Starting phenix.real_space_refine on Wed Sep 17 14:38:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xst_38628/09_2025/8xst_38628.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xst_38628/09_2025/8xst_38628.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8xst_38628/09_2025/8xst_38628.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xst_38628/09_2025/8xst_38628.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8xst_38628/09_2025/8xst_38628.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xst_38628/09_2025/8xst_38628.map" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.080 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 2 5.49 5 Mg 1 5.21 5 S 33 5.16 5 C 5781 2.51 5 N 1612 2.21 5 O 1690 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 31 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9119 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4348 Number of conformers: 1 Conformer: "" Number of residues, atoms: 574, 4348 Classifications: {'peptide': 574} Link IDs: {'PTRANS': 19, 'TRANS': 554} Chain: "B" Number of atoms: 4743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 619, 4743 Classifications: {'peptide': 619} Link IDs: {'PTRANS': 18, 'TRANS': 600} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.11, per 1000 atoms: 0.23 Number of scatterers: 9119 At special positions: 0 Unit cell: (69.056, 92.352, 149.76, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 33 16.00 P 2 15.00 Mg 1 11.99 O 1690 8.00 N 1612 7.00 C 5781 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: 0.87 Conformation dependent library (CDL) restraints added in 261.4 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2378 Ramachandran restraints generated. 1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2194 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 5 sheets defined 60.4% alpha, 3.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'A' and resid -1 through 10 removed outlier: 3.743A pdb=" N TRP A 3 " --> pdb=" O SER A -1 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ALA A 4 " --> pdb=" O ASN A 0 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLN A 8 " --> pdb=" O ALA A 4 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N TYR A 9 " --> pdb=" O LEU A 5 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N VAL A 10 " --> pdb=" O LEU A 6 " (cutoff:3.500A) Processing helix chain 'A' and resid 22 through 27 removed outlier: 3.692A pdb=" N ILE A 26 " --> pdb=" O VAL A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 32 through 45 removed outlier: 3.828A pdb=" N THR A 36 " --> pdb=" O LEU A 32 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA A 40 " --> pdb=" O THR A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 57 removed outlier: 3.836A pdb=" N ILE A 54 " --> pdb=" O ASP A 50 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N VAL A 55 " --> pdb=" O THR A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 71 removed outlier: 3.608A pdb=" N MET A 61 " --> pdb=" O LEU A 57 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N VAL A 69 " --> pdb=" O THR A 65 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N CYS A 71 " --> pdb=" O LEU A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 83 removed outlier: 3.948A pdb=" N ARG A 81 " --> pdb=" O PHE A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 99 removed outlier: 3.675A pdb=" N ARG A 91 " --> pdb=" O GLY A 87 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N THR A 96 " --> pdb=" O ALA A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 110 removed outlier: 3.722A pdb=" N PHE A 109 " --> pdb=" O GLU A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 130 removed outlier: 4.180A pdb=" N ILE A 125 " --> pdb=" O ASP A 121 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLN A 130 " --> pdb=" O GLN A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 153 Processing helix chain 'A' and resid 154 through 157 Processing helix chain 'A' and resid 158 through 165 removed outlier: 3.814A pdb=" N VAL A 165 " --> pdb=" O LEU A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 203 removed outlier: 3.899A pdb=" N ILE A 175 " --> pdb=" O ALA A 171 " (cutoff:3.500A) Proline residue: A 181 - end of helix removed outlier: 3.889A pdb=" N MET A 186 " --> pdb=" O VAL A 182 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLN A 187 " --> pdb=" O PHE A 183 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N SER A 188 " --> pdb=" O THR A 184 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLY A 192 " --> pdb=" O SER A 188 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ILE A 193 " --> pdb=" O LEU A 189 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ARG A 195 " --> pdb=" O ASP A 191 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N VAL A 196 " --> pdb=" O GLY A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 208 removed outlier: 3.874A pdb=" N ARG A 208 " --> pdb=" O ILE A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 238 removed outlier: 3.580A pdb=" N GLN A 225 " --> pdb=" O ALA A 221 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N THR A 226 " --> pdb=" O GLU A 222 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ASP A 229 " --> pdb=" O GLN A 225 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEU A 232 " --> pdb=" O SER A 228 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLU A 233 " --> pdb=" O ASP A 229 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ARG A 236 " --> pdb=" O LEU A 232 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N TRP A 237 " --> pdb=" O GLU A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 267 removed outlier: 3.567A pdb=" N TRP A 258 " --> pdb=" O VAL A 254 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ARG A 263 " --> pdb=" O PHE A 259 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ALA A 266 " --> pdb=" O LEU A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 293 removed outlier: 3.928A pdb=" N ILE A 275 " --> pdb=" O VAL A 271 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N MET A 290 " --> pdb=" O MET A 286 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ALA A 291 " --> pdb=" O ALA A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 302 removed outlier: 3.731A pdb=" N ARG A 300 " --> pdb=" O VAL A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 313 Processing helix chain 'A' and resid 373 through 382 removed outlier: 3.520A pdb=" N LEU A 377 " --> pdb=" O GLY A 373 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N ILE A 378 " --> pdb=" O LYS A 374 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N SER A 379 " --> pdb=" O SER A 375 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU A 380 " --> pdb=" O THR A 376 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ILE A 381 " --> pdb=" O LEU A 377 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N CYS A 382 " --> pdb=" O ILE A 378 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 373 through 382' Processing helix chain 'A' and resid 398 through 402 Processing helix chain 'A' and resid 403 through 409 Processing