Starting phenix.real_space_refine on Sun Jul 27 07:19:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xst_38628/07_2025/8xst_38628.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xst_38628/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8xst_38628/07_2025/8xst_38628.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xst_38628/07_2025/8xst_38628.map" model { file = "/net/cci-nas-00/data/ceres_data/8xst_38628/07_2025/8xst_38628.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xst_38628/07_2025/8xst_38628.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 5.68, per 1000 atoms: 0.62 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: 2.19 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 0.96 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: 2.40 Time building geometry restraints manager: 2.63 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: 2.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 23.000 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.040 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.780 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.030 0.001 TRP B 246 HIS 0.002 0.001 HIS A 152 PHE 0.012 0.001 PHE A 453 TYR 0.034 0.001 TYR B 354 ARG 0.008 0.000 ARG B 575 Details of bonding type rmsd hydrogen bonds : bond 0.21429 ( 384) hydrogen bonds : angle 8.47394 ( 1128) covalent geometry : bond 0.00360 ( 9274) covalent geometry : angle 0.82353 (12628) *********************** 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 : 0.964 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: 0.2371 time to fit residues: 41.3152 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 : 1.010 ------------------------------------------------------------------------------- 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 99 optimal weight: 2.9990 chunk 89 optimal weight: 0.8980 chunk 49 optimal weight: 0.6980 chunk 30 optimal weight: 0.7980 chunk 60 optimal weight: 1.9990 chunk 47 optimal weight: 7.9990 chunk 92 optimal weight: 0.8980 chunk 35 optimal weight: 3.9990 chunk 56 optimal weight: 0.7980 chunk 68 optimal weight: 0.7980 chunk 107 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3591 r_free = 0.3591 target = 0.140864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.110402 restraints weight = 11207.652| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 1.96 r_work: 0.3110 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2974 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.0986 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= 0.143 Angle : 0.665 9.321 12628 Z= 0.342 Chirality : 0.043 0.250 1520 Planarity : 0.004 0.056 1617 Dihedral : 8.663 174.862 1322 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.40 % Favored : 92.60 % Rotamer: Outliers : 3.66 % Allowed : 15.15 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.94 (0.23), residues: 1189 helix: -1.65 (0.18), residues: 742 sheet: -2.61 (0.61), residues: 64 loop : -2.07 (0.30), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 246 HIS 0.002 0.000 HIS A 152 PHE 0.012 0.001 PHE A 453 TYR 0.023 0.001 TYR B 354 ARG 0.004 0.000 ARG A 477 Details of bonding type rmsd hydrogen bonds : bond 0.04032 ( 384) hydrogen bonds : angle 4.79505 ( 1128) covalent geometry : bond 0.00327 ( 9274) covalent geometry : angle 0.66515 (12628) *********************** 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 171 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 136 time to evaluate : 1.028 Fit side-chains REVERT: A 8 GLN cc_start: 0.8582 (OUTLIER) cc_final: 0.7074 (tt0) REVERT: A 43 ASP cc_start: 0.7884 (m-30) cc_final: 0.7643 (m-30) REVERT: A 226 THR cc_start: 0.8415 (m) cc_final: 0.8136 (m) REVERT: A 427 GLU cc_start: 0.8389 (mt-10) cc_final: 0.7471 (tp30) REVERT: A 512 ASP cc_start: 0.8028 (m-30) cc_final: 0.7469 (m-30) REVERT: B 46 ILE cc_start: 0.8085 (OUTLIER) cc_final: 0.7699 (tp) REVERT: B 79 GLU cc_start: 0.8311 (mm-30) cc_final: 0.7699 (tp30) REVERT: B 152 GLU cc_start: 0.7834 (tp30) cc_final: 0.7611 (tp30) REVERT: B 494 GLU cc_start: 0.7489 (pt0) cc_final: 0.6992 (tt0) outliers start: 35 outliers final: 18 residues processed: 162 average time/residue: 0.2143 time to fit residues: 48.9635 Evaluate side-chains 139 