Starting phenix.real_space_refine on Fri Jun 5 10:02:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9tak_55749/06_2026/9tak_55749.cif Found real_map, /net/cci-nas-00/data/ceres_data/9tak_55749/06_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_55749/06_2026/9tak_55749.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9tak_55749/06_2026/9tak_55749.map" model { file = "/net/cci-nas-00/data/ceres_data/9tak_55749/06_2026/9tak_55749.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9tak_55749/06_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-6079/lib/python3.9/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: 5.92, per 1000 atoms: 0.30 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: 1.76 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 0.52 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: 3.45 Time building geometry restraints manager: 2.38 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=" CB7 CDL L 703 " pdb=" OB8 CDL L 703 " ideal model delta sigma weight residual 1.334 1.407 -0.073 1.10e-02 8.26e+03 4.43e+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 ... (remaining 19724 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.11: 26120 2.11 - 4.22: 317 4.22 - 6.33: 142 6.33 - 8.45: 22 8.45 - 10.56: 11 Bond angle restraints: 26612 Sorted by residual: angle pdb=" C11 CDL L 703 " pdb=" CA5 CDL L 703 " pdb=" OA6 CDL L 703 " ideal model delta sigma weight residual 111.33 119.89 -8.56 1.32e+00 5.72e-01 4.19e+01 angle pdb=" C51 CDL L 703 " pdb=" CB5 CDL L 703 " pdb=" OB6 CDL L 703 " ideal model delta sigma weight residual 111.33 119.89 -8.56 1.32e+00 5.72e-01 4.19e+01 angle pdb=" C71 CDL L 703 " pdb=" CB7 CDL L 703 " pdb=" OB8 CDL L 703 " ideal model delta sigma weight residual 111.64 120.47 -8.83 1.65e+00 3.69e-01 2.88e+01 angle pdb=" C31 CDL L 703 " pdb=" CA7 CDL L 703 " pdb=" OA8 CDL L 703 " ideal model delta sigma weight residual 111.64 120.06 -8.42 1.65e+00 3.69e-01 2.62e+01 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 ... (remaining 26607 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.00: 11033 34.00 - 68.00: 563 68.00 - 102.00: 38 102.00 - 136.00: 6 136.00 - 170.00: 1 Dihedral angle restraints: 11641 sinusoidal: 4916 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 11638 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 2361 0.045 - 0.091: 569 0.091 - 0.136: 79 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: 39.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.400 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 20.770 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9003 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= 0.215 Angle : 0.674 10.557 26612 Z= 0.318 Chirality : 0.037 0.227 3013 Planarity : 0.003 0.065 3143 Dihedral : 18.492 170.001 7341 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 0.00405 / 0.22 (19729) covalent geometry : angle 0.67399 / 0.32 (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 : 0.710 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: 0.6612 time to fit residues: 218.3715 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 : 0.687 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.087784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.066519 restraints weight = 38605.175| |-----------------------------------------------------------------------------| r_work (start): 0.2851 rms_B_bonded: 2.21 r_work: 0.2736 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2622 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2622 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2626 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2626 r_free = 0.2626 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 = 0.2626 r_free = 0.2626 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2626 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.0843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 19729 Z= 0.139 Angle : 0.522 7.450 26612 Z= 0.265 Chirality : 0.038 0.149 3013 Planarity : 0.004 0.066 3143 Dihedral : 15.874 169.598 3454 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 2.89 % Allowed : 19.56 % Favored : 77.55 % 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: 2.08 (0.12), residues: 1753 sheet: -0.12 (1.09), residues: 28 loop : -1.00 (0.28), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 80 TYR 0.021 0.001 TYR M 435 PHE 0.024 0.001 PHE H 277 TRP 0.013 0.001 TRP L 143 HIS 0.003 0.001 HIS L 411 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.14 (19729) covalent geometry : angle 0.52191 / 0.26 (26612) hydrogen bonds : bond 0.04800 / 3.19 ( 1301) hydrogen bonds : angle 4.18875 / 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 : 0.795 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 71 GLU cc_start: 0.7819 (tt0) cc_final: 0.6649 (mm-30) REVERT: K 94 SER cc_start: 0.8791 (m) cc_final: 0.8321 (p) REVERT: M 22 ARG cc_start: 0.8701 (mtp180) cc_final: 0.6869 (mmt180) REVERT: M 36 MET cc_start: 0.8955 (OUTLIER) cc_final: 0.8510 (mmm) REVERT: M 150 MET cc_start: 0.8838 (tpp) cc_final: 0.8463 (mmt) REVERT: M 303 TRP cc_start: 0.9209 (OUTLIER) cc_final: 0.8036 (m-10) REVERT: M 373 MET cc_start: 0.8965 (mmm) cc_final: 0.8727 (mmt) REVERT: B 45 MET cc_start: 0.6500 (mmt) cc_final: 0.5744 (pmm) REVERT: B 91 ARG cc_start: 0.8228 (mmt180) cc_final: 0.7921 (mmt180) REVERT: B 119 GLU cc_start: 0.8595 (mm-30) cc_final: 