helix chain 'A' and resid 425 through 429 Processing helix chain 'A' and resid 430 through 433 Processing helix chain 'A' and resid 440 through 448 removed outlier: 3.809A pdb=" N ALA A 444 " --> pdb=" O GLU A 440 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LEU A 445 " --> pdb=" O MET A 441 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ARG A 446 " --> pdb=" O TRP A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 455 removed outlier: 3.732A pdb=" N VAL A 454 " --> pdb=" O ALA A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 487 Processing helix chain 'A' and resid 503 through 518 Processing helix chain 'A' and resid 552 through 558 removed outlier: 3.988A pdb=" N ALA A 558 " --> pdb=" O ASP A 554 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 569 removed outlier: 3.820A pdb=" N SER A 569 " --> pdb=" O GLU A 565 " (cutoff:3.500A) Processing helix chain 'B' and resid 17 through 27 removed outlier: 3.522A pdb=" N ALA B 21 " --> pdb=" O PHE B 17 " (cutoff:3.500A) Processing helix chain 'B' and resid 32 through 40 removed outlier: 4.111A pdb=" N VAL B 38 " --> pdb=" O LEU B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 68 removed outlier: 4.093A pdb=" N ARG B 54 " --> pdb=" O VAL B 50 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU B 63 " --> pdb=" O ALA B 59 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLY B 66 " --> pdb=" O LEU B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 88 Processing helix chain 'B' and resid 90 through 100 removed outlier: 3.689A pdb=" N MET B 100 " --> pdb=" O LEU B 96 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 158 removed outlier: 3.599A pdb=" N VAL B 113 " --> pdb=" O ASP B 109 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU B 129 " --> pdb=" O LEU B 125 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL B 131 " --> pdb=" O ALA B 127 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N VAL B 133 " --> pdb=" O LEU B 129 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N GLN B 134 " --> pdb=" O LEU B 130 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N VAL B 147 " --> pdb=" O GLN B 143 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA B 148 " --> pdb=" O ARG B 144 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N HIS B 158 " --> pdb=" O GLN B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 166 removed outlier: 3.644A pdb=" N PHE B 165 " --> pdb=" O PRO B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 178 Processing helix chain 'B' and resid 178 through 190 removed outlier: 3.874A pdb=" N ASP B 182 " --> pdb=" O THR B 178 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASN B 183 " --> pdb=" O ASN B 179 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ILE B 184 " --> pdb=" O ASP B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 196 through 208 removed outlier: 5.387A pdb=" N VAL B 202 " --> pdb=" O SER B 198 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N VAL B 205 " --> pdb=" O THR B 201 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LEU B 206 " --> pdb=" O VAL B 202 " (cutoff:3.500A) Processing helix chain 'B' and resid 215 through 219 Processing helix chain 'B' and resid 222 through 236 removed outlier: 3.801A pdb=" N ALA B 226 " --> pdb=" O VAL B 222 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N THR B 235 " --> pdb=" O THR B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 243 removed outlier: 3.730A pdb=" N VAL B 243 " --> pdb=" O GLN B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 261 removed outlier: 3.562A pdb=" N HIS B 255 " --> pdb=" O ARG B 251 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N GLU B 258 " --> pdb=" O ALA B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 268 Processing helix chain 'B' and resid 271 through 297 removed outlier: 3.533A pdb=" N SER B 284 " --> pdb=" O ALA B 280 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N GLU B 285 " --> pdb=" O GLU B 281 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N THR B 286 " --> pdb=" O LEU B 282 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLN B 288 " --> pdb=" O SER B 284 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLY B 292 " --> pdb=" O GLN B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 300 through 305 removed outlier: 3.699A pdb=" N THR B 304 " --> pdb=" O VAL B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 308 No H-bonds generated for 'chain 'B' and resid 306 through 308' Processing helix chain 'B' and resid 309 through 324 removed outlier: 3.567A pdb=" N ALA B 314 " --> pdb=" O LEU B 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 344 removed outlier: 3.572A pdb=" N ALA B 335 " --> pdb=" O GLY B 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 354 through 363 removed outlier: 3.674A pdb=" N GLY B 360 " --> pdb=" O THR B 356 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 372 removed outlier: 3.941A pdb=" N PHE B 368 " --> pdb=" O ALA B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 438 Processing helix chain 'B' and resid 454 through 458 removed outlier: 3.606A pdb=" N SER B 457 " --> pdb=" O ASP B 454 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL B 458 " --> pdb=" O ILE B 455 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 454 through 458' Processing helix chain 'B' and resid 459 through 468 removed outlier: 3.625A pdb=" N SER B 466 " --> pdb=" O SER B 462 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N GLY B 468 " --> pdb=" O ARG B 464 " (cutoff:3.500A) Processing helix chain 'B' and resid 480 through 486 Processing helix chain 'B' and resid 493 through 498 Processing helix chain 'B' and resid 499 through 502 removed outlier: 3.536A pdb=" N THR B 502 " --> pdb=" O GLU B 499 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 499 through 502' Processing helix chain 'B' and resid 506 through 511 removed outlier: 3.682A pdb=" N HIS B 511 " --> pdb=" O ASP B 507 " (cutoff:3.500A) Processing helix chain 'B' and resid 531 through 544 removed outlier: 3.600A pdb=" N THR B 537 " --> pdb=" O LYS B 533 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ALA B 544 " --> pdb=" O ARG B 540 " (cutoff:3.500A) Processing helix chain 'B' and resid 559 through 570 removed outlier: 3.541A pdb=" N LEU B 564 " --> pdb=" O THR B 560 " (cutoff:3.500A) Processing helix chain 'B' and resid 608 through 614 Processing helix chain 'B' and resid 617 through 627 removed outlier: 3.974A pdb=" N ARG B 624 " --> pdb=" O TRP B 620 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N VAL B 625 " --> pdb=" O GLU B 621 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N HIS B 626 " --> pdb=" O MET B 622 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 335 through 339 removed outlier: 5.074A pdb=" N HIS A 337 " --> pdb=" O PHE A 356 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N PHE A 356 " --> pdb=" O HIS A 337 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 411 through 414 removed outlier: 6.454A pdb=" N GLY A 412 " --> pdb=" O LEU A 494 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N ASP A 496 " --> pdb=" O