain N residue 263 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 110 optimal weight: 1.9990 chunk 94 optimal weight: 0.7980 chunk 114 optimal weight: 0.7980 chunk 52 optimal weight: 0.9980 chunk 100 optimal weight: 0.0270 chunk 231 optimal weight: 0.6980 chunk 165 optimal weight: 0.9990 chunk 113 optimal weight: 0.5980 chunk 76 optimal weight: 3.9990 chunk 127 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 overall best weight: 0.5838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 481 GLN N 317 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.088048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.066552 restraints weight = 50073.475| |-----------------------------------------------------------------------------| r_work (start): 0.2849 rms_B_bonded: 2.48 r_work: 0.2726 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.2726 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2725 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2725 r_free = 0.2725 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2725 r_free = 0.2725 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.2725 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8823 moved from start: 0.1444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 19729 Z= 0.125 Angle : 0.533 9.286 26612 Z= 0.267 Chirality : 0.038 0.157 3013 Planarity : 0.004 0.068 3143 Dihedral : 14.086 171.273 3455 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 1.74 % Allowed : 22.77 % Favored : 75.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.26 (0.18), residues: 2333 helix: 2.28 (0.12), residues: 1751 sheet: -0.43 (1.00), residues: 28 loop : -1.01 (0.28), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG H 209 TYR 0.023 0.001 TYR M 435 PHE 0.023 0.001 PHE L 341 TRP 0.029 0.001 TRP B 122 HIS 0.003 0.000 HIS H 210 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 (19729) covalent geometry : angle 0.53274 / 0.27 (26612) hydrogen bonds : bond 0.03990 / 2.66 ( 1301) hydrogen bonds : angle 3.87262 / 2.73 ( 3812) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7927.31 seconds wall clock time: 135 minutes 45.96 seconds (8145.96 seconds total)