0.7963 (tp30) REVERT: B 122 TRP cc_start: 0.8747 (m-90) cc_final: 0.8455 (m-90) REVERT: B 173 GLN cc_start: 0.8420 (tt0) cc_final: 0.7864 (tm-30) REVERT: B 179 GLU cc_start: 0.8606 (pt0) cc_final: 0.7458 (tm-30) REVERT: B 180 ARG cc_start: 0.7329 (mmp80) cc_final: 0.6518 (ppt-90) REVERT: B 181 ARG cc_start: 0.7662 (tpp-160) cc_final: 0.6669 (tpt-90) REVERT: L 58 GLN cc_start: 0.8604 (mt0) cc_final: 0.7992 (mm110) REVERT: L 275 MET cc_start: 0.9124 (mtt) cc_final: 0.8897 (mtt) REVERT: L 359 GLU cc_start: 0.6960 (OUTLIER) cc_final: 0.6624 (pm20) REVERT: L 578 PHE cc_start: 0.8110 (m-10) cc_final: 0.7220 (t80) REVERT: N 104 GLU cc_start: 0.9259 (mp0) cc_final: 0.8669 (mp0) outliers start: 55 outliers final: 18 residues processed: 301 average time/residue: 0.6749 time to fit residues: 227.7441 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 : 0.706 ------------------------------------------------------------------------------- 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: 0.5980 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: 0.7980 chunk 1 optimal weight: 0.7980 chunk 78 optimal weight: 0.5980 chunk 49 optimal weight: 0.9990 chunk 179 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3225 r_free = 0.3225 target = 0.088012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.066679 restraints weight = 39410.459| |-----------------------------------------------------------------------------| r_work (start): 0.2820 rms_B_bonded: 2.24 r_work: 0.2698 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2582 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2582 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2623 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2623 r_free = 0.2623 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 = 0.2623 r_free = 0.2623 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2623 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 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 0.068 19729 Z= 0.131 Angle : 0.506 7.691 26612 Z= 0.255 Chirality : 0.038 0.148 3013 Planarity : 0.004 0.052 3143 Dihedral : 15.452 169.351 3439 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 2.52 % Allowed : 20.61 % Favored : 76.87 % 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: 2.13 (0.18), residues: 2333 helix: 2.17 (0.12), residues: 1750 sheet: -0.18 (1.06), residues: 28 loop : -1.00 (0.28), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 91 TYR 0.023 0.001 TYR M 435 PHE 0.024 0.001 PHE L 341 TRP 0.013 0.001 TRP L 143 HIS 0.003 0.000 HIS N 124 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 (19729) covalent geometry : angle 0.50611 / 0.26 (26612) hydrogen bonds : bond 0.04377 / 2.91 ( 1301) hydrogen bonds : angle 4.02780 / 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 312 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 264 time to evaluate : 0.686 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 71 GLU cc_start: 0.7774 (tt0) cc_final: 0.6618 (mm-30) REVERT: H 88 MET cc_start: 0.8649 (mtp) cc_final: 0.8440 (mtm) REVERT: H 286 ARG cc_start: 0.8067 (tpt-90) cc_final: 0.7653 (tpt-90) REVERT: K 94 SER cc_start: 0.8755 (m) cc_final: 0.8317 (p) REVERT: M 22 ARG cc_start: 0.8689 (mtp180) cc_final: 0.6866 (mmt180) REVERT: M 115 PHE cc_start: 0.7677 (t80) cc_final: 0.7177 (m-80) REVERT: M 144 GLU cc_start: 0.9148 (OUTLIER) cc_final: 0.7968 (mt-10) REVERT: M 146 MET cc_start: 0.8951 (pmm) cc_final: 0.8684 (pmt) REVERT: M 150 MET cc_start: 0.8820 (tpp) cc_final: 0.8417 (mmt) REVERT: M 303 TRP cc_start: 0.9197 (OUTLIER) cc_final: 0.8044 (m-10) REVERT: M 373 MET cc_start: 0.8929 (mmm) cc_final: 0.8660 (mmt) REVERT: B 45 MET cc_start: 0.6545 (mmt) cc_final: 0.5741 (pmm) REVERT: B 91 ARG cc_start: 0.8280 (mmt180) cc_final: 0.7894 (mmt180) REVERT: B 119 GLU cc_start: 0.8581 (mm-30) cc_final: 0.7955 (tp30) REVERT: B 122 TRP cc_start: 0.8718 (m-90) cc_final: 0.8444 (m-90) REVERT: B 171 LEU cc_start: 0.9473 (mp) cc_final: 0.8972 (tm) REVERT: B 173 GLN cc_start: 0.8401 (tt0) cc_final: 0.7867 (tm-30) REVERT: B 179 GLU cc_start: 0.8577 (pt0) cc_final: 0.6968 (pm20) REVERT: B 180 ARG cc_start: 0.7340 (mmp80) cc_final: 0.6475 (ppt-90) REVERT: B 181 ARG cc_start: 0.7640 (tpp-160) cc_final: 0.7346 (tpt-90) REVERT: L 58 GLN cc_start: 0.8560 (mt0) cc_final: 0.7924 (mm110) REVERT: L 359 GLU cc_start: 0.6886 (OUTLIER) cc_final: 0.6571 (pm20) REVERT: L 578 PHE cc_start: 0.8087 (m-10) cc_final: 0.7201 (t80) REVERT: N 104 GLU cc_start: 0.9248 (mp0) cc_final: 0.8617 (mp0) outliers start: 48 outliers final: 26 residues processed: 294 average time/residue: 0.6582 time to fit residues: 217.7904 Evaluate side-chains 277 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 248 time to evaluate : 0.697 ------------------------------------------------------------------------------- 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 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: 0.4980 chunk 69 optimal weight: 0.9980 chunk 204 optimal weight: 0.8980 chunk 52 optimal weight: 0.6980 chunk 71 optimal weight: 1.9990 chunk 118 optimal weight: 6.9990 chunk 49 optimal weight: 0.9980 chunk 230 optimal weight: 0.6980 chunk 104 optimal weight: 0.0170 overall best weight: 0.5018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3237 r_free = 0.3237 target = 0.088720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.067207 restraints weight = 42325.048| |-----------------------------------------------------------------------------| r_work (start): 0.2833 rms_B_bonded: 2.33 r_work: 0.2710 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.2710 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2750 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2750 r_free = 0.2750 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2750 r_free = 0.2750 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2750 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.1161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 19729 Z= 0.115 Angle : 0.492 7.554 26612 Z= 0.249 Chirality : 0.038 0.148 3013 Planarity : 0.004 0.055 3143 Dihedral : 15.013 169.077 3439 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 2.42 % Allowed : 21.35 % 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: 1752 sheet: -0.19 (1.06), residues: 28 loop : -1.06 (0.28), residues: 553 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 0.000 HIS H 210 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.12 (19729) covalent geometry : angle 0.49214 / 0.25 (26612) hydrogen bonds : bond 0.04014 / 2.67 ( 1301) hydrogen bonds : angle 3.90185 / 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 307 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 261 time to evaluate : 0.738 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 71 GLU cc_start: 0.7709 (tt0) cc_final: 0.6557 (mm-30) REVERT: H 141 TYR cc_start: 0.7497 (m-80) cc_final: 0.7141 (m-10) REVERT: H 286 ARG cc_start: 0.8063 (tpt-90) cc_final: 0.7710 (tpt-90) REVERT: K 94 SER cc_start: 0.8701 (m) cc_final: 0.8249 (p) REVERT: M 22 ARG cc_start: 0.8650 (mtp180) cc_final: 0.6846 (mmt180) REVERT: M 115 PHE cc_start: 0.7523 (t80) cc_final: 0.7086 (m-80) REVERT: M 146 MET cc_start: 0.8878 (pmm) cc_final: 0.8627 (pmt) REVERT: M 150 MET cc_start: 0.8712 (tpp) cc_final: 0.8232 (mmt) REVERT: M 303 TRP cc_start: 0.9116 (OUTLIER) cc_final: 0.8058 (m-10) REVERT: M 373 MET cc_start: 0.8869 (mmm) cc_final: 0.8614 (mmt) REVERT: B 45 MET cc_start: 0.6417 (mmt) cc_final: 0.5751 (pmm) REVERT: B 91 ARG cc_start: 0.8245 (mmt180) cc_final: 0.7782 (mmt180) REVERT: B 119 GLU cc_start: 0.8495 (mm-30) cc_final: 0.7864 (tp30) REVERT: B 122 TRP cc_start: 0.8695 (m-90) cc_final: 0.8424 (m-90) REVERT: B 171 LEU cc_start: 0.9467 (mp) cc_final: 0.8964 (tm) REVERT: B 173 GLN cc_start: 0.8386 (tt0) cc_final: 0.7844 (tm-30) REVERT: B 179 GLU cc_start: 0.8583 (pt0) cc_final: 0.7460 (tm-30) REVERT: B 180 ARG cc_start: 0.7363 (mmp80) cc_final: 0.6619 (ppt-90) REVERT: B 181 ARG cc_start: 0.7546 (tpp-160) cc_final: 0.6727 (tpt-90) REVERT: L 58 GLN cc_start: 0.8506 (mt0) cc_final: 0.7864 (mm110) REVERT: L 359 GLU cc_start: 0.6856 (OUTLIER) cc_final: 0.6510 (pm20) REVERT: L 578 PHE cc_start: 0.8012 (m-10) cc_final: 0.7171 (t80) REVERT: N 96 GLU cc_start: 0.8739 (mm-30) cc_final: 0.8536 (tp30) REVERT: N 104 GLU cc_start: 0.9178 (mp0) cc_final: 0.8499 (mp0) outliers start: 46 outliers final: 24 residues processed: 289 average time/residue: 0.6860 time to fit residues: 222.5773 Evaluate side-chains 276 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 250 time to evaluate : 0.781 ------------------------------------------------------------------------------- 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 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 316 LEU 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: 0.8980 chunk 67 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 231 optimal weight: 3.9990 chunk 61 optimal weight: 6.9990 chunk 229 optimal weight: 0.8980 chunk 162 optimal weight: 3.9990 chunk 72 optimal weight: 3.9990 chunk 120 optimal weight: 7.9990 chunk 49 optimal weight: 1.9990 chunk 127 optimal weight: 3.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 115 ASN L 62 GLN L 481 GLN N 317 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.085588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2812 r_free = 0.2812 target = 0.063645 restraints weight = 47649.972| |-----------------------------------------------------------------------------| r_work (start): 0.2796 rms_B_bonded: 2.43 r_work: 0.2675 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2675 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2669 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2669 r_free = 0.2669 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2669 r_free = 0.2669 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2669 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.1244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 19729 Z= 0.197 Angle : 0.557 8.995 26612 Z= 0.281 Chirality : 0.040 0.171 3013 Planarity : 0.004 0.056 3143 Dihedral : 15.082 168.935 3439 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 2.63 % Allowed : 21.14 % 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: 2.09 (0.18), residues: 2333 helix: 2.14 (0.12), residues: 1752 sheet: -0.29 (1.04), residues: 28 loop : -1.06 (0.28), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 209 TYR 0.020 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 0.00469 / 0.20 (19729) covalent geometry : angle 0.55739 / 0.28 (26612) hydrogen bonds : bond 0.04717 / 3.14 ( 1301) hydrogen bonds : angle 4.04523 / 2.85 ( 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 300 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 250 time to