GLY A 412 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N VAL A 414 " --> pdb=" O ASP A 496 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N TYR A 493 " --> pdb=" O VAL A 524 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N VAL A 526 " --> pdb=" O TYR A 493 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N PHE A 495 " --> pdb=" O VAL A 526 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N THR A 364 " --> pdb=" O ILE A 525 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N THR A 363 " --> pdb=" O GLN A 538 " (cutoff:3.500A) removed outlier: 8.039A pdb=" N VAL A 540 " --> pdb=" O THR A 363 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N ALA A 365 " --> pdb=" O VAL A 540 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N ILE A 542 " --> pdb=" O ALA A 365 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N VAL A 367 " --> pdb=" O ILE A 542 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLY A 549 " --> pdb=" O VAL A 541 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 423 through 424 removed outlier: 3.523A pdb=" N GLY A 423 " --> pdb=" O VAL A 465 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 421 through 423 removed outlier: 3.578A pdb=" N GLU B 605 " --> pdb=" O VAL B 597 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 469 through 470 removed outlier: 6.666A pdb=" N VAL B 470 " --> pdb=" O ASP B 552 " (cutoff:3.500A) 384 hydrogen bonds defined for protein. 1128 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: 1.40 Time building geometry restraints manager: 1.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1503 1.31 - 1.43: 2394 1.43 - 1.56: 5313 1.56 - 1.68: 3 1.68 - 1.81: 61 Bond restraints: 9274 Sorted by residual: bond pdb=" CA GLN B 239 " pdb=" C GLN B 239 " ideal model delta sigma weight residual 1.524 1.460 0.063 1.26e-02 6.30e+03 2.53e+01 bond pdb=" C GLN B 239 " pdb=" O GLN B 239 " ideal model delta sigma weight residual 1.238 1.186 0.052 1.28e-02 6.10e+03 1.64e+01 bond pdb=" CA GLN B 239 " pdb=" CB GLN B 239 " ideal model delta sigma weight residual 1.530 1.474 0.055 1.58e-02 4.01e+03 1.23e+01 bond pdb=" CG GLN B 239 " pdb=" CD GLN B 239 " ideal model delta sigma weight residual 1.516 1.460 0.056 2.50e-02 1.60e+03 4.95e+00 bond pdb=" CD GLN B 239 " pdb=" NE2 GLN B 239 " ideal model delta sigma weight residual 1.328 1.283 0.045 2.10e-02 2.27e+03 4.57e+00 ... (remaining 9269 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.54: 12403 2.54 - 5.08: 193 5.08 - 7.62: 25 7.62 - 10.16: 6 10.16 - 12.70: 1 Bond angle restraints: 12628 Sorted by residual: angle pdb=" N ILE B 48 " pdb=" CA ILE B 48 " pdb=" C ILE B 48 " ideal model delta sigma weight residual 113.53 106.46 7.07 9.80e-01 1.04e+00 5.21e+01 angle pdb=" C GLN B 239 " pdb=" N PRO B 240 " pdb=" CA PRO B 240 " ideal model delta sigma weight residual 119.87 112.45 7.42 1.04e+00 9.25e-01 5.09e+01 angle pdb=" N VAL B 202 " pdb=" CA VAL B 202 " pdb=" C VAL B 202 " ideal model delta sigma weight residual 113.71 106.98 6.73 9.50e-01 1.11e+00 5.02e+01 angle pdb=" N ILE B 192 " pdb=" CA ILE B 192 " pdb=" C ILE B 192 " ideal model delta sigma weight residual 113.71 107.13 6.58 9.50e-01 1.11e+00 4.80e+01 angle pdb=" N ARG A 360 " pdb=" CA ARG A 360 " pdb=" C ARG A 360 " ideal model delta sigma weight residual 111.37 120.29 -8.92 1.64e+00 3.72e-01 2.96e+01 ... (remaining 12623 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.48: 5347 32.48 - 64.96: 147 64.96 - 97.43: 14 97.43 - 129.91: 1 129.91 - 162.39: 2 Dihedral angle restraints: 5511 sinusoidal: 2102 harmonic: 3409 Sorted by residual: dihedral pdb=" O2A ADP B 701 " pdb=" O3A ADP B 701 " pdb=" PA ADP B 701 " pdb=" PB ADP B 701 " ideal model delta sinusoidal sigma weight residual -60.00 102.39 -162.39 1 2.00e+01 2.50e-03 4.69e+01 dihedral pdb=" O1B ADP B 701 " pdb=" O3A ADP B 701 " pdb=" PB ADP B 701 " pdb=" PA ADP B 701 " ideal model delta sinusoidal sigma weight residual -60.00 76.04 -136.05 1 2.00e+01 2.50e-03 4.13e+01 dihedral pdb=" CA PHE B 269 " pdb=" C PHE B 269 " pdb=" N GLY B 270 " pdb=" CA GLY B 270 " ideal model delta harmonic sigma weight residual 180.00 -151.98 -28.02 0 5.00e+00 4.00e-02 3.14e+01 ... (remaining 5508 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 1391 0.078 - 0.155: 124 0.155 - 0.233: 1 0.233 - 0.311: 3 0.311 - 0.388: 1 Chirality restraints: 1520 Sorted by residual: chirality pdb=" CA GLN B 239 " pdb=" N GLN B 239 " pdb=" C GLN B 239 " pdb=" CB GLN B 239 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.77e+00 chirality pdb=" CA ARG A 360 " pdb=" N ARG A 360 " pdb=" C ARG A 360 " pdb=" CB ARG A 360 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.14e+00 chirality pdb=" CB ILE A 487 " pdb=" CA ILE A 487 " pdb=" CG1 ILE A 487 " pdb=" CG2 ILE A 487 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.24 2.00e-01 2.50e+01 1.45e+00 ... (remaining 1517 not shown) Planarity restraints: 1617 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU A 213 " -0.046 5.00e-02 4.00e+02 6.95e-02 7.74e+00 pdb=" N PRO A 214 " 0.120 5.00e-02 4.00e+02 pdb=" CA PRO A 214 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 214 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 594 " -0.012 2.00e-02 2.50e+03 2.37e-02 5.63e+00 pdb=" C LEU B 594 " 0.041 2.00e-02 2.50e+03 pdb=" O LEU B 594 " -0.016 2.00e-02 2.50e+03 pdb=" N ILE B 595 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL B 401 " 0.034 5.00e-02 4.00e+02 5.14e-02 4.23e+00 pdb=" N PRO B 402 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO B 402 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 402 " 0.028 5.00e-02 4.00e+02 ... (remaining 1614 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 107 2.62 - 3.19: 8207 3.19 - 3.76: 14030 3.76 - 4.33: 20057 4.33 - 4.90: 33080 Nonbonded interactions: 75481 Sorted by model distance: nonbonded pdb=" OG1 THR B 431 " pdb="MG MG B 702 " model vdw 2.048 2.170 nonbonded pdb=" O3B ADP B 701 " pdb="MG MG B 702 " model vdw 2.179 2.170 nonbonded pdb=" OD2 ASP B 166 " pdb=" OH TYR B 441 " model vdw 2.212 3.040 nonbonded pdb=" O PHE A 421 " pdb=" ND2 ASN A 428 " model vdw 2.232 3.120 nonbonded pdb=" O VAL B 50 " pdb=" OH TYR B 339 " model vdw 2.242 3.040 ... (remaining 75476 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 9.680 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 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 0.063 9274 Z= 0.190 Angle : 0.824 12.699 12628 Z= 0.500 Chirality : 0.046 0.388 1520 Planarity : 0.004 0.070 1617 Dihedral : 15.104 162.388 3317 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.91 % Favored : 92.01 % Rotamer: Outliers : 0.31 % Allowed : 16.41 % Favored : 83.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.57 (0.23), residues: 1189 helix: -2.22 (0.18), residues: 740 sheet: -2.73 (0.59), residues: 64 loop : -2.18 (0.30), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 575 TYR 0.034 0.001 TYR B 354 PHE 0.012 0.001 PHE A 453 TRP 0.030 0.001 TRP B 246 HIS 0.002 0.001 HIS A 152 Details of bonding type rmsd covalent geometry : bond 0.00360 ( 9274) covalent geometry : angle 0.82353 (12628) hydrogen bonds : bond 0.21429 ( 384) hydrogen bonds : angle 8.47394 ( 1128) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2378 Ramachandran restraints generated. 