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 119 time to evaluate : 1.028 ------------------------------------------------------------------------------- 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 311 VAL Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 470 ILE Chi-restraints excluded: chain A residue 543 ASP 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 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 32 optimal weight: 0.0270 chunk 26 optimal weight: 1.9990 chunk 86 optimal weight: 0.9980 chunk 9 optimal weight: 0.9990 chunk 28 optimal weight: 0.7980 chunk 45 optimal weight: 10.0000 chunk 102 optimal weight: 4.9990 chunk 53 optimal weight: 5.9990 chunk 93 optimal weight: 0.9990 chunk 99 optimal weight: 0.5980 chunk 35 optimal weight: 5.9990 overall best weight: 0.6840 ------------------------------------------------------------------------------- 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 = 0.3599 r_free = 0.3599 target = 0.141724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.110749 restraints weight = 11236.691| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 1.99 r_work: 0.3113 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2975 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.1319 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= 0.127 Angle : 0.624 9.100 12628 Z= 0.319 Chirality : 0.042 0.201 1520 Planarity : 0.004 0.058 1617 Dihedral : 7.978 165.786 1320 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.64 % Favored : 93.36 % Rotamer: Outliers : 3.76 % Allowed : 15.99 % Favored : 80.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.51 (0.24), residues: 1189 helix: -1.30 (0.19), residues: 749 sheet: -2.45 (0.62), residues: 64 loop : -1.93 (0.31), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 246 HIS 0.002 0.000 HIS A 152 PHE 0.011 0.001 PHE A 453 TYR 0.019 0.001 TYR B 354 ARG 0.003 0.000 ARG A 477 Details of bonding type rmsd hydrogen bonds : bond 0.03703 ( 384) hydrogen bonds : angle 4.39389 ( 1128) covalent geometry : bond 0.00288 ( 9274) covalent geometry : angle 0.62449 (12628) *********************** 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 165 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 129 time to evaluate : 0.944 Fit side-chains REVERT: A 8 GLN cc_start: 0.8600 (OUTLIER) cc_final: 0.7043 (tt0) REVERT: A 48 LYS cc_start: 0.8419 (mttp) cc_final: 0.8065 (mttp) REVERT: A 191 ASP cc_start: 0.8101 (t0) cc_final: 0.7767 (m-30) REVERT: A 427 GLU cc_start: 0.8380 (mt-10) cc_final: 0.7423 (tp30) REVERT: A 557 LEU cc_start: 0.8100 (tp) cc_final: 0.7806 (tp) REVERT: B 46 ILE cc_start: 0.8129 (OUTLIER) cc_final: 0.7727 (tp) REVERT: B 79 GLU cc_start: 0.8308 (mm-30) cc_final: 0.7751 (tp30) REVERT: B 152 GLU cc_start: 0.7838 (tp30) cc_final: 0.7512 (tp30) REVERT: B 172 GLU cc_start: 0.7913 (tm-30) cc_final: 0.7489 (tm-30) REVERT: B 494 GLU cc_start: 0.7508 (pt0) cc_final: 0.7006 (tt0) REVERT: B 575 ARG cc_start: 0.8772 (mmm160) cc_final: 0.8154 (mpt180) outliers start: 36 outliers final: 28 residues processed: 156 average time/residue: 0.2518 time to fit residues: 55.1698 Evaluate side-chains 153 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 123 time to evaluate : 0.969 ------------------------------------------------------------------------------- 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 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 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 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 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 95 optimal weight: 4.9990 chunk 68 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 93 optimal weight: 0.0060 chunk 65 optimal weight: 3.9990 chunk 80 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 103 optimal weight: 2.9990 chunk 112 optimal weight: 3.9990 chunk 100 optimal weight: 2.9990 overall best weight: 1.1600 ------------------------------------------------------------------------------- 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 = 0.3612 r_free = 0.3612 target = 0.140245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.107947 restraints weight = 11189.715| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 2.15 r_work: 0.3093 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2955 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.1572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 9274 Z= 0.164 Angle : 0.648 9.402 12628 Z= 0.327 Chirality : 0.044 0.242 1520 Planarity : 0.004 0.060 1617 Dihedral : 7.781 159.235 1320 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.06 % Favored : 92.94 % Rotamer: Outliers : 4.60 % Allowed : 16.30 % Favored : 79.