evaluate : 0.834 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 71 GLU cc_start: 0.7731 (tt0) cc_final: 0.6541 (mm-30) REVERT: H 141 TYR cc_start: 0.7606 (m-80) cc_final: 0.7240 (m-10) REVERT: H 281 MET cc_start: 0.8617 (tpp) cc_final: 0.8355 (mpp) REVERT: H 294 TYR cc_start: 0.8578 (t80) cc_final: 0.8352 (t80) REVERT: K 94 SER cc_start: 0.8853 (m) cc_final: 0.8353 (p) REVERT: M 22 ARG cc_start: 0.8656 (mtp180) cc_final: 0.6896 (mmt180) REVERT: M 115 PHE cc_start: 0.7682 (t80) cc_final: 0.7203 (m-80) REVERT: M 146 MET cc_start: 0.8861 (pmm) cc_final: 0.8599 (pmt) REVERT: M 150 MET cc_start: 0.8797 (tpp) cc_final: 0.8292 (mmt) REVERT: M 303 TRP cc_start: 0.9168 (OUTLIER) cc_final: 0.8020 (m-10) REVERT: M 373 MET cc_start: 0.8904 (mmm) cc_final: 0.8662 (mmt) REVERT: B 45 MET cc_start: 0.6501 (mmt) cc_final: 0.5762 (pmm) REVERT: B 91 ARG cc_start: 0.8267 (mmt180) cc_final: 0.7749 (mmt180) REVERT: B 116 GLN cc_start: 0.7520 (OUTLIER) cc_final: 0.7158 (mp10) REVERT: B 119 GLU cc_start: 0.8443 (mm-30) cc_final: 0.7798 (tp30) REVERT: B 122 TRP cc_start: 0.8616 (m-90) cc_final: 0.8273 (m-90) REVERT: B 173 GLN cc_start: 0.8425 (tt0) cc_final: 0.7890 (tm-30) REVERT: B 179 GLU cc_start: 0.8563 (pt0) cc_final: 0.7455 (tm-30) REVERT: B 180 ARG cc_start: 0.7439 (mmp80) cc_final: 0.6657 (ppt-90) REVERT: B 181 ARG cc_start: 0.7571 (tpp-160) cc_final: 0.6684 (tpt-90) REVERT: B 192 VAL cc_start: 0.7481 (m) cc_final: 0.7080 (t) REVERT: L 58 GLN cc_start: 0.8523 (mt0) cc_final: 0.7880 (mm110) REVERT: L 359 GLU cc_start: 0.6795 (OUTLIER) cc_final: 0.6414 (pm20) REVERT: L 547 LYS cc_start: 0.8777 (OUTLIER) cc_final: 0.8510 (mptm) REVERT: L 578 PHE cc_start: 0.8056 (m-10) cc_final: 0.7220 (t80) REVERT: N 104 GLU cc_start: 0.9225 (mp0) cc_final: 0.8622 (mp0) REVERT: N 200 GLU cc_start: 0.8569 (OUTLIER) cc_final: 0.8071 (tm-30) outliers start: 50 outliers final: 26 residues processed: 283 average time/residue: 0.6848 time to fit residues: 216.9773 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 : 0.756 ------------------------------------------------------------------------------- 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 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 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 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: 0.9990 chunk 223 optimal weight: 0.9980 chunk 203 optimal weight: 0.0070 chunk 104 optimal weight: 1.9990 chunk 165 optimal weight: 0.8980 chunk 77 optimal weight: 0.8980 chunk 144 optimal weight: 2.9990 chunk 79 optimal weight: 0.6980 chunk 54 optimal weight: 2.9990 chunk 148 optimal weight: 0.6980 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 481 GLN N 46 ASN N 317 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.088603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.067065 restraints weight = 47252.105| |-----------------------------------------------------------------------------| r_work (start): 0.2856 rms_B_bonded: 2.41 r_work: 0.2733 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.2733 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2722 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2722 r_free = 0.2722 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2722 r_free = 0.2722 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2722 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.1298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 19729 Z= 0.126 Angle : 0.515 8.476 26612 Z= 0.260 Chirality : 0.038 0.160 3013 Planarity : 0.004 0.059 3143 Dihedral : 14.708 169.098 3439 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 2.05 % Allowed : 21.82 % 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: 2.22 (0.18), residues: 2333 helix: 2.25 (0.12), residues: 1746 sheet: -0.29 (1.04), residues: 28 loop : -1.02 (0.28), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 209 TYR 0.023 0.001 TYR M 435 PHE 0.024 0.001 PHE L 341 TRP 0.014 0.001 TRP L 143 HIS 0.003 0.000 HIS N 124 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 (19729) covalent geometry : angle 0.51506 / 0.26 (26612) hydrogen bonds : bond 0.04107 / 2.73 ( 1301) hydrogen bonds : angle 3.90255 / 2.75 ( 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: 39 poor density : 256 time to evaluate : 0.722 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 71 GLU cc_start: 0.7760 (tt0) cc_final: 0.6609 (mm-30) REVERT: H 141 TYR cc_start: 0.7555 (m-80) cc_final: 0.7337 (m-10) REVERT: K 94 SER cc_start: 0.8812 (m) cc_final: 0.8362 (p) REVERT: M 22 ARG cc_start: 0.8670 (mtp180) cc_final: 0.6891 (mmt180) REVERT: M 115 PHE cc_start: 0.7622 (t80) cc_final: 0.7153 (m-80) REVERT: M 146 MET cc_start: 0.8894 (pmm) cc_final: 0.8685 (pmt) REVERT: M 150 MET cc_start: 0.8768 (tpp) cc_final: 0.8291 (mmt) REVERT: M 303 TRP cc_start: 0.9221 (OUTLIER) cc_final: 0.8048 (m-10) REVERT: M 373 MET cc_start: 0.8962 (mmm) cc_final: 0.8715 (mmt) REVERT: B 45 MET cc_start: 0.6448 (mmt) cc_final: 0.5736 (pmm) REVERT: B 91 ARG cc_start: 0.8296 (mmt180) cc_final: 0.7706 (mmt180) REVERT: B 116 GLN cc_start: 0.7520 (OUTLIER) cc_final: 0.7174 (mp10) REVERT: B 119 GLU cc_start: 0.8504 (mm-30) cc_final: 0.7870 (tp30) REVERT: B 122 TRP cc_start: 0.8707 (m-90) cc_final: 0.8442 (m-90) REVERT: B 171 LEU cc_start: 0.9442 (mp) cc_final: 0.8934 (tm) REVERT: B 173 GLN cc_start: 0.8417 (tt0) cc_final: 0.7893 (tm-30) REVERT: B 179 GLU cc_start: 0.8584 (pt0) cc_final: 0.7480 (tm-30) REVERT: B 180 ARG cc_start: 0.7422 (mmp80) cc_final: 0.6678 (ppt-90) REVERT: B 181 ARG cc_start: 0.7632 (tpp-160) cc_final: 0.6810 (tpt-90) REVERT: B 192 VAL cc_start: 0.7590 (m) cc_final: 0.7135 (t) REVERT: L 58 GLN cc_start: 0.8555 (mt0) cc_final: 0.7920 (mm110) REVERT: L 354 LEU cc_start: 0.7935 (mt) cc_final: 0.7530 (pp) REVERT: L 547 LYS cc_start: 0.8860 (OUTLIER) cc_final: 0.8613 (mptm) REVERT: L 578 PHE cc_start: 0.8117 (m-10) cc_final: 0.7269 (t80) REVERT: N 104 GLU cc_start: 0.9219 (mp0) cc_final: 0.8502 (mp0) REVERT: N 200 GLU cc_start: 0.8636 (OUTLIER) cc_final: 0.7650 (tm-30) outliers start: 39 outliers final: 26 residues processed: 278 average time/residue: 0.6714 time to fit residues: 209.3276 Evaluate side-chains 273 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 243 time to evaluate : 0.783 ------------------------------------------------------------------------------- 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 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 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 200 GLU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 177 optimal weight: 1.9990 chunk 131 optimal weight: 0.9990 chunk 67 optimal weight: 0.6980 chunk 206 optimal weight: 0.9980 chunk 6 optimal weight: 0.9990 chunk 117 optimal weight: 5.9990 chunk 223 optimal weight: 0.9990 chunk 158 optimal weight: 0.0000 chunk 186 optimal weight: 0.9980 chunk 37 optimal weight: 4.9990 chunk 175 optimal weight: 0.0470 overall best weight: 0.5482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.088138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.066600 restraints weight = 47107.425| |-----------------------------------------------------------------------------| r_work (start): 0.2860 rms_B_bonded: 2.42 r_work: 0.2742 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.2742 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2737 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2737 r_free = 0.2737 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2737 r_free = 0.2737 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2737 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.1336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 19729 Z= 0.121 Angle : 0.514 8.788 26612 Z= 0.261 Chirality : 0.038 0.156 3013 Planarity : 0.004 0.061 3143 Dihedral : 14.465 169.327 3439 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 2.21 % Allowed : 21.98 % 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: 2.27 (0.18), residues: 2333 helix: 2.29 (0.12), residues: 1747 sheet: -0.29 (1.03), residues: 28 loop : -1.01 (0.28), residues: 558 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 0.014 0.001 TRP L 143 HIS 0.003 0.000 HIS H 210 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 (19729) covalent geometry : angle 0.51354 / 0.26 (26612) hydrogen bonds : bond 0.04002 / 2.67 ( 1301) hydrogen bonds : angle 3.85518 / 2.71 ( 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: 42 poor density : 250 time to evaluate : 0.683 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 71 GLU cc_start: 0.7723 (tt0) cc_final: 0.6551 (mm-30) REVERT: H 214 GLN cc_start: 0.8690 (mt0) cc_final: 0.7774 (pp30) REVERT: K 86 ARG cc_start: 0.8686 (mtp85) cc_final: 0.8484 (mtp85) REVERT: K 94 SER cc_start: 0.8765 (m) cc_final: 0.8313 (p) REVERT: M 22 ARG cc_start: 0.8633 (mtp180) cc_final: 0.6868 (mmt180) REVERT: M 115 PHE cc_start: 0.7596 (t80) cc_final: 0.7133 (m-80) REVERT: M 146 MET cc_start: 0.8900 (pmm) cc_final: 0.8698 (pmt) REVERT: M 150 MET cc_start: 0.8739 (tpp) cc_final: 0.8255 (mmt) REVERT: M 303 TRP cc_start: 0.9143 (OUTLIER) cc_final: 0.7979 (m-10) REVERT: M 373 MET cc_start: 0.8924 (mmm) cc_final: 0.8678 (mmt) REVERT: M 398 MET cc_start: 0.9029 (tpp) cc_final: 0.8781 (tpp) REVERT: B 45 MET cc_start: 0.6408 (mmt) cc_final: 0.5749 (pmm) REVERT: B 91 ARG cc_start: 0.8259 (mmt180) cc_final: 0.7677 (mmt180) REVERT: B 116 GLN cc_start: 0.7490 (OUTLIER) cc_final: 0.7128 (mp10) REVERT: B 119 GLU cc_start: 0.8480 (mm-30) cc_final: 0.7852 (tp30) REVERT: B 122 TRP cc_start: 0.8638 (m-90) cc_final: 0.8299 (m-90) REVERT: B 171 LEU cc_start: 0.9451 (mp) cc_final: 0.8930 (tm) REVERT: B 173 GLN cc_start: 0.8403 (tt0) cc_final: 0.7876 (tm-30) REVERT: B 179 GLU cc_start: 0.8607 (pt0) cc_final: 0.7465 (tm-30) REVERT: B 180 ARG cc_start: 0.7443 (mmp80) cc_final: 0.6679 (ppt-90) REVERT: B 181 ARG cc_start: 0.7564 (tpp-160) cc_final: 0.6729 (tpt-90) REVERT: B 192 VAL cc_start: 0.7597 (m) cc_final: 0.7131 (t) REVERT: L 58 GLN cc_start: 0.8524 (mt0) cc_final: 0.7876 (mm110) REVERT: L 547 LYS cc_start: 0.8822 (OUTLIER) cc_final: 0.8573 (mptm) REVERT: L 578 PHE cc_start: 0.8083 (m-10) cc_final: 0.7217 (t80) REVERT: N 104 GLU cc_start: 0.9199 (mp0) cc_final: 0.8457 (mp0) REVERT: N 207 PHE cc_start: 0.9059 (OUTLIER) cc_final: 0.8068 (t80) REVERT: N 255 MET cc_start: 0.9063 (tpt) cc_final: 0.8678 (tpt) outliers start: 42 outliers final: 27 residues processed: 274 average time/residue: 0.6869 time to fit residues: 210.4620 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 : 0.726 ------------------------------------------------------------------------------- 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 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 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 