1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2378 Ramachandran restraints generated. 1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 126 time to evaluate : 0.382 Fit side-chains REVERT: A 427 GLU cc_start: 0.8032 (mt-10) cc_final: 0.7266 (tp30) REVERT: A 461 LEU cc_start: 0.8059 (OUTLIER) cc_final: 0.7609 (pp) outliers start: 3 outliers final: 1 residues processed: 127 average time/residue: 0.1035 time to fit residues: 18.1284 Evaluate side-chains 120 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 118 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain B residue 210 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 108 optimal weight: 6.9990 chunk 49 optimal weight: 0.6980 chunk 97 optimal weight: 1.9990 chunk 113 optimal weight: 4.9990 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 9.9990 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 0.9990 chunk 117 optimal weight: 2.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 283 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.139554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.108808 restraints weight = 11305.288| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 1.98 r_work: 0.3084 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2947 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.0959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9274 Z= 0.169 Angle : 0.684 9.326 12628 Z= 0.351 Chirality : 0.044 0.258 1520 Planarity : 0.005 0.055 1617 Dihedral : 8.722 174.394 1322 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.32 % Favored : 92.68 % Rotamer: Outliers : 3.76 % Allowed : 15.05 % Favored : 81.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.98 (0.23), residues: 1189 helix: -1.69 (0.18), residues: 740 sheet: -2.61 (0.61), residues: 64 loop : -2.06 (0.30), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 477 TYR 0.023 0.001 TYR B 354 PHE 0.013 0.001 PHE A 453 TRP 0.013 0.001 TRP B 246 HIS 0.002 0.000 HIS A 152 Details of bonding type rmsd covalent geometry : bond 0.00399 ( 9274) covalent geometry : angle 0.68364 (12628) hydrogen bonds : bond 0.04312 ( 384) hydrogen bonds : angle 4.88138 ( 1128) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2378 Ramachandran restraints generated. 1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2378 Ramachandran restraints generated. 1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 131 time to evaluate : 0.368 Fit side-chains REVERT: A 8 GLN cc_start: 0.8608 (OUTLIER) cc_final: 0.7184 (tt0) REVERT: A 43 ASP cc_start: 0.7913 (m-30) cc_final: 0.7651 (m-30) REVERT: A 136 LEU cc_start: 0.8290 (OUTLIER) cc_final: 0.7946 (tt) REVERT: A 186 MET cc_start: 0.8293 (ttt) cc_final: 0.8092 (ttm) REVERT: A 226 THR cc_start: 0.8476 (m) cc_final: 0.8204 (m) REVERT: A 427 GLU cc_start: 0.8385 (mt-10) cc_final: 0.7457 (tp30) REVERT: B 46 ILE cc_start: 0.8116 (OUTLIER) cc_final: 0.7730 (tp) REVERT: B 79 GLU cc_start: 0.8315 (mm-30) cc_final: 0.7704 (tp30) REVERT: B 152 GLU cc_start: 0.7850 (tp30) cc_final: 0.7640 (tp30) outliers start: 36 outliers final: 20 residues processed: 158 average time/residue: 0.0956 time to fit residues: 21.2205 Evaluate side-chains 139 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 116 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 GLN Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 470 ILE Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 325 THR Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 372 ASP Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 411 SER Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 549 LEU Chi-restraints excluded: chain B residue 555 THR Chi-restraints excluded: chain B residue 579 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 74 optimal weight: 3.9990 chunk 103 optimal weight: 2.9990 chunk 66 optimal weight: 0.0970 chunk 39 optimal weight: 7.9990 chunk 73 optimal weight: 0.0270 chunk 102 optimal weight: 3.9990 chunk 61 optimal weight: 0.8980 chunk 55 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 90 optimal weight: 3.9990 chunk 80 optimal weight: 0.9990 overall best weight: 1.0040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.139579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.108588 restraints weight = 11118.427| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 1.98 r_work: 0.3078 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2942 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.1361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 9274 Z= 0.153 Angle : 0.643 9.219 12628 Z= 0.329 Chirality : 0.043 0.216 1520 Planarity : 0.004 0.057 1617 Dihedral : 8.092 163.181 1322 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.06 % Favored : 92.94 % Rotamer: Outliers : 4.28 % Allowed : 15.88 % Favored : 79.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.58 (0.24), residues: 1189 helix: -1.38 (0.19), residues: 749 sheet: -2.30 (0.64), residues: 62 loop : -1.93 (0.31), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 477 TYR 0.017 0.001 TYR B 354 PHE 0.011 0.001 PHE A 453 TRP 0.013 0.001 TRP B 246 HIS 0.002 0.001 HIS A 152 Details of bonding type rmsd covalent geometry : bond 0.00357 ( 9274) covalent geometry : angle 0.64267 (12628) hydrogen bonds : bond 0.03895 ( 384) hydrogen bonds : angle 4.45680 ( 1128) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2378 Ramachandran restraints generated. 1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2378 Ramachandran restraints generated. 1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 125 time to evaluate : 0.358 Fit side-chains REVERT: A 8 GLN cc_start: 0.8626 (OUTLIER) cc_final: 0.7189 (tt0) REVERT: A 43 ASP cc_start: 0.7920 (m-30) cc_final: 0.7712 (m-30) REVERT: A 226 THR cc_start: 0.8486 (m) cc_final: 0.8220 (m) REVERT: A 400 ARG cc_start: 0.8375 (OUTLIER) cc_final: 0.8114 (ptt180) REVERT: A 427 GLU cc_start: 0.8450 (mt-10) cc_final: 0.7552 (tp30) REVERT: A 461 LEU cc_start: 0.7991 (OUTLIER) cc_final: 0.7319 (pp) REVERT: A 557 LEU cc_start: 0.8085 (tp) cc_final: 0.7786 (tp) REVERT: B 46 ILE cc_start: 0.8153 (OUTLIER) cc_final: 0.7721 (tp) REVERT: B 79 GLU cc_start: 0.8297 (mm-30) cc_final: 0.7743 (tp30) REVERT: B 152 GLU cc_start: 0.7859 (tp30) cc_final: 0.7530 (tp30) REVERT: B 172 GLU cc_start: 0.7897 (tm-30) cc_final: 0.7442 (tm-30) REVERT: B 494 GLU cc_start: 0.7511 (pt0) cc_final: 0.7023 (tt0) REVERT: B 575 ARG cc_start: 0.8762 (mmm160) cc_final: 0.8168 (mpt180) outliers start: 41 outliers final: 31 residues processed: 159 average time/residue: 0.0916 time to fit residues: 20.3377 Evaluate side-chains 155 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 120 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 GLN Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 400 ARG Chi-restraints excluded: chain A residue 452 ASP Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 470 