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.31 (0.24), residues: 1189 helix: -1.17 (0.19), residues: 747 sheet: -2.06 (0.68), residues: 62 loop : -1.86 (0.31), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 246 HIS 0.002 0.001 HIS A 88 PHE 0.011 0.001 PHE B 269 TYR 0.014 0.001 TYR B 354 ARG 0.003 0.000 ARG B 618 Details of bonding type rmsd hydrogen bonds : bond 0.03804 ( 384) hydrogen bonds : angle 4.31963 ( 1128) covalent geometry : bond 0.00389 ( 9274) covalent geometry : angle 0.64776 (12628) *********************** 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 169 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 125 time to evaluate : 0.955 Fit side-chains REVERT: A 8 GLN cc_start: 0.8782 (OUTLIER) cc_final: 0.7359 (tt0) REVERT: A 191 ASP cc_start: 0.8340 (t0) cc_final: 0.8056 (m-30) REVERT: A 226 THR cc_start: 0.8778 (m) cc_final: 0.8536 (m) REVERT: A 246 THR cc_start: 0.8678 (OUTLIER) cc_final: 0.8325 (m) REVERT: A 427 GLU cc_start: 0.8527 (mt-10) cc_final: 0.7629 (tp30) REVERT: A 452 ASP cc_start: 0.8722 (OUTLIER) cc_final: 0.8214 (t0) REVERT: A 512 ASP cc_start: 0.7850 (m-30) cc_final: 0.7320 (m-30) REVERT: A 557 LEU cc_start: 0.8410 (tp) cc_final: 0.8144 (tp) REVERT: B 46 ILE cc_start: 0.8455 (OUTLIER) cc_final: 0.8013 (tp) REVERT: B 79 GLU cc_start: 0.8322 (mm-30) cc_final: 0.7793 (tp30) REVERT: B 83 GLU cc_start: 0.8522 (mm-30) cc_final: 0.8232 (mt-10) REVERT: B 257 GLU cc_start: 0.8376 (tp30) cc_final: 0.8050 (mt-10) REVERT: B 494 GLU cc_start: 0.7725 (pt0) cc_final: 0.7236 (tt0) REVERT: B 575 ARG cc_start: 0.8679 (mmm160) cc_final: 0.8230 (mpt180) REVERT: B 620 TRP cc_start: 0.8656 (t60) cc_final: 0.8320 (t60) outliers start: 44 outliers final: 34 residues processed: 161 average time/residue: 0.2230 time to fit residues: 49.6676 Evaluate side-chains 160 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 122 time to evaluate : 1.056 ------------------------------------------------------------------------------- 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 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 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 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 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 Chi-restraints excluded: chain B residue 615 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 104 optimal weight: 0.8980 chunk 17 optimal weight: 0.7980 chunk 64 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 88 optimal weight: 2.9990 chunk 70 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 115 optimal weight: 3.9990 chunk 57 optimal weight: 10.0000 overall best weight: 1.0782 ------------------------------------------------------------------------------- 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 = 0.3610 r_free = 0.3610 target = 0.140187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.108076 restraints weight = 11237.591| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 2.12 r_work: 0.3098 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2962 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.1749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 9274 Z= 0.155 Angle : 0.638 10.077 12628 Z= 0.321 Chirality : 0.044 0.230 1520 Planarity : 0.004 0.060 1617 Dihedral : 7.556 151.114 1320 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.81 % Favored : 93.19 % Rotamer: Outliers : 4.39 % Allowed : 17.35 % Favored : 78.