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 246 SER 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: 0.9990 chunk 115 optimal weight: 9.9990 chunk 198 optimal weight: 0.9980 chunk 105 optimal weight: 1.9990 chunk 181 optimal weight: 2.9990 chunk 11 optimal weight: 0.6980 chunk 224 optimal weight: 1.9990 chunk 142 optimal weight: 3.9990 chunk 19 optimal weight: 0.4980 chunk 201 optimal weight: 2.9990 chunk 193 optimal weight: 0.0870 overall best weight: 0.6560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 317 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.088049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.067149 restraints weight = 38432.775| |-----------------------------------------------------------------------------| r_work (start): 0.2874 rms_B_bonded: 2.18 r_work: 0.2761 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2653 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2653 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2649 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2649 r_free = 0.2649 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 = 0.2649 r_free = 0.2649 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2649 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.1386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 19729 Z= 0.129 Angle : 0.522 9.037 26612 Z= 0.263 Chirality : 0.038 0.157 3013 Planarity : 0.004 0.065 3143 Dihedral : 14.327 169.715 3439 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 2.37 % Allowed : 21.77 % 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: 2.27 (0.18), residues: 2333 helix: 2.28 (0.12), residues: 1748 sheet: -0.31 (1.03), residues: 28 loop : -0.99 (0.28), residues: 557 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 0.014 0.001 TRP L 143 HIS 0.003 0.000 HIS H 210 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 (19729) covalent geometry : angle 0.52210 / 0.26 (26612) hydrogen bonds : bond 0.04009 / 2.67 ( 1301) hydrogen bonds : angle 3.86302 / 2.72 ( 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 297 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 252 time to evaluate : 0.732 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 71 GLU cc_start: 0.7810 (tt0) cc_final: 0.6597 (mm-30) REVERT: H 80 ARG cc_start: 0.7685 (mtp-110) cc_final: 0.7479 (mtp-110) REVERT: H 214 GLN cc_start: 0.8710 (mt0) cc_final: 0.7692 (pp30) REVERT: K 86 ARG cc_start: 0.8762 (mtp85) cc_final: 0.8547 (mtp85) REVERT: K 94 SER cc_start: 0.8838 (m) cc_final: 0.8398 (p) REVERT: M 22 ARG cc_start: 0.8666 (mtp180) cc_final: 0.6890 (mmt180) REVERT: M 115 PHE cc_start: 0.7744 (t80) cc_final: 0.7238 (m-80) REVERT: M 150 MET cc_start: 0.8845 (tpp) cc_final: 0.8381 (mmt) REVERT: M 303 TRP cc_start: 0.9204 (OUTLIER) cc_final: 0.8036 (m-10) REVERT: M 373 MET cc_start: 0.8957 (mmm) cc_final: 0.8720 (mmt) REVERT: M 381 MET cc_start: 0.9111 (mtt) cc_final: 0.8792 (mtt) REVERT: B 45 MET cc_start: 0.6455 (mmt) cc_final: 0.5709 (pmm) REVERT: B 91 ARG cc_start: 0.8331 (mmt180) cc_final: 0.7785 (mmt180) REVERT: B 116 GLN cc_start: 0.7512 (OUTLIER) cc_final: 0.7133 (mp10) REVERT: B 119 GLU cc_start: 0.8571 (mm-30) cc_final: 0.7949 (tp30) REVERT: B 122 TRP cc_start: 0.8643 (m-90) cc_final: 0.8324 (m-90) REVERT: B 171 LEU cc_start: 0.9459 (mp) cc_final: 0.8939 (tm) REVERT: B 173 GLN cc_start: 0.8448 (tt0) cc_final: 0.7913 (tm-30) REVERT: B 179 GLU cc_start: 0.8628 (pt0) cc_final: 0.7482 (tm-30) REVERT: B 180 ARG cc_start: 0.7437 (mmp80) cc_final: 0.6735 (ppt-90) REVERT: B 181 ARG cc_start: 0.7610 (tpp-160) cc_final: 0.6830 (tpt-90) REVERT: B 192 VAL cc_start: 0.7662 (m) cc_final: 0.7201 (t) REVERT: L 58 GLN cc_start: 0.8559 (mt0) cc_final: 0.7891 (mm110) REVERT: L 354 LEU cc_start: 0.7964 (mt) cc_final: 0.7565 (pp) REVERT: L 547 LYS cc_start: 0.8815 (OUTLIER) cc_final: 0.8581 (mptm) REVERT: L 578 PHE cc_start: 0.8153 (m-10) cc_final: 0.7249 (t80) REVERT: N 104 GLU cc_start: 0.9284 (mp0) cc_final: 0.8583 (mp0) REVERT: N 207 PHE cc_start: 0.9114 (OUTLIER) cc_final: 0.8123 (t80) REVERT: N 255 MET cc_start: 0.9085 (tpt) cc_final: 0.8730 (tpt) outliers start: 45 outliers final: 30 residues processed: 278 average time/residue: 0.6682 time to fit residues: 208.1540 Evaluate side-chains 279 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 245 time to evaluate : 0.777 ------------------------------------------------------------------------------- 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 81 ILE 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 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 117 MET 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 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 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: 0.8980 chunk 86 optimal weight: 2.9990 chunk 125 optimal weight: 0.7980 chunk 218 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 chunk 219 optimal weight: 0.6980 chunk 97 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 166 optimal weight: 0.5980 chunk 145 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3224 r_free = 0.3224 target = 0.087487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.066016 restraints weight = 49491.698| |-----------------------------------------------------------------------------| r_work (start): 0.2850 rms_B_bonded: 2.44 r_work: 0.2730 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2730 