ILE Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 543 ASP Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 325 THR Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 549 LEU Chi-restraints excluded: chain B residue 555 THR Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 579 SER Chi-restraints excluded: chain B residue 615 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 16 optimal weight: 1.9990 chunk 66 optimal weight: 0.0470 chunk 86 optimal weight: 0.7980 chunk 22 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 69 optimal weight: 0.9980 chunk 88 optimal weight: 2.9990 chunk 95 optimal weight: 4.9990 overall best weight: 0.9682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 505 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.140690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.108579 restraints weight = 11250.609| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 2.15 r_work: 0.3098 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2961 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.1560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9274 Z= 0.148 Angle : 0.632 9.177 12628 Z= 0.321 Chirality : 0.043 0.232 1520 Planarity : 0.004 0.059 1617 Dihedral : 7.848 158.313 1322 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer: Outliers : 4.39 % Allowed : 16.82 % Favored : 78.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.36 (0.24), residues: 1189 helix: -1.18 (0.19), residues: 749 sheet: -2.18 (0.66), residues: 62 loop : -1.91 (0.31), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 117 TYR 0.016 0.001 TYR B 354 PHE 0.011 0.001 PHE A 453 TRP 0.008 0.001 TRP B 246 HIS 0.002 0.000 HIS A 152 Details of bonding type rmsd covalent geometry : bond 0.00348 ( 9274) covalent geometry : angle 0.63225 (12628) hydrogen bonds : bond 0.03666 ( 384) hydrogen bonds : angle 4.31585 ( 1128) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2378 Ramachandran restraints generated. 1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2378 Ramachandran restraints generated. 1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 125 time to evaluate : 0.327 Fit side-chains REVERT: A 8 GLN cc_start: 0.8775 (OUTLIER) cc_final: 0.7322 (tt0) REVERT: A 191 ASP cc_start: 0.8343 (t0) cc_final: 0.8030 (m-30) REVERT: A 226 THR cc_start: 0.8739 (m) cc_final: 0.8510 (m) REVERT: A 246 THR cc_start: 0.8671 (OUTLIER) cc_final: 0.8332 (m) REVERT: A 427 GLU cc_start: 0.8552 (mt-10) cc_final: 0.7725 (tp30) REVERT: A 452 ASP cc_start: 0.8714 (OUTLIER) cc_final: 0.8192 (t0) REVERT: A 557 LEU cc_start: 0.8418 (tp) cc_final: 0.8181 (tp) REVERT: B 46 ILE cc_start: 0.8429 (OUTLIER) cc_final: 0.8010 (tp) REVERT: B 79 GLU cc_start: 0.8291 (mm-30) cc_final: 0.7772 (tp30) REVERT: B 83 GLU cc_start: 0.8556 (mm-30) cc_final: 0.8248 (mt-10) REVERT: B 106 GLN cc_start: 0.8784 (tt0) cc_final: 0.8390 (tt0) REVERT: B 152 GLU cc_start: 0.8127 (tp30) cc_final: 0.7923 (tp30) REVERT: B 172 GLU cc_start: 0.8052 (tm-30) cc_final: 0.7573 (tm-30) REVERT: B 200 LEU cc_start: 0.8236 (OUTLIER) cc_final: 0.7994 (mp) REVERT: B 494 GLU cc_start: 0.7710 (pt0) cc_final: 0.7233 (tt0) REVERT: B 575 ARG cc_start: 0.8643 (mmm160) cc_final: 0.8235 (mpt180) outliers start: 42 outliers final: 32 residues processed: 158 average time/residue: 0.0950 time to fit residues: 21.2018 Evaluate side-chains 155 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 118 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 GLN Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 452 ASP Chi-restraints excluded: chain A residue 470 ILE Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 242 PHE Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 325 THR Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 372 ASP Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 411 SER Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 549 LEU Chi-restraints excluded: chain B residue 555 THR Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 578 THR Chi-restraints excluded: chain B residue 579 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 61 optimal weight: 0.5980 chunk 96 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 90 optimal weight: 0.8980 chunk 16 optimal weight: 0.9980 chunk 52 optimal weight: 0.2980 chunk 46 optimal weight: 3.9990 chunk 111 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 chunk 104 optimal weight: 0.9990 chunk 73 optimal weight: 0.0040 overall best weight: 0.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.142909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.110748 restraints weight = 11184.338| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 2.16 r_work: 0.3129 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2993 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.1725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 9274 Z= 0.115 Angle : 0.607 10.891 12628 Z= 0.306 Chirality : 0.042 0.216 1520 Planarity : 0.004 0.061 1617 Dihedral : 7.497 152.327 1320 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 3.97 % Allowed : 17.66 % Favored : 78.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.07 (0.24), residues: 1189 helix: -0.93 (0.19), residues: 747 sheet: -2.13 (0.68), residues: 64 loop : -1.84 (0.31), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 477 TYR 0.014 0.001 TYR B 354 PHE 0.010 0.001 PHE A 453 TRP 0.008 0.001 TRP B 620 HIS 0.001 0.000 HIS A 152 Details of bonding type rmsd covalent geometry : bond 0.00260 ( 9274) covalent geometry : angle 0.60702 (12628) hydrogen bonds : bond 0.03315 ( 384) hydrogen bonds : angle 4.12132 ( 1128) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2378 Ramachandran restraints generated. 1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2378 Ramachandran restraints generated. 1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 130 time to evaluate : 0.369 Fit side-chains REVERT: A 8 GLN cc_start: 0.8740 (OUTLIER) cc_final: 0.7046 (tp40) REVERT: A 135 MET cc_start: 0.8438 (mtt) cc_final: 0.8151 (mtp) REVERT: A 191 ASP cc_start: 0.8293 (t0) cc_final: 0.8009 (m-30) REVERT: A 226 THR cc_start: 0.8692 (m) cc_final: 0.8475 (m) REVERT: A 427 GLU cc_start: 0.8536 (mt-10) cc_final: 0.7700 (tp30) REVERT: A 452 ASP cc_start: 0.8698 (OUTLIER) cc_final: 0.8155 (t0) REVERT: A 557 LEU cc_start: 0.8368 (tp) cc_final: 0.8103 (tp) REVERT: B 46 ILE cc_start: 0.8392 (OUTLIER) cc_final: 0.7991 (tp) REVERT: B 79 GLU cc_start: 0.8279 (mm-30) cc_final: 0.7779 (tp30) REVERT: B 83 GLU cc_start: 0.8551 (mm-30) cc_final: 0.8281 (mt-10) REVERT: B 106 GLN cc_start: 0.8757 (tt0) cc_final: 0.8390 (tt0) REVERT: B 152 GLU cc_start: 0.8171 (tp30) cc_final: 0.7949 (tp30) REVERT: B 172 GLU cc_start: 0.8024 (tm-30) cc_final: 0.7485 (tm-30) REVERT: B 257 GLU cc_start: 0.8370 (tp30) cc_final: 0.7966 (mt-10) REVERT: B 494 GLU cc_start: 0.7632 (pt0) cc_final: 0.7159 (tt0) REVERT: B 575 ARG cc_start: 0.8580 (mmm160) cc_final: 0.8236 (mpt180) REVERT: B 620 TRP cc_start: 0.8625 (t60) cc_final: 0.8352 (t60) outliers start: 38 outliers final: 28 residues processed: 157 average time/residue: 0.0917 