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.13 (0.24), residues: 1189 helix: -1.03 (0.19), residues: 746 sheet: -1.92 (0.70), residues: 62 loop : -1.78 (0.31), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 246 HIS 0.002 0.000 HIS A 152 PHE 0.010 0.001 PHE A 453 TYR 0.013 0.001 TYR A 9 ARG 0.003 0.000 ARG A 117 Details of bonding type rmsd hydrogen bonds : bond 0.03640 ( 384) hydrogen bonds : angle 4.28348 ( 1128) covalent geometry : bond 0.00368 ( 9274) covalent geometry : angle 0.63777 (12628) *********************** 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 170 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 128 time to evaluate : 0.995 Fit side-chains REVERT: A 8 GLN cc_start: 0.8810 (OUTLIER) cc_final: 0.7409 (tt0) REVERT: A 135 MET cc_start: 0.8467 (mtt) cc_final: 0.8176 (mtp) REVERT: A 191 ASP cc_start: 0.8360 (t0) cc_final: 0.8086 (m-30) REVERT: A 226 THR cc_start: 0.8745 (m) cc_final: 0.8523 (m) REVERT: A 427 GLU cc_start: 0.8562 (mt-10) cc_final: 0.7723 (tp30) REVERT: A 452 ASP cc_start: 0.8741 (OUTLIER) cc_final: 0.8249 (t0) REVERT: A 557 LEU cc_start: 0.8375 (tp) cc_final: 0.8083 (tp) REVERT: B 46 ILE cc_start: 0.8403 (OUTLIER) cc_final: 0.7926 (tp) REVERT: B 79 GLU cc_start: 0.8290 (mm-30) cc_final: 0.7781 (tp30) REVERT: B 83 GLU cc_start: 0.8574 (mm-30) cc_final: 0.8298 (mt-10) REVERT: B 106 GLN cc_start: 0.8784 (tt0) cc_final: 0.8397 (tt0) REVERT: B 152 GLU cc_start: 0.8069 (tp30) cc_final: 0.7793 (tp30) REVERT: B 257 GLU cc_start: 0.8400 (tp30) cc_final: 0.8052 (mt-10) REVERT: B 494 GLU cc_start: 0.7684 (pt0) cc_final: 0.7192 (tt0) REVERT: B 575 ARG cc_start: 0.8625 (mmm160) cc_final: 0.8262 (mpt180) outliers start: 42 outliers final: 32 residues processed: 160 average time/residue: 0.2133 time to fit residues: 47.5744 Evaluate side-chains 158 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 123 time to evaluate : 1.018 ------------------------------------------------------------------------------- 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 389 SER 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 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 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 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 2 optimal weight: 0.5980 chunk 96 optimal weight: 0.8980 chunk 98 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 97 optimal weight: 6.9990 chunk 42 optimal weight: 0.1980 chunk 38 optimal weight: 4.9990 chunk 116 optimal weight: 2.9990 chunk 70 optimal weight: 0.9990 chunk 43 optimal weight: 0.7980 chunk 50 optimal weight: 5.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- 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 = 0.3628 r_free = 0.3628 target = 0.141966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.109761 restraints weight = 11116.108| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 2.13 r_work: 0.3119 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2983 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.1848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9274 Z= 0.126 Angle : 0.612 9.058 12628 Z= 0.309 Chirality : 0.043 0.234 1520 Planarity : 0.004 0.060 1617 Dihedral : 7.300 143.977 1320 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.81 % Favored : 93.19 % Rotamer: Outliers : 4.39 % Allowed : 17.76 % Favored : 77.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.89 (0.25), residues: 1189 helix: -0.82 (0.19), residues: 748 sheet: -1.99 (0.69), residues: 64 loop : -1.73 (0.32), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 620 HIS 0.001 0.000 HIS A 553 PHE 0.010 0.001 PHE A 453 TYR 0.013 0.001 TYR B 354 ARG 0.002 0.000 ARG B 618 Details of bonding type rmsd hydrogen bonds : bond 0.03385 ( 384) hydrogen bonds : angle 4.15374 ( 1128) covalent geometry : bond 0.00291 ( 9274) covalent geometry : angle 0.61198 (12628) *********************** 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 171 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 129 time to evaluate : 1.427 Fit side-chains REVERT: A 8 GLN cc_start: 0.8769 (OUTLIER) cc_final: 0.7273 (tt0) REVERT: A 135 MET cc_start: 0.8404 (mtt) cc_final: 0.8096 (mtp) REVERT: A 183 PHE cc_start: 0.8736 (OUTLIER) cc_final: 0.8338 (t80) REVERT: A 191 ASP cc_start: 0.8303 (t0) cc_final: 0.7990 (m-30) REVERT: A 246 THR cc_start: 0.8517 (OUTLIER) cc_final: 0.8200 (m) REVERT: A 427 GLU cc_start: 0.8548 (mt-10) cc_final: 0.7630 (tp30) REVERT: A 452 ASP cc_start: 0.8679 (OUTLIER) cc_final: 0.8121 (t0) REVERT: A 557 LEU cc_start: 0.8281 (tp) cc_final: 0.8033 (tp) REVERT: B 46 ILE cc_start: 0.8271 (OUTLIER) cc_final: 0.7828 (tp) REVERT: B 56 LEU cc_start: 0.8073 (OUTLIER) cc_final: 0.7714 (mp) REVERT: B 79 GLU cc_start: 0.8247 (mm-30) cc_final: 0.7717 (tp30) REVERT: B 83 GLU cc_start: 0.8533 (mm-30) cc_final: 0.8272 (mt-10) REVERT: B 106 GLN cc_start: 0.8735 (tt0) cc_final: 0.8355 (tt0) REVERT: B 146 MET cc_start: 0.8407 (mmp) cc_final: 0.8167 (mmp) REVERT: B 152 GLU cc_start: 0.7995 (tp30) cc_final: 0.7699 (tp30) REVERT: B 257 GLU cc_start: 0.8381 (tp30) cc_final: 0.7977 (mt-10) REVERT: B 382 ARG cc_start: 0.7982 (tpt-90) cc_final: 0.7742 (tpt-90) REVERT: B 494 GLU cc_start: 0.7546 (pt0) cc_final: 0.7107 (tt0) REVERT: B 575 ARG cc_start: 0.8582 (mmm160) cc_final: 0.8243 (mpt180) REVERT: B 620 TRP cc_start: 0.8622 (t60) cc_final: 0.8296 (t60) outliers start: 42 outliers final: 31 residues processed: 159 average time/residue: 0.2745 time to fit residues: 61.6678 Evaluate side-chains 163 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 126 time to evaluate : 0.984 ------------------------------------------------------------------------------- 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 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 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 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 B residue 46 ILE Chi-restraints excluded: chain B residue 56 LEU 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 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 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 39 optimal weight: 0.8980 chunk 50 optimal weight: 6.9990 chunk 54 optimal weight: 2.9990 chunk 89 optimal weight: 0.7980 chunk 114 optimal weight: 0.1980 chunk 98 optimal weight: 0.9990 chunk 2 optimal weight: 0.0010 chunk 76 optimal weight: 0.8980 chunk 29 optimal weight: 0.8980 chunk 37 optimal weight: 3.9990 chunk 93 optimal weight: 3.9990 overall best weight: 0.5586 ------------------------------------------------------------------------------- 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 = 0.3630 r_free = 0.3630 target = 0.142787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.110773 restraints weight = 11140.789| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 2.14 r_work: 0.3127 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2990 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.1999 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 : 0.604 12.405 12628 Z= 0.302 Chirality : 0.042 0.224 1520 Planarity : 0.004 0.062 1617 Dihedral : 6.932 131.517 1320 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 4.49 % Allowed : 18.18 % Favored : 77.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.64 (0.25), residues: 1189 helix: -0.60 (0.20), residues: 748 sheet: -1.95 (0.69), residues: 64 loop : -1.66 (0.32), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 620 HIS 0.001 0.000 HIS A 152 PHE 0.009 0.001 PHE A 453 TYR 0.012 0.001 TYR A 9 ARG 0.002 0.000 ARG B 618 Details of bonding type rmsd hydrogen bonds : bond 0.03190 ( 384) hydrogen bonds : angle 4.01451 ( 1128) covalent geometry : bond 0.00258 ( 9274) covalent geometry : angle 0.60400 (12628) *********************** 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 172 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 129 time to evaluate : 1.230 Fit side-chains REVERT: A 8 GLN cc_start: 0.8608 (OUTLIER) cc_final: 0.6919 (tp40) REVERT: A 135 MET cc_start: 0.8302 (mtt) cc_final: 0.7975 (mtp) REVERT: A 183 PHE cc_start: 0.8663 (OUTLIER) cc_final: 0.8227 (t80) REVERT: A 191 ASP cc_start: 0.8158 (t0) cc_final: 0.7793 (m-30) REVERT: A 427 GLU cc_start: 0.8503 (mt-10) cc_final: 0.7543 (tp30) REVERT: B 46 ILE cc_start: 0.8035 (OUTLIER) cc_final: 0.7602 (tp) REVERT: B 56 LEU cc_start: 0.7778 (OUTLIER) cc_final: 0.7459 (mp) REVERT: B 79 GLU cc_start: 0.8233 (mm-30) cc_final: 0.7714 (tp30) REVERT: B 83 GLU cc_start: 0.8503 (mm-30) cc_final: 0.8252 (mt-10) REVERT: B 106 GLN cc_start: 0.8662 (tt0) cc_final: 0.8275 (tt0) REVERT: B 152 GLU cc_start: 0.7875 (tp30) cc_final: 0.7552 (tp30) REVERT: B 257 GLU cc_start: 0.8318 (tp30) cc_final: 0.7816 (mt-10) REVERT: B 494 GLU cc_start: 0.7366 (pt0) cc_final: 0.6944 (tt0) REVERT: B 575 ARG cc_start: 0.8503 (mmm160) cc_final: 0.8207 (mpt180) REVERT: B 620 TRP cc_start: 0.8545 (t60) cc_final: 0.8285 (t60) outliers start: 43 outliers final: 33 residues processed: 158 average time/residue: 0.2536 time to fit residues: 57.4974 Evaluate side-chains 162 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 125 time to evaluate : 1.475 ------------------------------------------------------------------------------- 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 136 LEU Chi-restraints excluded: chain A residue 183 PHE Chi-restraints excluded: chain A residue 206 VAL 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 461 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 56 LEU 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 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 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 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 81 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 91 optimal weight: 0.8980 chunk 7 optimal weight: 0.1980 chunk 19 optimal weight: 2.9990 chunk 40 optimal weight: 0.7980 chunk 96 optimal weight: 0.4980 chunk 35 optimal weight: 0.0980 chunk 6 optimal weight: 0.5980 chunk 72 optimal weight: 0.9990 overall best weight: 0.4380 ------------------------------------------------------------------------------- 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 = 0.3646 r_free = 0.3646 target = 0.144217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.112150 restraints weight = 11305.207| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 2.18 r_work: 0.3146 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3009 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.2146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9274 Z= 0.107 Angle : 0.601 11.969 12628 Z= 0.298 Chirality : 0.042 0.245 1520 Planarity : 0.004 0.062 1617 Dihedral : 6.517 114.981 1320 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 4.39 % Allowed : 18.50 % Favored : 77.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.42 (0.25), residues: 1189 helix: -0.40 (0.20), residues: 748 sheet: -1.93 (0.69), residues: 64 loop : -1.62 (0.32), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 620 HIS 0.001 0.000 HIS A 152 PHE 0.008 0.001 PHE A 453 TYR 0.014 0.001 TYR B 354 ARG 0.002 0.000 ARG A 477 Details of bonding type rmsd hydrogen bonds : bond 0.03054 ( 384) hydrogen bonds : angle 3.89572 ( 1128) covalent geometry : bond 0.00240 ( 9274) covalent geometry : angle 0.60112 (12628) *********************** 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 170 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 128 time to evaluate : 0.944 Fit side-chains REVERT: A 8 GLN cc_start: 0.8548 (OUTLIER) cc_final: 0.6750 (tp40) REVERT: A 135 MET cc_start: 0.8300 (mtt) cc_final: 0.7966 (mtp) REVERT: A 183 PHE cc_start: 0.8636 (OUTLIER) cc_final: 0.8143 (t80) REVERT: A 191 ASP cc_start: 0.8167 (t0) cc_final: 0.7775 (m-30) REVERT: A 246 THR cc_start: 0.8136 (OUTLIER) cc_final: 0.7905 (m) REVERT: A 427 GLU cc_start: 0.8488 (mt-10) cc_final: 0.7509 (tp30) REVERT: B 46 ILE cc_start: 0.7997 (OUTLIER) cc_final: 0.7574 (tp) REVERT: B 56 LEU cc_start: 0.7775 (OUTLIER) cc_final: 0.7424 (mp) REVERT: B 79 GLU cc_start: 0.8222 (mm-30) cc_final: 0.7706 (tp30) REVERT: B 83 GLU cc_start: 0.8505 (mm-30) cc_final: 0.8260 (mt-10) REVERT: B 106 GLN cc_start: 0.8615 (tt0) cc_final: 0.8237 (tt0) REVERT: B 152 GLU cc_start: 0.7870 (tp30) cc_final: 0.7553 (tp30) REVERT: B 257 GLU cc_start: 0.8304 (tp30) cc_final: 0.7824 (mt-10) REVERT: B 494 GLU cc_start: 0.7341 (pt0) cc_final: 0.6834 (tt0) REVERT: B 575 ARG cc_start: 0.8489 (mmm160) cc_final: 0.8211 (mpt180) outliers start: 42 outliers final: 31 residues processed: 157 average time/residue: 0.2032 time to fit residues: 45.2104 Evaluate side-chains 158 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 122 time to evaluate : 0.933 ------------------------------------------------------------------------------- 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 136 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 461 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 56 LEU 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 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 