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2722 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2722 r_free = 0.2722 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 = 0.2722 r_free = 0.2722 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2722 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.1404 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= 0.139 Angle : 0.534 8.966 26612 Z= 0.268 Chirality : 0.039 0.159 3013 Planarity : 0.004 0.067 3143 Dihedral : 14.250 170.209 3439 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 1.95 % Allowed : 22.56 % 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: 2.23 (0.18), residues: 2333 helix: 2.25 (0.12), residues: 1753 sheet: -0.33 (1.03), residues: 28 loop : -1.04 (0.28), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 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 H 210 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 (19729) covalent geometry : angle 0.53356 / 0.27 (26612) hydrogen bonds : bond 0.04110 / 2.74 ( 1301) hydrogen bonds : angle 3.88914 / 2.74 ( 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 289 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 252 time to evaluate : 0.755 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 71 GLU cc_start: 0.7775 (tt0) cc_final: 0.6562 (mm-30) REVERT: H 80 ARG cc_start: 0.7645 (mtp-110) cc_final: 0.7410 (mtp-110) REVERT: H 214 GLN cc_start: 0.8729 (mt0) cc_final: 0.7781 (pp30) REVERT: H 216 GLU cc_start: 0.7844 (pm20) cc_final: 0.7419 (pm20) REVERT: K 1 MET cc_start: 0.7314 (pmt) cc_final: 0.7080 (pmm) REVERT: K 86 ARG cc_start: 0.8721 (mtp85) cc_final: 0.8492 (mtp85) REVERT: K 94 SER cc_start: 0.8837 (m) cc_final: 0.8382 (p) REVERT: M 22 ARG cc_start: 0.8624 (mtp180) cc_final: 0.6858 (mmt180) REVERT: M 115 PHE cc_start: 0.7679 (t80) cc_final: 0.7228 (m-80) REVERT: M 150 MET cc_start: 0.8718 (tpp) cc_final: 0.8226 (mmt) REVERT: M 303 TRP cc_start: 0.9145 (OUTLIER) cc_final: 0.7975 (m-10) REVERT: M 373 MET cc_start: 0.8910 (mmm) cc_final: 0.8664 (mmt) REVERT: B 45 MET cc_start: 0.6383 (mmt) cc_final: 0.5687 (pmm) REVERT: B 91 ARG cc_start: 0.8260 (mmt180) cc_final: 0.7700 (mmt180) REVERT: B 116 GLN cc_start: 0.7494 (OUTLIER) cc_final: 0.7111 (mp10) REVERT: B 119 GLU cc_start: 0.8495 (mm-30) cc_final: 0.7841 (tp30) REVERT: B 122 TRP cc_start: 0.8627 (m-90) cc_final: 0.8286 (m-90) REVERT: B 171 LEU cc_start: 0.9453 (mp) cc_final: 0.8942 (tm) REVERT: B 173 GLN cc_start: 0.8429 (tt0) cc_final: 0.7907 (tm-30) REVERT: B 179 GLU cc_start: 0.8619 (pt0) cc_final: 0.7489 (tm-30) REVERT: B 180 ARG cc_start: 0.7443 (mmp80) cc_final: 0.6686 (ppt-90) REVERT: B 181 ARG cc_start: 0.7540 (tpp-160) cc_final: 0.6749 (tpt-90) REVERT: B 192 VAL cc_start: 0.7672 (m) cc_final: 0.7230 (t) REVERT: L 58 GLN cc_start: 0.8489 (mt0) cc_final: 0.7827 (mm110) REVERT: L 354 LEU cc_start: 0.7961 (mt) cc_final: 0.7562 (pp) REVERT: L 547 LYS cc_start: 0.8782 (OUTLIER) cc_final: 0.8540 (mptm) REVERT: L 578 PHE cc_start: 0.8073 (m-10) cc_final: 0.7204 (t80) REVERT: N 104 GLU cc_start: 0.9206 (mp0) cc_final: 0.8473 (mp0) REVERT: N 207 PHE cc_start: 0.9060 (OUTLIER) cc_final: 0.8049 (t80) outliers start: 37 outliers final: 30 residues processed: 273 average time/residue: 0.6653 time to fit residues: 203.1390 Evaluate side-chains 282 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 248 time to evaluate : 0.686 ------------------------------------------------------------------------------- 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 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 81 ILE 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 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 117 MET 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 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 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 Chi-restraints excluded: chain N residue 477 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 13 optimal weight: 1.9990 chunk 160 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 170 optimal weight: 0.0670 chunk 204 optimal weight: 0.7980 chunk 188 optimal weight: 0.6980 chunk 227 optimal weight: 0.8980 chunk 20 optimal weight: 6.9990 chunk 134 optimal weight: 1.9990 chunk 179 optimal weight: 0.0070 chunk 69 optimal weight: 0.5980 overall best weight: 0.4336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 317 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.089030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.067860 restraints weight = 42371.789| |-----------------------------------------------------------------------------| r_work (start): 0.2886 rms_B_bonded: 2.30 r_work: 0.2772 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2658 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2658 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2659 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2659 r_free = 0.2659 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2659 r_free = 0.2659 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2659 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 moved from start: 0.1468 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= 0.114 Angle : 0.524 9.081 26612 Z= 0.264 Chirality : 0.038 0.173 3013 Planarity : 0.004 0.069 3143 Dihedral : 14.018 170.864 3439 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 1.95 % Allowed : 22.61 % Favored : 75.45 % 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: 2.30 (0.18), residues: 2333 helix: 2.31 (0.12), residues: 1746 sheet: -0.34 (1.03), residues: 28 loop : -0.98 (0.28), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG H 209 TYR 0.024 0.001 TYR M 435 PHE 0.023 0.001 PHE L 341 TRP 0.017 0.001 TRP L 143 HIS 0.003 0.000 HIS H 210 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.11 (19729) covalent geometry : angle 0.52432 / 0.26 (26612) hydrogen bonds : bond 0.03847 / 2.57 ( 1301) hydrogen bonds : angle 3.82199 / 2.69 ( 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 299 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 262 time to evaluate : 0.