time to fit residues: 20.3054 Evaluate side-chains 158 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 127 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 GLN Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 452 ASP Chi-restraints excluded: chain A residue 470 ILE Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 242 PHE Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 325 THR Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 372 ASP Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 411 SER Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 549 LEU Chi-restraints excluded: chain B residue 555 THR Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 579 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 110 optimal weight: 0.2980 chunk 49 optimal weight: 2.9990 chunk 41 optimal weight: 0.5980 chunk 111 optimal weight: 4.9990 chunk 113 optimal weight: 0.8980 chunk 58 optimal weight: 6.9990 chunk 11 optimal weight: 0.0270 chunk 82 optimal weight: 1.9990 chunk 55 optimal weight: 7.9990 chunk 88 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 overall best weight: 0.7640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.142317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.110054 restraints weight = 11194.608| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 2.15 r_work: 0.3121 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2983 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.1853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9274 Z= 0.129 Angle : 0.610 9.001 12628 Z= 0.308 Chirality : 0.043 0.241 1520 Planarity : 0.004 0.061 1617 Dihedral : 7.282 144.867 1320 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer: Outliers : 4.70 % Allowed : 17.66 % Favored : 77.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.92 (0.24), residues: 1189 helix: -0.82 (0.19), residues: 748 sheet: -2.04 (0.69), residues: 64 loop : -1.77 (0.32), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 117 TYR 0.013 0.001 TYR B 354 PHE 0.010 0.001 PHE A 453 TRP 0.006 0.001 TRP B 246 HIS 0.001 0.000 HIS A 88 Details of bonding type rmsd covalent geometry : bond 0.00300 ( 9274) covalent geometry : angle 0.61033 (12628) hydrogen bonds : bond 0.03377 ( 384) hydrogen bonds : angle 4.10162 ( 1128) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2378 Ramachandran restraints generated. 1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2378 Ramachandran restraints generated. 1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 128 time to evaluate : 0.301 Fit side-chains REVERT: A 8 GLN cc_start: 0.8747 (OUTLIER) cc_final: 0.7156 (tt0) REVERT: A 135 MET cc_start: 0.8440 (mtt) cc_final: 0.8148 (mtp) REVERT: A 183 PHE cc_start: 0.8777 (OUTLIER) cc_final: 0.8402 (t80) REVERT: A 191 ASP cc_start: 0.8295 (t0) cc_final: 0.7982 (m-30) REVERT: A 427 GLU cc_start: 0.8558 (mt-10) cc_final: 0.7721 (tp30) REVERT: A 452 ASP cc_start: 0.8663 (OUTLIER) cc_final: 0.8083 (t0) REVERT: A 461 LEU cc_start: 0.8317 (pt) cc_final: 0.8106 (pp) REVERT: A 546 ARG cc_start: 0.8069 (mtp-110) cc_final: 0.7780 (ttm110) REVERT: B 46 ILE cc_start: 0.8411 (OUTLIER) cc_final: 0.7967 (tp) REVERT: B 79 GLU cc_start: 0.8255 (mm-30) cc_final: 0.7759 (tp30) REVERT: B 83 GLU cc_start: 0.8548 (mm-30) cc_final: 0.8286 (mt-10) REVERT: B 106 GLN cc_start: 0.8737 (tt0) cc_final: 0.8380 (tt0) REVERT: B 257 GLU cc_start: 0.8455 (tp30) cc_final: 0.8011 (mt-10) REVERT: B 494 GLU cc_start: 0.7614 (pt0) cc_final: 0.7166 (tt0) REVERT: B 575 ARG cc_start: 0.8550 (mmm160) cc_final: 0.8251 (mpt180) REVERT: B 610 GLU cc_start: 0.8277 (mm-30) cc_final: 0.7841 (tp30) REVERT: B 620 TRP cc_start: 0.8633 (t60) cc_final: 0.8346 (t60) outliers start: 45 outliers final: 36 residues processed: 160 average time/residue: 0.0944 time to fit residues: 21.4651 Evaluate side-chains 164 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 124 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 GLN Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 183 PHE Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 452 ASP Chi-restraints excluded: chain A residue 470 ILE Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 242 PHE Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 325 THR Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 411 SER Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 549 LEU Chi-restraints excluded: chain B residue 555 THR Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 578 THR Chi-restraints excluded: chain B residue 579 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 31 optimal weight: 0.9980 chunk 97 optimal weight: 9.9990 chunk 56 optimal weight: 5.9990 chunk 108 optimal weight: 0.9990 chunk 66 optimal weight: 0.9980 chunk 21 optimal weight: 0.7980 chunk 6 optimal weight: 0.9980 chunk 36 optimal weight: 3.9990 chunk 109 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.141334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.108922 restraints weight = 11183.060| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 2.16 r_work: 0.3110 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2974 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.1973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9274 Z= 0.144 Angle : 0.627 12.487 12628 Z= 0.314 Chirality : 0.043 0.247 1520 Planarity : 0.004 0.061 1617 Dihedral : 7.099 134.592 1320 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 4.81 % Allowed : 17.97 % Favored : 77.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.79 (0.25), residues: 1189 helix: -0.73 (0.19), residues: 747 sheet: -2.00 (0.69), residues: 64 loop : -1.68 (0.32), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 382 TYR 0.013 0.001 TYR A 9 PHE 0.010 0.001 PHE B 509 TRP 0.006 0.001 TRP B 620 HIS 0.002 0.000 HIS A 88 Details of bonding type rmsd covalent geometry : bond 0.00338 ( 9274) covalent geometry : angle 0.62704 (12628) hydrogen bonds : bond 0.03521 ( 384) hydrogen bonds : angle 4.16487 ( 1128) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2378 Ramachandran restraints generated. 1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2378 Ramachandran restraints generated. 