411 SER Chi-restraints excluded: chain B residue 549 LEU 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 15 optimal weight: 0.5980 chunk 85 optimal weight: 0.5980 chunk 22 optimal weight: 2.9990 chunk 63 optimal weight: 5.9990 chunk 12 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 94 optimal weight: 9.9990 chunk 77 optimal weight: 0.8980 chunk 80 optimal weight: 0.6980 chunk 56 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3644 r_free = 0.3644 target = 0.143906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.112224 restraints weight = 11070.831| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 2.09 r_work: 0.3130 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2994 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.2208 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= 0.127 Angle : 0.617 11.570 12628 Z= 0.305 Chirality : 0.043 0.237 1520 Planarity : 0.004 0.062 1617 Dihedral : 6.344 101.918 1320 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.64 % Favored : 93.36 % Rotamer: Outliers : 4.28 % Allowed : 18.50 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.25), residues: 1189 helix: -0.32 (0.20), residues: 746 sheet: -1.86 (0.69), residues: 64 loop : -1.60 (0.32), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 620 HIS 0.001 0.000 HIS A 152 PHE 0.009 0.001 PHE B 269 TYR 0.013 0.001 TYR B 354 ARG 0.007 0.000 ARG B 341 Details of bonding type rmsd hydrogen bonds : bond 0.03255 ( 384) hydrogen bonds : angle 3.94063 ( 1128) covalent geometry : bond 0.00299 ( 9274) covalent geometry : angle 0.61704 (12628) *********************** 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 166 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 125 time to evaluate : 0.931 Fit side-chains REVERT: A 8 GLN cc_start: 0.8575 (OUTLIER) cc_final: 0.7002 (tt0) REVERT: A 135 MET cc_start: 0.8351 (mtt) cc_final: 0.8027 (mtp) REVERT: A 183 PHE cc_start: 0.8600 (OUTLIER) cc_final: 0.8072 (t80) REVERT: A 191 ASP cc_start: 0.8195 (t0) cc_final: 0.7804 (m-30) REVERT: A 246 THR cc_start: 0.8199 (OUTLIER) cc_final: 0.7935 (m) REVERT: A 427 GLU cc_start: 0.8478 (mt-10) cc_final: 0.7498 (tp30) REVERT: B 46 ILE cc_start: 0.7979 (OUTLIER) cc_final: 0.7539 (tp) REVERT: B 56 LEU cc_start: 0.7828 (OUTLIER) cc_final: 0.7474 (mp) REVERT: B 79 GLU cc_start: 0.8177 (mm-30) cc_final: 0.7662 (tp30) REVERT: B 83 GLU cc_start: 0.8518 (mm-30) cc_final: 0.8271 (mt-10) REVERT: B 106 GLN cc_start: 0.8607 (tt0) cc_final: 0.8395 (tt0) REVERT: B 257 GLU cc_start: 0.8292 (tp30) cc_final: 0.7828 (mt-10) REVERT: B 494 GLU cc_start: 0.7354 (pt0) cc_final: 0.6868 (tt0) REVERT: B 575 ARG cc_start: 0.8456 (mmm160) cc_final: 0.8235 (mpt180) outliers start: 41 outliers final: 32 residues processed: 153 average time/residue: 0.2007 time to fit residues: 43.4344 Evaluate side-chains 160 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 123 time to evaluate : 0.934 ------------------------------------------------------------------------------- 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 127 GLN 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 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 461 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 56 LEU 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 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 549 LEU 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 44 optimal weight: 3.9990 chunk 100 optimal weight: 4.9990 chunk 117 optimal weight: 5.9990 chunk 105 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 107 optimal weight: 3.9990 chunk 69 optimal weight: 0.6980 chunk 9 optimal weight: 0.9980 chunk 108 optimal weight: 0.0970 chunk 43 optimal weight: 2.9990 chunk 84 optimal weight: 0.7980 overall best weight: 0.9180 ------------------------------------------------------------------------------- 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 = 0.3620 r_free = 0.3620 target = 0.141974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.109294 restraints weight = 11209.644| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 2.18 r_work: 0.3107 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2969 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.2233 