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 71 GLU cc_start: 0.7809 (tt0) cc_final: 0.6598 (mm-30) REVERT: H 80 ARG cc_start: 0.7615 (mtp-110) cc_final: 0.7384 (mtp-110) REVERT: H 214 GLN cc_start: 0.8704 (mt0) cc_final: 0.7824 (pp30) REVERT: H 216 GLU cc_start: 0.7860 (pm20) cc_final: 0.7450 (pm20) REVERT: J 89 LYS cc_start: 0.8721 (mttm) cc_final: 0.8439 (mptm) REVERT: K 46 PHE cc_start: 0.9084 (OUTLIER) cc_final: 0.8467 (t80) REVERT: K 86 ARG cc_start: 0.8779 (mtp85) cc_final: 0.8557 (mtp85) REVERT: K 94 SER cc_start: 0.8803 (m) cc_final: 0.8371 (p) REVERT: M 22 ARG cc_start: 0.8638 (mtp180) cc_final: 0.6870 (mmt180) REVERT: M 115 PHE cc_start: 0.7756 (t80) cc_final: 0.7245 (m-80) REVERT: M 150 MET cc_start: 0.8809 (tpp) cc_final: 0.8381 (mmt) REVERT: M 303 TRP cc_start: 0.9201 (OUTLIER) cc_final: 0.8133 (m-10) REVERT: M 373 MET cc_start: 0.8972 (mmm) cc_final: 0.8733 (mmt) REVERT: B 45 MET cc_start: 0.6408 (mmt) cc_final: 0.5647 (pmm) REVERT: B 91 ARG cc_start: 0.8348 (mmt180) cc_final: 0.7879 (mmp80) REVERT: B 116 GLN cc_start: 0.7529 (OUTLIER) cc_final: 0.6977 (mp10) REVERT: B 119 GLU cc_start: 0.8589 (mm-30) cc_final: 0.7976 (tp30) REVERT: B 122 TRP cc_start: 0.8655 (m-90) cc_final: 0.8344 (m-90) REVERT: B 171 LEU cc_start: 0.9464 (mp) cc_final: 0.8945 (tm) REVERT: B 173 GLN cc_start: 0.8457 (tt0) cc_final: 0.7892 (tm-30) REVERT: B 179 GLU cc_start: 0.8630 (pt0) cc_final: 0.7487 (tm-30) REVERT: B 180 ARG cc_start: 0.7428 (mmp80) cc_final: 0.6757 (ppt-90) REVERT: B 181 ARG cc_start: 0.7609 (tpp-160) cc_final: 0.6829 (tpt-90) REVERT: B 192 VAL cc_start: 0.7653 (m) cc_final: 0.7177 (t) REVERT: L 58 GLN cc_start: 0.8576 (mt0) cc_final: 0.7904 (mm110) REVERT: L 354 LEU cc_start: 0.7951 (mt) cc_final: 0.7546 (pp) REVERT: L 547 LYS cc_start: 0.8810 (OUTLIER) cc_final: 0.8591 (mptm) REVERT: L 578 PHE cc_start: 0.8149 (m-10) cc_final: 0.7240 (t80) REVERT: N 104 GLU cc_start: 0.9288 (mp0) cc_final: 0.8574 (mp0) REVERT: N 207 PHE cc_start: 0.9105 (OUTLIER) cc_final: 0.8121 (t80) REVERT: N 255 MET cc_start: 0.9061 (tpt) cc_final: 0.8762 (tpt) outliers start: 37 outliers final: 27 residues processed: 283 average time/residue: 0.6405 time to fit residues: 203.6038 Evaluate side-chains 281 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 249 time to evaluate : 0.716 ------------------------------------------------------------------------------- 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 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 81 ILE 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 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 117 MET 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 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 246 SER Chi-restraints excluded: chain N residue 263 VAL Chi-restraints excluded: chain N residue 477 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 110 optimal weight: 2.9990 chunk 94 optimal weight: 0.8980 chunk 114 optimal weight: 0.6980 chunk 52 optimal weight: 0.6980 chunk 100 optimal weight: 0.6980 chunk 231 optimal weight: 0.7980 chunk 165 optimal weight: 0.9990 chunk 113 optimal weight: 0.5980 chunk 76 optimal weight: 1.9990 chunk 127 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3235 r_free = 0.3235 target = 0.088143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.066539 restraints weight = 50068.585| |-----------------------------------------------------------------------------| r_work (start): 0.2859 rms_B_bonded: 2.49 r_work: 0.2738 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2734 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2734 r_free = 0.2734 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2734 r_free = 0.2734 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2734 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.1467 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= 0.135 Angle : 0.540 9.359 26612 Z= 0.270 Chirality : 0.038 0.156 3013 Planarity : 0.004 0.067 3143 Dihedral : 13.965 171.442 3439 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 1.84 % Allowed : 22.82 % Favored : 75.34 % 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: 2.25 (0.18), residues: 2333 helix: 2.26 (0.12), residues: 1754 sheet: -0.35 (1.02), residues: 28 loop : -1.02 (0.28), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 209 TYR 0.031 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 0.00315 / 0.13 (19729) covalent geometry : angle 0.54029 / 0.27 (26612) hydrogen bonds : bond 0.03995 / 2.66 ( 1301) hydrogen bonds : angle 3.85372 / 2.71 ( 3812) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8498.25 seconds wall clock time: 145 minutes 18.21 seconds (8718.21 seconds total)