1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 121 time to evaluate : 0.344 Fit side-chains REVERT: A 8 GLN cc_start: 0.8779 (OUTLIER) cc_final: 0.7256 (tt0) REVERT: A 135 MET cc_start: 0.8414 (mtt) cc_final: 0.8104 (mtp) REVERT: A 183 PHE cc_start: 0.8755 (OUTLIER) cc_final: 0.8335 (t80) REVERT: A 191 ASP cc_start: 0.8223 (t0) cc_final: 0.7886 (m-30) REVERT: A 427 GLU cc_start: 0.8587 (mt-10) cc_final: 0.7726 (tp30) REVERT: A 452 ASP cc_start: 0.8713 (OUTLIER) cc_final: 0.8134 (t0) REVERT: A 557 LEU cc_start: 0.8456 (tp) cc_final: 0.8216 (mt) REVERT: B 46 ILE cc_start: 0.8289 (OUTLIER) cc_final: 0.7837 (tp) REVERT: B 79 GLU cc_start: 0.8238 (mm-30) cc_final: 0.7745 (tp30) REVERT: B 83 GLU cc_start: 0.8545 (mm-30) cc_final: 0.8291 (mt-10) REVERT: B 106 GLN cc_start: 0.8729 (tt0) cc_final: 0.8353 (tt0) REVERT: B 146 MET cc_start: 0.8442 (mmp) cc_final: 0.8207 (mmp) REVERT: B 152 GLU cc_start: 0.8014 (tp30) cc_final: 0.7756 (tp30) REVERT: B 257 GLU cc_start: 0.8428 (tp30) cc_final: 0.8151 (tt0) REVERT: B 494 GLU cc_start: 0.7505 (pt0) cc_final: 0.7070 (tt0) REVERT: B 575 ARG cc_start: 0.8559 (mmm160) cc_final: 0.8261 (mpt180) REVERT: B 610 GLU cc_start: 0.8261 (mm-30) cc_final: 0.7808 (tp30) outliers start: 46 outliers final: 38 residues processed: 156 average time/residue: 0.0880 time to fit residues: 19.5849 Evaluate side-chains 161 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 119 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 GLN Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 183 PHE Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 452 ASP Chi-restraints excluded: chain A residue 470 ILE Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 242 PHE Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 325 THR Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 411 SER Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 549 LEU Chi-restraints excluded: chain B residue 555 THR Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 578 THR Chi-restraints excluded: chain B residue 579 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 105 optimal weight: 5.9990 chunk 67 optimal weight: 0.7980 chunk 46 optimal weight: 0.8980 chunk 30 optimal weight: 0.0980 chunk 41 optimal weight: 4.9990 chunk 31 optimal weight: 0.8980 chunk 74 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 106 optimal weight: 0.7980 chunk 37 optimal weight: 3.9990 chunk 55 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.142840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.110416 restraints weight = 11065.289| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 2.16 r_work: 0.3127 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2989 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.2062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 9274 Z= 0.124 Angle : 0.617 11.744 12628 Z= 0.306 Chirality : 0.043 0.244 1520 Planarity : 0.004 0.061 1617 Dihedral : 6.773 121.845 1320 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer: Outliers : 4.28 % Allowed : 18.70 % Favored : 77.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.60 (0.25), residues: 1189 helix: -0.58 (0.19), residues: 747 sheet: -1.98 (0.69), residues: 64 loop : -1.61 (0.32), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 477 TYR 0.012 0.001 TYR A 9 PHE 0.009 0.001 PHE A 453 TRP 0.010 0.001 TRP B 620 HIS 0.001 0.000 HIS A 152 Details of bonding type rmsd covalent geometry : bond 0.00285 ( 9274) covalent geometry : angle 0.61727 (12628) hydrogen bonds : bond 0.03276 ( 384) hydrogen bonds : angle 4.03508 ( 1128) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2378 Ramachandran restraints generated. 1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2378 Ramachandran restraints generated. 1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 120 time to evaluate : 0.338 Fit side-chains REVERT: A 8 GLN cc_start: 0.8752 (OUTLIER) cc_final: 0.7142 (tt0) REVERT: A 121 ASP cc_start: 0.8424 (t70) cc_final: 0.7565 (t0) REVERT: A 135 MET cc_start: 0.8440 (mtt) cc_final: 0.8150 (mtp) REVERT: A 183 PHE cc_start: 0.8795 (OUTLIER) cc_final: 0.8395 (t80) REVERT: A 191 ASP cc_start: 0.8283 (t0) cc_final: 0.7969 (m-30) REVERT: A 246 THR cc_start: 0.8530 (OUTLIER) cc_final: 0.8215 (m) REVERT: A 427 GLU cc_start: 0.8558 (mt-10) cc_final: 0.7641 (tp30) REVERT: A 557 LEU cc_start: 0.8529 (tp) cc_final: 0.8283 (mt) REVERT: B 46 ILE cc_start: 0.8290 (OUTLIER) cc_final: 0.7855 (tp) REVERT: B 79 GLU cc_start: 0.8217 (mm-30) cc_final: 0.7729 (tp30) REVERT: B 83 GLU cc_start: 0.8560 (mm-30) cc_final: 0.8308 (mt-10) REVERT: B 106 GLN cc_start: 0.8737 (tt0) cc_final: 0.8388 (tt0) REVERT: B 146 MET cc_start: 0.8445 (mmp) cc_final: 0.8202 (mmp) REVERT: B 152 GLU cc_start: 0.8088 (tp30) cc_final: 0.7828 (tp30) REVERT: B 257 GLU cc_start: 0.8452 (tp30) cc_final: 0.8189 (tt0) REVERT: B 494 GLU cc_start: 0.7550 (pt0) cc_final: 0.7012 (tt0) REVERT: B 575 ARG cc_start: 0.8500 (mmm160) cc_final: 0.8280 (mpt180) REVERT: B 610 GLU cc_start: 0.8238 (mm-30) cc_final: 0.7797 (tp30) REVERT: B 620 TRP cc_start: 0.8661 (t60) cc_final: 0.8347 (t60) outliers start: 41 outliers final: 34 residues processed: 149 average time/residue: 0.0884 time to fit residues: 18.7185 Evaluate side-chains 157 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 119 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 GLN Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 183 PHE Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 470 ILE Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 242 PHE Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 325 THR Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 411 SER Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 549 LEU Chi-restraints excluded: chain B residue 555 THR Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 578 THR Chi-restraints excluded: chain B residue 579 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 74 optimal weight: 0.8980 chunk 12 optimal weight: 0.6980 chunk 4 optimal weight: 4.9990 chunk 15 optimal weight: 0.0040 chunk 103 optimal weight: 0.0970 chunk 6 optimal weight: 0.7980 chunk 79 optimal weight: 1.9990 chunk 39 optimal weight: 7.9990 chunk 110 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 overall best weight: 0.4990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.144513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.112182 restraints weight = 11100.105| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 2.16 r_work: 0.3151 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3011 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.2176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9274 Z= 0.110 Angle : 0.609 11.775 12628 Z= 0.301 Chirality : 0.042 0.233 1520 Planarity : 0.004 0.062 1617 Dihedral : 6.327 102.149 1320 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.64 % Favored : 93.36 % Rotamer: Outliers : 3.66 % Allowed : 19.54 % Favored : 76.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.35 (0.25), residues: 1189 helix: -0.35 (0.20), residues: 748 sheet: -1.95 (0.69), residues: 64 loop : -1.56 (0.32), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 341 TYR 0.012 0.001 TYR B 354 PHE 0.008 0.001 PHE A 453 TRP 0.008 0.001 TRP B 620 HIS 0.001 0.000 HIS A 152 Details of bonding type rmsd covalent geometry : bond 0.00249 ( 9274) covalent geometry : angle 0.60900 (12628) hydrogen bonds : bond 0.03077 ( 384) hydrogen bonds : angle 3.92332 ( 1128) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2378 Ramachandran restraints generated. 1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2378 Ramachandran restraints generated. 