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= 0.140 Angle : 0.628 11.108 12628 Z= 0.310 Chirality : 0.044 0.239 1520 Planarity : 0.004 0.061 1617 Dihedral : 6.118 78.996 1320 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 3.97 % Allowed : 19.02 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.25), residues: 1189 helix: -0.30 (0.20), residues: 746 sheet: -1.77 (0.70), residues: 64 loop : -1.56 (0.32), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 620 HIS 0.002 0.000 HIS A 152 PHE 0.010 0.001 PHE B 509 TYR 0.014 0.001 TYR B 354 ARG 0.007 0.000 ARG B 341 Details of bonding type rmsd hydrogen bonds : bond 0.03377 ( 384) hydrogen bonds : angle 4.00475 ( 1128) covalent geometry : bond 0.00332 ( 9274) covalent geometry : angle 0.62808 (12628) ********************** 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 165 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 127 time to evaluate : 0.983 Fit side-chains REVERT: A 8 GLN cc_start: 0.8683 (OUTLIER) cc_final: 0.7235 (tt0) REVERT: A 135 MET cc_start: 0.8374 (mtt) cc_final: 0.8060 (mtp) REVERT: A 183 PHE cc_start: 0.8759 (OUTLIER) cc_final: 0.8383 (t80) REVERT: A 191 ASP cc_start: 0.8271 (t0) cc_final: 0.7867 (m-30) REVERT: A 246 THR cc_start: 0.8369 (OUTLIER) cc_final: 0.8073 (m) REVERT: A 427 GLU cc_start: 0.8524 (mt-10) cc_final: 0.7592 (tp30) REVERT: B 46 ILE cc_start: 0.7982 (OUTLIER) cc_final: 0.7508 (tp) REVERT: B 56 LEU cc_start: 0.7943 (OUTLIER) cc_final: 0.7583 (mp) REVERT: B 79 GLU cc_start: 0.8175 (mm-30) cc_final: 0.7736 (tp30) REVERT: B 83 GLU cc_start: 0.8516 (mm-30) cc_final: 0.8267 (mt-10) REVERT: B 106 GLN cc_start: 0.8632 (tt0) cc_final: 0.8431 (tt0) REVERT: B 146 MET cc_start: 0.8420 (mmp) cc_final: 0.8194 (mmp) REVERT: B 257 GLU cc_start: 0.8354 (tp30) cc_final: 0.8059 (tt0) REVERT: B 494 GLU cc_start: 0.7414 (pt0) cc_final: 0.6924 (tt0) outliers start: 38 outliers final: 32 residues processed: 153 average time/residue: 0.2013 time to fit residues: 43.9324 Evaluate side-chains 161 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 124 time to evaluate : 0.931 ------------------------------------------------------------------------------- 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 136 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 461 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 56 LEU 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 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 549 LEU 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 87 optimal weight: 0.9980 chunk 112 optimal weight: 3.9990 chunk 79 optimal weight: 3.9990 chunk 25 optimal weight: 0.9980 chunk 78 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 69 optimal weight: 0.6980 chunk 6 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 113 optimal weight: 2.9990 chunk 111 optimal weight: 1.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- 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 = 0.3614 r_free = 0.3614 target = 0.141318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.109087 restraints weight = 11074.715| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 2.13 r_work: 0.3117 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2980 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.2235 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= 0.140 Angle : 0.634 10.967 12628 Z= 0.313 Chirality : 0.043 0.239 1520 Planarity : 0.004 0.061 1617 Dihedral : 5.888 55.651 1320 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.64 % Favored : 93.36 % Rotamer: Outliers : 4.18 % Allowed : 19.23 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.25), residues: 1189 helix: -0.24 (0.20), residues: 745 sheet: -1.70 (0.70), residues: 64 loop : -1.45 (0.33), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 620 HIS 0.001 0.000 HIS A 88 PHE 0.010 0.001 PHE B 509 TYR 0.014 0.001 TYR B 354 ARG 0.007 0.000 ARG B 341 Details of bonding type rmsd hydrogen bonds : bond 0.03363 ( 384) hydrogen bonds : angle 4.00132 ( 1128) covalent geometry : bond 0.00333 ( 9274) covalent geometry : angle 0.63413 (12628) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4964.52 seconds wall clock time: 89 minutes 10.37 seconds (5350.37 seconds total)