1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 124 time to evaluate : 0.397 Fit side-chains REVERT: A 8 GLN cc_start: 0.8721 (OUTLIER) cc_final: 0.6879 (tp40) REVERT: A 135 MET cc_start: 0.8437 (mtt) cc_final: 0.8154 (mtp) REVERT: A 183 PHE cc_start: 0.8809 (OUTLIER) cc_final: 0.8367 (t80) REVERT: A 191 ASP cc_start: 0.8273 (t0) cc_final: 0.7953 (m-30) REVERT: A 246 THR cc_start: 0.8449 (OUTLIER) cc_final: 0.8195 (m) REVERT: A 427 GLU cc_start: 0.8535 (mt-10) cc_final: 0.7598 (tp30) REVERT: A 546 ARG cc_start: 0.7984 (mtp-110) cc_final: 0.7690 (ttm110) REVERT: A 557 LEU cc_start: 0.8508 (tp) cc_final: 0.8281 (mt) REVERT: B 46 ILE cc_start: 0.8209 (OUTLIER) cc_final: 0.7783 (tp) REVERT: B 79 GLU cc_start: 0.8158 (mm-30) cc_final: 0.7669 (tp30) REVERT: B 83 GLU cc_start: 0.8544 (mm-30) cc_final: 0.8299 (mt-10) REVERT: B 106 GLN cc_start: 0.8676 (tt0) cc_final: 0.8332 (tt0) REVERT: B 146 MET cc_start: 0.8425 (mmp) cc_final: 0.8190 (mmp) REVERT: B 152 GLU cc_start: 0.8016 (tp30) cc_final: 0.7749 (tp30) REVERT: B 257 GLU cc_start: 0.8455 (tp30) cc_final: 0.8146 (mt-10) REVERT: B 494 GLU cc_start: 0.7514 (pt0) cc_final: 0.7027 (tt0) REVERT: B 610 GLU cc_start: 0.8228 (mm-30) cc_final: 0.7792 (tp30) outliers start: 35 outliers final: 27 residues processed: 147 average time/residue: 0.1000 time to fit residues: 20.3490 Evaluate side-chains 154 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 123 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 GLN Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 183 PHE Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 470 ILE Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 242 PHE Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 325 THR Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 411 SER Chi-restraints excluded: chain B residue 549 LEU Chi-restraints excluded: chain B residue 555 THR Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 578 THR Chi-restraints excluded: chain B residue 579 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 47 optimal weight: 0.0670 chunk 112 optimal weight: 4.9990 chunk 92 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 chunk 14 optimal weight: 0.6980 chunk 58 optimal weight: 4.9990 chunk 116 optimal weight: 5.9990 chunk 21 optimal weight: 0.6980 chunk 4 optimal weight: 4.9990 chunk 49 optimal weight: 0.7980 chunk 114 optimal weight: 0.8980 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 270 GLN ** A 459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.143855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.111587 restraints weight = 11162.383| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 2.16 r_work: 0.3144 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3005 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.2200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9274 Z= 0.119 Angle : 0.618 11.487 12628 Z= 0.305 Chirality : 0.043 0.229 1520 Planarity : 0.004 0.062 1617 Dihedral : 6.090 85.597 1320 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.81 % Favored : 93.19 % Rotamer: Outliers : 3.66 % Allowed : 19.75 % Favored : 76.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.25 (0.25), residues: 1189 helix: -0.26 (0.20), residues: 748 sheet: -1.88 (0.69), residues: 64 loop : -1.57 (0.32), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 382 TYR 0.016 0.001 TYR B 354 PHE 0.008 0.001 PHE B 509 TRP 0.010 0.001 TRP B 620 HIS 0.001 0.000 HIS A 152 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 9274) covalent geometry : angle 0.61799 (12628) hydrogen bonds : bond 0.03154 ( 384) hydrogen bonds : angle 3.91960 ( 1128) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2378 Ramachandran restraints generated. 1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2378 Ramachandran restraints generated. 1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 124 time to evaluate : 0.367 Fit side-chains REVERT: A 8 GLN cc_start: 0.8713 (OUTLIER) cc_final: 0.6851 (tp40) REVERT: A 135 MET cc_start: 0.8425 (mtt) cc_final: 0.8138 (mtp) REVERT: A 183 PHE cc_start: 0.8732 (OUTLIER) cc_final: 0.8279 (t80) REVERT: A 186 MET cc_start: 0.8649 (ttp) cc_final: 0.8378 (ttm) REVERT: A 191 ASP cc_start: 0.8279 (t0) cc_final: 0.7962 (m-30) REVERT: A 246 THR cc_start: 0.8449 (OUTLIER) cc_final: 0.8191 (m) REVERT: A 427 GLU cc_start: 0.8551 (mt-10) cc_final: 0.7614 (tp30) REVERT: A 546 ARG cc_start: 0.7992 (mtp-110) cc_final: 0.7699 (ttm110) REVERT: A 557 LEU cc_start: 0.8513 (tp) cc_final: 0.8288 (mt) REVERT: B 46 ILE cc_start: 0.8171 (OUTLIER) cc_final: 0.7745 (tp) REVERT: B 79 GLU cc_start: 0.8160 (mm-30) cc_final: 0.7674 (tp30) REVERT: B 83 GLU cc_start: 0.8553 (mm-30) cc_final: 0.8303 (mt-10) REVERT: B 146 MET cc_start: 0.8440 (mmp) cc_final: 0.8200 (mmp) REVERT: B 257 GLU cc_start: 0.8437 (tp30) cc_final: 0.8142 (mt-10) REVERT: B 494 GLU cc_start: 0.7510 (pt0) cc_final: 0.7163 (tt0) REVERT: B 610 GLU cc_start: 0.8229 (mm-30) cc_final: 0.7775 (tp30) outliers start: 35 outliers final: 30 residues processed: 148 average time/residue: 0.0961 time to fit residues: 19.8475 Evaluate side-chains 155 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 121 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 GLN Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 183 PHE Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 470 ILE Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 242 PHE Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 325 THR Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 549 LEU Chi-restraints excluded: chain B residue 555 THR Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 578 THR Chi-restraints excluded: chain B residue 579 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 43 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 101 optimal weight: 0.6980 chunk 64 optimal weight: 4.9990 chunk 12 optimal weight: 3.9990 chunk 95 optimal weight: 0.7980 chunk 66 optimal weight: 0.0370 chunk 83 optimal weight: 4.9990 chunk 74 optimal weight: 0.9980 chunk 86 optimal weight: 0.4980 chunk 11 optimal weight: 0.7980 overall best weight: 0.5658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.144525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.112295 restraints weight = 10966.080| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 2.14 r_work: 0.3155 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3017 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.2263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9274 Z= 0.114 Angle : 0.613 11.363 12628 Z= 0.302 Chirality : 0.042 0.227 1520 Planarity : 0.004 0.062 1617 Dihedral : 5.768 57.798 1320 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.64 % Favored : 93.36 % Rotamer: Outliers : 3.97 % Allowed : 19.64 % Favored : 76.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.16 (0.25), residues: 1189 helix: -0.18 (0.20), residues: 747 sheet: -1.85 (0.69), residues: 64 loop : -1.55 (0.32), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 575 TYR 0.014 0.001 TYR B 354 PHE 0.007 0.001 PHE B 509 TRP 0.010 0.001 TRP B 620 HIS 0.001 0.000 HIS A 152 Details of bonding type rmsd covalent geometry : bond 0.00261 ( 9274) covalent geometry : angle 0.61275 (12628) hydrogen bonds : bond 0.03098 ( 384) hydrogen bonds : angle 3.88525 ( 1128) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2438.93 seconds wall clock time: 42 minutes 21.72 seconds (2541.72 seconds total)